Starting phenix.real_space_refine on Mon Mar 11 12:18:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odv_16819/03_2024/8odv_16819.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odv_16819/03_2024/8odv_16819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odv_16819/03_2024/8odv_16819.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odv_16819/03_2024/8odv_16819.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odv_16819/03_2024/8odv_16819.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odv_16819/03_2024/8odv_16819.pdb" } resolution = 4.7 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= 0.000 sd= 0.021 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 52 5.16 5 C 5330 2.51 5 N 1366 2.21 5 O 1484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C GLU 1047": "OE1" <-> "OE2" Residue "C GLU 1089": "OE1" <-> "OE2" Residue "C GLU 1143": "OE1" <-> "OE2" Residue "D GLU 309": "OE1" <-> "OE2" Residue "D GLU 1047": "OE1" <-> "OE2" Residue "D GLU 1089": "OE1" <-> "OE2" Residue "D GLU 1143": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8233 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2317 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 2 Chain: "B" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2317 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 2 Chain: "C" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1799 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 8, 'TRANS': 209} Chain breaks: 2 Chain: "D" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1799 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 8, 'TRANS': 209} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1822 SG CYS A 281 44.572 43.672 14.092 1.00167.44 S ATOM 1846 SG CYS A 284 41.703 43.987 16.312 1.00153.79 S ATOM 4139 SG CYS B 281 41.903 47.146 14.049 1.00167.06 S ATOM 4163 SG CYS B 284 44.773 46.863 16.271 1.00154.18 S Time building chain proxies: 4.65, per 1000 atoms: 0.56 Number of scatterers: 8233 At special positions: 0 Unit cell: (87.69, 93.24, 146.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 52 16.00 O 1484 8.00 N 1366 7.00 C 5330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.15 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 281 " pdb="ZN ZN A 401 " - pdb=" SG CYS B 281 " pdb="ZN ZN A 401 " - pdb=" SG CYS B 284 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 284 " Number of angles added : 6 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 2 sheets defined 65.9% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 18 through 25 removed outlier: 3.607A pdb=" N LEU A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A 24 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 52 removed outlier: 3.534A pdb=" N THR A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 67 through 74 removed outlier: 4.070A pdb=" N ASP A 71 " --> pdb=" O HIS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 105 removed outlier: 3.812A pdb=" N MET A 101 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'A' and resid 132 through 146 Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 206 through 229 removed outlier: 4.102A pdb=" N VAL A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 259 Processing helix chain 'A' and resid 281 through 303 removed outlier: 3.755A pdb=" N ALA A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 removed outlier: 4.137A pdb=" N MET A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 25 removed outlier: 3.608A pdb=" N LEU B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 52 removed outlier: 3.533A pdb=" N THR B 43 " --> pdb=" O GLY B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 67 through 74 removed outlier: 4.070A pdb=" N ASP B 71 " --> pdb=" O HIS B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 105 removed outlier: 3.812A pdb=" N MET B 101 " --> pdb=" O PRO B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'B' and resid 132 through 146 Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 168 through 185 Processing helix chain 'B' and resid 206 through 229 removed outlier: 4.101A pdb=" N VAL B 210 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS B 229 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 259 Processing helix chain 'B' and resid 281 through 303 removed outlier: 3.756A pdb=" N ALA B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 removed outlier: 4.138A pdb=" N MET B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 310 removed outlier: 3.738A pdb=" N PHE C 310 " --> pdb=" O LEU C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 356 removed outlier: 3.900A pdb=" N TRP C 354 " --> pdb=" O GLY C 350 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TRP C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG C 356 " --> pdb=" O VAL C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1019 Processing helix chain 'C' and resid 1023 through 1034 removed outlier: 3.630A pdb=" N ARG C1031 " --> pdb=" O ASN C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1065 removed outlier: 3.551A pdb=" N LYS C1043 " --> pdb=" O SER C1039 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1124 removed outlier: 3.674A pdb=" N ASP C1086 " --> pdb=" O ASP C1082 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU C1087 " --> pdb=" O LYS C1083 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU C1089 " --> pdb=" O MET C1085 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS C1090 " --> pdb=" O ASP C1086 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS C1091 " --> pdb=" O GLU C1087 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS C1092 " --> pdb=" O LEU C1088 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C1097 " --> pdb=" O SER C1093 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE C1108 " --> pdb=" O ARG C1104 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU C1113 " --> pdb=" O TYR C1109 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU C1121 " --> pdb=" O MET C1117 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N CYS C1122 " --> pdb=" O GLN C1118 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1148 removed outlier: 4.616A pdb=" N LEU C1145 " --> pdb=" O TRP C1141 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N VAL C1146 " --> pdb=" O VAL C1142 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER C1147 " --> pdb=" O GLU C1143 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C1148 " --> pdb=" O TRP C1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 1164 through 1181 removed outlier: 3.932A pdb=" N VAL C1168 " --> pdb=" O ALA C1164 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C1169 " --> pdb=" O CYS C1165 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C1171 " --> pdb=" O GLY C1167 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL C1172 " --> pdb=" O VAL C1168 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C1181 " --> pdb=" O MET C1177 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 310 removed outlier: 3.737A pdb=" N PHE D 310 " --> pdb=" O LEU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 356 removed outlier: 3.900A pdb=" N TRP D 354 " --> pdb=" O GLY D 350 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TRP D 355 " --> pdb=" O ALA D 351 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG D 356 " --> pdb=" O VAL D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 1002 through 1019 Processing helix chain 'D' and resid 1023 through 1034 removed outlier: 3.631A pdb=" N ARG D1031 " --> pdb=" O ASN D1027 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1065 removed outlier: 3.551A pdb=" N LYS D1043 " --> pdb=" O SER D1039 " (cutoff:3.500A) Processing helix chain 'D' and resid 1070 through 1124 removed outlier: 3.674A pdb=" N ASP D1086 " --> pdb=" O ASP D1082 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU D1087 " --> pdb=" O LYS D1083 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU D1089 " --> pdb=" O MET D1085 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS D1090 " --> pdb=" O ASP D1086 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS D1091 " --> pdb=" O GLU D1087 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS D1092 " --> pdb=" O LEU D1088 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D1097 " --> pdb=" O SER D1093 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE D1108 " --> pdb=" O ARG D1104 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU D1113 " --> pdb=" O TYR D1109 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET D1117 " --> pdb=" O LEU D1113 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU D1121 " --> pdb=" O MET D1117 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N CYS D1122 " --> pdb=" O GLN D1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 1139 through 1148 removed outlier: 4.616A pdb=" N LEU D1145 " --> pdb=" O TRP D1141 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N VAL D1146 " --> pdb=" O VAL D1142 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER D1147 " --> pdb=" O GLU D1143 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE D1148 " --> pdb=" O TRP D1144 " (cutoff:3.500A) Processing helix chain 'D' and resid 1164 through 1181 removed outlier: 3.931A pdb=" N VAL D1168 " --> pdb=" O ALA D1164 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU D1169 " --> pdb=" O CYS D1165 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D1171 " --> pdb=" O GLY D1167 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL D1172 " --> pdb=" O VAL D1168 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG D1181 " --> pdb=" O MET D1177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.895A pdb=" N TYR A 91 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP A 29 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL A 237 " --> pdb=" O TRP A 29 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE A 31 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N VAL A 239 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY A 33 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 11.078A pdb=" N CYS A 266 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N PHE A 236 " --> pdb=" O CYS A 266 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N VAL A 268 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N CYS A 238 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.895A pdb=" N TYR B 91 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP B 29 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N VAL B 237 " --> pdb=" O TRP B 29 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE B 31 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL B 239 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY B 33 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 11.077A pdb=" N CYS B 266 " --> pdb=" O THR B 234 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N PHE B 236 " --> pdb=" O CYS B 266 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N VAL B 268 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N CYS B 238 " --> pdb=" O VAL B 268 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1314 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: 1.98 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2601 1.34 - 1.46: 1741 1.46 - 1.58: 3982 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 8412 Sorted by residual: bond pdb=" CB THR A 163 " pdb=" CG2 THR A 163 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.62e+00 bond pdb=" CB THR B 163 " pdb=" CG2 THR B 163 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.53e+00 bond pdb=" CB PHE A 228 " pdb=" CG PHE A 228 " ideal model delta sigma weight residual 1.502 1.468 0.034 2.30e-02 1.89e+03 2.18e+00 bond pdb=" CB VAL B 180 " pdb=" CG1 VAL B 180 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.09e+00 bond pdb=" CB VAL A 180 " pdb=" CG1 VAL A 180 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.09e+00 ... (remaining 8407 not shown) Histogram of bond angle deviations from ideal: 99.48 - 106.39: 234 106.39 - 113.30: 4643 113.30 - 120.21: 3383 120.21 - 127.12: 3014 127.12 - 134.03: 110 Bond angle restraints: 11384 Sorted by residual: angle pdb=" N PHE D1148 " pdb=" CA PHE D1148 " pdb=" C PHE D1148 " ideal model delta sigma weight residual 109.81 118.96 -9.15 2.21e+00 2.05e-01 1.72e+01 angle pdb=" N PHE C1148 " pdb=" CA PHE C1148 " pdb=" C PHE C1148 " ideal model delta sigma weight residual 109.81 118.91 -9.10 2.21e+00 2.05e-01 1.70e+01 angle pdb=" C ASP A 230 " pdb=" N GLU A 231 " pdb=" CA GLU A 231 " ideal model delta sigma weight residual 121.54 129.37 -7.83 1.91e+00 2.74e-01 1.68e+01 angle pdb=" C ASP B 230 " pdb=" N GLU B 231 " pdb=" CA GLU B 231 " ideal model delta sigma weight residual 121.54 129.31 -7.77 1.91e+00 2.74e-01 1.66e+01 angle pdb=" C GLU A 94 " pdb=" N ILE A 95 " pdb=" CA ILE A 95 " ideal model delta sigma weight residual 122.48 118.28 4.20 1.13e+00 7.83e-01 1.38e+01 ... (remaining 11379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 4497 16.26 - 32.51: 416 32.51 - 48.77: 109 48.77 - 65.02: 22 65.02 - 81.28: 6 Dihedral angle restraints: 5050 sinusoidal: 2064 harmonic: 2986 Sorted by residual: dihedral pdb=" CA PRO B 159 " pdb=" C PRO B 159 " pdb=" N THR B 160 " pdb=" CA THR B 160 " ideal model delta harmonic sigma weight residual -180.00 -153.05 -26.95 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA PRO A 159 " pdb=" C PRO A 159 " pdb=" N THR A 160 " pdb=" CA THR A 160 " ideal model delta harmonic sigma weight residual -180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA ILE D1020 " pdb=" C ILE D1020 " pdb=" N GLY D1021 " pdb=" CA GLY D1021 " ideal model delta harmonic sigma weight residual 180.00 155.69 24.31 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 5047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 771 0.043 - 0.085: 384 0.085 - 0.128: 109 0.128 - 0.171: 18 0.171 - 0.213: 4 Chirality restraints: 1286 Sorted by residual: chirality pdb=" CB ILE C1036 " pdb=" CA ILE C1036 " pdb=" CG1 ILE C1036 " pdb=" CG2 ILE C1036 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE D1036 " pdb=" CA ILE D1036 " pdb=" CG1 ILE D1036 " pdb=" CG2 ILE D1036 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA TYR B 302 " pdb=" N TYR B 302 " pdb=" C TYR B 302 " pdb=" CB TYR B 302 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.55e-01 ... (remaining 1283 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C1092 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.28e+00 pdb=" C LYS C1092 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS C1092 " -0.020 2.00e-02 2.50e+03 pdb=" N SER C1093 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D1092 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C LYS D1092 " -0.052 2.00e-02 2.50e+03 pdb=" O LYS D1092 " 0.020 2.00e-02 2.50e+03 pdb=" N SER D1093 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 293 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.46e+00 pdb=" C LYS B 293 " -0.047 2.00e-02 2.50e+03 pdb=" O LYS B 293 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR B 294 " 0.016 2.00e-02 2.50e+03 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1178 2.73 - 3.28: 8988 3.28 - 3.82: 13647 3.82 - 4.36: 15866 4.36 - 4.90: 24146 Nonbonded interactions: 63825 Sorted by model distance: nonbonded pdb=" O PHE C1032 " pdb=" OG SER C1035 " model vdw 2.192 2.440 nonbonded pdb=" O PHE D1032 " pdb=" OG SER D1035 " model vdw 2.193 2.440 nonbonded pdb=" O HIS A 265 " pdb=" ND2 ASN A 307 " model vdw 2.220 2.520 nonbonded pdb=" O HIS B 265 " pdb=" ND2 ASN B 307 " model vdw 2.221 2.520 nonbonded pdb=" OE1 GLU B 251 " pdb=" OH TYR B 302 " model vdw 2.232 2.440 ... (remaining 63820 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 339) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 group one per residue 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: 0.820 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: 3.870 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 25.420 Find NCS groups from input model: 0.430 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 : 0.007 0.053 8412 Z= 0.420 Angle : 1.105 9.883 11384 Z= 0.614 Chirality : 0.052 0.213 1286 Planarity : 0.008 0.055 1426 Dihedral : 14.056 81.277 3098 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 25.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.04 (0.21), residues: 998 helix: -2.54 (0.15), residues: 628 sheet: -2.19 (0.54), residues: 78 loop : -2.58 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 29 HIS 0.007 0.003 HIS A 265 PHE 0.024 0.002 PHE B 169 TYR 0.019 0.002 TYR A 302 ARG 0.006 0.001 ARG C1099 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8201 (mmt) cc_final: 0.7461 (mtp) REVERT: A 55 ARG cc_start: 0.7240 (mmt180) cc_final: 0.5304 (mmm160) REVERT: A 136 MET cc_start: 0.9038 (ptm) cc_final: 0.8824 (ptm) REVERT: A 223 GLU cc_start: 0.9358 (mt-10) cc_final: 0.8602 (mm-30) REVERT: A 311 MET cc_start: 0.8447 (tpp) cc_final: 0.7978 (mmm) REVERT: A 330 MET cc_start: 0.8806 (mtm) cc_final: 0.8473 (mmm) REVERT: A 331 LEU cc_start: 0.9495 (mt) cc_final: 0.9207 (mm) REVERT: B 14 MET cc_start: 0.7817 (mmt) cc_final: 0.6771 (mtp) REVERT: B 127 TYR cc_start: 0.8579 (t80) cc_final: 0.8309 (t80) REVERT: B 223 GLU cc_start: 0.9398 (mt-10) cc_final: 0.8678 (mm-30) REVERT: B 294 TYR cc_start: 0.9439 (m-80) cc_final: 0.8869 (m-10) REVERT: B 304 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8595 (mp0) REVERT: B 311 MET cc_start: 0.8544 (tpp) cc_final: 0.8140 (mmp) REVERT: B 330 MET cc_start: 0.8792 (mtm) cc_final: 0.8221 (mmm) REVERT: C 340 ARG cc_start: 0.8614 (mmt-90) cc_final: 0.8200 (tpt170) REVERT: C 1033 TYR cc_start: 0.8982 (m-80) cc_final: 0.8757 (m-80) REVERT: C 1073 LYS cc_start: 0.9466 (mmpt) cc_final: 0.9262 (mmmt) REVERT: C 1088 LEU cc_start: 0.9401 (mt) cc_final: 0.9181 (mt) REVERT: C 1153 MET cc_start: 0.7657 (tpt) cc_final: 0.7368 (mmp) REVERT: D 336 MET cc_start: 0.3465 (ptt) cc_final: 0.3085 (ptp) REVERT: D 1088 LEU cc_start: 0.9349 (mt) cc_final: 0.9136 (mt) REVERT: D 1153 MET cc_start: 0.7514 (tpt) cc_final: 0.7164 (tpt) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.2432 time to fit residues: 63.0626 Evaluate side-chains 125 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.6980 chunk 75 optimal weight: 30.0000 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS A 297 GLN A 307 ASN B 162 HIS B 297 GLN B 307 ASN C1068 GLN ** D1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1068 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8412 Z= 0.196 Angle : 0.691 9.108 11384 Z= 0.348 Chirality : 0.042 0.133 1286 Planarity : 0.005 0.056 1426 Dihedral : 5.179 21.242 1086 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.22 % Allowed : 4.42 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.57 (0.25), residues: 998 helix: -0.58 (0.19), residues: 628 sheet: -1.19 (0.50), residues: 86 loop : -1.70 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 29 HIS 0.006 0.002 HIS D1060 PHE 0.013 0.001 PHE B 236 TYR 0.015 0.001 TYR D1109 ARG 0.004 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8289 (mmt) cc_final: 0.7592 (mtp) REVERT: A 35 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8551 (mmmt) REVERT: A 101 MET cc_start: 0.8198 (tmm) cc_final: 0.7536 (mtt) REVERT: A 223 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8585 (mm-30) REVERT: A 253 MET cc_start: 0.9297 (ttm) cc_final: 0.9004 (ttm) REVERT: A 311 MET cc_start: 0.8326 (tpp) cc_final: 0.7805 (mmm) REVERT: A 330 MET cc_start: 0.8851 (mtm) cc_final: 0.8418 (mmm) REVERT: A 331 LEU cc_start: 0.9415 (mt) cc_final: 0.9181 (mm) REVERT: B 14 MET cc_start: 0.8037 (mmt) cc_final: 0.6935 (mtp) REVERT: B 101 MET cc_start: 0.8264 (tmm) cc_final: 0.7645 (mtt) REVERT: B 223 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8708 (mm-30) REVERT: B 239 VAL cc_start: 0.9172 (m) cc_final: 0.8953 (p) REVERT: B 253 MET cc_start: 0.9266 (ttm) cc_final: 0.9042 (ttm) REVERT: B 294 TYR cc_start: 0.9280 (m-80) cc_final: 0.9073 (m-10) REVERT: B 295 LEU cc_start: 0.9518 (tp) cc_final: 0.9312 (tt) REVERT: B 299 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8518 (mt-10) REVERT: B 311 MET cc_start: 0.8483 (tpp) cc_final: 0.7834 (mmt) REVERT: B 330 MET cc_start: 0.8991 (mtm) cc_final: 0.8223 (tpp) REVERT: C 340 ARG cc_start: 0.8656 (mmt-90) cc_final: 0.8386 (mmm160) REVERT: C 1028 LEU cc_start: 0.9456 (tp) cc_final: 0.9109 (tp) REVERT: C 1032 PHE cc_start: 0.8333 (m-10) cc_final: 0.7735 (m-80) REVERT: C 1061 ASP cc_start: 0.9372 (m-30) cc_final: 0.9079 (m-30) REVERT: C 1088 LEU cc_start: 0.9330 (mt) cc_final: 0.9128 (tp) REVERT: C 1153 MET cc_start: 0.7488 (tpt) cc_final: 0.7276 (mmp) REVERT: D 336 MET cc_start: 0.3790 (ptt) cc_final: 0.3567 (ptp) REVERT: D 1028 LEU cc_start: 0.9535 (tp) cc_final: 0.9136 (tp) REVERT: D 1032 PHE cc_start: 0.8202 (m-10) cc_final: 0.7662 (m-80) REVERT: D 1153 MET cc_start: 0.7430 (tpt) cc_final: 0.7178 (mmp) outliers start: 2 outliers final: 0 residues processed: 178 average time/residue: 0.1969 time to fit residues: 49.9096 Evaluate side-chains 117 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 30.0000 chunk 25 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 0.0000 chunk 72 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 ASN B 265 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 ASN D1052 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8412 Z= 0.221 Angle : 0.678 8.422 11384 Z= 0.344 Chirality : 0.040 0.150 1286 Planarity : 0.005 0.054 1426 Dihedral : 4.953 21.586 1086 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.22 % Allowed : 5.09 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.27), residues: 998 helix: 0.13 (0.20), residues: 628 sheet: -0.78 (0.52), residues: 88 loop : -1.26 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 339 HIS 0.013 0.002 HIS D1060 PHE 0.013 0.002 PHE B 236 TYR 0.022 0.002 TYR A 302 ARG 0.003 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 160 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8583 (mmmt) REVERT: A 55 ARG cc_start: 0.6754 (mmt180) cc_final: 0.5293 (mmm160) REVERT: A 101 MET cc_start: 0.8220 (tmm) cc_final: 0.7413 (mtt) REVERT: A 136 MET cc_start: 0.8672 (ptt) cc_final: 0.7932 (ppp) REVERT: A 223 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8543 (mm-30) REVERT: A 253 MET cc_start: 0.9271 (ttm) cc_final: 0.9060 (ttm) REVERT: A 294 TYR cc_start: 0.9386 (m-10) cc_final: 0.9027 (m-80) REVERT: A 330 MET cc_start: 0.8977 (mtm) cc_final: 0.8374 (tpp) REVERT: B 14 MET cc_start: 0.8451 (mmt) cc_final: 0.7238 (mtp) REVERT: B 101 MET cc_start: 0.8704 (tmm) cc_final: 0.7720 (mtt) REVERT: B 104 LEU cc_start: 0.6565 (mt) cc_final: 0.6201 (mt) REVERT: B 223 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8545 (mm-30) REVERT: B 294 TYR cc_start: 0.9292 (m-80) cc_final: 0.8737 (m-80) REVERT: B 330 MET cc_start: 0.8985 (mtm) cc_final: 0.8348 (tpp) REVERT: C 340 ARG cc_start: 0.8559 (mmt-90) cc_final: 0.8266 (mmm160) REVERT: C 1032 PHE cc_start: 0.8409 (m-10) cc_final: 0.8027 (m-80) REVERT: C 1033 TYR cc_start: 0.8751 (m-80) cc_final: 0.8424 (m-80) REVERT: C 1061 ASP cc_start: 0.9357 (m-30) cc_final: 0.9120 (m-30) REVERT: D 1032 PHE cc_start: 0.8292 (m-10) cc_final: 0.7949 (m-80) REVERT: D 1088 LEU cc_start: 0.9435 (mt) cc_final: 0.9034 (tp) REVERT: D 1153 MET cc_start: 0.7374 (tpt) cc_final: 0.7145 (mmp) outliers start: 2 outliers final: 0 residues processed: 160 average time/residue: 0.1798 time to fit residues: 40.9385 Evaluate side-chains 105 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 43 optimal weight: 0.2980 chunk 61 optimal weight: 30.0000 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS C1052 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8412 Z= 0.164 Angle : 0.641 8.110 11384 Z= 0.318 Chirality : 0.041 0.134 1286 Planarity : 0.004 0.053 1426 Dihedral : 4.759 19.784 1086 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 998 helix: 0.37 (0.21), residues: 628 sheet: -0.57 (0.53), residues: 88 loop : -1.14 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 339 HIS 0.004 0.001 HIS D1098 PHE 0.015 0.001 PHE D1102 TYR 0.016 0.001 TYR C1033 ARG 0.002 0.000 ARG D1049 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8533 (mmt) cc_final: 0.7609 (mtp) REVERT: A 101 MET cc_start: 0.8483 (tmm) cc_final: 0.7676 (mtt) REVERT: A 136 MET cc_start: 0.8725 (ptt) cc_final: 0.7949 (ppp) REVERT: A 223 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8570 (mm-30) REVERT: A 256 GLU cc_start: 0.9379 (tp30) cc_final: 0.9028 (tm-30) REVERT: A 294 TYR cc_start: 0.9371 (m-10) cc_final: 0.9095 (m-80) REVERT: A 330 MET cc_start: 0.9082 (mtm) cc_final: 0.8383 (tpp) REVERT: B 14 MET cc_start: 0.8592 (mmt) cc_final: 0.7356 (mtp) REVERT: B 101 MET cc_start: 0.8806 (tmm) cc_final: 0.7952 (mtt) REVERT: B 136 MET cc_start: 0.8659 (ptt) cc_final: 0.7920 (ppp) REVERT: B 223 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8565 (mm-30) REVERT: B 227 GLN cc_start: 0.8870 (tp-100) cc_final: 0.8482 (tp-100) REVERT: B 256 GLU cc_start: 0.9359 (tp30) cc_final: 0.9009 (tm-30) REVERT: B 294 TYR cc_start: 0.9299 (m-80) cc_final: 0.8797 (m-80) REVERT: B 299 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8822 (mt-10) REVERT: B 311 MET cc_start: 0.8462 (tpp) cc_final: 0.7803 (mmp) REVERT: B 330 MET cc_start: 0.9043 (mtm) cc_final: 0.8326 (tpp) REVERT: C 1032 PHE cc_start: 0.8362 (m-10) cc_final: 0.7996 (m-80) REVERT: C 1033 TYR cc_start: 0.8678 (m-80) cc_final: 0.8160 (m-80) REVERT: C 1061 ASP cc_start: 0.9365 (m-30) cc_final: 0.9146 (m-30) REVERT: D 1028 LEU cc_start: 0.9497 (tp) cc_final: 0.9094 (tp) REVERT: D 1032 PHE cc_start: 0.8561 (m-10) cc_final: 0.7870 (m-80) REVERT: D 1153 MET cc_start: 0.7267 (tpt) cc_final: 0.7015 (tpt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2372 time to fit residues: 52.7312 Evaluate side-chains 118 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 30.0000 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 0.0010 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1052 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8412 Z= 0.155 Angle : 0.632 8.038 11384 Z= 0.311 Chirality : 0.040 0.139 1286 Planarity : 0.004 0.050 1426 Dihedral : 4.611 20.388 1086 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.11 % Allowed : 3.32 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.27), residues: 998 helix: 0.48 (0.21), residues: 630 sheet: -0.25 (0.53), residues: 88 loop : -0.97 (0.41), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D1074 HIS 0.010 0.001 HIS C1060 PHE 0.009 0.001 PHE A 169 TYR 0.014 0.001 TYR B 127 ARG 0.002 0.000 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8545 (mmt) cc_final: 0.7653 (mtp) REVERT: A 55 ARG cc_start: 0.6673 (mmt180) cc_final: 0.5355 (mmm160) REVERT: A 101 MET cc_start: 0.8719 (tmm) cc_final: 0.7951 (mtt) REVERT: A 136 MET cc_start: 0.8734 (ptt) cc_final: 0.7971 (ppp) REVERT: A 223 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8563 (mm-30) REVERT: A 256 GLU cc_start: 0.9333 (tp30) cc_final: 0.9037 (tm-30) REVERT: A 330 MET cc_start: 0.9074 (mtm) cc_final: 0.8434 (tpp) REVERT: B 14 MET cc_start: 0.8617 (mmt) cc_final: 0.7537 (mtp) REVERT: B 101 MET cc_start: 0.8455 (tmm) cc_final: 0.7675 (mtt) REVERT: B 223 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8555 (mm-30) REVERT: B 227 GLN cc_start: 0.8702 (tp-100) cc_final: 0.8476 (tp-100) REVERT: B 256 GLU cc_start: 0.9360 (tp30) cc_final: 0.9021 (tm-30) REVERT: B 294 TYR cc_start: 0.9309 (m-80) cc_final: 0.8885 (m-80) REVERT: B 299 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8781 (mt-10) REVERT: B 311 MET cc_start: 0.8491 (tpp) cc_final: 0.7818 (mmp) REVERT: B 330 MET cc_start: 0.9039 (mtm) cc_final: 0.8333 (tpp) REVERT: C 340 ARG cc_start: 0.6682 (mtt180) cc_final: 0.6387 (mmm-85) REVERT: C 1028 LEU cc_start: 0.9387 (tp) cc_final: 0.9140 (tp) REVERT: C 1032 PHE cc_start: 0.8317 (m-10) cc_final: 0.7847 (m-80) REVERT: C 1033 TYR cc_start: 0.8734 (m-80) cc_final: 0.8274 (m-80) REVERT: C 1061 ASP cc_start: 0.9354 (m-30) cc_final: 0.9110 (m-30) REVERT: D 1153 MET cc_start: 0.7339 (tpt) cc_final: 0.7084 (tpt) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.2015 time to fit residues: 45.0012 Evaluate side-chains 112 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.0370 chunk 56 optimal weight: 0.0570 chunk 23 optimal weight: 30.0000 chunk 96 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1052 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8412 Z= 0.148 Angle : 0.633 9.300 11384 Z= 0.308 Chirality : 0.040 0.142 1286 Planarity : 0.004 0.053 1426 Dihedral : 4.494 19.462 1086 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.16 (0.27), residues: 998 helix: 0.65 (0.21), residues: 628 sheet: -0.14 (0.53), residues: 90 loop : -0.85 (0.41), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1074 HIS 0.006 0.001 HIS C1060 PHE 0.015 0.001 PHE B 274 TYR 0.014 0.001 TYR B 127 ARG 0.002 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8538 (mmt) cc_final: 0.7761 (mtp) REVERT: A 55 ARG cc_start: 0.6710 (mmt180) cc_final: 0.5364 (mmm160) REVERT: A 136 MET cc_start: 0.8848 (ptt) cc_final: 0.8088 (ppp) REVERT: A 221 ILE cc_start: 0.9346 (tt) cc_final: 0.8978 (tt) REVERT: A 223 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8544 (mm-30) REVERT: A 256 GLU cc_start: 0.9366 (tp30) cc_final: 0.8968 (tm-30) REVERT: A 330 MET cc_start: 0.9064 (mtm) cc_final: 0.8414 (tpp) REVERT: B 14 MET cc_start: 0.8641 (mmt) cc_final: 0.7612 (mtp) REVERT: B 123 GLN cc_start: 0.7976 (mp10) cc_final: 0.7768 (tm-30) REVERT: B 221 ILE cc_start: 0.9301 (tt) cc_final: 0.8958 (tt) REVERT: B 223 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8583 (mm-30) REVERT: B 227 GLN cc_start: 0.8680 (tp-100) cc_final: 0.8454 (tp-100) REVERT: B 256 GLU cc_start: 0.9316 (tp30) cc_final: 0.8977 (tm-30) REVERT: B 294 TYR cc_start: 0.9280 (m-80) cc_final: 0.8832 (m-80) REVERT: B 330 MET cc_start: 0.9031 (mtm) cc_final: 0.8481 (tpp) REVERT: C 340 ARG cc_start: 0.6750 (mtt180) cc_final: 0.6222 (mmm160) REVERT: C 1033 TYR cc_start: 0.8746 (m-80) cc_final: 0.8429 (m-80) REVERT: C 1073 LYS cc_start: 0.9508 (mmtm) cc_final: 0.9306 (mmmt) REVERT: D 308 LEU cc_start: 0.7409 (tt) cc_final: 0.7024 (pp) REVERT: D 340 ARG cc_start: 0.6293 (mtt180) cc_final: 0.5600 (mmp-170) REVERT: D 343 MET cc_start: 0.6952 (ppp) cc_final: 0.6620 (ppp) REVERT: D 1073 LYS cc_start: 0.9531 (mmtm) cc_final: 0.9314 (mmmt) REVERT: D 1085 MET cc_start: 0.8920 (tpp) cc_final: 0.8571 (tpp) REVERT: D 1153 MET cc_start: 0.7447 (tpt) cc_final: 0.7234 (tpt) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1969 time to fit residues: 43.0966 Evaluate side-chains 119 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8412 Z= 0.313 Angle : 0.753 9.755 11384 Z= 0.379 Chirality : 0.042 0.171 1286 Planarity : 0.004 0.043 1426 Dihedral : 4.927 21.365 1086 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 998 helix: 0.62 (0.21), residues: 618 sheet: 0.28 (0.61), residues: 72 loop : -1.03 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP D1030 HIS 0.005 0.001 HIS B 162 PHE 0.024 0.002 PHE A 31 TYR 0.015 0.002 TYR A 248 ARG 0.005 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8729 (mmt) cc_final: 0.7885 (mtp) REVERT: A 51 LEU cc_start: 0.8623 (tp) cc_final: 0.8246 (tp) REVERT: A 55 ARG cc_start: 0.7152 (mmt180) cc_final: 0.5533 (mmm160) REVERT: A 223 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8513 (mm-30) REVERT: A 330 MET cc_start: 0.9106 (mtm) cc_final: 0.8315 (tpp) REVERT: B 14 MET cc_start: 0.8767 (mmt) cc_final: 0.7837 (mtp) REVERT: B 164 LEU cc_start: 0.7666 (mt) cc_final: 0.7453 (mt) REVERT: B 223 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8577 (mm-30) REVERT: B 294 TYR cc_start: 0.9387 (m-80) cc_final: 0.9047 (m-80) REVERT: B 330 MET cc_start: 0.9079 (mtm) cc_final: 0.8404 (tpp) REVERT: C 340 ARG cc_start: 0.6753 (mtt180) cc_final: 0.6204 (mmm160) REVERT: C 1032 PHE cc_start: 0.8399 (m-10) cc_final: 0.8152 (m-80) REVERT: C 1033 TYR cc_start: 0.8963 (m-80) cc_final: 0.8574 (m-80) REVERT: C 1073 LYS cc_start: 0.9632 (mmtm) cc_final: 0.9404 (mmmt) REVERT: D 308 LEU cc_start: 0.7237 (tt) cc_final: 0.6829 (pp) REVERT: D 340 ARG cc_start: 0.6333 (mtt180) cc_final: 0.5651 (mmp-170) REVERT: D 1073 LYS cc_start: 0.9621 (mmtm) cc_final: 0.9392 (mmmt) REVERT: D 1153 MET cc_start: 0.7481 (tpt) cc_final: 0.7252 (tpt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1836 time to fit residues: 36.8555 Evaluate side-chains 105 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 0.3980 chunk 61 optimal weight: 30.0000 chunk 65 optimal weight: 0.0170 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1052 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8412 Z= 0.151 Angle : 0.661 8.505 11384 Z= 0.322 Chirality : 0.041 0.150 1286 Planarity : 0.004 0.043 1426 Dihedral : 4.712 21.756 1086 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.27), residues: 998 helix: 0.81 (0.21), residues: 620 sheet: 0.31 (0.59), residues: 72 loop : -0.80 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP D1030 HIS 0.003 0.001 HIS C1060 PHE 0.020 0.001 PHE D1102 TYR 0.013 0.001 TYR B 302 ARG 0.006 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8728 (mmt) cc_final: 0.7918 (mtp) REVERT: A 55 ARG cc_start: 0.6864 (mmt180) cc_final: 0.5304 (mmm160) REVERT: A 123 GLN cc_start: 0.8005 (mp10) cc_final: 0.7771 (tm-30) REVERT: A 136 MET cc_start: 0.8713 (ptt) cc_final: 0.7896 (ppp) REVERT: A 330 MET cc_start: 0.9096 (mtm) cc_final: 0.8386 (tpp) REVERT: B 14 MET cc_start: 0.8733 (mmt) cc_final: 0.7747 (mtp) REVERT: B 223 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8603 (mm-30) REVERT: B 227 GLN cc_start: 0.8703 (tp-100) cc_final: 0.8389 (tp-100) REVERT: B 230 ASP cc_start: 0.8412 (m-30) cc_final: 0.8176 (m-30) REVERT: B 294 TYR cc_start: 0.9352 (m-80) cc_final: 0.9015 (m-80) REVERT: B 330 MET cc_start: 0.9094 (mtm) cc_final: 0.8446 (tpp) REVERT: C 340 ARG cc_start: 0.6750 (mtt180) cc_final: 0.6203 (mmm160) REVERT: C 1032 PHE cc_start: 0.8338 (m-10) cc_final: 0.8124 (m-80) REVERT: C 1033 TYR cc_start: 0.8935 (m-80) cc_final: 0.8541 (m-80) REVERT: D 308 LEU cc_start: 0.7331 (tt) cc_final: 0.6922 (pp) REVERT: D 340 ARG cc_start: 0.6375 (mtt180) cc_final: 0.5704 (mmp-170) REVERT: D 343 MET cc_start: 0.7026 (ppp) cc_final: 0.6761 (ppp) REVERT: D 1073 LYS cc_start: 0.9596 (mmtm) cc_final: 0.9375 (mmtm) REVERT: D 1153 MET cc_start: 0.7333 (tpt) cc_final: 0.7110 (tpt) REVERT: D 1177 MET cc_start: 0.8850 (tmm) cc_final: 0.8560 (mmm) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1851 time to fit residues: 39.5406 Evaluate side-chains 115 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 57 optimal weight: 0.0030 overall best weight: 0.5570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1081 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8412 Z= 0.156 Angle : 0.674 9.866 11384 Z= 0.327 Chirality : 0.041 0.144 1286 Planarity : 0.004 0.051 1426 Dihedral : 4.516 18.980 1086 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.27), residues: 998 helix: 0.75 (0.21), residues: 630 sheet: 0.49 (0.59), residues: 72 loop : -0.71 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP D1030 HIS 0.002 0.001 HIS C1060 PHE 0.018 0.001 PHE D1045 TYR 0.011 0.001 TYR D1055 ARG 0.001 0.000 ARG D1079 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8722 (mmt) cc_final: 0.7896 (mtp) REVERT: A 136 MET cc_start: 0.8814 (ptt) cc_final: 0.7970 (ppp) REVERT: A 330 MET cc_start: 0.9098 (mtm) cc_final: 0.8444 (tpp) REVERT: B 14 MET cc_start: 0.8670 (mmt) cc_final: 0.7688 (mtp) REVERT: B 223 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8519 (mm-30) REVERT: B 227 GLN cc_start: 0.8589 (tp-100) cc_final: 0.8242 (tp-100) REVERT: B 230 ASP cc_start: 0.8395 (m-30) cc_final: 0.8191 (m-30) REVERT: B 294 TYR cc_start: 0.9279 (m-80) cc_final: 0.8823 (m-80) REVERT: B 330 MET cc_start: 0.9094 (mtm) cc_final: 0.8528 (tpp) REVERT: C 340 ARG cc_start: 0.6738 (mtt180) cc_final: 0.6197 (mmm160) REVERT: D 308 LEU cc_start: 0.7178 (tt) cc_final: 0.6449 (mt) REVERT: D 340 ARG cc_start: 0.6368 (mtt180) cc_final: 0.5683 (mmp-170) REVERT: D 343 MET cc_start: 0.7001 (ppp) cc_final: 0.6656 (ppp) REVERT: D 1073 LYS cc_start: 0.9588 (mmtm) cc_final: 0.9376 (mmtm) REVERT: D 1080 LYS cc_start: 0.9721 (mttt) cc_final: 0.9401 (mmmm) REVERT: D 1153 MET cc_start: 0.7353 (tpt) cc_final: 0.7130 (tpt) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1993 time to fit residues: 42.6785 Evaluate side-chains 113 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 61 optimal weight: 30.0000 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8412 Z= 0.235 Angle : 0.713 9.150 11384 Z= 0.356 Chirality : 0.041 0.129 1286 Planarity : 0.004 0.045 1426 Dihedral : 4.700 20.117 1086 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.27), residues: 998 helix: 0.71 (0.21), residues: 630 sheet: 0.52 (0.62), residues: 72 loop : -0.58 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D1030 HIS 0.003 0.001 HIS B 162 PHE 0.017 0.002 PHE A 31 TYR 0.017 0.002 TYR D1055 ARG 0.004 0.000 ARG D1099 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8725 (mmt) cc_final: 0.7836 (mtp) REVERT: A 123 GLN cc_start: 0.7683 (mp10) cc_final: 0.7420 (mp10) REVERT: A 136 MET cc_start: 0.8885 (ptt) cc_final: 0.8011 (ppp) REVERT: A 330 MET cc_start: 0.9094 (mtm) cc_final: 0.8376 (tpp) REVERT: B 14 MET cc_start: 0.8745 (mmt) cc_final: 0.7870 (mtp) REVERT: B 223 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8516 (mm-30) REVERT: B 294 TYR cc_start: 0.9398 (m-80) cc_final: 0.9127 (m-80) REVERT: B 330 MET cc_start: 0.9019 (mtm) cc_final: 0.8609 (tpp) REVERT: C 340 ARG cc_start: 0.6738 (mtt180) cc_final: 0.6186 (mmm160) REVERT: C 1073 LYS cc_start: 0.9608 (mmtm) cc_final: 0.9395 (mmmt) REVERT: D 308 LEU cc_start: 0.7199 (tt) cc_final: 0.6444 (mt) REVERT: D 340 ARG cc_start: 0.6371 (mtt180) cc_final: 0.5685 (mmp-170) REVERT: D 343 MET cc_start: 0.6977 (ppp) cc_final: 0.6650 (ppp) REVERT: D 1073 LYS cc_start: 0.9637 (mmtm) cc_final: 0.9405 (mmtm) REVERT: D 1153 MET cc_start: 0.7440 (tpt) cc_final: 0.7211 (tpt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2005 time to fit residues: 40.5995 Evaluate side-chains 107 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.0570 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.103815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.071294 restraints weight = 31790.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.071597 restraints weight = 22338.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.072271 restraints weight = 16690.877| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8412 Z= 0.152 Angle : 0.681 9.114 11384 Z= 0.329 Chirality : 0.041 0.144 1286 Planarity : 0.004 0.049 1426 Dihedral : 4.507 19.827 1086 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.27), residues: 998 helix: 0.82 (0.21), residues: 630 sheet: 0.60 (0.61), residues: 72 loop : -0.58 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D1030 HIS 0.002 0.001 HIS D1098 PHE 0.017 0.001 PHE D1045 TYR 0.015 0.001 TYR D1055 ARG 0.002 0.000 ARG A 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1767.33 seconds wall clock time: 33 minutes 4.72 seconds (1984.72 seconds total)