Starting phenix.real_space_refine on Sun May 11 23:40:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zfc_60056/05_2025/8zfc_60056.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zfc_60056/05_2025/8zfc_60056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zfc_60056/05_2025/8zfc_60056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zfc_60056/05_2025/8zfc_60056.map" model { file = "/net/cci-nas-00/data/ceres_data/8zfc_60056/05_2025/8zfc_60056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zfc_60056/05_2025/8zfc_60056.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5454 2.51 5 N 1477 2.21 5 O 1561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8545 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1826 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 95 Chain: "B" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2469 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 98 Chain: "G" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 343 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "S" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1676 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "R" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2231 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 12, 'TRANS': 281} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 114 Time building chain proxies: 5.05, per 1000 atoms: 0.59 Number of scatterers: 8545 At special positions: 0 Unit cell: (87.98, 121.9, 127.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1561 8.00 N 1477 7.00 C 5454 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 92 " - pdb=" SG CYS R 170 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 974.2 milliseconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 36.4% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 6 through 38 removed outlier: 3.636A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.680A pdb=" N GLN A 246 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A 247 " --> pdb=" O TRP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.527A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.618A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.714A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'R' and resid 20 through 50 removed outlier: 3.602A pdb=" N PHE R 28 " --> pdb=" O SER R 24 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Proline residue: R 35 - end of helix removed outlier: 3.705A pdb=" N GLN R 50 " --> pdb=" O ARG R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 70 removed outlier: 3.935A pdb=" N TYR R 57 " --> pdb=" O GLU R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 81 removed outlier: 4.155A pdb=" N TRP R 75 " --> pdb=" O THR R 71 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP R 77 " --> pdb=" O PRO R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 101 removed outlier: 3.696A pdb=" N SER R 91 " --> pdb=" O HIS R 87 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N CYS R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY R 96 " --> pdb=" O CYS R 92 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE R 97 " --> pdb=" O LYS R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 123 removed outlier: 3.681A pdb=" N ALA R 108 " --> pdb=" O TYR R 104 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS R 111 " --> pdb=" O ILE R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 146 Processing helix chain 'R' and resid 152 through 157 removed outlier: 3.580A pdb=" N HIS R 157 " --> pdb=" O PRO R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 191 removed outlier: 3.634A pdb=" N ALA R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TRP R 182 " --> pdb=" O ARG R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 213 removed outlier: 3.889A pdb=" N SER R 212 " --> pdb=" O ARG R 208 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER R 213 " --> pdb=" O ALA R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 256 removed outlier: 3.677A pdb=" N SER R 230 " --> pdb=" O ARG R 226 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE R 232 " --> pdb=" O ALA R 228 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL R 235 " --> pdb=" O LEU R 231 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU R 236 " --> pdb=" O ILE R 232 " (cutoff:3.500A) Proline residue: R 241 - end of helix removed outlier: 4.060A pdb=" N TYR R 253 " --> pdb=" O ARG R 249 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU R 254 " --> pdb=" O SER R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 277 removed outlier: 3.712A pdb=" N GLU R 264 " --> pdb=" O CYS R 260 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG R 265 " --> pdb=" O GLY R 261 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N SER R 268 " --> pdb=" O GLU R 264 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA R 269 " --> pdb=" O ARG R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 280 No H-bonds generated for 'chain 'R' and resid 278 through 280' Processing helix chain 'R' and resid 282 through 290 removed outlier: 3.811A pdb=" N ILE R 286 " --> pdb=" O VAL R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 304 Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 224 removed outlier: 4.645A pdb=" N VAL A 234 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLY A 47 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A 253 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 254 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE A 290 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE A 256 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN A 292 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 258 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.554A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.552A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.720A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.752A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.602A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.509A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.319A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.509A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.982A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 5.458A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1892 1.33 - 1.45: 2058 1.45 - 1.57: 4719 1.57 - 1.69: 0 1.69 - 1.82: 74 Bond restraints: 8743 Sorted by residual: bond pdb=" CA CYS R 170 " pdb=" C CYS R 170 " ideal model delta sigma weight residual 1.520 1.489 0.031 1.12e-02 7.97e+03 7.46e+00 bond pdb=" CA PHE R 174 " pdb=" CB PHE R 174 " ideal model delta sigma weight residual 1.530 1.489 0.041 1.58e-02 4.01e+03 6.62e+00 bond pdb=" C CYS R 170 " pdb=" O CYS R 170 " ideal model delta sigma weight residual 1.235 1.206 0.028 1.18e-02 7.18e+03 5.73e+00 bond pdb=" CA GLU R 172 " pdb=" CB GLU R 172 " ideal model delta sigma weight residual 1.534 1.500 0.034 1.57e-02 4.06e+03 4.58e+00 bond pdb=" C PHE R 174 " pdb=" N PRO R 175 " ideal model delta sigma weight residual 1.334 1.287 0.047 2.34e-02 1.83e+03 4.09e+00 ... (remaining 8738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.82: 11870 3.82 - 7.64: 44 7.64 - 11.47: 3 11.47 - 15.29: 2 15.29 - 19.11: 1 Bond angle restraints: 11920 Sorted by residual: angle pdb=" N LYS R 173 " pdb=" CA LYS R 173 " pdb=" C LYS R 173 " ideal model delta sigma weight residual 110.80 91.69 19.11 2.13e+00 2.20e-01 8.05e+01 angle pdb=" C LYS R 173 " pdb=" CA LYS R 173 " pdb=" CB LYS R 173 " ideal model delta sigma weight residual 110.42 124.89 -14.47 1.99e+00 2.53e-01 5.29e+01 angle pdb=" C PHE R 174 " pdb=" CA PHE R 174 " pdb=" CB PHE R 174 " ideal model delta sigma weight residual 110.17 121.65 -11.48 1.97e+00 2.58e-01 3.39e+01 angle pdb=" N CYS R 170 " pdb=" CA CYS R 170 " pdb=" C CYS R 170 " ideal model delta sigma weight residual 108.13 100.51 7.62 1.72e+00 3.38e-01 1.96e+01 angle pdb=" C GLU R 172 " pdb=" N LYS R 173 " pdb=" CA LYS R 173 " ideal model delta sigma weight residual 121.54 129.27 -7.73 1.91e+00 2.74e-01 1.64e+01 ... (remaining 11915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 4670 17.36 - 34.71: 358 34.71 - 52.07: 45 52.07 - 69.42: 9 69.42 - 86.78: 4 Dihedral angle restraints: 5086 sinusoidal: 1745 harmonic: 3341 Sorted by residual: dihedral pdb=" CB CYS R 92 " pdb=" SG CYS R 92 " pdb=" SG CYS R 170 " pdb=" CB CYS R 170 " ideal model delta sinusoidal sigma weight residual 93.00 145.43 -52.43 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" C PHE R 174 " pdb=" N PHE R 174 " pdb=" CA PHE R 174 " pdb=" CB PHE R 174 " ideal model delta harmonic sigma weight residual -122.60 -135.40 12.80 0 2.50e+00 1.60e-01 2.62e+01 dihedral pdb=" CA THR R 216 " pdb=" C THR R 216 " pdb=" N GLU R 217 " pdb=" CA GLU R 217 " ideal model delta harmonic sigma weight residual 180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 5083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1259 0.089 - 0.177: 110 0.177 - 0.266: 4 0.266 - 0.354: 0 0.354 - 0.443: 1 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CA PHE R 174 " pdb=" N PHE R 174 " pdb=" C PHE R 174 " pdb=" CB PHE R 174 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CB VAL G 54 " pdb=" CA VAL G 54 " pdb=" CG1 VAL G 54 " pdb=" CG2 VAL G 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA PHE R 171 " pdb=" N PHE R 171 " pdb=" C PHE R 171 " pdb=" CB PHE R 171 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1371 not shown) Planarity restraints: 1517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 174 " -0.053 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO R 175 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO R 175 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO R 175 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 174 " 0.027 2.00e-02 2.50e+03 2.26e-02 8.91e+00 pdb=" CG PHE R 174 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE R 174 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE R 174 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE R 174 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE R 174 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE R 174 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 102 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.99e+00 pdb=" C ASN R 102 " -0.049 2.00e-02 2.50e+03 pdb=" O ASN R 102 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE R 103 " 0.017 2.00e-02 2.50e+03 ... (remaining 1514 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 81 2.62 - 3.19: 7481 3.19 - 3.76: 13072 3.76 - 4.33: 18710 4.33 - 4.90: 31346 Nonbonded interactions: 70690 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.051 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.095 3.040 nonbonded pdb=" NH1 ARG A 238 " pdb=" OD1 ASP B 186 " model vdw 2.148 3.120 nonbonded pdb=" OG SER A 6 " pdb=" OD1 ASP A 9 " model vdw 2.166 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.190 3.040 ... (remaining 70685 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.260 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8745 Z= 0.270 Angle : 0.736 19.110 11924 Z= 0.406 Chirality : 0.050 0.443 1374 Planarity : 0.005 0.080 1517 Dihedral : 12.449 86.778 2924 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.12 % Allowed : 0.36 % Favored : 99.53 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.24), residues: 1133 helix: 0.54 (0.27), residues: 372 sheet: -0.40 (0.31), residues: 281 loop : -1.39 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 244 HIS 0.011 0.002 HIS A 230 PHE 0.052 0.002 PHE R 174 TYR 0.026 0.002 TYR R 104 ARG 0.006 0.001 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.17772 ( 416) hydrogen bonds : angle 7.23422 ( 1200) SS BOND : bond 0.01669 ( 2) SS BOND : angle 1.89958 ( 4) covalent geometry : bond 0.00633 ( 8743) covalent geometry : angle 0.73570 (11920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 0.963 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 1.1698 time to fit residues: 211.8994 Evaluate side-chains 151 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 47 optimal weight: 0.0370 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN A 278 ASN A 294 GLN B 32 GLN B 75 GLN B 237 ASN B 259 GLN B 340 ASN G 24 ASN S 186 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.099604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.087441 restraints weight = 14559.770| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.88 r_work: 0.3166 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8745 Z= 0.158 Angle : 0.607 8.702 11924 Z= 0.324 Chirality : 0.044 0.173 1374 Planarity : 0.004 0.047 1517 Dihedral : 5.065 29.566 1236 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.49 % Allowed : 10.08 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.25), residues: 1133 helix: 0.81 (0.27), residues: 386 sheet: 0.00 (0.31), residues: 285 loop : -1.35 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS B 62 PHE 0.026 0.002 PHE R 28 TYR 0.017 0.001 TYR R 270 ARG 0.007 0.001 ARG R 132 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 416) hydrogen bonds : angle 5.21156 ( 1200) SS BOND : bond 0.00632 ( 2) SS BOND : angle 1.29504 ( 4) covalent geometry : bond 0.00368 ( 8743) covalent geometry : angle 0.60666 (11920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.000 Fit side-chains REVERT: A 343 ASP cc_start: 0.7953 (m-30) cc_final: 0.7619 (m-30) REVERT: B 17 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8387 (tp-100) REVERT: B 239 ASN cc_start: 0.8978 (m110) cc_final: 0.8685 (m110) REVERT: R 179 TRP cc_start: 0.8401 (p-90) cc_final: 0.8087 (p-90) outliers start: 21 outliers final: 13 residues processed: 160 average time/residue: 1.1886 time to fit residues: 202.7937 Evaluate side-chains 163 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 99 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 75 GLN B 237 ASN B 259 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 24 ASN S 186 GLN S 194 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.098148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.085997 restraints weight = 14770.470| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.92 r_work: 0.3144 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8745 Z= 0.170 Angle : 0.587 8.577 11924 Z= 0.312 Chirality : 0.044 0.145 1374 Planarity : 0.004 0.048 1517 Dihedral : 4.913 29.199 1236 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.61 % Allowed : 12.93 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.25), residues: 1133 helix: 0.95 (0.27), residues: 389 sheet: 0.05 (0.31), residues: 261 loop : -1.27 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.006 0.001 HIS A 230 PHE 0.028 0.002 PHE R 28 TYR 0.020 0.002 TYR R 253 ARG 0.007 0.001 ARG R 208 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 416) hydrogen bonds : angle 4.91438 ( 1200) SS BOND : bond 0.00104 ( 2) SS BOND : angle 1.18462 ( 4) covalent geometry : bond 0.00404 ( 8743) covalent geometry : angle 0.58677 (11920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.891 Fit side-chains REVERT: A 343 ASP cc_start: 0.7963 (m-30) cc_final: 0.7524 (m-30) REVERT: B 239 ASN cc_start: 0.8987 (m110) cc_final: 0.8657 (m110) REVERT: R 179 TRP cc_start: 0.8333 (p-90) cc_final: 0.8112 (p-90) outliers start: 22 outliers final: 14 residues processed: 167 average time/residue: 1.2051 time to fit residues: 214.1768 Evaluate side-chains 167 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 32 GLN B 75 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 24 ASN S 186 GLN R 167 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.097452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.085385 restraints weight = 14715.421| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.92 r_work: 0.3134 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8745 Z= 0.191 Angle : 0.595 9.161 11924 Z= 0.316 Chirality : 0.044 0.137 1374 Planarity : 0.005 0.071 1517 Dihedral : 4.906 30.144 1236 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.08 % Allowed : 15.07 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1133 helix: 1.06 (0.27), residues: 387 sheet: -0.02 (0.31), residues: 262 loop : -1.22 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 99 HIS 0.003 0.001 HIS R 167 PHE 0.019 0.002 PHE R 174 TYR 0.021 0.002 TYR R 253 ARG 0.009 0.001 ARG R 187 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 416) hydrogen bonds : angle 4.87146 ( 1200) SS BOND : bond 0.00212 ( 2) SS BOND : angle 1.13796 ( 4) covalent geometry : bond 0.00458 ( 8743) covalent geometry : angle 0.59454 (11920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.874 Fit side-chains REVERT: A 343 ASP cc_start: 0.7995 (m-30) cc_final: 0.7582 (m-30) REVERT: B 17 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8520 (tp40) REVERT: B 57 LYS cc_start: 0.9076 (ptpt) cc_final: 0.8753 (mtmt) REVERT: B 239 ASN cc_start: 0.8991 (m110) cc_final: 0.8686 (m110) REVERT: R 179 TRP cc_start: 0.8306 (p-90) cc_final: 0.8093 (p-90) REVERT: R 226 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7682 (mtm110) outliers start: 26 outliers final: 17 residues processed: 165 average time/residue: 1.1305 time to fit residues: 198.9602 Evaluate side-chains 169 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 226 ARG Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 32 GLN B 75 GLN B 237 ASN B 259 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN S 186 GLN R 84 ASN R 167 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.098058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.086036 restraints weight = 14564.204| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.91 r_work: 0.3143 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8745 Z= 0.164 Angle : 0.569 9.214 11924 Z= 0.303 Chirality : 0.043 0.134 1374 Planarity : 0.004 0.049 1517 Dihedral : 4.791 29.425 1236 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.44 % Allowed : 16.25 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1133 helix: 1.19 (0.27), residues: 387 sheet: -0.03 (0.31), residues: 263 loop : -1.17 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 244 HIS 0.003 0.001 HIS A 230 PHE 0.028 0.002 PHE R 28 TYR 0.017 0.002 TYR R 104 ARG 0.008 0.001 ARG R 126 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 416) hydrogen bonds : angle 4.76175 ( 1200) SS BOND : bond 0.00086 ( 2) SS BOND : angle 1.07796 ( 4) covalent geometry : bond 0.00391 ( 8743) covalent geometry : angle 0.56863 (11920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.964 Fit side-chains REVERT: A 343 ASP cc_start: 0.7965 (m-30) cc_final: 0.7601 (m-30) REVERT: B 57 LYS cc_start: 0.9072 (ptpt) cc_final: 0.8688 (mtmt) REVERT: B 59 TYR cc_start: 0.8756 (m-80) cc_final: 0.8375 (m-80) REVERT: B 239 ASN cc_start: 0.8947 (m110) cc_final: 0.8674 (m110) REVERT: R 226 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7656 (mtm110) outliers start: 29 outliers final: 18 residues processed: 167 average time/residue: 1.1348 time to fit residues: 202.2754 Evaluate side-chains 169 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 211 GLN Chi-restraints excluded: chain R residue 226 ARG Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 89 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 0.0970 chunk 63 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 32 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 24 ASN S 186 GLN R 167 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.098080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.085996 restraints weight = 14487.255| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.91 r_work: 0.3148 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8745 Z= 0.151 Angle : 0.563 9.392 11924 Z= 0.299 Chirality : 0.042 0.135 1374 Planarity : 0.004 0.049 1517 Dihedral : 4.699 27.695 1236 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.68 % Allowed : 17.32 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1133 helix: 1.24 (0.27), residues: 394 sheet: 0.04 (0.31), residues: 269 loop : -1.13 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP R 179 HIS 0.003 0.001 HIS R 167 PHE 0.017 0.002 PHE R 171 TYR 0.016 0.001 TYR R 104 ARG 0.009 0.001 ARG R 249 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 416) hydrogen bonds : angle 4.68067 ( 1200) SS BOND : bond 0.00142 ( 2) SS BOND : angle 0.97834 ( 4) covalent geometry : bond 0.00358 ( 8743) covalent geometry : angle 0.56257 (11920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 1.004 Fit side-chains REVERT: A 238 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8412 (mtm110) REVERT: B 17 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8496 (tp40) REVERT: B 57 LYS cc_start: 0.9066 (ptpt) cc_final: 0.8716 (mtmt) REVERT: B 59 TYR cc_start: 0.8736 (m-80) cc_final: 0.8422 (m-80) REVERT: B 239 ASN cc_start: 0.8940 (m110) cc_final: 0.8693 (m110) REVERT: S 183 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8584 (pm20) REVERT: R 226 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7646 (mtm110) outliers start: 31 outliers final: 20 residues processed: 162 average time/residue: 1.1591 time to fit residues: 200.3370 Evaluate side-chains 172 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 211 GLN Chi-restraints excluded: chain R residue 226 ARG Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 100 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 84 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 24 ASN S 186 GLN R 167 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.099044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.086924 restraints weight = 14570.019| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.93 r_work: 0.3161 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8745 Z= 0.137 Angle : 0.556 9.541 11924 Z= 0.295 Chirality : 0.042 0.135 1374 Planarity : 0.004 0.049 1517 Dihedral : 4.601 27.187 1236 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.03 % Allowed : 17.32 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1133 helix: 1.34 (0.27), residues: 394 sheet: 0.10 (0.31), residues: 268 loop : -1.11 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP R 179 HIS 0.005 0.001 HIS A 230 PHE 0.018 0.001 PHE R 171 TYR 0.016 0.001 TYR R 104 ARG 0.009 0.001 ARG R 249 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 416) hydrogen bonds : angle 4.62799 ( 1200) SS BOND : bond 0.00150 ( 2) SS BOND : angle 0.90027 ( 4) covalent geometry : bond 0.00322 ( 8743) covalent geometry : angle 0.55551 (11920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.905 Fit side-chains REVERT: B 57 LYS cc_start: 0.9064 (ptpt) cc_final: 0.8717 (mtmp) REVERT: B 59 TYR cc_start: 0.8735 (m-80) cc_final: 0.8473 (m-80) REVERT: B 239 ASN cc_start: 0.8934 (m110) cc_final: 0.8729 (m110) REVERT: S 183 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8566 (pm20) REVERT: R 226 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.6439 (mmm160) outliers start: 34 outliers final: 21 residues processed: 172 average time/residue: 1.0915 time to fit residues: 200.6193 Evaluate side-chains 178 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 211 GLN Chi-restraints excluded: chain R residue 226 ARG Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 0.0040 chunk 55 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN S 186 GLN R 167 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.098547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.086370 restraints weight = 14841.692| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.95 r_work: 0.3157 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8745 Z= 0.144 Angle : 0.568 9.706 11924 Z= 0.300 Chirality : 0.043 0.133 1374 Planarity : 0.004 0.050 1517 Dihedral : 4.609 26.464 1236 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.03 % Allowed : 18.51 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.25), residues: 1133 helix: 1.37 (0.27), residues: 394 sheet: 0.12 (0.31), residues: 268 loop : -1.11 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP R 179 HIS 0.006 0.001 HIS A 230 PHE 0.019 0.002 PHE R 21 TYR 0.017 0.001 TYR R 270 ARG 0.009 0.001 ARG R 126 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 416) hydrogen bonds : angle 4.63780 ( 1200) SS BOND : bond 0.00154 ( 2) SS BOND : angle 0.89106 ( 4) covalent geometry : bond 0.00340 ( 8743) covalent geometry : angle 0.56828 (11920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.871 Fit side-chains REVERT: B 57 LYS cc_start: 0.9066 (ptpt) cc_final: 0.8742 (mtmp) REVERT: B 59 TYR cc_start: 0.8762 (m-80) cc_final: 0.8533 (m-80) REVERT: B 268 ASN cc_start: 0.8294 (p0) cc_final: 0.8081 (p0) REVERT: S 183 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8566 (pm20) REVERT: R 152 SER cc_start: 0.8460 (p) cc_final: 0.8257 (t) REVERT: R 226 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.6455 (mmm160) outliers start: 34 outliers final: 22 residues processed: 171 average time/residue: 1.1300 time to fit residues: 206.7486 Evaluate side-chains 180 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 211 GLN Chi-restraints excluded: chain R residue 226 ARG Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 0.0670 chunk 45 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN S 186 GLN R 167 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.099586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.087472 restraints weight = 14593.730| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.91 r_work: 0.3166 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8745 Z= 0.141 Angle : 0.575 10.399 11924 Z= 0.302 Chirality : 0.043 0.132 1374 Planarity : 0.004 0.050 1517 Dihedral : 4.610 27.311 1236 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.56 % Allowed : 19.57 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1133 helix: 1.47 (0.28), residues: 387 sheet: 0.07 (0.31), residues: 270 loop : -1.05 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP R 179 HIS 0.006 0.001 HIS A 230 PHE 0.016 0.001 PHE R 171 TYR 0.018 0.001 TYR R 270 ARG 0.009 0.001 ARG R 208 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 416) hydrogen bonds : angle 4.62698 ( 1200) SS BOND : bond 0.00195 ( 2) SS BOND : angle 0.98257 ( 4) covalent geometry : bond 0.00331 ( 8743) covalent geometry : angle 0.57463 (11920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.872 Fit side-chains REVERT: S 183 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8531 (pm20) REVERT: R 152 SER cc_start: 0.8415 (p) cc_final: 0.8209 (t) REVERT: R 226 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.6478 (mmm160) outliers start: 30 outliers final: 21 residues processed: 171 average time/residue: 1.0562 time to fit residues: 193.4916 Evaluate side-chains 180 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 211 GLN Chi-restraints excluded: chain R residue 226 ARG Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 0.0570 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.0370 chunk 106 optimal weight: 0.0980 chunk 69 optimal weight: 0.0970 chunk 59 optimal weight: 0.0870 chunk 83 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 overall best weight: 0.0752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN R 167 HIS R 271 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.103769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.091574 restraints weight = 14508.562| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.93 r_work: 0.3240 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8745 Z= 0.099 Angle : 0.548 12.490 11924 Z= 0.285 Chirality : 0.042 0.160 1374 Planarity : 0.004 0.050 1517 Dihedral : 4.212 23.216 1236 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.90 % Allowed : 21.00 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1133 helix: 1.64 (0.27), residues: 390 sheet: 0.22 (0.31), residues: 277 loop : -1.13 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP R 179 HIS 0.007 0.001 HIS A 230 PHE 0.020 0.001 PHE R 21 TYR 0.019 0.001 TYR R 253 ARG 0.009 0.001 ARG R 126 Details of bonding type rmsd hydrogen bonds : bond 0.02934 ( 416) hydrogen bonds : angle 4.40450 ( 1200) SS BOND : bond 0.00273 ( 2) SS BOND : angle 0.53388 ( 4) covalent geometry : bond 0.00210 ( 8743) covalent geometry : angle 0.54813 (11920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 1.014 Fit side-chains REVERT: B 76 ASP cc_start: 0.8233 (p0) cc_final: 0.8033 (p0) REVERT: B 243 THR cc_start: 0.8724 (p) cc_final: 0.8458 (p) REVERT: S 82 GLN cc_start: 0.8055 (tp-100) cc_final: 0.7784 (tp40) REVERT: R 152 SER cc_start: 0.8339 (p) cc_final: 0.8130 (t) outliers start: 16 outliers final: 6 residues processed: 180 average time/residue: 1.0866 time to fit residues: 209.1863 Evaluate side-chains 170 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 164 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN A 294 GLN B 75 GLN B 125 ASN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN R 167 HIS R 271 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.099556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.087287 restraints weight = 14778.011| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.94 r_work: 0.3165 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8745 Z= 0.169 Angle : 0.609 14.721 11924 Z= 0.318 Chirality : 0.044 0.133 1374 Planarity : 0.004 0.053 1517 Dihedral : 4.641 26.175 1236 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.19 % Allowed : 23.13 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1133 helix: 1.60 (0.27), residues: 387 sheet: 0.08 (0.31), residues: 273 loop : -1.10 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP R 179 HIS 0.010 0.001 HIS R 157 PHE 0.031 0.002 PHE R 99 TYR 0.022 0.002 TYR R 186 ARG 0.008 0.001 ARG R 249 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 416) hydrogen bonds : angle 4.57720 ( 1200) SS BOND : bond 0.00241 ( 2) SS BOND : angle 0.91140 ( 4) covalent geometry : bond 0.00404 ( 8743) covalent geometry : angle 0.60843 (11920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6723.14 seconds wall clock time: 116 minutes 26.85 seconds (6986.85 seconds total)