Starting phenix.real_space_refine on Wed Mar 4 23:17:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s0t_24793/03_2026/7s0t_24793.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s0t_24793/03_2026/7s0t_24793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s0t_24793/03_2026/7s0t_24793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s0t_24793/03_2026/7s0t_24793.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s0t_24793/03_2026/7s0t_24793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s0t_24793/03_2026/7s0t_24793.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.022 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 P 27 5.49 5 S 76 5.16 5 C 11076 2.51 5 N 2828 2.21 5 O 3083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "A PHE 598": not complete - not flipped Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17095 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 9196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1231, 9196 Classifications: {'peptide': 1231} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 161} Link IDs: {'PTRANS': 60, 'TRANS': 1170} Chain breaks: 16 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 852 Unresolved non-hydrogen angles: 1053 Unresolved non-hydrogen dihedrals: 681 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ASP:plan': 32, 'GLU:plan': 48, 'GLN:plan1': 17, 'ARG:plan': 22, 'PHE:plan': 4, 'ASN:plan1': 11, 'TYR:plan': 5, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 504 Chain: "D" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1284 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 152} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1624 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 195} Chain breaks: 2 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 6, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "F" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3510 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 27, 'TRANS': 438} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 23, 'HIS:plan': 2, 'GLU:plan': 18, 'GLN:plan1': 6, 'ARG:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 177 Chain: "G" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 921 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 28 Chain: "P" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 193 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 299 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 54 Unusual residues: {' CA': 1, 'DCP': 1, 'SF4': 1} Classifications: {'undetermined': 3, 'water': 17} Link IDs: {None: 19} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9008 SG CYS A1473 41.278 82.041 85.282 1.00 64.88 S ATOM 8827 SG CYS A1449 45.629 87.243 84.420 1.00 68.55 S ATOM 8970 SG CYS A1468 38.906 88.990 82.407 1.00 62.69 S Time building chain proxies: 3.80, per 1000 atoms: 0.22 Number of scatterers: 17095 At special positions: 0 Unit cell: (87.68, 143.576, 168.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 76 16.00 P 27 15.00 O 3083 8.00 N 2828 7.00 C 11076 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 - 3.00 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: 1.39 Conformation dependent library (CDL) restraints added in 728.7 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1601 " pdb="FE1 SF4 A1601 " - pdb=" SG CYS A1473 " pdb="FE3 SF4 A1601 " - pdb=" SG CYS A1468 " pdb="FE2 SF4 A1601 " - pdb=" SG CYS A1449 " pdb="FE4 SF4 A1601 " - pdb=" SG CYS A1446 " Number of angles added : 12 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4188 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 19 sheets defined 39.5% alpha, 13.9% beta 4 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 95 through 116 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 178 Processing helix chain 'A' and resid 194 through 203 Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.899A pdb=" N LEU A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 246 Processing helix chain 'A' and resid 285 through 289 removed outlier: 3.851A pdb=" N HIS A 288 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A 289 " --> pdb=" O ILE A 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 285 through 289' Processing helix chain 'A' and resid 306 through 320 Processing helix chain 'A' and resid 345 through 360 removed outlier: 3.501A pdb=" N PHE A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 373 removed outlier: 3.781A pdb=" N PHE A 373 " --> pdb=" O PHE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.625A pdb=" N LEU A 390 " --> pdb=" O PRO A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 540 removed outlier: 4.356A pdb=" N ASN A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 725 through 735 Processing helix chain 'A' and resid 744 through 760 Processing helix chain 'A' and resid 772 through 784 Processing helix chain 'A' and resid 788 through 794 Processing helix chain 'A' and resid 806 through 812 removed outlier: 3.835A pdb=" N HIS A 812 " --> pdb=" O TRP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 834 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 857 through 866 Processing helix chain 'A' and resid 870 through 895 removed outlier: 3.602A pdb=" N LEU A 874 " --> pdb=" O SER A 870 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE A 889 " --> pdb=" O ALA A 885 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 895 " --> pdb=" O LEU A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 909 Processing helix chain 'A' and resid 911 through 917 removed outlier: 4.360A pdb=" N TYR A 916 " --> pdb=" O PHE A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 934 removed outlier: 4.340A pdb=" N LYS A 923 " --> pdb=" O GLY A 919 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 924 " --> pdb=" O SER A 920 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER A 934 " --> pdb=" O ARG A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 949 Processing helix chain 'A' and resid 978 through 988 Processing helix chain 'A' and resid 1018 through 1023 Processing helix chain 'A' and resid 1044 through 1064 WARNING: missing atoms! Processing helix chain 'A' and resid 1073 through 1095 removed outlier: 4.137A pdb=" N TYR A1093 " --> pdb=" O ALA A1089 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY A1094 " --> pdb=" O ASN A1090 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1131 removed outlier: 3.690A pdb=" N ASP A1131 " --> pdb=" O ILE A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1156 No H-bonds generated for 'chain 'A' and resid 1154 through 1156' Processing helix chain 'A' and resid 1157 through 1171 Processing helix chain 'A' and resid 1224 through 1242 Processing helix chain 'A' and resid 1243 through 1261 removed outlier: 3.551A pdb=" N ILE A1247 " --> pdb=" O ASP A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1297 Processing helix chain 'A' and resid 1329 through 1330 No H-bonds generated for 'chain 'A' and resid 1329 through 1330' Processing helix chain 'A' and resid 1332 through 1334 No H-bonds generated for 'chain 'A' and resid 1332 through 1334' Processing helix chain 'A' and resid 1342 through 1360 removed outlier: 3.733A pdb=" N TYR A1346 " --> pdb=" O ASP A1342 " (cutoff:3.500A) Proline residue: A1353 - end of helix Processing helix chain 'A' and resid 1365 through 1373 removed outlier: 3.962A pdb=" N TRP A1369 " --> pdb=" O ASN A1365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A1372 " --> pdb=" O ASN A1368 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A1373 " --> pdb=" O TRP A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1455 removed outlier: 4.189A pdb=" N ARG A1452 " --> pdb=" O THR A1448 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR A1453 " --> pdb=" O CYS A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1466 Processing helix chain 'A' and resid 1473 through 1487 removed outlier: 3.915A pdb=" N TYR A1477 " --> pdb=" O CYS A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1502 Processing helix chain 'D' and resid 3 through 24 removed outlier: 4.349A pdb=" N LYS D 7 " --> pdb=" O ARG D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 68 removed outlier: 3.549A pdb=" N LYS D 68 " --> pdb=" O ASP D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.842A pdb=" N VAL D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS D 130 " --> pdb=" O MET D 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 24 Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 51 through 68 Processing helix chain 'E' and resid 109 through 130 removed outlier: 3.797A pdb=" N VAL E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS E 130 " --> pdb=" O MET E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 175 Processing helix chain 'F' and resid 0 through 10 Processing helix chain 'F' and resid 52 through 76 removed outlier: 3.749A pdb=" N ILE F 56 " --> pdb=" O GLN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 96 removed outlier: 3.592A pdb=" N ILE F 96 " --> pdb=" O VAL F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 124 Processing helix chain 'F' and resid 132 through 138 removed outlier: 3.697A pdb=" N TYR F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 241 Processing helix chain 'F' and resid 247 through 252 Processing helix chain 'F' and resid 272 through 291 removed outlier: 3.915A pdb=" N LEU F 276 " --> pdb=" O ASN F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 325 Processing helix chain 'F' and resid 357 through 365 Processing helix chain 'F' and resid 391 through 406 Processing helix chain 'F' and resid 411 through 416 Processing helix chain 'G' and resid 3 through 15 Processing helix chain 'G' and resid 22 through 30 Processing helix chain 'G' and resid 32 through 45 Processing helix chain 'G' and resid 76 through 80 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 35 removed outlier: 7.906A pdb=" N ILE A 268 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU A 72 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE A 270 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N HIS A 74 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 189 removed outlier: 3.528A pdb=" N ILE A 84 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 139 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ILE A 938 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A 146 " --> pdb=" O ILE A 938 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 521 through 522 removed outlier: 3.617A pdb=" N ARG D 74 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU D 89 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN D 81 " --> pdb=" O CYS D 87 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N CYS D 87 " --> pdb=" O ASN D 81 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLN D 214 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 581 through 582 removed outlier: 6.421A pdb=" N ILE A 581 " --> pdb=" O GLN D 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 177 through 180 removed outlier: 4.375A pdb=" N SER A 603 " --> pdb=" O CYS E 180 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ALA E 143 " --> pdb=" O TYR A 606 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR E 140 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG E 74 " --> pdb=" O ASN E 146 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN E 81 " --> pdb=" O CYS E 87 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS E 87 " --> pdb=" O ASN E 81 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS E 213 " --> pdb=" O ASP E 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 739 through 742 removed outlier: 6.874A pdb=" N LEU A 670 " --> pdb=" O SER A 765 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 965 through 967 removed outlier: 3.721A pdb=" N ALA A 965 " --> pdb=" O LEU A1190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1137 through 1141 removed outlier: 6.798A pdb=" N PHE A1147 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY A1141 " --> pdb=" O SER A1145 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N SER A1145 " --> pdb=" O GLY A1141 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ARG A1195 " --> pdb=" O ILE A1191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 994 through 997 removed outlier: 6.416A pdb=" N VAL A1035 " --> pdb=" O ILE A 995 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1270 through 1274 removed outlier: 3.675A pdb=" N LYS A1272 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A1310 " --> pdb=" O LYS A1272 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A1308 " --> pdb=" O VAL A1274 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 32 through 33 Processing sheet with id=AB3, first strand: chain 'E' and resid 32 through 37 removed outlier: 9.026A pdb=" N PHE E 32 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N VAL E 46 " --> pdb=" O PHE E 32 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N TYR E 34 " --> pdb=" O GLN E 44 " (cutoff:3.500A) removed outlier: 10.377A pdb=" N GLN E 44 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR E 36 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 23 through 24 removed outlier: 6.454A pdb=" N ARG F 23 " --> pdb=" O LYS G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 88 through 89 removed outlier: 6.874A pdb=" N LEU F 88 " --> pdb=" O TRP F 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 147 through 149 removed outlier: 3.584A pdb=" N GLY F 106 " --> pdb=" O VAL F 173 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 113 through 114 Processing sheet with id=AB8, first strand: chain 'F' and resid 156 through 158 removed outlier: 5.830A pdb=" N LEU F 156 " --> pdb=" O PHE F 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 336 through 338 removed outlier: 4.320A pdb=" N SER F 295 " --> pdb=" O GLY F 255 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LYS F 213 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG F 256 " --> pdb=" O LYS F 213 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE G 65 " --> pdb=" O THR F 482 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LYS F 484 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE G 67 " --> pdb=" O LYS F 484 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR G 64 " --> pdb=" O TYR G 60 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE G 57 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE G 85 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N CYS G 59 " --> pdb=" O CYS G 83 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS G 83 " --> pdb=" O CYS G 59 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 343 through 347 735 hydrogen bonds defined for protein. 2106 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 3.60 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.38: 6181 1.38 - 1.57: 11162 1.57 - 1.76: 53 1.76 - 1.95: 96 1.95 - 2.14: 12 Bond restraints: 17504 Sorted by residual: bond pdb=" C4' DCP A1603 " pdb=" O4' DCP A1603 " ideal model delta sigma weight residual 1.444 1.614 -0.170 1.00e-02 1.00e+04 2.91e+02 bond pdb=" C3' DCP A1603 " pdb=" C4' DCP A1603 " ideal model delta sigma weight residual 1.527 1.348 0.179 1.10e-02 8.26e+03 2.64e+02 bond pdb=" C4 DCP A1603 " pdb=" N4 DCP A1603 " ideal model delta sigma weight residual 1.334 1.475 -0.141 1.20e-02 6.94e+03 1.37e+02 bond pdb=" C1' DCP A1603 " pdb=" O4' DCP A1603 " ideal model delta sigma weight residual 1.418 1.302 0.116 1.20e-02 6.94e+03 9.34e+01 bond pdb=" C5 DCP A1603 " pdb=" C6 DCP A1603 " ideal model delta sigma weight residual 1.345 1.503 -0.158 1.80e-02 3.09e+03 7.69e+01 ... (remaining 17499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 23837 3.57 - 7.13: 54 7.13 - 10.70: 4 10.70 - 14.27: 6 14.27 - 17.84: 20 Bond angle restraints: 23921 Sorted by residual: angle pdb=" PB DCP A1603 " pdb=" O3B DCP A1603 " pdb=" PG DCP A1603 " ideal model delta sigma weight residual 139.87 122.03 17.84 1.00e+00 1.00e+00 3.18e+02 angle pdb=" PA DCP A1603 " pdb=" O3A DCP A1603 " pdb=" PB DCP A1603 " ideal model delta sigma weight residual 136.83 124.59 12.24 1.00e+00 1.00e+00 1.50e+02 angle pdb="FE3 SF4 A1601 " pdb=" S1 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 73.70 91.00 -17.30 1.50e+00 4.44e-01 1.33e+02 angle pdb="FE2 SF4 A1601 " pdb=" S1 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 73.70 90.56 -16.86 1.50e+00 4.44e-01 1.26e+02 angle pdb="FE1 SF4 A1601 " pdb=" S2 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 73.70 90.53 -16.83 1.50e+00 4.44e-01 1.26e+02 ... (remaining 23916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 9482 17.90 - 35.79: 675 35.79 - 53.69: 180 53.69 - 71.58: 29 71.58 - 89.48: 11 Dihedral angle restraints: 10377 sinusoidal: 3942 harmonic: 6435 Sorted by residual: dihedral pdb=" CA SER A 220 " pdb=" C SER A 220 " pdb=" N PRO A 221 " pdb=" CA PRO A 221 " ideal model delta harmonic sigma weight residual -180.00 -151.50 -28.50 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA PHE A 772 " pdb=" C PHE A 772 " pdb=" N SER A 773 " pdb=" CA SER A 773 " ideal model delta harmonic sigma weight residual -180.00 -152.20 -27.80 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA LYS F 36 " pdb=" C LYS F 36 " pdb=" N SER F 37 " pdb=" CA SER F 37 " ideal model delta harmonic sigma weight residual 180.00 155.71 24.29 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 10374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.044: 2794 4.044 - 8.087: 0 8.087 - 12.131: 0 12.131 - 16.174: 0 16.174 - 20.218: 4 Chirality restraints: 2798 Sorted by residual: chirality pdb="FE3 SF4 A1601 " pdb=" S1 SF4 A1601 " pdb=" S2 SF4 A1601 " pdb=" S4 SF4 A1601 " both_signs ideal model delta sigma weight residual False -10.55 9.66 -20.22 2.00e-01 2.50e+01 1.02e+04 chirality pdb="FE2 SF4 A1601 " pdb=" S1 SF4 A1601 " pdb=" S3 SF4 A1601 " pdb=" S4 SF4 A1601 " both_signs ideal model delta sigma weight residual False 10.55 -9.58 20.14 2.00e-01 2.50e+01 1.01e+04 chirality pdb="FE1 SF4 A1601 " pdb=" S2 SF4 A1601 " pdb=" S3 SF4 A1601 " pdb=" S4 SF4 A1601 " both_signs ideal model delta sigma weight residual False -10.55 9.58 -20.13 2.00e-01 2.50e+01 1.01e+04 ... (remaining 2795 not shown) Planarity restraints: 2900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 220 " 0.033 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 221 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 221 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 221 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 385 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.79e+00 pdb=" N PRO A 386 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 386 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 386 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 685 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO A 686 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 686 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 686 " 0.024 5.00e-02 4.00e+02 ... (remaining 2897 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 711 2.72 - 3.27: 16934 3.27 - 3.81: 27689 3.81 - 4.36: 33256 4.36 - 4.90: 58208 Nonbonded interactions: 136798 Sorted by model distance: nonbonded pdb=" O VAL F 122 " pdb=" OG1 THR F 126 " model vdw 2.181 3.040 nonbonded pdb=" OD1 ASN F 341 " pdb=" OG SER F 356 " model vdw 2.213 3.040 nonbonded pdb=" O ASP A1456 " pdb=" ND2 ASN A1461 " model vdw 2.229 3.120 nonbonded pdb=" N LYS A1316 " pdb=" OH TYR A1346 " model vdw 2.233 3.120 nonbonded pdb=" OD1 ASN G 10 " pdb=" OH TYR G 43 " model vdw 2.252 3.040 ... (remaining 136793 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: 1.070 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: 0.030 Extract box with map and model: 0.250 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.210 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 : 0.013 0.833 17508 Z= 0.456 Angle : 0.959 45.530 23933 Z= 0.453 Chirality : 0.762 20.218 2798 Planarity : 0.004 0.051 2900 Dihedral : 13.864 89.476 6189 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.19), residues: 2121 helix: 2.25 (0.19), residues: 771 sheet: 0.01 (0.30), residues: 299 loop : -1.41 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1309 TYR 0.011 0.001 TYR A 880 PHE 0.016 0.001 PHE A 927 TRP 0.025 0.001 TRP A 343 HIS 0.009 0.001 HIS A 732 Details of bonding type rmsd covalent geometry : bond 0.00575 (17504) covalent geometry : angle 0.72413 (23921) hydrogen bonds : bond 0.16646 ( 743) hydrogen bonds : angle 6.63075 ( 2126) metal coordination : bond 0.73455 ( 4) metal coordination : angle 28.06563 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.606 Fit side-chains REVERT: A 261 VAL cc_start: 0.8942 (m) cc_final: 0.8718 (p) REVERT: F 100 GLN cc_start: 0.8462 (pt0) cc_final: 0.8170 (pt0) REVERT: F 277 MET cc_start: 0.7849 (tpt) cc_final: 0.7511 (tpt) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1193 time to fit residues: 26.6968 Evaluate side-chains 123 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN E 30 GLN F 221 ASN ** F 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.077738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.066654 restraints weight = 51042.063| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.54 r_work: 0.3229 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.259 17508 Z= 0.312 Angle : 1.501 51.202 23933 Z= 0.854 Chirality : 0.243 6.418 2798 Planarity : 0.005 0.051 2900 Dihedral : 10.778 78.356 2603 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.07 % Favored : 92.88 % Rotamer: Outliers : 0.64 % Allowed : 7.09 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.19), residues: 2121 helix: 2.07 (0.19), residues: 769 sheet: -0.20 (0.28), residues: 321 loop : -1.46 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1435 TYR 0.013 0.001 TYR D 23 PHE 0.015 0.002 PHE A 787 TRP 0.012 0.001 TRP F 76 HIS 0.005 0.001 HIS F 316 Details of bonding type rmsd covalent geometry : bond 0.00816 (17504) covalent geometry : angle 1.33041 (23921) hydrogen bonds : bond 0.04713 ( 743) hydrogen bonds : angle 5.23926 ( 2126) metal coordination : bond 0.03156 ( 4) metal coordination : angle 31.02041 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: D 77 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7614 (mt) outliers start: 10 outliers final: 9 residues processed: 131 average time/residue: 0.1198 time to fit residues: 25.0463 Evaluate side-chains 123 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 191 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 137 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 167 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN F 221 ASN ** F 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.078608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.067500 restraints weight = 51829.406| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.58 r_work: 0.3249 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 17508 Z= 0.251 Angle : 1.458 50.416 23933 Z= 0.834 Chirality : 0.243 6.370 2798 Planarity : 0.004 0.051 2900 Dihedral : 10.661 74.721 2603 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.09 % Allowed : 10.03 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.19), residues: 2121 helix: 2.21 (0.19), residues: 769 sheet: -0.22 (0.29), residues: 305 loop : -1.53 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1435 TYR 0.015 0.001 TYR A 880 PHE 0.013 0.001 PHE A1333 TRP 0.011 0.001 TRP F 76 HIS 0.003 0.001 HIS F 316 Details of bonding type rmsd covalent geometry : bond 0.00700 (17504) covalent geometry : angle 1.28705 (23921) hydrogen bonds : bond 0.04051 ( 743) hydrogen bonds : angle 4.86168 ( 2126) metal coordination : bond 0.04381 ( 4) metal coordination : angle 30.64990 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.622 Fit side-chains REVERT: D 16 TYR cc_start: 0.8678 (t80) cc_final: 0.8148 (t80) REVERT: D 116 GLU cc_start: 0.8760 (mp0) cc_final: 0.8354 (mp0) outliers start: 17 outliers final: 12 residues processed: 132 average time/residue: 0.1168 time to fit residues: 24.9501 Evaluate side-chains 125 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 415 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 115 optimal weight: 5.9990 chunk 142 optimal weight: 0.0570 chunk 209 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 221 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.077635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.066521 restraints weight = 51753.219| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.58 r_work: 0.3228 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.241 17508 Z= 0.263 Angle : 1.464 50.445 23933 Z= 0.837 Chirality : 0.243 6.352 2798 Planarity : 0.004 0.057 2900 Dihedral : 10.679 73.938 2603 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.21 % Favored : 92.74 % Rotamer: Outliers : 1.72 % Allowed : 11.05 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.19), residues: 2121 helix: 2.17 (0.19), residues: 768 sheet: -0.25 (0.29), residues: 311 loop : -1.55 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1435 TYR 0.015 0.001 TYR A 880 PHE 0.013 0.001 PHE A1333 TRP 0.010 0.001 TRP F 76 HIS 0.004 0.001 HIS F 316 Details of bonding type rmsd covalent geometry : bond 0.00725 (17504) covalent geometry : angle 1.29408 (23921) hydrogen bonds : bond 0.04050 ( 743) hydrogen bonds : angle 4.77375 ( 2126) metal coordination : bond 0.02859 ( 4) metal coordination : angle 30.58835 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.480 Fit side-chains REVERT: A 343 TRP cc_start: 0.5856 (m-10) cc_final: 0.5397 (m-10) REVERT: D 38 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8161 (pt0) REVERT: D 77 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.7867 (mt) REVERT: D 116 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8397 (mp0) outliers start: 27 outliers final: 18 residues processed: 143 average time/residue: 0.1210 time to fit residues: 27.4623 Evaluate side-chains 136 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 112 MET Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain G residue 20 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 168 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 50 optimal weight: 0.0170 chunk 181 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 173 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN A1006 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.078074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.066993 restraints weight = 51218.476| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.57 r_work: 0.3237 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.242 17508 Z= 0.249 Angle : 1.458 50.428 23933 Z= 0.833 Chirality : 0.243 6.347 2798 Planarity : 0.004 0.055 2900 Dihedral : 10.623 75.029 2603 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.17 % Allowed : 11.17 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.19), residues: 2121 helix: 2.25 (0.19), residues: 768 sheet: -0.21 (0.29), residues: 311 loop : -1.56 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1435 TYR 0.016 0.001 TYR D 73 PHE 0.015 0.001 PHE A1333 TRP 0.010 0.001 TRP F 76 HIS 0.012 0.001 HIS F 316 Details of bonding type rmsd covalent geometry : bond 0.00696 (17504) covalent geometry : angle 1.28637 (23921) hydrogen bonds : bond 0.03787 ( 743) hydrogen bonds : angle 4.65481 ( 2126) metal coordination : bond 0.02652 ( 4) metal coordination : angle 30.64891 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.653 Fit side-chains REVERT: A 343 TRP cc_start: 0.5868 (m-10) cc_final: 0.5378 (m-10) REVERT: A 830 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8444 (mm) REVERT: D 38 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8153 (pt0) REVERT: D 77 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.7987 (mt) REVERT: D 112 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: D 116 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8412 (mp0) outliers start: 34 outliers final: 23 residues processed: 147 average time/residue: 0.1181 time to fit residues: 27.9959 Evaluate side-chains 144 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 112 MET Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain G residue 20 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 36 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 chunk 172 optimal weight: 0.0010 chunk 86 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** 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 = 0.3579 r_free = 0.3579 target = 0.078293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.067260 restraints weight = 50950.448| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.56 r_work: 0.3244 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.242 17508 Z= 0.242 Angle : 1.454 50.418 23933 Z= 0.831 Chirality : 0.242 6.342 2798 Planarity : 0.004 0.055 2900 Dihedral : 10.538 75.516 2603 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.23 % Allowed : 11.49 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.19), residues: 2121 helix: 2.31 (0.19), residues: 768 sheet: -0.27 (0.28), residues: 321 loop : -1.52 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1435 TYR 0.019 0.001 TYR D 73 PHE 0.010 0.001 PHE A1181 TRP 0.010 0.001 TRP F 76 HIS 0.006 0.001 HIS F 316 Details of bonding type rmsd covalent geometry : bond 0.00682 (17504) covalent geometry : angle 1.28222 (23921) hydrogen bonds : bond 0.03601 ( 743) hydrogen bonds : angle 4.53384 ( 2126) metal coordination : bond 0.02437 ( 4) metal coordination : angle 30.63119 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.715 Fit side-chains REVERT: A 251 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.8053 (t0) REVERT: A 343 TRP cc_start: 0.5854 (m-10) cc_final: 0.5280 (m-10) REVERT: A 830 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8434 (mm) REVERT: D 38 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8154 (pt0) REVERT: D 77 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.7984 (mt) REVERT: D 112 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7819 (pm20) REVERT: D 116 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8399 (mp0) outliers start: 35 outliers final: 26 residues processed: 148 average time/residue: 0.1176 time to fit residues: 27.9527 Evaluate side-chains 148 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 112 MET Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 72 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 113 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 79 optimal weight: 0.0040 overall best weight: 2.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.076578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.065551 restraints weight = 51353.419| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.55 r_work: 0.3203 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.239 17508 Z= 0.276 Angle : 1.470 50.439 23933 Z= 0.840 Chirality : 0.243 6.355 2798 Planarity : 0.004 0.058 2900 Dihedral : 10.651 75.086 2603 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.62 % Allowed : 11.69 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.19), residues: 2121 helix: 2.18 (0.19), residues: 768 sheet: -0.28 (0.29), residues: 311 loop : -1.57 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1435 TYR 0.021 0.001 TYR D 73 PHE 0.017 0.001 PHE A1333 TRP 0.010 0.001 TRP F 76 HIS 0.004 0.001 HIS F 394 Details of bonding type rmsd covalent geometry : bond 0.00752 (17504) covalent geometry : angle 1.30154 (23921) hydrogen bonds : bond 0.04156 ( 743) hydrogen bonds : angle 4.69115 ( 2126) metal coordination : bond 0.02770 ( 4) metal coordination : angle 30.56929 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 0.630 Fit side-chains REVERT: A 343 TRP cc_start: 0.6139 (m-10) cc_final: 0.5465 (m-10) REVERT: A 830 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8520 (mm) REVERT: D 38 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8361 (pp30) REVERT: D 77 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.7987 (mt) REVERT: D 112 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: D 116 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8469 (mp0) outliers start: 41 outliers final: 28 residues processed: 144 average time/residue: 0.1153 time to fit residues: 26.7376 Evaluate side-chains 145 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 112 MET Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 72 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 80 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 127 optimal weight: 0.0570 chunk 37 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 145 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.077422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.066435 restraints weight = 51458.224| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.56 r_work: 0.3223 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.242 17508 Z= 0.248 Angle : 1.457 50.437 23933 Z= 0.833 Chirality : 0.242 6.343 2798 Planarity : 0.004 0.056 2900 Dihedral : 10.600 76.574 2603 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.55 % Allowed : 12.32 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.19), residues: 2121 helix: 2.27 (0.19), residues: 768 sheet: -0.20 (0.29), residues: 310 loop : -1.52 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1435 TYR 0.022 0.001 TYR D 73 PHE 0.018 0.001 PHE A1333 TRP 0.011 0.001 TRP F 76 HIS 0.003 0.001 HIS F 394 Details of bonding type rmsd covalent geometry : bond 0.00696 (17504) covalent geometry : angle 1.28630 (23921) hydrogen bonds : bond 0.03732 ( 743) hydrogen bonds : angle 4.55495 ( 2126) metal coordination : bond 0.02400 ( 4) metal coordination : angle 30.62925 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.636 Fit side-chains REVERT: A 251 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.7996 (t0) REVERT: A 343 TRP cc_start: 0.6138 (m-10) cc_final: 0.5471 (m-10) REVERT: A 830 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8467 (mm) REVERT: D 16 TYR cc_start: 0.8696 (t80) cc_final: 0.8147 (t80) REVERT: D 38 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8192 (pt0) REVERT: D 77 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7995 (mt) REVERT: D 112 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: D 116 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8445 (mp0) outliers start: 40 outliers final: 29 residues processed: 147 average time/residue: 0.1155 time to fit residues: 27.6653 Evaluate side-chains 148 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 112 MET Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 72 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 106 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 125 optimal weight: 0.0270 chunk 12 optimal weight: 0.0980 chunk 26 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 overall best weight: 0.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.079015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.068023 restraints weight = 51288.671| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.58 r_work: 0.3262 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 17508 Z= 0.231 Angle : 1.450 50.419 23933 Z= 0.829 Chirality : 0.242 6.329 2798 Planarity : 0.004 0.053 2900 Dihedral : 10.426 77.296 2603 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.85 % Allowed : 12.64 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.19), residues: 2121 helix: 2.36 (0.19), residues: 769 sheet: -0.26 (0.29), residues: 309 loop : -1.43 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1435 TYR 0.025 0.001 TYR D 73 PHE 0.008 0.001 PHE D 215 TRP 0.011 0.001 TRP F 76 HIS 0.003 0.001 HIS F 316 Details of bonding type rmsd covalent geometry : bond 0.00660 (17504) covalent geometry : angle 1.27693 (23921) hydrogen bonds : bond 0.03303 ( 743) hydrogen bonds : angle 4.39143 ( 2126) metal coordination : bond 0.02064 ( 4) metal coordination : angle 30.67721 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.576 Fit side-chains REVERT: A 251 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.7967 (t0) REVERT: A 343 TRP cc_start: 0.6086 (m-10) cc_final: 0.5405 (m-10) REVERT: D 16 TYR cc_start: 0.8634 (t80) cc_final: 0.8099 (t80) REVERT: D 38 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8128 (pt0) REVERT: D 77 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.7952 (mt) REVERT: D 112 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7719 (pm20) REVERT: D 116 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8404 (mp0) outliers start: 29 outliers final: 18 residues processed: 138 average time/residue: 0.1119 time to fit residues: 25.3392 Evaluate side-chains 137 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 112 MET Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain G residue 20 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 189 optimal weight: 0.8980 chunk 216 optimal weight: 5.9990 chunk 213 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 143 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** 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 = 0.3575 r_free = 0.3575 target = 0.078081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.067138 restraints weight = 51044.969| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.55 r_work: 0.3240 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.241 17508 Z= 0.244 Angle : 1.457 50.417 23933 Z= 0.833 Chirality : 0.242 6.337 2798 Planarity : 0.004 0.055 2900 Dihedral : 10.436 76.024 2603 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.60 % Allowed : 13.28 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 2121 helix: 2.39 (0.19), residues: 767 sheet: -0.31 (0.28), residues: 326 loop : -1.41 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1435 TYR 0.025 0.001 TYR D 73 PHE 0.021 0.001 PHE A1333 TRP 0.009 0.001 TRP A 343 HIS 0.003 0.001 HIS F 394 Details of bonding type rmsd covalent geometry : bond 0.00688 (17504) covalent geometry : angle 1.28622 (23921) hydrogen bonds : bond 0.03514 ( 743) hydrogen bonds : angle 4.41585 ( 2126) metal coordination : bond 0.02248 ( 4) metal coordination : angle 30.60408 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.697 Fit side-chains REVERT: A 251 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.7992 (t0) REVERT: A 343 TRP cc_start: 0.6046 (m-10) cc_final: 0.5456 (m-10) REVERT: D 16 TYR cc_start: 0.8647 (t80) cc_final: 0.8105 (t80) REVERT: D 38 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8161 (pt0) REVERT: D 77 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.7985 (mt) REVERT: D 112 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7734 (pm20) REVERT: D 116 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8412 (mp0) outliers start: 25 outliers final: 19 residues processed: 131 average time/residue: 0.1176 time to fit residues: 24.8674 Evaluate side-chains 134 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 72 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 144 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 212 optimal weight: 0.0970 chunk 119 optimal weight: 5.9990 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 0.0050 chunk 68 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** 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 = 0.3584 r_free = 0.3584 target = 0.078423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.067539 restraints weight = 51284.984| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.54 r_work: 0.3250 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.242 17508 Z= 0.237 Angle : 1.453 50.421 23933 Z= 0.831 Chirality : 0.242 6.333 2798 Planarity : 0.004 0.053 2900 Dihedral : 10.410 75.966 2603 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.66 % Allowed : 13.15 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 2121 helix: 2.37 (0.19), residues: 768 sheet: -0.29 (0.28), residues: 321 loop : -1.40 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1435 TYR 0.026 0.001 TYR D 73 PHE 0.008 0.001 PHE D 215 TRP 0.010 0.001 TRP F 76 HIS 0.003 0.001 HIS F 394 Details of bonding type rmsd covalent geometry : bond 0.00673 (17504) covalent geometry : angle 1.28132 (23921) hydrogen bonds : bond 0.03410 ( 743) hydrogen bonds : angle 4.38377 ( 2126) metal coordination : bond 0.02167 ( 4) metal coordination : angle 30.62670 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3106.47 seconds wall clock time: 54 minutes 8.07 seconds (3248.07 seconds total)