Starting phenix.real_space_refine on Mon Sep 14 14:54:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7aoe_11842/09_2026/7aoe_11842.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aoe_11842/09_2026/7aoe_11842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7aoe_11842/09_2026/7aoe_11842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aoe_11842/09_2026/7aoe_11842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7aoe_11842/09_2026/7aoe_11842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aoe_11842/09_2026/7aoe_11842.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7aoe_11842/09_2026/7aoe_11842.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7aoe_11842/09_2026/7aoe_11842.cif" } resolution = 3.9 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= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 569 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 44 5.49 5 S 165 5.16 5 C 19404 2.51 5 N 5347 2.21 5 O 5862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 217 residue(s): 0.16s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30828 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 11102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1401, 11102 Classifications: {'peptide': 1401} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1334} Chain breaks: 11 Chain: "B" Number of atoms: 9254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1174, 9254 Classifications: {'peptide': 1174} Link IDs: {'PTRANS': 60, 'TRANS': 1113} Chain: "C" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2533 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "D" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 322 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain breaks: 1 Chain: "E" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1663 Classifications: {'peptide': 207} Link IDs: {'CIS': 5, 'PTRANS': 7, 'TRANS': 194} Chain: "F" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 650 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1267 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 10, 'TRANS': 149} Chain breaks: 1 Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 990 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 119} Chain: "I" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 431 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "J" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 550 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "L" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 368 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "U" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 509 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "R" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 153 Classifications: {'RNAv2': 7} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 483 SG CYS A 63 105.178 56.173 89.829 1.00 73.94 S ATOM 501 SG CYS A 66 104.500 54.333 89.518 1.00 69.95 S ATOM 565 SG CYS A 73 102.390 56.260 89.059 1.00 69.42 S ATOM 809 SG CYS A 103 74.652 45.015 131.808 1.00 93.16 S ATOM 835 SG CYS A 106 75.286 41.093 132.530 1.00 94.91 S ATOM 1540 SG CYS A 228 72.874 44.805 132.585 1.00102.92 S ATOM 1562 SG CYS A 231 75.022 43.102 136.179 1.00105.69 S ATOM 19731 SG CYS B1089 95.549 39.542 95.331 1.00 47.27 S ATOM 19756 SG CYS B1092 94.762 41.006 97.061 1.00 52.44 S ATOM 19912 SG CYS B1115 97.730 42.128 96.500 1.00 57.89 S ATOM 19935 SG CYS B1118 96.363 38.955 98.731 1.00 67.35 S ATOM 27820 SG CYS I 10 36.598 102.678 138.458 1.00 85.76 S ATOM 27841 SG CYS I 13 40.186 102.456 138.365 1.00 84.93 S ATOM 27946 SG CYS I 27 38.860 101.194 140.972 1.00104.55 S ATOM 27969 SG CYS I 30 39.264 102.522 140.348 1.00 95.27 S ATOM 28268 SG CYS J 7 63.115 93.491 42.813 1.00 17.17 S ATOM 28563 SG CYS J 44 59.353 91.760 42.704 1.00 20.42 S ATOM 28569 SG CYS J 45 61.478 94.155 41.227 1.00 18.78 S ATOM 29556 SG CYS L 24 90.933 112.237 71.571 1.00 36.02 S ATOM 29575 SG CYS L 27 91.349 114.118 71.395 1.00 36.10 S ATOM 29682 SG CYS L 41 93.551 113.693 72.623 1.00 50.40 S ATOM 29708 SG CYS L 44 91.838 114.994 72.540 1.00 52.02 S Time building chain proxies: 6.04, per 1000 atoms: 0.20 Number of scatterers: 30828 At special positions: 0 Unit cell: (161.652, 137.192, 156.335, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 165 16.00 P 44 15.00 O 5862 8.00 N 5347 7.00 C 19404 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: 2.80 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A 76 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 73 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 66 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 63 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 103 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 228 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 106 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 231 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1118 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1089 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1115 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 27 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 44 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 24 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 41 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 27 " Number of angles added : 27 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7062 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 45 sheets defined 37.6% alpha, 13.1% beta 11 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 112 through 127 Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.789A pdb=" N VAL A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 195 removed outlier: 3.694A pdb=" N GLN A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 223 removed outlier: 3.885A pdb=" N LEU A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 213 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.630A pdb=" N VAL A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 removed outlier: 3.721A pdb=" N LEU A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 411 Processing helix chain 'A' and resid 422 through 446 Processing helix chain 'A' and resid 463 through 470 Processing helix chain 'A' and resid 506 through 513 Processing helix chain 'A' and resid 523 through 534 Processing helix chain 'A' and resid 558 through 568 removed outlier: 3.593A pdb=" N GLN A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 633 through 641 removed outlier: 3.923A pdb=" N CYS A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN A 638 " --> pdb=" O TYR A 634 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 667 removed outlier: 3.570A pdb=" N ARG A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 673 Processing helix chain 'A' and resid 686 through 698 removed outlier: 3.683A pdb=" N CYS A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 717 Processing helix chain 'A' and resid 717 through 722 removed outlier: 3.837A pdb=" N THR A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 754 Processing helix chain 'A' and resid 771 through 775 Processing helix chain 'A' and resid 807 through 817 Processing helix chain 'A' and resid 817 through 840 removed outlier: 3.906A pdb=" N ARG A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 851 through 865 Processing helix chain 'A' and resid 867 through 878 removed outlier: 3.615A pdb=" N GLU A 871 " --> pdb=" O SER A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 896 Processing helix chain 'A' and resid 899 through 925 Processing helix chain 'A' and resid 936 through 944 removed outlier: 4.047A pdb=" N MET A 941 " --> pdb=" O HIS A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 958 removed outlier: 3.748A pdb=" N VAL A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 992 Processing helix chain 'A' and resid 1004 through 1026 removed outlier: 3.637A pdb=" N PHE A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A1024 " --> pdb=" O ILE A1020 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A1026 " --> pdb=" O THR A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1031 removed outlier: 4.039A pdb=" N TYR A1031 " --> pdb=" O ARG A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1077 removed outlier: 4.068A pdb=" N HIS A1075 " --> pdb=" O LYS A1072 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A1076 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A1077 " --> pdb=" O LYS A1074 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1072 through 1077' Processing helix chain 'A' and resid 1078 through 1086 removed outlier: 3.709A pdb=" N SER A1082 " --> pdb=" O GLN A1078 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A1085 " --> pdb=" O PHE A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1094 removed outlier: 3.768A pdb=" N ILE A1090 " --> pdb=" O TYR A1086 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1102 removed outlier: 4.188A pdb=" N SER A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA A1101 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A1102 " --> pdb=" O VAL A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1116 removed outlier: 3.865A pdb=" N LYS A1112 " --> pdb=" O SER A1108 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A1113 " --> pdb=" O SER A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 3.582A pdb=" N LYS A1127 " --> pdb=" O PRO A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1152 Processing helix chain 'A' and resid 1163 through 1167 Processing helix chain 'A' and resid 1171 through 1186 Processing helix chain 'A' and resid 1194 through 1209 Proline residue: A1205 - end of helix removed outlier: 3.757A pdb=" N MET A1209 " --> pdb=" O PRO A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1236 Processing helix chain 'A' and resid 1256 through 1268 Processing helix chain 'A' and resid 1271 through 1275 removed outlier: 3.785A pdb=" N VAL A1275 " --> pdb=" O VAL A1271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1271 through 1275' Processing helix chain 'A' and resid 1305 through 1313 Processing helix chain 'A' and resid 1316 through 1345 removed outlier: 3.533A pdb=" N GLN A1345 " --> pdb=" O ALA A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1515 Processing helix chain 'A' and resid 1548 through 1555 removed outlier: 3.622A pdb=" N GLU A1554 " --> pdb=" O LYS A1550 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A1555 " --> pdb=" O ALA A1551 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1577 removed outlier: 3.741A pdb=" N GLY A1577 " --> pdb=" O LEU A1573 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1595 removed outlier: 3.587A pdb=" N VAL A1595 " --> pdb=" O SER A1591 " (cutoff:3.500A) Processing helix chain 'A' and resid 1601 through 1613 removed outlier: 3.826A pdb=" N LEU A1605 " --> pdb=" O ASP A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1627 Processing helix chain 'A' and resid 1633 through 1639 removed outlier: 4.442A pdb=" N GLU A1639 " --> pdb=" O LYS A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1652 Processing helix chain 'A' and resid 1659 through 1666 removed outlier: 3.682A pdb=" N VAL A1666 " --> pdb=" O SER A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1672 through 1676 Processing helix chain 'B' and resid 5 through 14 removed outlier: 3.556A pdb=" N ASN B 14 " --> pdb=" O ARG B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 41 removed outlier: 4.237A pdb=" N GLN B 26 " --> pdb=" O PHE B 22 " (cutoff:3.500A) Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 44 through 53 removed outlier: 3.851A pdb=" N GLY B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.577A pdb=" N ALA B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.858A pdb=" N ASN B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 removed outlier: 3.796A pdb=" N LEU B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 278 through 296 removed outlier: 3.750A pdb=" N GLU B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 312 Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'B' and resid 341 through 361 Processing helix chain 'B' and resid 379 through 410 removed outlier: 3.689A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N SER B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 429 removed outlier: 3.849A pdb=" N LEU B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 444 Processing helix chain 'B' and resid 468 through 478 removed outlier: 3.531A pdb=" N MET B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 535 through 544 Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.687A pdb=" N ASN B 596 " --> pdb=" O VAL B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 683 through 688 Processing helix chain 'B' and resid 696 through 708 removed outlier: 3.563A pdb=" N ASN B 700 " --> pdb=" O GLN B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 745 Processing helix chain 'B' and resid 746 through 750 removed outlier: 3.618A pdb=" N HIS B 749 " --> pdb=" O GLY B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 795 through 800 removed outlier: 4.174A pdb=" N LYS B 799 " --> pdb=" O ASP B 795 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 800 " --> pdb=" O LEU B 796 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 795 through 800' Processing helix chain 'B' and resid 821 through 826 Processing helix chain 'B' and resid 935 through 939 Processing helix chain 'B' and resid 944 through 961 removed outlier: 3.896A pdb=" N PHE B 948 " --> pdb=" O THR B 944 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS B 959 " --> pdb=" O LYS B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 989 Processing helix chain 'B' and resid 1059 through 1068 Processing helix chain 'B' and resid 1069 through 1079 Processing helix chain 'B' and resid 1152 through 1165 removed outlier: 3.581A pdb=" N ASN B1156 " --> pdb=" O PRO B1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 66 through 79 removed outlier: 3.522A pdb=" N ALA C 70 " --> pdb=" O ASP C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 110 removed outlier: 3.707A pdb=" N VAL C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 119 removed outlier: 3.724A pdb=" N PHE C 119 " --> pdb=" O PRO C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 186 Processing helix chain 'C' and resid 223 through 227 removed outlier: 3.605A pdb=" N PHE C 226 " --> pdb=" O HIS C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 258 removed outlier: 3.613A pdb=" N VAL C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE C 258 " --> pdb=" O PHE C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 283 removed outlier: 4.053A pdb=" N LYS C 282 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 319 through 344 Processing helix chain 'D' and resid 18 through 33 Processing helix chain 'D' and resid 45 through 58 Processing helix chain 'E' and resid 6 through 11 removed outlier: 3.692A pdb=" N VAL E 11 " --> pdb=" O ASN E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 15 Processing helix chain 'E' and resid 37 through 45 removed outlier: 3.739A pdb=" N PHE E 41 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 98 Processing helix chain 'E' and resid 112 through 122 removed outlier: 3.520A pdb=" N LYS E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR E 120 " --> pdb=" O LYS E 116 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL E 121 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR E 122 " --> pdb=" O ILE E 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 112 through 122' Processing helix chain 'E' and resid 152 through 163 removed outlier: 3.594A pdb=" N LEU E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 78 through 93 Processing helix chain 'F' and resid 108 through 117 removed outlier: 3.742A pdb=" N GLN F 117 " --> pdb=" O LYS F 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 24 through 37 removed outlier: 3.874A pdb=" N ALA G 28 " --> pdb=" O ASP G 24 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET G 36 " --> pdb=" O HIS G 32 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE G 37 " --> pdb=" O MET G 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 71 removed outlier: 4.086A pdb=" N LYS H 69 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 62 Processing helix chain 'J' and resid 18 through 26 removed outlier: 3.902A pdb=" N THR J 23 " --> pdb=" O ASP J 19 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU J 24 " --> pdb=" O THR J 20 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.658A pdb=" N LEU J 35 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 50 removed outlier: 4.522A pdb=" N ILE J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU J 50 " --> pdb=" O ARG J 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 45 through 50' Processing helix chain 'K' and resid 43 through 56 removed outlier: 3.616A pdb=" N GLY K 47 " --> pdb=" O ASP K 43 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 113 removed outlier: 3.731A pdb=" N LEU K 113 " --> pdb=" O PHE K 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 15 removed outlier: 4.471A pdb=" N SER A 13 " --> pdb=" O GLU B1172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 3.927A pdb=" N ILE A 365 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 491 removed outlier: 3.623A pdb=" N SER A 490 " --> pdb=" O MET A 649 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS A 619 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 493 through 494 removed outlier: 6.986A pdb=" N SER A 493 " --> pdb=" O MET A 632 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 514 through 517 removed outlier: 6.852A pdb=" N LYS A 592 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ILE A 544 " --> pdb=" O LYS A 592 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR A 594 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AA7, first strand: chain 'A' and resid 734 through 736 removed outlier: 6.201A pdb=" N ILE H 75 " --> pdb=" O GLN A 735 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 764 through 767 removed outlier: 7.609A pdb=" N ASP A 787 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 961 through 962 removed outlier: 3.753A pdb=" N GLY A 961 " --> pdb=" O ILE A 995 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 995 " --> pdb=" O GLY A 961 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1050 through 1052 removed outlier: 7.111A pdb=" N VAL A1051 " --> pdb=" O VAL A1059 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1524 through 1530 removed outlier: 4.751A pdb=" N ARG A1526 " --> pdb=" O GLU A1545 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS A1530 " --> pdb=" O LYS A1541 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS A1541 " --> pdb=" O LYS A1530 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG A1250 " --> pdb=" O ASN A1562 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN A1562 " --> pdb=" O ARG A1250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1477 through 1482 removed outlier: 5.371A pdb=" N GLN A1278 " --> pdb=" O ASP A1302 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL I 44 " --> pdb=" O GLU A1283 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1678 through 1679 Processing sheet with id=AB5, first strand: chain 'B' and resid 55 through 58 removed outlier: 3.548A pdb=" N ARG B 78 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS B 120 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL B 82 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 118 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE B 84 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG B 116 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N SER B 115 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N MET B 139 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU B 117 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 180 through 182 Processing sheet with id=AB7, first strand: chain 'B' and resid 375 through 378 removed outlier: 3.632A pdb=" N LEU B 185 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N MET B 184 " --> pdb=" O HIS B 480 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 194 through 197 removed outlier: 5.577A pdb=" N TYR B 211 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 250 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AC1, first strand: chain 'B' and resid 567 through 572 removed outlier: 4.022A pdb=" N GLY B 569 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 561 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N LEU B 625 " --> pdb=" O TRP B 558 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N CYS B 560 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU B 627 " --> pdb=" O CYS B 560 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN B 562 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE B 628 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 610 " --> pdb=" O PHE B 628 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 646 through 649 Processing sheet with id=AC3, first strand: chain 'B' and resid 725 through 729 removed outlier: 3.917A pdb=" N GLU B 870 " --> pdb=" O LYS B 889 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL B 871 " --> pdb=" O LYS L 51 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET L 49 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 737 through 738 Processing sheet with id=AC5, first strand: chain 'B' and resid 932 through 934 removed outlier: 8.297A pdb=" N ILE B 932 " --> pdb=" O ASN B 755 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL B 757 " --> pdb=" O ILE B 932 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE B 934 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA B 759 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR B 754 " --> pdb=" O TYR B1018 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR B1012 " --> pdb=" O VAL B 760 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 809 through 810 Processing sheet with id=AC7, first strand: chain 'B' and resid 843 through 845 removed outlier: 7.307A pdb=" N GLU B 858 " --> pdb=" O ILE B 844 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 923 through 924 Processing sheet with id=AC9, first strand: chain 'B' and resid 1085 through 1089 Processing sheet with id=AD1, first strand: chain 'B' and resid 1098 through 1099 Processing sheet with id=AD2, first strand: chain 'B' and resid 1119 through 1121 removed outlier: 3.592A pdb=" N TRP B1132 " --> pdb=" O PHE B1140 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 47 through 53 removed outlier: 6.722A pdb=" N VAL C 59 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU C 53 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 10.705A pdb=" N ARG C 303 " --> pdb=" O HIS C 241 " (cutoff:3.500A) removed outlier: 11.202A pdb=" N HIS C 241 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 10.338A pdb=" N ARG C 305 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 11.541A pdb=" N THR C 239 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N HIS C 307 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 237 " --> pdb=" O HIS C 307 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 175 through 177 removed outlier: 4.441A pdb=" N VAL C 140 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLU C 208 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN C 94 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP C 210 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE C 216 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N PHE C 86 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 112 through 113 removed outlier: 4.059A pdb=" N ARG C 192 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 148 through 149 removed outlier: 3.738A pdb=" N GLU C 148 " --> pdb=" O VAL C 165 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 168 through 170 removed outlier: 6.798A pdb=" N VAL C 169 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 263 through 264 Processing sheet with id=AD9, first strand: chain 'D' and resid 13 through 15 removed outlier: 3.541A pdb=" N LYS D 13 " --> pdb=" O THR G 10 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS G 8 " --> pdb=" O GLU D 15 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG G 55 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASP G 77 " --> pdb=" O ASN G 53 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASN G 53 " --> pdb=" O ASP G 77 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 13 through 15 removed outlier: 3.541A pdb=" N LYS D 13 " --> pdb=" O THR G 10 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS G 8 " --> pdb=" O GLU D 15 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 58 through 61 removed outlier: 3.789A pdb=" N GLY E 102 " --> pdb=" O THR E 126 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 148 through 149 Processing sheet with id=AE4, first strand: chain 'G' and resid 40 through 41 removed outlier: 3.894A pdb=" N GLY G 46 " --> pdb=" O LEU G 41 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 109 through 114 removed outlier: 7.124A pdb=" N HIS G 100 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL G 96 " --> pdb=" O HIS G 100 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLY G 102 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL G 153 " --> pdb=" O THR G 169 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR G 169 " --> pdb=" O VAL G 153 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 15 through 17 removed outlier: 3.612A pdb=" N SER H 15 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE H 42 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL H 95 " --> pdb=" O MET H 102 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG H 82 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 57 through 59 Processing sheet with id=AE8, first strand: chain 'K' and resid 22 through 24 removed outlier: 3.518A pdb=" N ILE K 23 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 34 through 35 1108 hydrogen bonds defined for protein. 3096 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 7.31 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9098 1.33 - 1.46: 6431 1.46 - 1.58: 15657 1.58 - 1.70: 87 1.70 - 1.83: 266 Bond restraints: 31539 Sorted by residual: bond pdb=" C3' DG U 28 " pdb=" C2' DG U 28 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C1' DC T 18 " pdb=" N1 DC T 18 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.27e+01 bond pdb=" C3' DG T 17 " pdb=" O3' DG T 17 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.18e+01 bond pdb=" C3' DC T 19 " pdb=" O3' DC T 19 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.14e+01 bond pdb=" C3' DC T 24 " pdb=" O3' DC T 24 " ideal model delta sigma weight residual 1.435 1.395 0.040 1.30e-02 5.92e+03 9.47e+00 ... (remaining 31534 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 42077 2.86 - 5.71: 672 5.71 - 8.57: 56 8.57 - 11.42: 7 11.42 - 14.28: 4 Bond angle restraints: 42816 Sorted by residual: angle pdb=" C GLU A1065 " pdb=" N ASP A1066 " pdb=" CA ASP A1066 " ideal model delta sigma weight residual 121.54 133.95 -12.41 1.91e+00 2.74e-01 4.22e+01 angle pdb=" C GLN K 112 " pdb=" N LEU K 113 " pdb=" CA LEU K 113 " ideal model delta sigma weight residual 123.15 108.87 14.28 2.23e+00 2.01e-01 4.10e+01 angle pdb=" C GLY E 49 " pdb=" N ARG E 50 " pdb=" CA ARG E 50 " ideal model delta sigma weight residual 121.70 132.32 -10.62 1.80e+00 3.09e-01 3.48e+01 angle pdb=" C ASP H 17 " pdb=" N LYS H 18 " pdb=" CA LYS H 18 " ideal model delta sigma weight residual 121.70 132.04 -10.34 1.80e+00 3.09e-01 3.30e+01 angle pdb=" C SER A1067 " pdb=" N LEU A1068 " pdb=" CA LEU A1068 " ideal model delta sigma weight residual 121.54 131.55 -10.01 1.91e+00 2.74e-01 2.75e+01 ... (remaining 42811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 16675 18.02 - 36.04: 1868 36.04 - 54.06: 398 54.06 - 72.08: 81 72.08 - 90.10: 31 Dihedral angle restraints: 19053 sinusoidal: 8101 harmonic: 10952 Sorted by residual: dihedral pdb=" CA ILE A 84 " pdb=" C ILE A 84 " pdb=" N PRO A 85 " pdb=" CA PRO A 85 " ideal model delta harmonic sigma weight residual -180.00 -118.49 -61.51 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA LYS B 274 " pdb=" C LYS B 274 " pdb=" N ASP B 275 " pdb=" CA ASP B 275 " ideal model delta harmonic sigma weight residual 180.00 133.59 46.41 0 5.00e+00 4.00e-02 8.61e+01 dihedral pdb=" CA PRO B 498 " pdb=" C PRO B 498 " pdb=" N GLU B 499 " pdb=" CA GLU B 499 " ideal model delta harmonic sigma weight residual 180.00 137.28 42.72 0 5.00e+00 4.00e-02 7.30e+01 ... (remaining 19050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3722 0.058 - 0.115: 936 0.115 - 0.173: 118 0.173 - 0.231: 9 0.231 - 0.289: 3 Chirality restraints: 4788 Sorted by residual: chirality pdb=" CA ASP E 24 " pdb=" N ASP E 24 " pdb=" C ASP E 24 " pdb=" CB ASP E 24 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" P G R 19 " pdb=" OP1 G R 19 " pdb=" OP2 G R 19 " pdb=" O5' G R 19 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" P A R 14 " pdb=" OP1 A R 14 " pdb=" OP2 A R 14 " pdb=" O5' A R 14 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 4785 not shown) Planarity restraints: 5346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 84 " -0.049 5.00e-02 4.00e+02 7.46e-02 8.90e+00 pdb=" N PRO A 85 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 73 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.79e+00 pdb=" N PRO A 74 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 675 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO A 676 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 676 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 676 " -0.033 5.00e-02 4.00e+02 ... (remaining 5343 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 292 2.51 - 3.11: 24661 3.11 - 3.70: 47054 3.70 - 4.30: 65632 4.30 - 4.90: 106496 Nonbonded interactions: 244135 Sorted by model distance: nonbonded pdb=" CB CYS J 10 " pdb="ZN ZN J 101 " model vdw 1.910 2.630 nonbonded pdb=" O VAL A 491 " pdb=" OG1 THR A 629 " model vdw 1.974 3.040 nonbonded pdb=" O LEU A1036 " pdb=" OG SER A1199 " model vdw 1.999 3.040 nonbonded pdb=" OE2 GLU A 893 " pdb=" OG SER B 617 " model vdw 2.064 3.040 nonbonded pdb=" O ALA E 61 " pdb=" OG1 THR E 71 " model vdw 2.065 3.040 ... (remaining 244130 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 33.830 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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 : 0.008 0.285 31562 Z= 0.380 Angle : 1.322 71.122 42843 Z= 0.575 Chirality : 0.050 0.289 4788 Planarity : 0.006 0.075 5346 Dihedral : 15.946 90.097 11991 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.38 % Favored : 88.30 % Rotamer: Outliers : 0.57 % Allowed : 11.04 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.39 % 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: -4.07 (0.11), residues: 3718 helix: -2.20 (0.12), residues: 1208 sheet: -2.67 (0.19), residues: 526 loop : -3.09 (0.12), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 183 TYR 0.031 0.002 TYR A1063 PHE 0.030 0.003 PHE A 786 TRP 0.023 0.002 TRP E 15 HIS 0.012 0.002 HIS B 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00756 / 0.36 (31539) covalent geometry : angle 0.93004 / 0.54 (42816) hydrogen bonds : bond 0.16619 / 11.15 ( 1125) hydrogen bonds : angle 7.87383 / 5.61 ( 3154) metal coordination : bond 0.12895 / 7.13 ( 23) metal coordination : angle 37.40904 / 22.05 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 669 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5504 (ttm) cc_final: 0.5019 (ttp) REVERT: A 12 LYS cc_start: 0.8068 (mttm) cc_final: 0.7817 (mttp) REVERT: A 362 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7824 (pp) REVERT: A 700 ASP cc_start: 0.7480 (t70) cc_final: 0.7153 (t70) REVERT: A 894 GLU cc_start: 0.7795 (tt0) cc_final: 0.7377 (tp30) REVERT: A 1016 ARG cc_start: 0.7577 (tmm160) cc_final: 0.7050 (tmm160) REVERT: A 1049 HIS cc_start: 0.7614 (t70) cc_final: 0.7323 (t-170) REVERT: A 1078 GLN cc_start: 0.8001 (mm110) cc_final: 0.7738 (tp40) REVERT: A 1179 MET cc_start: 0.7733 (mmp) cc_final: 0.7281 (mmp) REVERT: A 1185 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7049 (tm-30) REVERT: A 1209 MET cc_start: 0.5031 (tpp) cc_final: 0.4829 (tpp) REVERT: A 1247 MET cc_start: 0.8112 (mtm) cc_final: 0.7291 (mtp) REVERT: B 190 ARG cc_start: 0.8396 (mtt-85) cc_final: 0.7477 (mtm180) REVERT: B 216 ARG cc_start: 0.8443 (ttt-90) cc_final: 0.8112 (ttt-90) REVERT: B 244 ARG cc_start: 0.8158 (mmt90) cc_final: 0.7754 (tpp-160) REVERT: B 332 GLN cc_start: 0.7622 (tt0) cc_final: 0.7364 (tm-30) REVERT: B 466 LYS cc_start: 0.8766 (tttt) cc_final: 0.8546 (ttpt) REVERT: B 645 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6476 (mm-30) REVERT: B 1024 MET cc_start: 0.7001 (pmm) cc_final: 0.6668 (pmm) REVERT: B 1114 ARG cc_start: 0.8254 (mmt-90) cc_final: 0.7701 (mmt-90) REVERT: C 29 TYR cc_start: 0.7159 (t80) cc_final: 0.6573 (p90) REVERT: C 141 PHE cc_start: 0.8575 (m-80) cc_final: 0.8211 (m-80) REVERT: C 323 LEU cc_start: 0.8045 (mm) cc_final: 0.7769 (mp) REVERT: F 113 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8313 (mttt) REVERT: H 125 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.7233 (mtp180) REVERT: K 69 HIS cc_start: 0.7812 (t-90) cc_final: 0.7486 (t-90) outliers start: 19 outliers final: 8 residues processed: 683 average time/residue: 0.2140 time to fit residues: 228.5303 Evaluate side-chains 494 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 485 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain K residue 22 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 HIS A 108 HIS ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 466 GLN A 497 ASN A 543 HIS A 545 GLN A 606 ASN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 GLN A 735 GLN A 860 GLN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1046 GLN A1075 HIS A1078 GLN ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1223 ASN A1317 GLN A1345 GLN A1486 ASN ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN B 83 GLN B 98 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 HIS B 203 ASN B 300 GLN B 305 GLN B 374 HIS B 386 GLN B 449 ASN ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 HIS B 562 GLN B 619 ASN B 680 ASN B 687 ASN B 733 GLN B 752 ASN ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 GLN B1005 GLN B1019 GLN B1038 HIS B1039 ASN ** B1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 GLN C 223 HIS ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS C 300 GLN D 27 ASN E 124 GLN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 GLN H 45 GLN H 58 GLN H 118 HIS I 15 ASN J 63 ASN ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.173556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.142696 restraints weight = 51702.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.143905 restraints weight = 41104.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.144943 restraints weight = 29367.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.144720 restraints weight = 22230.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.145032 restraints weight = 20400.572| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31562 Z= 0.177 Angle : 0.913 41.811 42843 Z= 0.427 Chirality : 0.047 0.258 4788 Planarity : 0.006 0.085 5346 Dihedral : 11.928 89.099 4624 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.98 % Favored : 90.88 % Rotamer: Outliers : 3.29 % Allowed : 16.71 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.39 % 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: -2.76 (0.13), residues: 3718 helix: -0.78 (0.14), residues: 1194 sheet: -2.09 (0.21), residues: 521 loop : -2.47 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 202 TYR 0.036 0.002 TYR G 65 PHE 0.025 0.002 PHE B 939 TRP 0.014 0.001 TRP B 395 HIS 0.014 0.002 HIS B 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (31539) covalent geometry : angle 0.80062 / 0.42 (42816) hydrogen bonds : bond 0.05433 / 3.58 ( 1125) hydrogen bonds : angle 6.12605 / 4.32 ( 3154) metal coordination : bond 0.01967 / 1.08 ( 23) metal coordination : angle 17.46750 / 10.12 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 576 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8134 (mttm) cc_final: 0.7880 (mttp) REVERT: A 92 PHE cc_start: 0.6092 (t80) cc_final: 0.5862 (p90) REVERT: A 359 MET cc_start: 0.8484 (mtm) cc_final: 0.8182 (mtp) REVERT: A 362 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8048 (pp) REVERT: A 479 MET cc_start: 0.8371 (mtt) cc_final: 0.8157 (mtt) REVERT: A 700 ASP cc_start: 0.7140 (t70) cc_final: 0.6850 (t0) REVERT: A 894 GLU cc_start: 0.7932 (tt0) cc_final: 0.7426 (tp30) REVERT: A 1016 ARG cc_start: 0.7356 (tmm160) cc_final: 0.6747 (tmm160) REVERT: A 1179 MET cc_start: 0.7572 (mmp) cc_final: 0.7164 (mmt) REVERT: A 1185 GLN cc_start: 0.7621 (tm-30) cc_final: 0.7317 (tm-30) REVERT: A 1209 MET cc_start: 0.4547 (tpp) cc_final: 0.4294 (tpp) REVERT: A 1223 ASN cc_start: 0.6850 (OUTLIER) cc_final: 0.6587 (m-40) REVERT: A 1645 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8092 (tt) REVERT: B 80 ASP cc_start: 0.7663 (t70) cc_final: 0.7180 (t0) REVERT: B 190 ARG cc_start: 0.8410 (mtt-85) cc_final: 0.7948 (mtm180) REVERT: B 238 MET cc_start: 0.7569 (mmt) cc_final: 0.7080 (mmt) REVERT: B 332 GLN cc_start: 0.7939 (tt0) cc_final: 0.7628 (tm-30) REVERT: B 645 GLU cc_start: 0.6594 (mm-30) cc_final: 0.6349 (mm-30) REVERT: B 662 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.7196 (m-10) REVERT: B 1024 MET cc_start: 0.6619 (pmm) cc_final: 0.6308 (pmm) REVERT: B 1114 ARG cc_start: 0.8273 (mmt-90) cc_final: 0.7315 (mmt-90) REVERT: C 29 TYR cc_start: 0.7107 (t80) cc_final: 0.6263 (p90) REVERT: E 33 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7166 (mm-30) REVERT: F 93 MET cc_start: 0.8202 (mmm) cc_final: 0.7961 (mtt) REVERT: K 65 TYR cc_start: 0.8794 (p90) cc_final: 0.8503 (p90) REVERT: K 69 HIS cc_start: 0.7995 (t-90) cc_final: 0.7725 (t-90) REVERT: L 31 ASN cc_start: 0.7870 (m-40) cc_final: 0.7603 (m110) outliers start: 109 outliers final: 68 residues processed: 643 average time/residue: 0.1976 time to fit residues: 204.7573 Evaluate side-chains 559 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 487 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1223 ASN Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1499 ASN Chi-restraints excluded: chain A residue 1505 MET Chi-restraints excluded: chain A residue 1538 THR Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1576 TYR Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1645 LEU Chi-restraints excluded: chain A residue 1661 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 876 ASN Chi-restraints excluded: chain B residue 903 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1064 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1134 ASP Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 22 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 242 optimal weight: 6.9990 chunk 250 optimal weight: 2.9990 chunk 118 optimal weight: 20.0000 chunk 276 optimal weight: 9.9990 chunk 321 optimal weight: 9.9990 chunk 290 optimal weight: 40.0000 chunk 53 optimal weight: 0.9990 chunk 333 optimal weight: 6.9990 chunk 296 optimal weight: 10.0000 chunk 310 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN A 608 GLN A 652 HIS ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1223 ASN ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN B 508 HIS B 619 ASN B 621 GLN ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 HIS ** B 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS E 138 ASN G 27 ASN G 167 GLN ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.169081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.138193 restraints weight = 52110.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.138839 restraints weight = 42421.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.139501 restraints weight = 35935.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.139701 restraints weight = 27528.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.139958 restraints weight = 23103.646| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 31562 Z= 0.269 Angle : 0.901 40.231 42843 Z= 0.431 Chirality : 0.048 0.274 4788 Planarity : 0.006 0.085 5346 Dihedral : 11.883 89.332 4623 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.49 % Favored : 89.38 % Rotamer: Outliers : 4.92 % Allowed : 19.48 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.36 % 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: -2.60 (0.13), residues: 3718 helix: -0.61 (0.14), residues: 1208 sheet: -2.06 (0.21), residues: 512 loop : -2.41 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 82 TYR 0.040 0.002 TYR G 65 PHE 0.023 0.002 PHE B 939 TRP 0.015 0.002 TRP B 395 HIS 0.011 0.002 HIS B 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.27 (31539) covalent geometry : angle 0.82333 / 0.43 (42816) hydrogen bonds : bond 0.05290 / 3.48 ( 1125) hydrogen bonds : angle 6.02989 / 4.25 ( 3154) metal coordination : bond 0.02066 / 1.18 ( 23) metal coordination : angle 14.59033 / 8.23 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 496 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7716 (mm-40) REVERT: A 12 LYS cc_start: 0.8076 (mttm) cc_final: 0.7799 (mttp) REVERT: A 136 MET cc_start: -0.0459 (ttt) cc_final: -0.1066 (ptm) REVERT: A 245 LYS cc_start: 0.7293 (mmtt) cc_final: 0.7072 (mmtm) REVERT: A 359 MET cc_start: 0.8439 (mtm) cc_final: 0.8232 (mtp) REVERT: A 362 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7814 (pp) REVERT: A 533 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8551 (m-40) REVERT: A 631 ARG cc_start: 0.8292 (mpt-90) cc_final: 0.8082 (mpt-90) REVERT: A 763 ASN cc_start: 0.7883 (p0) cc_final: 0.7221 (p0) REVERT: A 894 GLU cc_start: 0.7936 (tt0) cc_final: 0.7420 (tp30) REVERT: A 1016 ARG cc_start: 0.7264 (tmm160) cc_final: 0.6660 (tmm160) REVERT: A 1179 MET cc_start: 0.7750 (mmp) cc_final: 0.7272 (mmt) REVERT: A 1185 GLN cc_start: 0.7697 (tm-30) cc_final: 0.7143 (tm-30) REVERT: A 1209 MET cc_start: 0.4745 (tpp) cc_final: 0.4412 (tpp) REVERT: B 190 ARG cc_start: 0.8516 (mtt-85) cc_final: 0.8168 (mtm180) REVERT: B 238 MET cc_start: 0.7698 (mmt) cc_final: 0.7186 (mmt) REVERT: B 332 GLN cc_start: 0.7884 (tt0) cc_final: 0.7661 (tm-30) REVERT: B 645 GLU cc_start: 0.6686 (mm-30) cc_final: 0.6448 (mm-30) REVERT: B 662 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: B 768 MET cc_start: 0.7363 (mmt) cc_final: 0.7084 (mmt) REVERT: B 1024 MET cc_start: 0.6859 (pmm) cc_final: 0.6442 (pmm) REVERT: B 1067 HIS cc_start: 0.7173 (OUTLIER) cc_final: 0.6915 (m90) REVERT: B 1074 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7154 (tm-30) REVERT: B 1104 MET cc_start: 0.4356 (OUTLIER) cc_final: 0.4067 (ptm) REVERT: B 1114 ARG cc_start: 0.8248 (mmt-90) cc_final: 0.7370 (mmt-90) REVERT: C 41 LYS cc_start: 0.7248 (tptt) cc_final: 0.7035 (tppt) REVERT: C 141 PHE cc_start: 0.8726 (m-80) cc_final: 0.8195 (m-80) REVERT: C 323 LEU cc_start: 0.8127 (mm) cc_final: 0.7862 (mp) REVERT: F 79 GLU cc_start: 0.8127 (mp0) cc_final: 0.7628 (mp0) REVERT: F 93 MET cc_start: 0.8321 (mmm) cc_final: 0.8039 (mtt) outliers start: 163 outliers final: 108 residues processed: 607 average time/residue: 0.1943 time to fit residues: 193.1187 Evaluate side-chains 563 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 450 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 471 LYS Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1328 PHE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1499 ASN Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1538 THR Chi-restraints excluded: chain A residue 1565 TYR Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1576 TYR Chi-restraints excluded: chain A residue 1608 ILE Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1661 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 876 ASN Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 903 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1027 ASP Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1072 LEU Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1134 ASP Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1170 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 23 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 123 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 276 optimal weight: 1.9990 chunk 263 optimal weight: 7.9990 chunk 213 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 109 optimal weight: 0.0670 chunk 200 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 chunk 176 optimal weight: 9.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN B 227 ASN ** B 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS ** L 31 ASN ** 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 = 0.4158 r_free = 0.4158 target = 0.172564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.141446 restraints weight = 51658.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.142426 restraints weight = 39504.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.143196 restraints weight = 30694.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.143213 restraints weight = 23287.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.143425 restraints weight = 20718.358| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31562 Z= 0.166 Angle : 0.798 36.921 42843 Z= 0.390 Chirality : 0.045 0.269 4788 Planarity : 0.005 0.087 5346 Dihedral : 11.715 89.052 4623 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.25 % Favored : 90.61 % Rotamer: Outliers : 4.67 % Allowed : 21.17 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.36 % 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: -2.29 (0.13), residues: 3718 helix: -0.25 (0.15), residues: 1197 sheet: -2.00 (0.21), residues: 516 loop : -2.24 (0.13), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 23 TYR 0.035 0.002 TYR A1297 PHE 0.026 0.002 PHE B 939 TRP 0.013 0.001 TRP B 395 HIS 0.016 0.001 HIS B 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (31539) covalent geometry : angle 0.74784 / 0.39 (42816) hydrogen bonds : bond 0.04685 / 3.07 ( 1125) hydrogen bonds : angle 5.69540 / 4.01 ( 3154) metal coordination : bond 0.01737 / 0.98 ( 23) metal coordination : angle 11.13400 / 6.04 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 522 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ILE cc_start: 0.8177 (mt) cc_final: 0.7962 (mt) REVERT: A 5 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7653 (mm110) REVERT: A 12 LYS cc_start: 0.8026 (mttm) cc_final: 0.7727 (mttp) REVERT: A 245 LYS cc_start: 0.7280 (mmtt) cc_final: 0.7052 (mmtm) REVERT: A 327 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.5870 (tm-30) REVERT: A 362 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7812 (pp) REVERT: A 631 ARG cc_start: 0.8052 (mpt-90) cc_final: 0.7841 (mpt-90) REVERT: A 847 ASP cc_start: 0.8196 (m-30) cc_final: 0.7723 (t0) REVERT: A 894 GLU cc_start: 0.7929 (tt0) cc_final: 0.7392 (tp30) REVERT: A 1078 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7603 (tp40) REVERT: A 1185 GLN cc_start: 0.7703 (tm-30) cc_final: 0.7381 (tm-30) REVERT: A 1209 MET cc_start: 0.4624 (tpp) cc_final: 0.4416 (tpp) REVERT: A 1339 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.6659 (t80) REVERT: A 1505 MET cc_start: 0.6875 (mmm) cc_final: 0.6674 (tpt) REVERT: A 1576 TYR cc_start: 0.6191 (OUTLIER) cc_final: 0.3157 (t80) REVERT: B 165 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7097 (pt0) REVERT: B 190 ARG cc_start: 0.8642 (mtt-85) cc_final: 0.8123 (mtm180) REVERT: B 238 MET cc_start: 0.7521 (mmt) cc_final: 0.6990 (mmt) REVERT: B 332 GLN cc_start: 0.7860 (tt0) cc_final: 0.7445 (tm-30) REVERT: B 662 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7228 (m-80) REVERT: B 688 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7080 (mtm) REVERT: B 768 MET cc_start: 0.7416 (mmt) cc_final: 0.7128 (mmp) REVERT: B 1024 MET cc_start: 0.6684 (pmm) cc_final: 0.6328 (pmm) REVERT: B 1104 MET cc_start: 0.4220 (OUTLIER) cc_final: 0.4007 (ptm) REVERT: B 1114 ARG cc_start: 0.8272 (mmt-90) cc_final: 0.7481 (mmt-90) REVERT: C 58 MET cc_start: 0.7812 (tpp) cc_final: 0.6942 (tpp) REVERT: C 141 PHE cc_start: 0.8706 (m-80) cc_final: 0.8149 (m-80) REVERT: C 323 LEU cc_start: 0.7975 (mm) cc_final: 0.7711 (mp) REVERT: F 79 GLU cc_start: 0.7691 (mp0) cc_final: 0.7477 (mp0) REVERT: F 93 MET cc_start: 0.8226 (mmm) cc_final: 0.7969 (mtt) REVERT: G 9 GLN cc_start: 0.4557 (mm-40) cc_final: 0.4200 (mp10) REVERT: H 47 TYR cc_start: 0.7184 (t80) cc_final: 0.6546 (t80) outliers start: 155 outliers final: 108 residues processed: 621 average time/residue: 0.1889 time to fit residues: 193.7420 Evaluate side-chains 583 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 467 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1309 TYR Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1339 TYR Chi-restraints excluded: chain A residue 1499 ASN Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1538 THR Chi-restraints excluded: chain A residue 1565 TYR Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1576 TYR Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 652 PHE Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 876 ASN Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 903 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1134 ASP Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1170 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 59 GLU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 113 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 249 optimal weight: 8.9990 chunk 210 optimal weight: 0.8980 chunk 321 optimal weight: 7.9990 chunk 348 optimal weight: 6.9990 chunk 296 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 326 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 HIS ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1548 ASN ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.169815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.139061 restraints weight = 52156.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.139837 restraints weight = 41564.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.140453 restraints weight = 32679.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.140873 restraints weight = 25120.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.140927 restraints weight = 22881.803| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 31562 Z= 0.242 Angle : 0.826 34.299 42843 Z= 0.407 Chirality : 0.047 0.275 4788 Planarity : 0.005 0.087 5346 Dihedral : 11.718 89.832 4623 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.66 % Favored : 90.21 % Rotamer: Outliers : 6.18 % Allowed : 21.59 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.34 % 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: -2.29 (0.13), residues: 3718 helix: -0.29 (0.14), residues: 1220 sheet: -1.98 (0.21), residues: 515 loop : -2.24 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 82 TYR 0.030 0.002 TYR A 896 PHE 0.023 0.002 PHE A1175 TRP 0.014 0.001 TRP B 395 HIS 0.009 0.002 HIS B 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 (31539) covalent geometry : angle 0.78668 / 0.40 (42816) hydrogen bonds : bond 0.04818 / 3.15 ( 1125) hydrogen bonds : angle 5.68834 / 4.01 ( 3154) metal coordination : bond 0.01682 / 0.92 ( 23) metal coordination : angle 10.03060 / 5.52 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 479 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5431 (ttm) cc_final: 0.4905 (ttm) REVERT: A 3 ILE cc_start: 0.8202 (mt) cc_final: 0.7892 (mt) REVERT: A 12 LYS cc_start: 0.8004 (mttm) cc_final: 0.7702 (mttp) REVERT: A 245 LYS cc_start: 0.7451 (mmtt) cc_final: 0.7202 (mmtm) REVERT: A 327 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.5949 (tm-30) REVERT: A 362 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7662 (pp) REVERT: A 467 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7246 (pt) REVERT: A 624 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.6865 (mp) REVERT: A 894 GLU cc_start: 0.7956 (tt0) cc_final: 0.7419 (tp30) REVERT: A 1068 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7468 (tt) REVERT: A 1078 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7637 (tp40) REVERT: A 1185 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7167 (tm-30) REVERT: A 1209 MET cc_start: 0.4788 (tpp) cc_final: 0.4501 (tpp) REVERT: A 1339 TYR cc_start: 0.7000 (OUTLIER) cc_final: 0.6719 (t80) REVERT: A 1505 MET cc_start: 0.6956 (mmm) cc_final: 0.6654 (tpt) REVERT: A 1572 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8089 (mt) REVERT: A 1576 TYR cc_start: 0.6175 (OUTLIER) cc_final: 0.3182 (t80) REVERT: B 165 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7137 (pt0) REVERT: B 190 ARG cc_start: 0.8680 (mtt-85) cc_final: 0.8148 (mtm180) REVERT: B 238 MET cc_start: 0.7604 (mmt) cc_final: 0.7037 (mmt) REVERT: B 332 GLN cc_start: 0.7768 (tt0) cc_final: 0.7421 (tm-30) REVERT: B 504 MET cc_start: 0.7178 (ptp) cc_final: 0.6769 (mtm) REVERT: B 662 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: B 688 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7179 (mtm) REVERT: B 1024 MET cc_start: 0.6926 (pmm) cc_final: 0.6588 (pmm) REVERT: B 1114 ARG cc_start: 0.8479 (mmt-90) cc_final: 0.7477 (mmt-90) REVERT: C 99 GLN cc_start: 0.8057 (mp10) cc_final: 0.7437 (mp10) REVERT: E 169 GLN cc_start: 0.7517 (mt0) cc_final: 0.7294 (mt0) REVERT: F 93 MET cc_start: 0.8220 (mmm) cc_final: 0.7953 (mtt) REVERT: G 65 TYR cc_start: 0.4992 (OUTLIER) cc_final: 0.4696 (t80) REVERT: G 66 ASP cc_start: 0.6847 (t0) cc_final: 0.6477 (t70) REVERT: H 47 TYR cc_start: 0.7166 (t80) cc_final: 0.6539 (t80) outliers start: 205 outliers final: 155 residues processed: 617 average time/residue: 0.1881 time to fit residues: 192.8306 Evaluate side-chains 614 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 447 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 898 ASP Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1309 TYR Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1339 TYR Chi-restraints excluded: chain A residue 1499 ASN Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1538 THR Chi-restraints excluded: chain A residue 1565 TYR Chi-restraints excluded: chain A residue 1572 ILE Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1576 TYR Chi-restraints excluded: chain A residue 1608 ILE Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1661 SER Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain A residue 1679 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 652 PHE Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 903 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1027 ASP Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1072 LEU Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1134 ASP Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 32 HIS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 65 TYR Chi-restraints excluded: chain G residue 69 PHE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 52 HIS Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 59 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 23 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 38 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 285 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 243 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN ** A 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN B 619 ASN ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.171665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.140015 restraints weight = 51744.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.141595 restraints weight = 37142.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.142234 restraints weight = 26772.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.142122 restraints weight = 21091.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.142329 restraints weight = 18743.698| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31562 Z= 0.152 Angle : 0.768 31.121 42843 Z= 0.378 Chirality : 0.045 0.352 4788 Planarity : 0.005 0.087 5346 Dihedral : 11.583 89.909 4623 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.55 % Favored : 91.31 % Rotamer: Outliers : 4.86 % Allowed : 23.49 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.34 % 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: -2.05 (0.13), residues: 3718 helix: -0.03 (0.15), residues: 1224 sheet: -1.94 (0.21), residues: 515 loop : -2.11 (0.13), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 92 TYR 0.027 0.002 TYR A 896 PHE 0.027 0.002 PHE A 247 TRP 0.013 0.001 TRP B 395 HIS 0.010 0.001 HIS B 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (31539) covalent geometry : angle 0.73445 / 0.38 (42816) hydrogen bonds : bond 0.04358 / 2.86 ( 1125) hydrogen bonds : angle 5.46853 / 3.85 ( 3154) metal coordination : bond 0.01284 / 0.67 ( 23) metal coordination : angle 9.01681 / 5.04 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 508 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7481 (mm110) REVERT: A 12 LYS cc_start: 0.7979 (mttm) cc_final: 0.7694 (mttp) REVERT: A 327 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.5277 (tm-30) REVERT: A 362 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7675 (pp) REVERT: A 624 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.6769 (mp) REVERT: A 723 MET cc_start: 0.6465 (ptt) cc_final: 0.6205 (ptt) REVERT: A 847 ASP cc_start: 0.8194 (m-30) cc_final: 0.7863 (t0) REVERT: A 894 GLU cc_start: 0.7946 (tt0) cc_final: 0.7372 (tp30) REVERT: A 1078 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7571 (tp40) REVERT: A 1185 GLN cc_start: 0.7838 (tm-30) cc_final: 0.7393 (tm-30) REVERT: A 1339 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.6611 (t80) REVERT: A 1505 MET cc_start: 0.6883 (mmm) cc_final: 0.6619 (tpt) REVERT: A 1572 ILE cc_start: 0.8503 (pt) cc_final: 0.8186 (mt) REVERT: A 1576 TYR cc_start: 0.6172 (OUTLIER) cc_final: 0.3157 (t80) REVERT: A 1641 THR cc_start: 0.8183 (m) cc_final: 0.7866 (m) REVERT: B 190 ARG cc_start: 0.8598 (mtt-85) cc_final: 0.8108 (mtm180) REVERT: B 238 MET cc_start: 0.7395 (mmt) cc_final: 0.6984 (mmt) REVERT: B 332 GLN cc_start: 0.7684 (tt0) cc_final: 0.7326 (tm-30) REVERT: B 504 MET cc_start: 0.7241 (ptp) cc_final: 0.6872 (mtm) REVERT: B 662 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7281 (m-80) REVERT: B 688 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.6947 (mtm) REVERT: B 838 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8470 (mp) REVERT: B 877 ASP cc_start: 0.6080 (OUTLIER) cc_final: 0.5157 (p0) REVERT: B 1007 MET cc_start: 0.7676 (mmm) cc_final: 0.7308 (mtt) REVERT: B 1024 MET cc_start: 0.6854 (pmm) cc_final: 0.6474 (pmm) REVERT: B 1076 ARG cc_start: 0.8364 (mmm-85) cc_final: 0.7819 (mmm-85) REVERT: E 169 GLN cc_start: 0.7377 (mt0) cc_final: 0.6990 (mt0) REVERT: G 9 GLN cc_start: 0.5991 (pm20) cc_final: 0.5510 (mm110) REVERT: G 66 ASP cc_start: 0.6849 (t0) cc_final: 0.6367 (t70) REVERT: H 47 TYR cc_start: 0.7001 (t80) cc_final: 0.6522 (t80) outliers start: 161 outliers final: 121 residues processed: 612 average time/residue: 0.1859 time to fit residues: 188.3029 Evaluate side-chains 597 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 467 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1339 TYR Chi-restraints excluded: chain A residue 1499 ASN Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1538 THR Chi-restraints excluded: chain A residue 1565 TYR Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1576 TYR Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 652 PHE Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 876 ASN Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1027 ASP Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1159 THR Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 32 HIS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 113 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 307 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 204 optimal weight: 9.9990 chunk 290 optimal weight: 50.0000 chunk 83 optimal weight: 6.9990 chunk 327 optimal weight: 30.0000 chunk 202 optimal weight: 0.0980 chunk 250 optimal weight: 0.0020 chunk 239 optimal weight: 7.9990 chunk 262 optimal weight: 7.9990 chunk 55 optimal weight: 0.4980 overall best weight: 2.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS F 90 GLN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.173227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.142406 restraints weight = 52087.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.143071 restraints weight = 40108.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.143852 restraints weight = 33853.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.144134 restraints weight = 24863.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.144343 restraints weight = 21601.010| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31562 Z= 0.165 Angle : 0.760 29.688 42843 Z= 0.374 Chirality : 0.045 0.322 4788 Planarity : 0.005 0.087 5346 Dihedral : 11.522 89.884 4623 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.74 % Favored : 91.18 % Rotamer: Outliers : 4.98 % Allowed : 23.55 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.28 % 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: -1.97 (0.13), residues: 3718 helix: 0.04 (0.15), residues: 1238 sheet: -1.92 (0.21), residues: 523 loop : -2.06 (0.13), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A1016 TYR 0.026 0.002 TYR A1297 PHE 0.021 0.002 PHE B 939 TRP 0.012 0.001 TRP B 395 HIS 0.009 0.001 HIS B 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (31539) covalent geometry : angle 0.72861 / 0.37 (42816) hydrogen bonds : bond 0.04283 / 2.80 ( 1125) hydrogen bonds : angle 5.39319 / 3.80 ( 3154) metal coordination : bond 0.01243 / 0.66 ( 23) metal coordination : angle 8.62512 / 4.84 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 497 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7491 (mm110) REVERT: A 12 LYS cc_start: 0.8003 (mttm) cc_final: 0.7718 (mttp) REVERT: A 362 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7672 (pp) REVERT: A 522 TYR cc_start: 0.7189 (OUTLIER) cc_final: 0.6614 (p90) REVERT: A 624 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.6724 (mp) REVERT: A 723 MET cc_start: 0.6479 (ptt) cc_final: 0.6204 (ptt) REVERT: A 847 ASP cc_start: 0.8143 (m-30) cc_final: 0.7696 (t0) REVERT: A 894 GLU cc_start: 0.7865 (tt0) cc_final: 0.7328 (tp30) REVERT: A 1003 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8463 (pt) REVERT: A 1078 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7576 (tp40) REVERT: A 1185 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7407 (tm-30) REVERT: A 1339 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.6613 (t80) REVERT: A 1505 MET cc_start: 0.6903 (mmm) cc_final: 0.6664 (tpt) REVERT: A 1572 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8248 (mt) REVERT: A 1576 TYR cc_start: 0.6169 (OUTLIER) cc_final: 0.3186 (t80) REVERT: A 1615 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7777 (tm-30) REVERT: B 190 ARG cc_start: 0.8604 (mtt-85) cc_final: 0.8112 (mtm180) REVERT: B 238 MET cc_start: 0.7468 (mmt) cc_final: 0.6971 (mmt) REVERT: B 330 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7439 (tt) REVERT: B 332 GLN cc_start: 0.7676 (tt0) cc_final: 0.7282 (tm-30) REVERT: B 504 MET cc_start: 0.7223 (ptp) cc_final: 0.6865 (mtm) REVERT: B 662 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7299 (m-80) REVERT: B 688 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.6934 (mtm) REVERT: B 838 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8435 (mp) REVERT: B 877 ASP cc_start: 0.6131 (OUTLIER) cc_final: 0.5272 (p0) REVERT: B 1076 ARG cc_start: 0.8311 (mmm-85) cc_final: 0.7772 (mmm-85) REVERT: B 1114 ARG cc_start: 0.8374 (mmt-90) cc_final: 0.7711 (mmt-90) REVERT: C 99 GLN cc_start: 0.7874 (mp10) cc_final: 0.7316 (mp10) REVERT: F 75 MET cc_start: 0.7899 (ttp) cc_final: 0.7605 (ttp) REVERT: G 9 GLN cc_start: 0.6015 (pm20) cc_final: 0.5373 (mm110) REVERT: H 47 TYR cc_start: 0.6881 (t80) cc_final: 0.6534 (t80) outliers start: 165 outliers final: 130 residues processed: 600 average time/residue: 0.1900 time to fit residues: 188.5799 Evaluate side-chains 607 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 465 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1309 TYR Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1339 TYR Chi-restraints excluded: chain A residue 1499 ASN Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1538 THR Chi-restraints excluded: chain A residue 1565 TYR Chi-restraints excluded: chain A residue 1572 ILE Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1576 TYR Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 652 PHE Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 876 ASN Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1027 ASP Chi-restraints excluded: chain B residue 1059 MET Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1159 THR Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 32 HIS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 69 PHE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 59 GLU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 23 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 267 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 258 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 354 optimal weight: 6.9990 chunk 316 optimal weight: 2.9990 chunk 141 optimal weight: 0.0570 chunk 255 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1046 GLN ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN B 619 ASN ** B 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS F 90 GLN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.175401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.144419 restraints weight = 51894.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.144771 restraints weight = 40030.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.145570 restraints weight = 31887.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.146110 restraints weight = 23118.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.146323 restraints weight = 20490.072| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31562 Z= 0.140 Angle : 0.749 27.158 42843 Z= 0.368 Chirality : 0.044 0.271 4788 Planarity : 0.005 0.087 5346 Dihedral : 11.416 89.457 4623 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.66 % Favored : 91.26 % Rotamer: Outliers : 4.46 % Allowed : 24.40 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.25 % 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: -1.78 (0.13), residues: 3718 helix: 0.25 (0.15), residues: 1222 sheet: -1.90 (0.21), residues: 539 loop : -1.94 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG B 92 TYR 0.023 0.001 TYR A 896 PHE 0.027 0.002 PHE B 329 TRP 0.012 0.001 TRP B 395 HIS 0.008 0.001 HIS B 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (31539) covalent geometry : angle 0.72199 / 0.37 (42816) hydrogen bonds : bond 0.04072 / 2.66 ( 1125) hydrogen bonds : angle 5.26279 / 3.71 ( 3154) metal coordination : bond 0.01065 / 0.56 ( 23) metal coordination : angle 8.00632 / 4.53 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 513 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4857 (ttm) cc_final: 0.4265 (mtm) REVERT: A 5 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7530 (mm-40) REVERT: A 12 LYS cc_start: 0.7939 (mttm) cc_final: 0.7664 (mttp) REVERT: A 247 PHE cc_start: 0.5601 (m-10) cc_final: 0.5354 (m-10) REVERT: A 327 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.5748 (tm-30) REVERT: A 362 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7734 (pp) REVERT: A 482 LYS cc_start: 0.8252 (pttt) cc_final: 0.7880 (pttm) REVERT: A 486 TYR cc_start: 0.8408 (m-80) cc_final: 0.8010 (m-10) REVERT: A 522 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.6590 (p90) REVERT: A 602 MET cc_start: 0.8169 (tpp) cc_final: 0.7822 (tpp) REVERT: A 624 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.6600 (mp) REVERT: A 723 MET cc_start: 0.6278 (OUTLIER) cc_final: 0.5967 (ptt) REVERT: A 847 ASP cc_start: 0.8152 (m-30) cc_final: 0.7729 (t0) REVERT: A 894 GLU cc_start: 0.7804 (tt0) cc_final: 0.7414 (tp30) REVERT: A 1078 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7528 (tp40) REVERT: A 1185 GLN cc_start: 0.7922 (tm-30) cc_final: 0.7527 (tm-30) REVERT: A 1572 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8272 (mt) REVERT: A 1576 TYR cc_start: 0.6060 (OUTLIER) cc_final: 0.3100 (t80) REVERT: B 88 MET cc_start: 0.8386 (mmt) cc_final: 0.7961 (mmt) REVERT: B 190 ARG cc_start: 0.8566 (mtt-85) cc_final: 0.8088 (mtm180) REVERT: B 238 MET cc_start: 0.7288 (mmt) cc_final: 0.6757 (mmt) REVERT: B 332 GLN cc_start: 0.7721 (tt0) cc_final: 0.7237 (tm-30) REVERT: B 504 MET cc_start: 0.7247 (ptp) cc_final: 0.6868 (mtm) REVERT: B 662 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7264 (m-80) REVERT: B 688 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.6954 (mtm) REVERT: B 838 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8456 (mp) REVERT: B 877 ASP cc_start: 0.5931 (OUTLIER) cc_final: 0.5241 (p0) REVERT: B 1024 MET cc_start: 0.6894 (pmm) cc_final: 0.6601 (pmm) REVERT: B 1076 ARG cc_start: 0.8256 (mmm-85) cc_final: 0.7832 (mmm-85) REVERT: G 9 GLN cc_start: 0.6328 (pm20) cc_final: 0.5609 (mm110) REVERT: G 30 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7219 (mm-40) REVERT: G 36 MET cc_start: 0.6246 (ptt) cc_final: 0.6023 (ptt) REVERT: H 47 TYR cc_start: 0.6751 (t80) cc_final: 0.6423 (t80) outliers start: 148 outliers final: 119 residues processed: 605 average time/residue: 0.1848 time to fit residues: 184.6881 Evaluate side-chains 607 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 477 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 723 MET Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1309 TYR Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1499 ASN Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1538 THR Chi-restraints excluded: chain A residue 1565 TYR Chi-restraints excluded: chain A residue 1572 ILE Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1576 TYR Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 652 PHE Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 876 ASN Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1059 MET Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1072 LEU Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1159 THR Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 32 HIS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 113 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 311 optimal weight: 6.9990 chunk 309 optimal weight: 8.9990 chunk 340 optimal weight: 9.9990 chunk 262 optimal weight: 0.9990 chunk 147 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 149 optimal weight: 0.0040 chunk 337 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 172 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1479 HIS ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN B 619 ASN B 621 GLN ** B 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.173844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.143099 restraints weight = 51736.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.143920 restraints weight = 39986.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.144721 restraints weight = 32225.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.144890 restraints weight = 24105.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.145164 restraints weight = 20847.053| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31562 Z= 0.172 Angle : 0.761 26.151 42843 Z= 0.376 Chirality : 0.045 0.272 4788 Planarity : 0.005 0.087 5346 Dihedral : 11.404 89.779 4623 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.69 % Favored : 91.23 % Rotamer: Outliers : 4.49 % Allowed : 24.64 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.22 % 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: -1.79 (0.13), residues: 3718 helix: 0.22 (0.15), residues: 1235 sheet: -1.86 (0.21), residues: 549 loop : -1.95 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 87 TYR 0.030 0.002 TYR B 172 PHE 0.040 0.002 PHE A 92 TRP 0.011 0.001 TRP B 395 HIS 0.018 0.001 HIS B 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (31539) covalent geometry : angle 0.73611 / 0.37 (42816) hydrogen bonds : bond 0.04150 / 2.70 ( 1125) hydrogen bonds : angle 5.29180 / 3.73 ( 3154) metal coordination : bond 0.01122 / 0.60 ( 23) metal coordination : angle 7.75057 / 4.38 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 494 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4908 (ttm) cc_final: 0.4559 (mtm) REVERT: A 5 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7483 (mm-40) REVERT: A 12 LYS cc_start: 0.8027 (mttm) cc_final: 0.7772 (mttp) REVERT: A 179 MET cc_start: 0.3202 (mmt) cc_final: 0.2451 (mmm) REVERT: A 362 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7758 (pp) REVERT: A 384 GLU cc_start: 0.6535 (pm20) cc_final: 0.6052 (pm20) REVERT: A 482 LYS cc_start: 0.8185 (pttt) cc_final: 0.7730 (pttm) REVERT: A 486 TYR cc_start: 0.8406 (m-80) cc_final: 0.8139 (m-10) REVERT: A 522 TYR cc_start: 0.7310 (OUTLIER) cc_final: 0.6653 (p90) REVERT: A 602 MET cc_start: 0.8165 (tpp) cc_final: 0.7943 (tpp) REVERT: A 617 MET cc_start: 0.8367 (mtt) cc_final: 0.8039 (mtt) REVERT: A 624 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.6605 (mp) REVERT: A 723 MET cc_start: 0.6376 (OUTLIER) cc_final: 0.6100 (ptt) REVERT: A 847 ASP cc_start: 0.8156 (m-30) cc_final: 0.7724 (t0) REVERT: A 894 GLU cc_start: 0.7802 (tt0) cc_final: 0.7405 (tp30) REVERT: A 1078 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7666 (tp40) REVERT: A 1185 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7436 (tm-30) REVERT: A 1505 MET cc_start: 0.6740 (mmm) cc_final: 0.6360 (tpt) REVERT: A 1572 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8286 (mt) REVERT: A 1576 TYR cc_start: 0.6120 (OUTLIER) cc_final: 0.3073 (t80) REVERT: B 190 ARG cc_start: 0.8611 (mtt-85) cc_final: 0.8109 (mtm180) REVERT: B 238 MET cc_start: 0.7329 (mmt) cc_final: 0.6785 (mmt) REVERT: B 332 GLN cc_start: 0.7735 (tt0) cc_final: 0.7266 (tm-30) REVERT: B 504 MET cc_start: 0.7333 (ptp) cc_final: 0.6923 (mtm) REVERT: B 662 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7322 (m-80) REVERT: B 688 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.6919 (mtm) REVERT: B 833 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7266 (m-80) REVERT: B 838 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8464 (mp) REVERT: B 877 ASP cc_start: 0.5885 (OUTLIER) cc_final: 0.5211 (p0) REVERT: B 1007 MET cc_start: 0.7801 (mmm) cc_final: 0.7372 (mtt) REVERT: B 1073 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7729 (ttp) REVERT: B 1076 ARG cc_start: 0.8281 (mmm-85) cc_final: 0.7771 (mmm-85) REVERT: C 99 GLN cc_start: 0.7845 (mp10) cc_final: 0.7322 (mp10) REVERT: C 235 ARG cc_start: 0.8759 (mtp-110) cc_final: 0.8543 (mtp-110) REVERT: G 9 GLN cc_start: 0.6332 (pm20) cc_final: 0.5618 (mm110) REVERT: G 30 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7302 (mm-40) REVERT: H 47 TYR cc_start: 0.6784 (t80) cc_final: 0.6430 (t80) outliers start: 149 outliers final: 123 residues processed: 593 average time/residue: 0.1851 time to fit residues: 180.8806 Evaluate side-chains 606 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 471 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 723 MET Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1309 TYR Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1499 ASN Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1538 THR Chi-restraints excluded: chain A residue 1565 TYR Chi-restraints excluded: chain A residue 1572 ILE Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1576 TYR Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 652 PHE Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1059 MET Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1072 LEU Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1159 THR Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 32 HIS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 23 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 237 optimal weight: 7.9990 chunk 352 optimal weight: 0.8980 chunk 140 optimal weight: 0.0270 chunk 262 optimal weight: 5.9990 chunk 349 optimal weight: 20.0000 chunk 147 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 252 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS ** A 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1479 HIS ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN B 619 ASN ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.172682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.141813 restraints weight = 51631.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.143020 restraints weight = 37323.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.143600 restraints weight = 30820.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.143827 restraints weight = 23496.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.143995 restraints weight = 20653.461| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31562 Z= 0.158 Angle : 0.758 24.852 42843 Z= 0.375 Chirality : 0.045 0.272 4788 Planarity : 0.005 0.087 5346 Dihedral : 11.382 89.579 4623 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.77 % Favored : 91.18 % Rotamer: Outliers : 4.28 % Allowed : 25.03 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.22 % 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: -1.72 (0.13), residues: 3718 helix: 0.28 (0.15), residues: 1229 sheet: -1.86 (0.21), residues: 552 loop : -1.90 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1061 TYR 0.029 0.002 TYR E 203 PHE 0.026 0.002 PHE B1056 TRP 0.011 0.001 TRP B 395 HIS 0.009 0.001 HIS B 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (31539) covalent geometry : angle 0.73530 / 0.37 (42816) hydrogen bonds : bond 0.04067 / 2.64 ( 1125) hydrogen bonds : angle 5.25167 / 3.70 ( 3154) metal coordination : bond 0.01053 / 0.56 ( 23) metal coordination : angle 7.44227 / 4.20 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 496 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8033 (mttm) cc_final: 0.7737 (mttp) REVERT: A 179 MET cc_start: 0.3520 (mmt) cc_final: 0.2925 (mmm) REVERT: A 359 MET cc_start: 0.8140 (ttm) cc_final: 0.7907 (ttp) REVERT: A 362 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7691 (pp) REVERT: A 482 LYS cc_start: 0.8186 (pttt) cc_final: 0.7709 (pttm) REVERT: A 486 TYR cc_start: 0.8437 (m-80) cc_final: 0.8156 (m-10) REVERT: A 522 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.6683 (p90) REVERT: A 602 MET cc_start: 0.8219 (tpp) cc_final: 0.7979 (tpp) REVERT: A 603 LEU cc_start: 0.8913 (pt) cc_final: 0.8680 (pp) REVERT: A 624 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.6565 (mp) REVERT: A 723 MET cc_start: 0.6454 (OUTLIER) cc_final: 0.6154 (ptt) REVERT: A 847 ASP cc_start: 0.8133 (m-30) cc_final: 0.7697 (t0) REVERT: A 894 GLU cc_start: 0.7889 (tt0) cc_final: 0.7331 (tp30) REVERT: A 1078 GLN cc_start: 0.7980 (mm-40) cc_final: 0.7675 (tp40) REVERT: A 1185 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7430 (tm-30) REVERT: A 1572 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8295 (mt) REVERT: A 1576 TYR cc_start: 0.5980 (OUTLIER) cc_final: 0.3048 (t80) REVERT: B 80 ASP cc_start: 0.7862 (t0) cc_final: 0.7222 (t0) REVERT: B 190 ARG cc_start: 0.8584 (mtt-85) cc_final: 0.8094 (mtm180) REVERT: B 238 MET cc_start: 0.7268 (mmt) cc_final: 0.6547 (mmt) REVERT: B 332 GLN cc_start: 0.7715 (tt0) cc_final: 0.7247 (tm-30) REVERT: B 504 MET cc_start: 0.7318 (ptp) cc_final: 0.6911 (mtm) REVERT: B 662 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7317 (m-80) REVERT: B 688 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.6942 (mtm) REVERT: B 838 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8503 (mp) REVERT: B 877 ASP cc_start: 0.5889 (OUTLIER) cc_final: 0.5256 (p0) REVERT: B 1076 ARG cc_start: 0.8270 (mmm-85) cc_final: 0.7747 (mmm-85) REVERT: C 99 GLN cc_start: 0.7835 (mp10) cc_final: 0.7284 (mp10) REVERT: G 9 GLN cc_start: 0.6322 (pm20) cc_final: 0.5767 (mm110) REVERT: G 30 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7252 (mm-40) REVERT: G 36 MET cc_start: 0.6077 (ptt) cc_final: 0.5813 (ptt) REVERT: H 47 TYR cc_start: 0.6739 (t80) cc_final: 0.6365 (t80) outliers start: 142 outliers final: 125 residues processed: 588 average time/residue: 0.1861 time to fit residues: 181.3745 Evaluate side-chains 616 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 481 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 723 MET Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1309 TYR Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1499 ASN Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1538 THR Chi-restraints excluded: chain A residue 1565 TYR Chi-restraints excluded: chain A residue 1572 ILE Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1576 TYR Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 652 PHE Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1059 MET Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1072 LEU Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1159 THR Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 32 HIS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 39 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 341 optimal weight: 1.9990 chunk 317 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 362 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 319 optimal weight: 0.3980 chunk 305 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 367 optimal weight: 0.0870 overall best weight: 1.0964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1479 HIS ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 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 = 0.4151 r_free = 0.4151 target = 0.172434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.141236 restraints weight = 51950.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.141894 restraints weight = 38787.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.142466 restraints weight = 34032.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.142858 restraints weight = 26092.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.143130 restraints weight = 21944.617| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.238 31562 Z= 0.216 Angle : 0.842 59.199 42843 Z= 0.443 Chirality : 0.048 1.239 4788 Planarity : 0.005 0.091 5346 Dihedral : 11.382 89.580 4623 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.88 % Favored : 91.07 % Rotamer: Outliers : 4.28 % Allowed : 25.03 % Favored : 70.69 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.22 % 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: -1.73 (0.13), residues: 3718 helix: 0.29 (0.15), residues: 1229 sheet: -1.86 (0.21), residues: 552 loop : -1.91 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 204 TYR 0.026 0.002 TYR E 203 PHE 0.026 0.002 PHE B1056 TRP 0.011 0.001 TRP B 395 HIS 0.010 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.22 (31539) covalent geometry : angle 0.82174 / 0.44 (42816) hydrogen bonds : bond 0.04061 / 2.64 ( 1125) hydrogen bonds : angle 5.25167 / 3.70 ( 3154) metal coordination : bond 0.01025 / 0.54 ( 23) metal coordination : angle 7.43613 / 4.20 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5021.53 seconds wall clock time: 88 minutes 19.26 seconds (5299.26 seconds total)