A "gamma file" contains keywords followed by a ":", followed by data as follows:



HMM: file name for HMMSTR model, prob_flag=1 (only sequence was used) or 3 (sequence and structure were used), number of HMMSTR states (always 282)
GCA: PDB code and chain ID, chainID, domainID, length, Filename= internal file name of sequence profile data.
RESIDUE: sequence number, PDB number, amino acid character, x, y, z of C-alpha if known, phi, psi, omega if known, secondary struct character if known, rotamer character if known.
PROFILE: amino acid probabilities from profile file A through Y in alphabetical order.
GPROFILE: calculated amino acid profile based on HMMSTR stage probabilities. This is an "extrapolated profile".
GAMMA: Probabilities for HMMSTR states 0 through 281. NOTE: for model_R.hmm state 0 is a non-emitting state. Probs for states 1-281 sum to 1.00.
DISTANCE: distance from current residue C-alpha to each of the other residues, rounded to the nearest integer. 
HMM: /home/users/bystrc/server/data/hmm/hmmstr/models/model_R.hmm, prob_flag= 1 num_nodes= 282
GCA:  pred_ _ _ 251 Filename= /home/users/bystrc/server/isites/tmp/example.28159.hssp.drct
RESIDUE: 1 1 M      0.0      0.0      0.0     0.00     0.00     0.00 . ? .
SS: H 0.366752 0.054006 0.046760 0.099915 0.077857 0.354378 
PROFILE: 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 
GPROFILE: 0.063983 0.015752 0.026249 0.028422 0.049344 0.037532 0.015355 0.060311 0.022829 0.125047 0.251804 0.020824 0.036615 0.018677 0.025715 0.039922 0.039949 0.067511 0.018750 0.035404 
GAMMA: 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.159559 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000108 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000151 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000298 0.000000 0.000000 0.000000 0.000000 0.000000 0.231349 0.000000 0.000000 0.000000 0.000000 0.000006 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000139 0.000000 0.000000 0.000000 0.000342 0.026321 0.074948 0.000000 0.000000 0.024324 0.000000 0.000000 0.000000 0.016499 0.000000 0.000000 0.000797 0.000000 0.000000 0.000000 0.000000 0.000000 0.003112 0.000000 0.000000 0.000001 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.007372 0.000000 0.005177 0.000000 0.000000 0.000003 0.004217 0.000000 0.000000 0.000000 0.006326 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.002116 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.206931 0.000000 0.000000 0.000000 0.000000 0.000000 0.003040 0.000000 0.000000 0.000000 0.000379 0.000000 0.000000 0.000000 0.000000 0.077108 0.000000 0.000000 0.000000 0.045273 0.000000 0.000000 0.008349 0.000000 0.000000 0.000000 0.000000 0.000000 0.004418 0.000000 0.000000 0.000000 0.004731 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.004432 0.000000 0.000000 0.000000 0.000000 0.000028 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000768 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000109 0.000000 0.000000 0.045090 0.000000 0.000000 0.031140 0.000000 0.000000 0.000000 0.000000 0.000000 0.000457 0.000000 0.000000 0.000000 0.000967 0.000225 0.000000 0.000275 0.000000 0.000385 0.000000 0.000010 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.002719 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 
DISTANCE: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
RESIDUE: 2 2 N      0.0      0.0      0.0     0.00     0.00     0.00 . ? .
SS: H 0.427384 0.062544 0.050599 0.090184 0.079718 0.289720 
PROFILE: 0.239446 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.412929 0.000000 0.000000 0.000000 0.347625 0.000000 0.000000 0.000000 0.000000 
GPROFILE: 0.086307 0.008956 0.080635 0.093175 0.018895 0.070751 0.021951 0.030551 0.072262 0.054127 0.015480 0.053976 0.056964 0.045667 0.058692 0.089979 0.069483 0.041026 0.009060 0.022067 
GAMMA: 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.206931 0.000000 0.000000 0.002417 0.000967 0.000457 0.000000 0.000000 0.004418 0.000000 0.000000 0.000000 0.000000 0.159559 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000225 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.008349 0.000000 0.000000 0.000000 0.000000 0.000000 0.000108 0.000342 0.007372 0.000000 0.000151 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.257670 0.000000 0.000000 0.000000 0.000000 0.000006 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000028 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000139 0.000000 0.000000 0.000000 0.000000 0.000000 0.074948 0.000000 0.000000 0.024324 0.000000 0.000000 0.000000 0.016499 0.000000 0.000000 0.000797 0.000000 0.000000 0.002719 0.000000 0.000000 0.003112 0.000000 0.000000 0.000001 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.005177 0.000000 0.000000 0.000000 0.004217 0.000000 0.000000 0.000000 0.006326 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.004731 0.000000 0.000000 0.000000 0.000000 0.045273 0.000000 0.000000 0.000000 0.000000 0.000000 0.003040 0.000000 0.000000 0.000000 0.000379 0.000000 0.000000 0.000768 0.000000 0.077108 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.004432 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.031140 0.000000 0.000000 0.000109 0.000000 0.000000 0.045090 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000275 0.000000 0.000385 0.000000 0.000010 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 
DISTANCE: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0