Starting phenix.real_space_refine on Tue Jul 7 06:23:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nfe_12301/07_2026/7nfe_12301.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nfe_12301/07_2026/7nfe_12301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nfe_12301/07_2026/7nfe_12301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nfe_12301/07_2026/7nfe_12301.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nfe_12301/07_2026/7nfe_12301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nfe_12301/07_2026/7nfe_12301.map" } resolution = 4.29 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 48 5.49 5 S 249 5.16 5 C 28370 2.51 5 N 7476 2.21 5 O 8411 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 44554 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 27665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3557, 27665 Classifications: {'peptide': 3557} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 222} Link IDs: {'PTRANS': 153, 'TRANS': 3403} Chain breaks: 36 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 918 Unresolved non-hydrogen angles: 1120 Unresolved non-hydrogen dihedrals: 776 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 33, 'ASP:plan': 11, 'GLU:plan': 20, 'ASN:plan1': 13, 'HIS:plan': 6, 'PHE:plan': 5, 'TYR:plan': 8, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 488 Chain: "A" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 141 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 27} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'UNK:plan-1': 27} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3673 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 26, 'TRANS': 448} Chain breaks: 4 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 5, 'ASN:plan1': 3, 'GLN:plan1': 3, 'ARG:plan': 9, 'ASP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "C" Number of atoms: 3999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3999 Classifications: {'peptide': 513} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 37} Link IDs: {'PTRANS': 22, 'TRANS': 490} Chain breaks: 4 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 4, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 61 Chain: "F" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1465 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 179} Chain breaks: 7 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "G" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1502 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain breaks: 6 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "H" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1575 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 197} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1521 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 190} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "J" Number of atoms: 2026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2026 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 247} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 493 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "E" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 494 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Time building chain proxies: 9.73, per 1000 atoms: 0.22 Number of scatterers: 44554 At special positions: 0 Unit cell: (195.6, 249.064, 181.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 249 16.00 P 48 15.00 O 8411 8.00 N 7476 7.00 C 28370 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: 3.67 Conformation dependent library (CDL) restraints added in 2.1 seconds 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10790 Finding SS restraints... Secondary structure from input PDB file: 261 helices and 24 sheets defined 63.5% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 27 through 46 Processing helix chain 'A' and resid 49 through 60 Processing helix chain 'A' and resid 60 through 69 removed outlier: 4.397A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 100 through 117 removed outlier: 4.623A pdb=" N VAL A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLU A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 141 Processing helix chain 'A' and resid 141 through 147 removed outlier: 3.642A pdb=" N PHE A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 172 through 179 removed outlier: 4.131A pdb=" N GLU A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.697A pdb=" N ILE A 190 " --> pdb=" O PRO A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 209 Processing helix chain 'A' and resid 217 through 232 Processing helix chain 'A' and resid 241 through 256 removed outlier: 4.482A pdb=" N ILE A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 282 through 289 removed outlier: 4.156A pdb=" N ASN A 289 " --> pdb=" O CYS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 305 through 328 removed outlier: 3.511A pdb=" N SER A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 355 through 369 Processing helix chain 'A' and resid 369 through 377 Processing helix chain 'A' and resid 377 through 396 Processing helix chain 'A' and resid 409 through 424 removed outlier: 3.843A pdb=" N TYR A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 446 removed outlier: 4.546A pdb=" N VAL A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 450 through 469 Processing helix chain 'A' and resid 470 through 471 No H-bonds generated for 'chain 'A' and resid 470 through 471' Processing helix chain 'A' and resid 472 through 475 Processing helix chain 'A' and resid 476 through 493 Processing helix chain 'A' and resid 523 through 526 Processing helix chain 'A' and resid 527 through 537 Processing helix chain 'A' and resid 537 through 546 removed outlier: 3.669A pdb=" N MET A 541 " --> pdb=" O SER A 537 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP A 542 " --> pdb=" O ASP A 538 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 579 removed outlier: 3.733A pdb=" N LEU A 563 " --> pdb=" O SER A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 634 Processing helix chain 'A' and resid 644 through 660 removed outlier: 4.726A pdb=" N SER A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 680 removed outlier: 3.921A pdb=" N TYR A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 718 Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 725 through 735 Processing helix chain 'A' and resid 744 through 760 removed outlier: 3.934A pdb=" N TYR A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Proline residue: A 750 - end of helix removed outlier: 3.621A pdb=" N LEU A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 780 removed outlier: 3.605A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 796 removed outlier: 4.102A pdb=" N LYS A 790 " --> pdb=" O GLN A 786 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASP A 791 " --> pdb=" O PRO A 787 " (cutoff:3.500A) Proline residue: A 794 - end of helix Processing helix chain 'A' and resid 796 through 801 removed outlier: 3.975A pdb=" N LEU A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 862 Processing helix chain 'A' and resid 863 through 868 Processing helix chain 'A' and resid 869 through 871 No H-bonds generated for 'chain 'A' and resid 869 through 871' Processing helix chain 'A' and resid 876 through 882 Processing helix chain 'A' and resid 910 through 920 Processing helix chain 'A' and resid 923 through 946 Processing helix chain 'A' and resid 958 through 974 Proline residue: A 967 - end of helix Processing helix chain 'A' and resid 977 through 997 Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 998 through 1001 Processing helix chain 'A' and resid 1004 through 1019 removed outlier: 3.700A pdb=" N ILE A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP A1019 " --> pdb=" O ASP A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1044 removed outlier: 3.680A pdb=" N ARG A1026 " --> pdb=" O ASP A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1069 removed outlier: 4.748A pdb=" N SER A1058 " --> pdb=" O VAL A1054 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU A1059 " --> pdb=" O ASN A1055 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A1060 " --> pdb=" O THR A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1090 removed outlier: 4.883A pdb=" N ARG A1087 " --> pdb=" O ASN A1083 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLU A1088 " --> pdb=" O ASN A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1116 removed outlier: 5.068A pdb=" N GLN A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU A1104 " --> pdb=" O VAL A1100 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA A1116 " --> pdb=" O ALA A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1146 removed outlier: 6.007A pdb=" N VAL A1143 " --> pdb=" O GLU A1139 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER A1144 " --> pdb=" O LYS A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1176 Processing helix chain 'A' and resid 1180 through 1195 Processing helix chain 'A' and resid 1203 through 1223 removed outlier: 3.924A pdb=" N LYS A1213 " --> pdb=" O LYS A1209 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU A1214 " --> pdb=" O ASP A1210 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL A1217 " --> pdb=" O LYS A1213 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N SER A1218 " --> pdb=" O GLU A1214 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE A1219 " --> pdb=" O GLU A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1273 Processing helix chain 'A' and resid 1277 through 1282 removed outlier: 3.814A pdb=" N VAL A1281 " --> pdb=" O GLY A1277 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A1282 " --> pdb=" O ALA A1278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1277 through 1282' Processing helix chain 'A' and resid 1289 through 1304 removed outlier: 4.539A pdb=" N ALA A1302 " --> pdb=" O LEU A1298 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET A1303 " --> pdb=" O GLU A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1352 Processing helix chain 'A' and resid 1360 through 1378 removed outlier: 4.223A pdb=" N CYS A1364 " --> pdb=" O LYS A1360 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N MET A1369 " --> pdb=" O ASN A1365 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1409 Proline residue: A1396 - end of helix Processing helix chain 'A' and resid 1411 through 1423 Processing helix chain 'A' and resid 1426 through 1435 removed outlier: 4.532A pdb=" N ASN A1435 " --> pdb=" O LEU A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1462 Processing helix chain 'A' and resid 1463 through 1468 Processing helix chain 'A' and resid 1476 through 1490 removed outlier: 3.785A pdb=" N TYR A1488 " --> pdb=" O LEU A1484 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1521 removed outlier: 3.577A pdb=" N PHE A1521 " --> pdb=" O LEU A1517 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1534 Processing helix chain 'A' and resid 1554 through 1574 removed outlier: 6.498A pdb=" N GLU A1565 " --> pdb=" O SER A1561 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR A1566 " --> pdb=" O LEU A1562 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS A1573 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A1574 " --> pdb=" O GLU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1586 removed outlier: 4.100A pdb=" N ALA A1578 " --> pdb=" O ASN A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1608 Processing helix chain 'A' and resid 1611 through 1625 removed outlier: 4.453A pdb=" N GLY A1615 " --> pdb=" O GLN A1611 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1634 removed outlier: 3.804A pdb=" N ALA A1634 " --> pdb=" O SER A1631 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1656 Processing helix chain 'A' and resid 1658 through 1663 removed outlier: 4.213A pdb=" N THR A1663 " --> pdb=" O VAL A1659 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1680 Processing helix chain 'A' and resid 1685 through 1696 Processing helix chain 'A' and resid 1696 through 1701 Processing helix chain 'A' and resid 1703 through 1705 No H-bonds generated for 'chain 'A' and resid 1703 through 1705' Processing helix chain 'A' and resid 1706 through 1722 Processing helix chain 'A' and resid 1733 through 1754 Processing helix chain 'A' and resid 1755 through 1767 removed outlier: 3.711A pdb=" N VAL A1765 " --> pdb=" O LEU A1761 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1789 removed outlier: 3.689A pdb=" N PHE A1778 " --> pdb=" O MET A1774 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1807 Processing helix chain 'A' and resid 1812 through 1823 removed outlier: 3.905A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A1823 " --> pdb=" O PHE A1819 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1831 Processing helix chain 'A' and resid 1832 through 1853 removed outlier: 5.251A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A1853 " --> pdb=" O ASP A1849 " (cutoff:3.500A) Processing helix chain 'A' and resid 1861 through 1882 Processing helix chain 'A' and resid 1910 through 1925 Processing helix chain 'A' and resid 1934 through 1955 Processing helix chain 'A' and resid 1972 through 1976 Processing helix chain 'A' and resid 2093 through 2108 Processing helix chain 'A' and resid 2123 through 2135 removed outlier: 4.075A pdb=" N ASN A2135 " --> pdb=" O GLY A2131 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2153 Processing helix chain 'A' and resid 2160 through 2171 removed outlier: 4.623A pdb=" N SER A2166 " --> pdb=" O LYS A2162 " (cutoff:3.500A) Proline residue: A2167 - end of helix Processing helix chain 'A' and resid 2183 through 2196 Processing helix chain 'A' and resid 2205 through 2223 removed outlier: 3.876A pdb=" N GLU A2209 " --> pdb=" O VAL A2205 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2245 removed outlier: 3.944A pdb=" N PHE A2231 " --> pdb=" O LYS A2227 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP A2245 " --> pdb=" O LEU A2241 " (cutoff:3.500A) Processing helix chain 'A' and resid 2254 through 2259 Processing helix chain 'A' and resid 2270 through 2283 removed outlier: 3.516A pdb=" N ASN A2283 " --> pdb=" O ILE A2279 " (cutoff:3.500A) Processing helix chain 'A' and resid 2298 through 2306 Processing helix chain 'A' and resid 2314 through 2328 Processing helix chain 'A' and resid 2339 through 2354 removed outlier: 3.578A pdb=" N GLU A2343 " --> pdb=" O GLU A2339 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS A2352 " --> pdb=" O GLN A2348 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2356 through 2369 Processing helix chain 'A' and resid 2371 through 2377 removed outlier: 3.752A pdb=" N ARG A2377 " --> pdb=" O LEU A2374 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2386 Processing helix chain 'A' and resid 2391 through 2404 removed outlier: 3.754A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A2404 " --> pdb=" O VAL A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2418 Processing helix chain 'A' and resid 2419 through 2426 Processing helix chain 'A' and resid 2428 through 2443 Processing helix chain 'A' and resid 2444 through 2446 No H-bonds generated for 'chain 'A' and resid 2444 through 2446' Processing helix chain 'A' and resid 2447 through 2459 Proline residue: A2457 - end of helix Processing helix chain 'A' and resid 2460 through 2462 No H-bonds generated for 'chain 'A' and resid 2460 through 2462' Processing helix chain 'A' and resid 2467 through 2485 Processing helix chain 'A' and resid 2492 through 2509 Processing helix chain 'A' and resid 2510 through 2512 No H-bonds generated for 'chain 'A' and resid 2510 through 2512' Processing helix chain 'A' and resid 2514 through 2527 Processing helix chain 'A' and resid 2534 through 2545 Processing helix chain 'A' and resid 2553 through 2568 removed outlier: 4.006A pdb=" N MET A2568 " --> pdb=" O GLU A2564 " (cutoff:3.500A) Processing helix chain 'A' and resid 2787 through 2801 Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2801 through 2824 removed outlier: 3.632A pdb=" N PHE A2823 " --> pdb=" O GLU A2819 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2847 Processing helix chain 'A' and resid 2851 through 2864 removed outlier: 3.666A pdb=" N GLN A2864 " --> pdb=" O ASP A2860 " (cutoff:3.500A) Processing helix chain 'A' and resid 2865 through 2871 removed outlier: 3.610A pdb=" N LEU A2871 " --> pdb=" O LEU A2868 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2884 Processing helix chain 'A' and resid 2885 through 2899 removed outlier: 3.532A pdb=" N ARG A2899 " --> pdb=" O GLU A2895 " (cutoff:3.500A) Processing helix chain 'A' and resid 2919 through 2934 Processing helix chain 'A' and resid 2935 through 2946 Processing helix chain 'A' and resid 2950 through 2962 removed outlier: 3.546A pdb=" N GLN A2954 " --> pdb=" O LYS A2950 " (cutoff:3.500A) Processing helix chain 'A' and resid 2964 through 2978 removed outlier: 3.762A pdb=" N ALA A2968 " --> pdb=" O ASP A2964 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3005 Processing helix chain 'A' and resid 3007 through 3017 Processing helix chain 'A' and resid 3028 through 3032 removed outlier: 3.580A pdb=" N TRP A3031 " --> pdb=" O ASN A3028 " (cutoff:3.500A) Processing helix chain 'A' and resid 3034 through 3054 Proline residue: A3042 - end of helix Processing helix chain 'A' and resid 3060 through 3070 removed outlier: 3.675A pdb=" N PHE A3064 " --> pdb=" O SER A3060 " (cutoff:3.500A) Processing helix chain 'A' and resid 3071 through 3082 Processing helix chain 'A' and resid 3082 through 3094 Processing helix chain 'A' and resid 3095 through 3117 Processing helix chain 'A' and resid 3121 through 3130 removed outlier: 3.709A pdb=" N GLN A3130 " --> pdb=" O LEU A3126 " (cutoff:3.500A) Processing helix chain 'A' and resid 3131 through 3147 Processing helix chain 'A' and resid 3148 through 3153 removed outlier: 3.762A pdb=" N SER A3152 " --> pdb=" O GLN A3148 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3166 Processing helix chain 'A' and resid 3175 through 3195 removed outlier: 3.557A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU A3195 " --> pdb=" O SER A3191 " (cutoff:3.500A) Processing helix chain 'A' and resid 3227 through 3250 Processing helix chain 'A' and resid 3251 through 3262 Processing helix chain 'A' and resid 3262 through 3269 removed outlier: 4.258A pdb=" N ARG A3269 " --> pdb=" O GLU A3265 " (cutoff:3.500A) Processing helix chain 'A' and resid 3269 through 3288 Processing helix chain 'A' and resid 3290 through 3305 removed outlier: 4.590A pdb=" N GLU A3295 " --> pdb=" O GLN A3291 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLN A3296 " --> pdb=" O GLY A3292 " (cutoff:3.500A) Processing helix chain 'A' and resid 3313 through 3319 removed outlier: 4.366A pdb=" N SER A3317 " --> pdb=" O SER A3313 " (cutoff:3.500A) Processing helix chain 'A' and resid 3320 through 3344 Processing helix chain 'A' and resid 3353 through 3364 removed outlier: 4.568A pdb=" N GLU A3361 " --> pdb=" O ARG A3357 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A3364 " --> pdb=" O LEU A3360 " (cutoff:3.500A) Processing helix chain 'A' and resid 3369 through 3394 removed outlier: 3.616A pdb=" N GLU A3394 " --> pdb=" O GLN A3390 " (cutoff:3.500A) Processing helix chain 'A' and resid 3407 through 3428 Processing helix chain 'A' and resid 3440 through 3456 removed outlier: 4.713A pdb=" N ALA A3444 " --> pdb=" O GLN A3440 " (cutoff:3.500A) Processing helix chain 'A' and resid 3458 through 3475 Proline residue: A3466 - end of helix Processing helix chain 'A' and resid 3479 through 3488 removed outlier: 4.095A pdb=" N MET A3483 " --> pdb=" O THR A3479 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU A3486 " --> pdb=" O LEU A3482 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3497 No H-bonds generated for 'chain 'A' and resid 3495 through 3497' Processing helix chain 'A' and resid 3498 through 3508 Processing helix chain 'A' and resid 3511 through 3525 removed outlier: 4.443A pdb=" N HIS A3516 " --> pdb=" O VAL A3512 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N SER A3517 " --> pdb=" O ALA A3513 " (cutoff:3.500A) Processing helix chain 'A' and resid 3530 through 3538 Processing helix chain 'A' and resid 3547 through 3562 Processing helix chain 'A' and resid 3563 through 3565 No H-bonds generated for 'chain 'A' and resid 3563 through 3565' Processing helix chain 'A' and resid 3566 through 3579 Processing helix chain 'A' and resid 3580 through 3598 removed outlier: 3.669A pdb=" N LEU A3584 " --> pdb=" O ASN A3580 " (cutoff:3.500A) Processing helix chain 'A' and resid 3604 through 3617 Processing helix chain 'A' and resid 3626 through 3643 removed outlier: 4.735A pdb=" N LYS A3638 " --> pdb=" O GLN A3634 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLU A3639 " --> pdb=" O THR A3635 " (cutoff:3.500A) Processing helix chain 'A' and resid 3659 through 3674 Processing helix chain 'A' and resid 3680 through 3683 Processing helix chain 'A' and resid 3684 through 3690 removed outlier: 3.831A pdb=" N SER A3688 " --> pdb=" O SER A3684 " (cutoff:3.500A) Processing helix chain 'A' and resid 3758 through 3778 Processing helix chain 'A' and resid 3779 through 3784 removed outlier: 3.683A pdb=" N ARG A3784 " --> pdb=" O ALA A3780 " (cutoff:3.500A) Processing helix chain 'A' and resid 3812 through 3820 Processing helix chain 'A' and resid 3821 through 3828 Processing helix chain 'A' and resid 3835 through 3845 Processing helix chain 'A' and resid 3852 through 3861 removed outlier: 3.936A pdb=" N MET A3856 " --> pdb=" O VAL A3852 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3878 Processing helix chain 'A' and resid 3881 through 3891 Processing helix chain 'A' and resid 3895 through 3918 Processing helix chain 'A' and resid 3924 through 3926 No H-bonds generated for 'chain 'A' and resid 3924 through 3926' Processing helix chain 'A' and resid 3964 through 3971 removed outlier: 4.071A pdb=" N MET A3971 " --> pdb=" O PHE A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3978 through 3994 removed outlier: 4.167A pdb=" N ASP A3994 " --> pdb=" O ALA A3990 " (cutoff:3.500A) Processing helix chain 'A' and resid 3995 through 4008 removed outlier: 3.712A pdb=" N GLU A4008 " --> pdb=" O VAL A4004 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4011 No H-bonds generated for 'chain 'A' and resid 4009 through 4011' Processing helix chain 'A' and resid 4012 through 4024 removed outlier: 3.935A pdb=" N LYS A4022 " --> pdb=" O GLN A4018 " (cutoff:3.500A) Processing helix chain 'A' and resid 4039 through 4053 Processing helix chain 'A' and resid 4055 through 4069 removed outlier: 3.910A pdb=" N GLU A4069 " --> pdb=" O LEU A4065 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4082 Processing helix chain 'A' and resid 4099 through 4113 Processing helix chain 'A' and resid 4113 through 4119 Processing helix chain 'A' and resid 4121 through 4125 removed outlier: 3.510A pdb=" N TRP A4124 " --> pdb=" O TRP A4121 " (cutoff:3.500A) Processing helix chain 'A' and resid 5010 through 5015 removed outlier: 3.613A pdb=" N UNK A5014 " --> pdb=" O UNK A5010 " (cutoff:3.500A) Processing helix chain 'A' and resid 6005 through 6019 Processing helix chain 'B' and resid 58 through 78 removed outlier: 3.611A pdb=" N MET B 62 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 121 Processing helix chain 'B' and resid 124 through 136 Processing helix chain 'B' and resid 142 through 157 removed outlier: 3.865A pdb=" N VAL B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'B' and resid 312 through 315 Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 376 through 392 removed outlier: 4.259A pdb=" N THR B 380 " --> pdb=" O ILE B 376 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU B 391 " --> pdb=" O ILE B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 468 removed outlier: 3.719A pdb=" N LYS B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 478 removed outlier: 4.311A pdb=" N PHE B 478 " --> pdb=" O SER B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 496 Processing helix chain 'B' and resid 510 through 515 Processing helix chain 'C' and resid 29 through 49 removed outlier: 3.571A pdb=" N GLN C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 106 through 122 Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 198 through 216 Processing helix chain 'C' and resid 217 through 224 removed outlier: 3.843A pdb=" N ILE C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 235 removed outlier: 3.673A pdb=" N CYS C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 324 through 331 removed outlier: 4.062A pdb=" N GLN C 330 " --> pdb=" O VAL C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 388 Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'C' and resid 447 through 461 Processing helix chain 'C' and resid 484 through 500 removed outlier: 3.934A pdb=" N GLN C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS C 500 " --> pdb=" O HIS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 517 removed outlier: 3.550A pdb=" N TRP C 513 " --> pdb=" O GLN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 537 removed outlier: 3.994A pdb=" N THR C 523 " --> pdb=" O PRO C 519 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE C 528 " --> pdb=" O THR C 524 " (cutoff:3.500A) Proline residue: C 529 - end of helix Processing helix chain 'F' and resid 50 through 62 Processing helix chain 'F' and resid 68 through 77 removed outlier: 3.981A pdb=" N PHE F 72 " --> pdb=" O PRO F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 135 removed outlier: 4.180A pdb=" N VAL F 131 " --> pdb=" O SER F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 170 removed outlier: 3.581A pdb=" N GLN F 147 " --> pdb=" O SER F 143 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET F 159 " --> pdb=" O THR F 155 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS F 160 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 193 Processing helix chain 'F' and resid 197 through 203 removed outlier: 3.720A pdb=" N CYS F 202 " --> pdb=" O PRO F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 217 removed outlier: 3.614A pdb=" N ASP F 216 " --> pdb=" O ASN F 213 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU F 217 " --> pdb=" O LEU F 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 213 through 217' Processing helix chain 'G' and resid 3 through 7 Processing helix chain 'G' and resid 50 through 61 Processing helix chain 'G' and resid 68 through 78 removed outlier: 3.785A pdb=" N PHE G 72 " --> pdb=" O PRO G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 135 removed outlier: 3.524A pdb=" N VAL G 131 " --> pdb=" O SER G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 159 removed outlier: 4.593A pdb=" N MET G 159 " --> pdb=" O THR G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 171 Processing helix chain 'G' and resid 186 through 193 Processing helix chain 'G' and resid 197 through 202 removed outlier: 3.959A pdb=" N CYS G 202 " --> pdb=" O PRO G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 60 removed outlier: 3.966A pdb=" N GLU H 55 " --> pdb=" O GLU H 51 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 75 Processing helix chain 'H' and resid 100 through 104 removed outlier: 3.633A pdb=" N ASP H 103 " --> pdb=" O ASN H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 200 removed outlier: 4.449A pdb=" N GLU H 170 " --> pdb=" O VAL H 166 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA H 171 " --> pdb=" O SER H 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 57 removed outlier: 4.490A pdb=" N ASP I 57 " --> pdb=" O SER I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 74 Processing helix chain 'I' and resid 118 through 201 removed outlier: 4.183A pdb=" N VAL I 122 " --> pdb=" O ASN I 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 685 Processing helix chain 'J' and resid 706 through 715 Processing helix chain 'J' and resid 722 through 733 removed outlier: 3.932A pdb=" N LEU J 726 " --> pdb=" O LYS J 722 " (cutoff:3.500A) Processing helix chain 'J' and resid 747 through 752 removed outlier: 3.938A pdb=" N GLU J 752 " --> pdb=" O PRO J 748 " (cutoff:3.500A) Processing helix chain 'J' and resid 752 through 757 removed outlier: 3.870A pdb=" N GLU J 757 " --> pdb=" O HIS J 753 " (cutoff:3.500A) Processing helix chain 'J' and resid 770 through 781 Processing helix chain 'J' and resid 788 through 795 removed outlier: 3.568A pdb=" N MET J 792 " --> pdb=" O THR J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 795 through 803 removed outlier: 3.947A pdb=" N GLU J 800 " --> pdb=" O ILE J 796 " (cutoff:3.500A) Processing helix chain 'J' and resid 839 through 847 Processing helix chain 'J' and resid 871 through 879 removed outlier: 3.623A pdb=" N ALA J 877 " --> pdb=" O ALA J 873 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE J 878 " --> pdb=" O ASP J 874 " (cutoff:3.500A) Processing helix chain 'J' and resid 890 through 894 Processing helix chain 'J' and resid 906 through 910 removed outlier: 3.726A pdb=" N LEU J 910 " --> pdb=" O ASN J 907 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 583 through 585 Processing sheet with id=AA2, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA3, first strand: chain 'A' and resid 1538 through 1539 Processing sheet with id=AA4, first strand: chain 'A' and resid 2587 through 2588 Processing sheet with id=AA5, first strand: chain 'A' and resid 3719 through 3728 removed outlier: 7.715A pdb=" N ASP A3723 " --> pdb=" O ARG A3741 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ARG A3741 " --> pdb=" O ASP A3723 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ARG A3725 " --> pdb=" O ILE A3739 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ILE A3739 " --> pdb=" O ARG A3725 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS A3736 " --> pdb=" O VAL A3752 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL A3752 " --> pdb=" O LYS A3736 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A3801 " --> pdb=" O LYS A3753 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 3810 through 3811 removed outlier: 3.659A pdb=" N VAL A3810 " --> pdb=" O VAL A3930 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A3930 " --> pdb=" O VAL A3810 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 102 through 109 removed outlier: 6.373A pdb=" N VAL B 85 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLU B 107 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU B 83 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU B 82 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 38 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA B 84 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 42 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N SER B 37 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N MET B 167 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE B 39 " --> pdb=" O MET B 167 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N PHE B 169 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU B 41 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS B 164 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ASP B 201 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE B 166 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N MET B 203 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU B 168 " --> pdb=" O MET B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 259 through 262 removed outlier: 3.635A pdb=" N LEU B 366 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA B 396 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 9.924A pdb=" N VAL B 394 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ALA B 395 " --> pdb=" O PHE B 350 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE B 350 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU B 397 " --> pdb=" O MET B 348 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS B 260 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU B 347 " --> pdb=" O LYS B 260 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LYS B 262 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N GLY B 349 " --> pdb=" O LYS B 262 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 286 through 289 removed outlier: 3.536A pdb=" N ASP C 319 " --> pdb=" O TYR C 316 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 325 through 330 removed outlier: 3.622A pdb=" N ILE B 327 " --> pdb=" O GLN B 320 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN B 320 " --> pdb=" O ILE B 327 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 77 through 84 removed outlier: 6.623A pdb=" N LEU C 56 " --> pdb=" O HIS C 80 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N HIS C 82 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ILE C 54 " --> pdb=" O HIS C 82 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ALA C 8 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ALA C 55 " --> pdb=" O ALA C 8 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL C 10 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL C 57 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU C 12 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE C 59 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N MET C 14 " --> pdb=" O PHE C 59 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ALA C 9 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLU C 133 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N VAL C 11 " --> pdb=" O GLU C 133 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 164 through 165 Processing sheet with id=AB4, first strand: chain 'C' and resid 249 through 252 removed outlier: 3.893A pdb=" N TYR C 264 " --> pdb=" O LYS C 363 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 363 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N GLN C 360 " --> pdb=" O GLN C 423 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLN C 423 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 362 " --> pdb=" O TYR C 421 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA C 366 " --> pdb=" O GLU C 417 " (cutoff:3.500A) removed outlier: 10.788A pdb=" N GLU C 417 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N MET C 389 " --> pdb=" O PRO C 410 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL C 390 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE C 345 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE C 392 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG C 250 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL C 342 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR C 252 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N GLY C 344 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 16 through 17 Processing sheet with id=AB6, first strand: chain 'G' and resid 105 through 106 Processing sheet with id=AB7, first strand: chain 'G' and resid 111 through 112 Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 4 removed outlier: 3.575A pdb=" N VAL H 22 " --> pdb=" O LYS H 4 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 7 through 8 removed outlier: 4.271A pdb=" N HIS H 18 " --> pdb=" O ILE H 8 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 36 through 37 removed outlier: 3.587A pdb=" N THR H 44 " --> pdb=" O GLU H 114 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 85 through 89 removed outlier: 3.572A pdb=" N GLU H 98 " --> pdb=" O THR H 85 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 4 through 9 Processing sheet with id=AC4, first strand: chain 'I' and resid 33 through 37 Processing sheet with id=AC5, first strand: chain 'J' and resid 688 through 690 removed outlier: 3.874A pdb=" N VAL J 666 " --> pdb=" O VAL J 690 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLU J 663 " --> pdb=" O CYS J 699 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE J 701 " --> pdb=" O GLU J 663 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS J 665 " --> pdb=" O ILE J 701 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N VAL J 721 " --> pdb=" O TYR J 698 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL J 700 " --> pdb=" O VAL J 721 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 818 through 819 removed outlier: 4.271A pdb=" N ILE J 864 " --> pdb=" O TYR J 819 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL J 863 " --> pdb=" O LEU J 889 " (cutoff:3.500A) 2464 hydrogen bonds defined for protein. 7242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.87 Time building geometry restraints manager: 4.95 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: 11016 1.33 - 1.45: 8524 1.45 - 1.57: 25491 1.57 - 1.69: 94 1.69 - 1.81: 385 Bond restraints: 45510 Sorted by residual: bond pdb=" C3' DA E 21 " pdb=" C2' DA E 21 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DA E 36 " pdb=" C2' DA E 36 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" N GLU A1958 " pdb=" CA GLU A1958 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.63e+00 bond pdb=" N ILE C 253 " pdb=" CA ILE C 253 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.25e+00 bond pdb=" C3' DT D 40 " pdb=" C2' DT D 40 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.88e+00 ... (remaining 45505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 60904 2.15 - 4.31: 786 4.31 - 6.46: 104 6.46 - 8.61: 19 8.61 - 10.77: 3 Bond angle restraints: 61816 Sorted by residual: angle pdb=" N TYR A3859 " pdb=" CA TYR A3859 " pdb=" C TYR A3859 " ideal model delta sigma weight residual 111.36 103.70 7.66 1.09e+00 8.42e-01 4.94e+01 angle pdb=" N MET A3858 " pdb=" CA MET A3858 " pdb=" C MET A3858 " ideal model delta sigma weight residual 112.90 105.30 7.60 1.31e+00 5.83e-01 3.37e+01 angle pdb=" N ALA A3854 " pdb=" CA ALA A3854 " pdb=" C ALA A3854 " ideal model delta sigma weight residual 111.71 105.45 6.26 1.15e+00 7.56e-01 2.96e+01 angle pdb=" CA VAL A1955 " pdb=" C VAL A1955 " pdb=" O VAL A1955 " ideal model delta sigma weight residual 122.63 118.09 4.54 8.70e-01 1.32e+00 2.72e+01 angle pdb=" N LYS A3860 " pdb=" CA LYS A3860 " pdb=" C LYS A3860 " ideal model delta sigma weight residual 111.28 105.98 5.30 1.09e+00 8.42e-01 2.37e+01 ... (remaining 61811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 26806 34.96 - 69.93: 631 69.93 - 104.89: 84 104.89 - 139.85: 0 139.85 - 174.81: 1 Dihedral angle restraints: 27522 sinusoidal: 11036 harmonic: 16486 Sorted by residual: dihedral pdb=" CA TRP A1633 " pdb=" C TRP A1633 " pdb=" N ALA A1634 " pdb=" CA ALA A1634 " ideal model delta harmonic sigma weight residual -180.00 -155.54 -24.46 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LEU A1359 " pdb=" C LEU A1359 " pdb=" N LYS A1360 " pdb=" CA LYS A1360 " ideal model delta harmonic sigma weight residual -180.00 -155.86 -24.14 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA LEU G 157 " pdb=" C LEU G 157 " pdb=" N HIS G 158 " pdb=" CA HIS G 158 " ideal model delta harmonic sigma weight residual -180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 27519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 5802 0.050 - 0.101: 1149 0.101 - 0.151: 150 0.151 - 0.202: 11 0.202 - 0.252: 4 Chirality restraints: 7116 Sorted by residual: chirality pdb=" CA MET A3856 " pdb=" N MET A3856 " pdb=" C MET A3856 " pdb=" CB MET A3856 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE A3351 " pdb=" CA ILE A3351 " pdb=" CG1 ILE A3351 " pdb=" CG2 ILE A3351 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA VAL A1955 " pdb=" N VAL A1955 " pdb=" C VAL A1955 " pdb=" CB VAL A1955 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 7113 not shown) Planarity restraints: 7722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS F 158 " 0.020 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C HIS F 158 " -0.067 2.00e-02 2.50e+03 pdb=" O HIS F 158 " 0.024 2.00e-02 2.50e+03 pdb=" N MET F 159 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 157 " 0.016 2.00e-02 2.50e+03 3.12e-02 9.76e+00 pdb=" C LEU G 157 " -0.054 2.00e-02 2.50e+03 pdb=" O LEU G 157 " 0.020 2.00e-02 2.50e+03 pdb=" N HIS G 158 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY H 79 " 0.045 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO H 80 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO H 80 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO H 80 " 0.038 5.00e-02 4.00e+02 ... (remaining 7719 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3461 2.74 - 3.28: 50862 3.28 - 3.82: 81090 3.82 - 4.36: 93220 4.36 - 4.90: 149259 Nonbonded interactions: 377892 Sorted by model distance: nonbonded pdb=" OH TYR B 369 " pdb=" O SER C 436 " model vdw 2.196 3.040 nonbonded pdb=" NH1 ARG A1184 " pdb=" OE1 GLU A1265 " model vdw 2.200 3.120 nonbonded pdb=" OE1 GLN A 982 " pdb=" OH TYR A2589 " model vdw 2.203 3.040 nonbonded pdb=" O ASP A3778 " pdb=" OG SER A3782 " model vdw 2.209 3.040 nonbonded pdb=" O TYR A1560 " pdb=" OG SER A1564 " model vdw 2.216 3.040 ... (remaining 377887 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 Found NCS groups: ncs_group { reference = (chain 'F' and (resid 2 through 13 or (resid 15 through 16 and (name N or name C \ A or name C or name O or name CB )) or resid 17 through 30 or (resid 31 and (nam \ e N or name CA or name C or name O or name CB )) or resid 32 through 45 or (resi \ d 46 through 47 and (name N or name CA or name C or name O or name CB )) or resi \ d 48 through 56 or (resid 57 through 58 and (name N or name CA or name C or name \ O or name CB )) or resid 59 through 79 or resid 93 through 109 or (resid 110 an \ d (name N or name CA or name C or name O or name CB )) or resid 111 through 137 \ or resid 143 through 152 or (resid 153 through 154 and (name N or name CA or nam \ e C or name O or name CB )) or resid 155 through 157 or (resid 158 and (name N o \ r name CA or name C or name O or name CB )) or resid 159 or (resid 160 and (name \ N or name CA or name C or name O or name CB )) or resid 161 through 203 or (res \ id 204 and (name N or name CA or name C or name O or name CB )) or resid 205 thr \ ough 207 or (resid 208 and (name N or name CA or name C or name O or name CB )) \ or resid 209 through 215)) selection = (chain 'G' and (resid 2 through 5 or resid 12 through 37 or (resid 38 and (name \ N or name CA or name C or name O or name CB )) or resid 39 or resid 43 through 4 \ 4 or (resid 45 through 47 and (name N or name CA or name C or name O or name CB \ )) or resid 48 through 122 or resid 126 through 136 or (resid 137 and (name N or \ name CA or name C or name O or name CB )) or resid 143 through 175 or (resid 17 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 177 through \ 179 or (resid 180 and (name N or name CA or name C or name O or name CB )) or re \ sid 181 or (resid 182 and (name N or name CA or name C or name O or name CB )) o \ r resid 183 through 193 or (resid 197 and (name N or name CA or name C or name O \ or name CB )) or resid 198 through 210 or (resid 213 and (name N or name CA or \ name C or name O or name CB )) or resid 214 through 215)) } ncs_group { reference = (chain 'H' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 4 or (resid 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 or (resid 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 23 or (resid 24 and (name N or name CA or name C \ or name O or name CB )) or resid 25 through 75 or resid 84 through 98 or (resid \ 99 and (name N or name CA or name C or name O or name CB )) or resid 100 through \ 106 or (resid 107 and (name N or name CA or name C or name O or name CB )) or r \ esid 108 through 114 or (resid 115 and (name N or name CA or name C or name O or \ name CB )) or resid 116 through 125 or (resid 126 through 128 and (name N or na \ me CA or name C or name O or name CB )) or resid 129 through 149 or (resid 150 a \ nd (name N or name CA or name C or name O or name CB )) or resid 151 through 165 \ or (resid 166 and (name N or name CA or name C or name O or name CB )) or resid \ 167 through 186 or (resid 187 and (name N or name CA or name C or name O or nam \ e CB )) or resid 188 through 201)) selection = (chain 'I' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 33 or (resid 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 73 or (resid 74 and (n \ ame N or name CA or name C or name O or name CB )) or resid 75 through 87 or (re \ sid 88 and (name N or name CA or name C or name O or name CB )) or resid 89 thro \ ugh 94 or (resid 95 and (name N or name CA or name C or name O or name CB )) or \ resid 96 through 127 or (resid 128 and (name N or name CA or name C or name O or \ name CB )) or resid 129 through 148 or (resid 149 through 150 and (name N or na \ me CA or name C or name O or name CB )) or resid 151 through 152 or (resid 153 a \ nd (name N or name CA or name C or name O or name CB )) or resid 154 through 156 \ or (resid 157 and (name N or name CA or name C or name O or name CB )) or resid \ 158 through 191 or (resid 192 and (name N or name CA or name C or name O or nam \ e CB )) or resid 193 through 196 or (resid 197 and (name N or name CA or name C \ or name O or name CB )) or resid 198 through 201)) } 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=0.00 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: 20.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 46.380 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.003 0.044 45510 Z= 0.164 Angle : 0.596 10.767 61816 Z= 0.354 Chirality : 0.040 0.252 7116 Planarity : 0.004 0.092 7722 Dihedral : 15.485 174.813 16732 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.12 % Favored : 94.83 % Rotamer: Outliers : 0.19 % Allowed : 0.32 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.12), residues: 5452 helix: 1.44 (0.10), residues: 3151 sheet: -0.99 (0.36), residues: 213 loop : -1.60 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG G 151 TYR 0.021 0.001 TYR A3828 PHE 0.017 0.001 PHE A1923 TRP 0.014 0.001 TRP A3272 HIS 0.013 0.001 HIS I 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.16 (45510) covalent geometry : angle 0.59568 / 0.35 (61816) hydrogen bonds : bond 0.14433 / 9.72 ( 2464) hydrogen bonds : angle 5.81567 / 4.20 ( 7242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 468 time to evaluate : 1.532 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.9749 (t80) cc_final: 0.9470 (t80) REVERT: A 115 TYR cc_start: 0.8333 (t80) cc_final: 0.7809 (t80) REVERT: A 144 MET cc_start: 0.9358 (mmp) cc_final: 0.9132 (mpp) REVERT: A 208 MET cc_start: 0.9389 (pmm) cc_final: 0.9166 (pmm) REVERT: A 421 LEU cc_start: 0.9770 (tp) cc_final: 0.9562 (mt) REVERT: A 441 MET cc_start: 0.9202 (mmt) cc_final: 0.8854 (mmp) REVERT: A 870 LEU cc_start: 0.9788 (tp) cc_final: 0.9568 (pt) REVERT: A 879 MET cc_start: 0.9083 (mmp) cc_final: 0.8580 (mpp) REVERT: A 880 MET cc_start: 0.8275 (ptp) cc_final: 0.7883 (ptt) REVERT: A 958 MET cc_start: 0.8058 (mmp) cc_final: 0.7856 (mmp) REVERT: A 1104 LEU cc_start: 0.9815 (tp) cc_final: 0.9610 (tp) REVERT: A 1270 PHE cc_start: 0.9490 (m-10) cc_final: 0.9180 (m-80) REVERT: A 1369 MET cc_start: 0.8419 (ttt) cc_final: 0.7716 (tpp) REVERT: A 1600 MET cc_start: 0.9124 (mmp) cc_final: 0.8734 (mmm) REVERT: A 1646 LEU cc_start: 0.9743 (tp) cc_final: 0.9516 (tt) REVERT: A 1877 LEU cc_start: 0.9815 (mt) cc_final: 0.9349 (mt) REVERT: A 1881 TYR cc_start: 0.8409 (m-10) cc_final: 0.8120 (m-80) REVERT: A 2419 ASP cc_start: 0.9604 (t0) cc_final: 0.9404 (t0) REVERT: A 2437 ASP cc_start: 0.9542 (t0) cc_final: 0.9245 (m-30) REVERT: A 2930 TYR cc_start: 0.9508 (m-80) cc_final: 0.9236 (m-80) REVERT: A 2943 PHE cc_start: 0.9124 (m-80) cc_final: 0.8695 (m-80) REVERT: A 3173 MET cc_start: 0.9290 (mmp) cc_final: 0.8968 (mmm) REVERT: A 3240 MET cc_start: 0.9582 (tpt) cc_final: 0.9291 (mmm) REVERT: A 3450 MET cc_start: 0.9203 (tmm) cc_final: 0.8993 (tpp) REVERT: A 3967 PHE cc_start: 0.9233 (m-80) cc_final: 0.9016 (m-80) REVERT: B 161 MET cc_start: 0.9089 (tpt) cc_final: 0.8791 (tpt) REVERT: B 345 LEU cc_start: 0.9731 (mp) cc_final: 0.9514 (mp) REVERT: B 347 LEU cc_start: 0.9440 (tp) cc_final: 0.9225 (tp) REVERT: B 348 MET cc_start: 0.8716 (mmp) cc_final: 0.7055 (mmm) REVERT: B 453 MET cc_start: 0.8057 (mmp) cc_final: 0.7834 (mmp) REVERT: C 84 MET cc_start: 0.9638 (ppp) cc_final: 0.9354 (ppp) REVERT: C 340 PHE cc_start: 0.8845 (t80) cc_final: 0.8363 (t80) REVERT: C 377 LEU cc_start: 0.9613 (tt) cc_final: 0.9390 (mt) REVERT: C 389 MET cc_start: 0.7321 (tpt) cc_final: 0.6826 (tpt) REVERT: G 159 MET cc_start: 0.9636 (ppp) cc_final: 0.9231 (ppp) REVERT: J 667 MET cc_start: 0.7992 (ppp) cc_final: 0.7554 (ppp) REVERT: J 688 TYR cc_start: 0.9694 (t80) cc_final: 0.9356 (t80) REVERT: J 743 MET cc_start: 0.9064 (tpt) cc_final: 0.8845 (tpt) REVERT: J 792 MET cc_start: 0.9039 (mpp) cc_final: 0.8480 (mmt) outliers start: 9 outliers final: 2 residues processed: 475 average time/residue: 0.2664 time to fit residues: 210.0407 Evaluate side-chains 308 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 306 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 394 optimal weight: 0.0570 chunk 430 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 265 optimal weight: 10.0000 chunk 523 optimal weight: 8.9990 chunk 497 optimal weight: 0.6980 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 4.9990 chunk 488 optimal weight: 4.9990 chunk 366 optimal weight: 4.9990 chunk 223 optimal weight: 0.9980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS A 613 HIS A 625 ASN ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN A1146 ASN A1603 GLN ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2527 HIS A3054 GLN A3108 GLN A3590 ASN ** A3697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN C 402 ASN ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 HIS I 137 ASN ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.046881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.038149 restraints weight = 724180.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.038403 restraints weight = 491474.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.038767 restraints weight = 409248.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.038968 restraints weight = 280719.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.039281 restraints weight = 249337.685| |-----------------------------------------------------------------------------| r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 45510 Z= 0.136 Angle : 0.607 10.188 61816 Z= 0.317 Chirality : 0.040 0.208 7116 Planarity : 0.005 0.121 7722 Dihedral : 11.505 177.080 6471 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.39 % Favored : 94.57 % Rotamer: Outliers : 0.15 % Allowed : 3.71 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.12), residues: 5452 helix: 1.18 (0.09), residues: 3217 sheet: -1.13 (0.34), residues: 240 loop : -1.67 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A2538 TYR 0.024 0.001 TYR I 84 PHE 0.029 0.001 PHE B 382 TRP 0.024 0.001 TRP A 776 HIS 0.011 0.001 HIS I 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (45510) covalent geometry : angle 0.60738 / 0.32 (61816) hydrogen bonds : bond 0.04288 / 2.89 ( 2464) hydrogen bonds : angle 5.00733 / 3.60 ( 7242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 359 time to evaluate : 1.726 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.9675 (t80) cc_final: 0.9452 (t80) REVERT: A 115 TYR cc_start: 0.8357 (t80) cc_final: 0.7812 (t80) REVERT: A 144 MET cc_start: 0.8921 (mmp) cc_final: 0.8686 (mpp) REVERT: A 208 MET cc_start: 0.9491 (pmm) cc_final: 0.9284 (pmm) REVERT: A 384 MET cc_start: 0.9585 (ptp) cc_final: 0.9360 (ptp) REVERT: A 441 MET cc_start: 0.9249 (mmt) cc_final: 0.8872 (mmp) REVERT: A 465 PHE cc_start: 0.9023 (t80) cc_final: 0.8685 (t80) REVERT: A 626 LEU cc_start: 0.9788 (mt) cc_final: 0.9571 (mt) REVERT: A 649 PHE cc_start: 0.9269 (t80) cc_final: 0.8877 (t80) REVERT: A 879 MET cc_start: 0.8952 (mmp) cc_final: 0.8487 (mpp) REVERT: A 880 MET cc_start: 0.8205 (ptp) cc_final: 0.7266 (ptp) REVERT: A 937 MET cc_start: 0.9429 (ptp) cc_final: 0.9226 (ptm) REVERT: A 1270 PHE cc_start: 0.9386 (m-10) cc_final: 0.9094 (m-80) REVERT: A 1342 MET cc_start: 0.9672 (mtm) cc_final: 0.9424 (mtp) REVERT: A 1344 PHE cc_start: 0.9531 (t80) cc_final: 0.9323 (t80) REVERT: A 1600 MET cc_start: 0.8998 (mmp) cc_final: 0.8645 (mmm) REVERT: A 1877 LEU cc_start: 0.9815 (mt) cc_final: 0.9349 (mt) REVERT: A 1881 TYR cc_start: 0.8320 (m-10) cc_final: 0.8042 (m-80) REVERT: A 2356 MET cc_start: 0.9224 (ptm) cc_final: 0.8987 (ptm) REVERT: A 2399 GLU cc_start: 0.9555 (OUTLIER) cc_final: 0.9330 (pm20) REVERT: A 2419 ASP cc_start: 0.9580 (t0) cc_final: 0.9343 (t0) REVERT: A 2473 MET cc_start: 0.9340 (ptt) cc_final: 0.9129 (ptt) REVERT: A 2554 PHE cc_start: 0.9144 (t80) cc_final: 0.8917 (t80) REVERT: A 2820 MET cc_start: 0.8917 (tmm) cc_final: 0.8658 (tmm) REVERT: A 2928 LYS cc_start: 0.9716 (mmtp) cc_final: 0.9390 (mttp) REVERT: A 2930 TYR cc_start: 0.9558 (m-80) cc_final: 0.9065 (m-80) REVERT: A 2943 PHE cc_start: 0.9038 (m-80) cc_final: 0.8440 (m-80) REVERT: A 3065 ILE cc_start: 0.9660 (mm) cc_final: 0.9318 (mm) REVERT: A 3173 MET cc_start: 0.9261 (mmp) cc_final: 0.9044 (mmm) REVERT: A 3414 MET cc_start: 0.9295 (mmt) cc_final: 0.9005 (mmm) REVERT: A 3694 PHE cc_start: 0.8484 (p90) cc_final: 0.8105 (p90) REVERT: A 3796 MET cc_start: 0.8844 (mmp) cc_final: 0.8517 (mmm) REVERT: A 3846 MET cc_start: 0.6572 (ptp) cc_final: 0.4294 (ptp) REVERT: B 87 PHE cc_start: 0.8952 (m-80) cc_final: 0.8560 (m-80) REVERT: B 167 MET cc_start: 0.6971 (tpt) cc_final: 0.6222 (tpt) REVERT: B 203 MET cc_start: 0.3392 (ttp) cc_final: 0.3158 (ttt) REVERT: B 345 LEU cc_start: 0.9688 (mp) cc_final: 0.9273 (tp) REVERT: B 348 MET cc_start: 0.8434 (mmp) cc_final: 0.7748 (mmm) REVERT: B 446 MET cc_start: 0.8420 (tpp) cc_final: 0.8072 (tpp) REVERT: B 453 MET cc_start: 0.8421 (mmp) cc_final: 0.8207 (mmp) REVERT: C 40 MET cc_start: 0.9627 (ptt) cc_final: 0.9318 (ppp) REVERT: C 251 LEU cc_start: 0.9870 (tp) cc_final: 0.9523 (tp) REVERT: C 290 GLN cc_start: 0.6572 (OUTLIER) cc_final: 0.6208 (pm20) REVERT: C 340 PHE cc_start: 0.9200 (t80) cc_final: 0.8667 (t80) REVERT: C 389 MET cc_start: 0.7704 (tpt) cc_final: 0.6770 (tpt) REVERT: C 461 MET cc_start: 0.8877 (tpt) cc_final: 0.8640 (tpp) REVERT: G 159 MET cc_start: 0.9445 (ppp) cc_final: 0.9172 (ppp) REVERT: H 59 MET cc_start: 0.8989 (mmm) cc_final: 0.8660 (mmm) REVERT: J 667 MET cc_start: 0.7929 (ppp) cc_final: 0.7143 (ppp) REVERT: J 792 MET cc_start: 0.8858 (mpp) cc_final: 0.8423 (mpp) outliers start: 7 outliers final: 2 residues processed: 366 average time/residue: 0.2501 time to fit residues: 153.8297 Evaluate side-chains 285 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 281 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 394 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 206 optimal weight: 0.0020 chunk 237 optimal weight: 0.6980 chunk 549 optimal weight: 8.9990 chunk 347 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 467 optimal weight: 7.9990 chunk 303 optimal weight: 5.9990 chunk 513 optimal weight: 40.0000 chunk 343 optimal weight: 0.4980 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN ** A1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 ASN ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3054 GLN ** A3697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 HIS I 21 GLN ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 718 HIS ** 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 = 0.3329 r_free = 0.3329 target = 0.046107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.037573 restraints weight = 727300.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.037742 restraints weight = 508754.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.038230 restraints weight = 386393.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.038296 restraints weight = 297481.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.038563 restraints weight = 248885.874| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 45510 Z= 0.127 Angle : 0.587 14.569 61816 Z= 0.303 Chirality : 0.040 0.185 7116 Planarity : 0.004 0.054 7722 Dihedral : 11.457 179.364 6471 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.32 % Favored : 94.64 % Rotamer: Outliers : 0.04 % Allowed : 3.24 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.12), residues: 5452 helix: 1.13 (0.09), residues: 3228 sheet: -1.39 (0.32), residues: 248 loop : -1.67 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG A2931 TYR 0.025 0.001 TYR B 103 PHE 0.026 0.001 PHE A2145 TRP 0.013 0.001 TRP A1039 HIS 0.009 0.001 HIS I 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (45510) covalent geometry : angle 0.58665 / 0.30 (61816) hydrogen bonds : bond 0.03794 / 2.55 ( 2464) hydrogen bonds : angle 4.85316 / 3.49 ( 7242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 341 time to evaluate : 1.679 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LEU cc_start: 0.9859 (mt) cc_final: 0.9640 (mt) REVERT: A 208 MET cc_start: 0.9494 (pmm) cc_final: 0.9203 (pmm) REVERT: A 384 MET cc_start: 0.9612 (ptp) cc_final: 0.9378 (ptp) REVERT: A 441 MET cc_start: 0.9240 (mmt) cc_final: 0.8864 (mmp) REVERT: A 465 PHE cc_start: 0.9035 (t80) cc_final: 0.8807 (t80) REVERT: A 649 PHE cc_start: 0.9280 (t80) cc_final: 0.8921 (t80) REVERT: A 879 MET cc_start: 0.9004 (mmp) cc_final: 0.8571 (mpp) REVERT: A 880 MET cc_start: 0.8261 (ptp) cc_final: 0.7315 (ptp) REVERT: A 937 MET cc_start: 0.9473 (ptp) cc_final: 0.9236 (ptm) REVERT: A 1270 PHE cc_start: 0.9376 (m-10) cc_final: 0.9079 (m-80) REVERT: A 1297 PHE cc_start: 0.9281 (m-10) cc_final: 0.9035 (m-80) REVERT: A 1342 MET cc_start: 0.9658 (mtm) cc_final: 0.9399 (mtp) REVERT: A 1600 MET cc_start: 0.9007 (mmp) cc_final: 0.8681 (mmm) REVERT: A 1757 MET cc_start: 0.9204 (tpt) cc_final: 0.8989 (tpt) REVERT: A 1877 LEU cc_start: 0.9800 (mt) cc_final: 0.9524 (mt) REVERT: A 1881 TYR cc_start: 0.8376 (m-10) cc_final: 0.8148 (m-80) REVERT: A 2094 MET cc_start: 0.8755 (ptt) cc_final: 0.8359 (ppp) REVERT: A 2220 MET cc_start: 0.9326 (ptp) cc_final: 0.8810 (ppp) REVERT: A 2419 ASP cc_start: 0.9605 (t0) cc_final: 0.9369 (t0) REVERT: A 2554 PHE cc_start: 0.9147 (t80) cc_final: 0.8926 (t80) REVERT: A 2820 MET cc_start: 0.8888 (tmm) cc_final: 0.8640 (tmm) REVERT: A 2930 TYR cc_start: 0.9574 (m-80) cc_final: 0.9051 (m-80) REVERT: A 3173 MET cc_start: 0.9457 (mmp) cc_final: 0.9156 (mmm) REVERT: A 3240 MET cc_start: 0.9204 (mmp) cc_final: 0.8859 (mmp) REVERT: A 3414 MET cc_start: 0.9281 (mmt) cc_final: 0.8898 (mmt) REVERT: A 3694 PHE cc_start: 0.8534 (p90) cc_final: 0.8128 (p90) REVERT: A 3796 MET cc_start: 0.8944 (mmp) cc_final: 0.8588 (mmm) REVERT: B 87 PHE cc_start: 0.9046 (m-80) cc_final: 0.8662 (m-80) REVERT: B 345 LEU cc_start: 0.9711 (mp) cc_final: 0.9281 (tp) REVERT: B 348 MET cc_start: 0.8434 (mmp) cc_final: 0.7519 (mmm) REVERT: B 350 PHE cc_start: 0.9053 (m-80) cc_final: 0.8743 (m-80) REVERT: B 446 MET cc_start: 0.8472 (tpp) cc_final: 0.8200 (tpp) REVERT: B 453 MET cc_start: 0.8413 (mmp) cc_final: 0.8196 (mmp) REVERT: C 40 MET cc_start: 0.9614 (ptt) cc_final: 0.9328 (ppp) REVERT: C 115 MET cc_start: 0.8969 (ppp) cc_final: 0.8733 (ppp) REVERT: C 340 PHE cc_start: 0.9375 (t80) cc_final: 0.8892 (t80) REVERT: C 389 MET cc_start: 0.7276 (tpt) cc_final: 0.6331 (tpt) REVERT: C 461 MET cc_start: 0.9004 (tpt) cc_final: 0.8599 (tpp) REVERT: H 59 MET cc_start: 0.9094 (mmm) cc_final: 0.8761 (mmm) REVERT: J 667 MET cc_start: 0.7908 (ppp) cc_final: 0.7068 (ppp) REVERT: J 792 MET cc_start: 0.9000 (mpp) cc_final: 0.8734 (mpp) outliers start: 2 outliers final: 2 residues processed: 343 average time/residue: 0.2594 time to fit residues: 149.8593 Evaluate side-chains 272 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 270 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 473 optimal weight: 50.0000 chunk 430 optimal weight: 6.9990 chunk 501 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 468 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 491 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 133 optimal weight: 0.6980 chunk 209 optimal weight: 2.9990 chunk 524 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 HIS A 771 ASN ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN ** A1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 ASN ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3133 GLN ** A3697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 HIS ** J 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.042324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.034054 restraints weight = 773538.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.034147 restraints weight = 525146.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.034342 restraints weight = 427750.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.034491 restraints weight = 334868.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.034760 restraints weight = 296077.845| |-----------------------------------------------------------------------------| r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 45510 Z= 0.243 Angle : 0.685 16.807 61816 Z= 0.361 Chirality : 0.041 0.285 7116 Planarity : 0.005 0.054 7722 Dihedral : 11.524 175.619 6471 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.89 % Favored : 94.08 % Rotamer: Outliers : 0.02 % Allowed : 3.80 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.12), residues: 5452 helix: 0.91 (0.09), residues: 3227 sheet: -1.58 (0.32), residues: 251 loop : -1.68 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 151 TYR 0.030 0.002 TYR A 883 PHE 0.031 0.002 PHE A1840 TRP 0.019 0.002 TRP A1039 HIS 0.010 0.002 HIS A1772 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.24 (45510) covalent geometry : angle 0.68519 / 0.36 (61816) hydrogen bonds : bond 0.04091 / 2.78 ( 2464) hydrogen bonds : angle 5.03303 / 3.62 ( 7242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 313 time to evaluate : 1.980 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 MET cc_start: 0.9258 (ppp) cc_final: 0.8944 (ppp) REVERT: A 384 MET cc_start: 0.9659 (ptp) cc_final: 0.9384 (ptp) REVERT: A 441 MET cc_start: 0.9242 (mmt) cc_final: 0.8907 (mmm) REVERT: A 465 PHE cc_start: 0.9031 (t80) cc_final: 0.8765 (t80) REVERT: A 649 PHE cc_start: 0.9365 (t80) cc_final: 0.8977 (t80) REVERT: A 879 MET cc_start: 0.9142 (mmp) cc_final: 0.8654 (mpp) REVERT: A 880 MET cc_start: 0.8648 (ptp) cc_final: 0.7926 (ptt) REVERT: A 937 MET cc_start: 0.9472 (ptp) cc_final: 0.9213 (ptm) REVERT: A 1108 MET cc_start: 0.9538 (tpt) cc_final: 0.9275 (tmm) REVERT: A 1119 LYS cc_start: 0.9531 (tmtt) cc_final: 0.9176 (mmmt) REVERT: A 1270 PHE cc_start: 0.9420 (m-10) cc_final: 0.9095 (m-80) REVERT: A 1342 MET cc_start: 0.9683 (mtm) cc_final: 0.9427 (mtp) REVERT: A 1600 MET cc_start: 0.9190 (mmp) cc_final: 0.8812 (mmm) REVERT: A 1871 MET cc_start: 0.8645 (mmp) cc_final: 0.8180 (mmm) REVERT: A 1877 LEU cc_start: 0.9772 (mt) cc_final: 0.9432 (mt) REVERT: A 1881 TYR cc_start: 0.8486 (m-80) cc_final: 0.7832 (m-80) REVERT: A 2094 MET cc_start: 0.8939 (ptt) cc_final: 0.8334 (ppp) REVERT: A 2220 MET cc_start: 0.9389 (ptp) cc_final: 0.8970 (ppp) REVERT: A 2820 MET cc_start: 0.8973 (tmm) cc_final: 0.8713 (tmm) REVERT: A 2930 TYR cc_start: 0.9638 (m-80) cc_final: 0.9168 (m-80) REVERT: A 2936 TYR cc_start: 0.9543 (m-10) cc_final: 0.9342 (m-10) REVERT: A 3044 MET cc_start: 0.9347 (mmt) cc_final: 0.8789 (mmm) REVERT: A 3240 MET cc_start: 0.9351 (mmp) cc_final: 0.9006 (mmp) REVERT: A 3414 MET cc_start: 0.9340 (mmt) cc_final: 0.8964 (mmm) REVERT: A 3694 PHE cc_start: 0.8899 (p90) cc_final: 0.8473 (p90) REVERT: A 3796 MET cc_start: 0.9103 (mmp) cc_final: 0.8774 (mmm) REVERT: A 3967 PHE cc_start: 0.9386 (m-80) cc_final: 0.9120 (m-80) REVERT: A 3971 MET cc_start: 0.9771 (pmm) cc_final: 0.9558 (pmm) REVERT: B 87 PHE cc_start: 0.8984 (m-80) cc_final: 0.8637 (m-80) REVERT: B 345 LEU cc_start: 0.9712 (mp) cc_final: 0.9372 (tp) REVERT: B 348 MET cc_start: 0.8825 (mmp) cc_final: 0.7851 (mmm) REVERT: B 446 MET cc_start: 0.8381 (tpp) cc_final: 0.8175 (tpp) REVERT: C 14 MET cc_start: 0.7336 (ppp) cc_final: 0.7047 (ppp) REVERT: C 115 MET cc_start: 0.9011 (ppp) cc_final: 0.8802 (ppp) REVERT: C 291 LYS cc_start: 0.8712 (mttt) cc_final: 0.7561 (tppt) REVERT: C 340 PHE cc_start: 0.9446 (t80) cc_final: 0.8922 (t80) REVERT: C 461 MET cc_start: 0.9158 (tpt) cc_final: 0.8873 (tpp) REVERT: G 159 MET cc_start: 0.9410 (ppp) cc_final: 0.9165 (tmm) REVERT: H 59 MET cc_start: 0.9231 (mmm) cc_final: 0.8990 (mmm) REVERT: J 667 MET cc_start: 0.8103 (ppp) cc_final: 0.7283 (ppp) REVERT: J 792 MET cc_start: 0.9050 (mpp) cc_final: 0.8843 (mpp) outliers start: 1 outliers final: 0 residues processed: 314 average time/residue: 0.2613 time to fit residues: 139.1412 Evaluate side-chains 247 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 492 optimal weight: 0.0770 chunk 147 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 279 optimal weight: 0.8980 chunk 408 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 456 optimal weight: 30.0000 chunk 200 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN ** A1115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 GLN A1146 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1665 HIS A1687 HIS ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 ASN ** A3697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3766 GLN ** A3969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 HIS ** J 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.044291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.035770 restraints weight = 739799.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.036122 restraints weight = 486433.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.036220 restraints weight = 370290.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.036459 restraints weight = 299851.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.036807 restraints weight = 245095.470| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 45510 Z= 0.120 Angle : 0.599 12.287 61816 Z= 0.307 Chirality : 0.040 0.243 7116 Planarity : 0.004 0.069 7722 Dihedral : 11.535 178.192 6471 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.15 % Favored : 94.81 % Rotamer: Outliers : 0.06 % Allowed : 2.39 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.12), residues: 5452 helix: 1.06 (0.09), residues: 3215 sheet: -1.59 (0.31), residues: 256 loop : -1.60 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3741 TYR 0.020 0.001 TYR C 421 PHE 0.025 0.001 PHE A2840 TRP 0.014 0.001 TRP A1039 HIS 0.008 0.001 HIS I 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (45510) covalent geometry : angle 0.59893 / 0.31 (61816) hydrogen bonds : bond 0.03539 / 2.37 ( 2464) hydrogen bonds : angle 4.75322 / 3.42 ( 7242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 324 time to evaluate : 1.744 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: 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: 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 144 MET cc_start: 0.8165 (mpp) cc_final: 0.7860 (mpp) REVERT: A 208 MET cc_start: 0.9460 (pmm) cc_final: 0.9153 (pmm) REVERT: A 342 MET cc_start: 0.9033 (ppp) cc_final: 0.8814 (ppp) REVERT: A 384 MET cc_start: 0.9638 (ptp) cc_final: 0.9423 (ptp) REVERT: A 441 MET cc_start: 0.9233 (mmt) cc_final: 0.8837 (mmp) REVERT: A 649 PHE cc_start: 0.9235 (t80) cc_final: 0.8745 (t80) REVERT: A 762 TYR cc_start: 0.9076 (t80) cc_final: 0.8845 (t80) REVERT: A 879 MET cc_start: 0.9104 (mmp) cc_final: 0.8620 (mpp) REVERT: A 880 MET cc_start: 0.8500 (ptp) cc_final: 0.7748 (ptt) REVERT: A 937 MET cc_start: 0.9437 (ptp) cc_final: 0.9228 (ptm) REVERT: A 1270 PHE cc_start: 0.9309 (m-10) cc_final: 0.9003 (m-80) REVERT: A 1297 PHE cc_start: 0.9282 (m-10) cc_final: 0.9071 (m-80) REVERT: A 1342 MET cc_start: 0.9657 (mtm) cc_final: 0.9375 (mtp) REVERT: A 1871 MET cc_start: 0.8463 (mmp) cc_final: 0.7986 (mmm) REVERT: A 1877 LEU cc_start: 0.9781 (mt) cc_final: 0.9571 (mt) REVERT: A 1881 TYR cc_start: 0.8469 (m-80) cc_final: 0.8144 (m-80) REVERT: A 2094 MET cc_start: 0.8755 (ptt) cc_final: 0.8198 (ppp) REVERT: A 2220 MET cc_start: 0.9256 (ptp) cc_final: 0.9054 (ptm) REVERT: A 2374 LEU cc_start: 0.9456 (mt) cc_final: 0.9233 (pp) REVERT: A 2442 MET cc_start: 0.9063 (tpt) cc_final: 0.8681 (tmm) REVERT: A 2473 MET cc_start: 0.9108 (ptt) cc_final: 0.8700 (ptt) REVERT: A 2554 PHE cc_start: 0.9269 (t80) cc_final: 0.9066 (t80) REVERT: A 2820 MET cc_start: 0.8975 (tmm) cc_final: 0.8742 (tmm) REVERT: A 2840 PHE cc_start: 0.9543 (m-80) cc_final: 0.9338 (m-80) REVERT: A 2936 TYR cc_start: 0.9525 (m-80) cc_final: 0.9273 (m-10) REVERT: A 2943 PHE cc_start: 0.9282 (m-80) cc_final: 0.8905 (m-80) REVERT: A 3173 MET cc_start: 0.9547 (mmp) cc_final: 0.9246 (mmm) REVERT: A 3240 MET cc_start: 0.9295 (mmp) cc_final: 0.8926 (mmp) REVERT: A 3414 MET cc_start: 0.9262 (mmt) cc_final: 0.8899 (mmp) REVERT: A 3694 PHE cc_start: 0.8535 (p90) cc_final: 0.8141 (p90) REVERT: A 3796 MET cc_start: 0.9154 (mmp) cc_final: 0.8703 (mmm) REVERT: B 87 PHE cc_start: 0.9091 (m-80) cc_final: 0.8701 (m-80) REVERT: B 345 LEU cc_start: 0.9694 (mp) cc_final: 0.9322 (tp) REVERT: B 348 MET cc_start: 0.8644 (mmp) cc_final: 0.7446 (mmm) REVERT: B 382 PHE cc_start: 0.9492 (m-80) cc_final: 0.9176 (m-80) REVERT: B 446 MET cc_start: 0.8421 (tpp) cc_final: 0.8192 (tpp) REVERT: C 14 MET cc_start: 0.6973 (ppp) cc_final: 0.6682 (ppp) REVERT: C 40 MET cc_start: 0.9661 (ptt) cc_final: 0.9303 (ppp) REVERT: C 115 MET cc_start: 0.8982 (ppp) cc_final: 0.8765 (ppp) REVERT: C 340 PHE cc_start: 0.9397 (t80) cc_final: 0.8809 (t80) REVERT: C 389 MET cc_start: 0.6918 (tpt) cc_final: 0.5821 (tpt) REVERT: C 457 LEU cc_start: 0.9588 (tp) cc_final: 0.9282 (pp) REVERT: C 461 MET cc_start: 0.9070 (tpt) cc_final: 0.8780 (tpp) REVERT: G 159 MET cc_start: 0.9445 (ppp) cc_final: 0.9113 (ppp) REVERT: H 59 MET cc_start: 0.9294 (mmm) cc_final: 0.9079 (mmm) REVERT: J 667 MET cc_start: 0.7931 (ppp) cc_final: 0.7411 (ppp) outliers start: 3 outliers final: 1 residues processed: 327 average time/residue: 0.2457 time to fit residues: 137.3341 Evaluate side-chains 265 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 477 optimal weight: 9.9990 chunk 92 optimal weight: 0.3980 chunk 498 optimal weight: 20.0000 chunk 129 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 456 optimal weight: 40.0000 chunk 119 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 273 optimal weight: 0.8980 chunk 522 optimal weight: 0.0870 chunk 62 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN ** A1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3766 GLN ** A3969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN ** H 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 718 HIS ** 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 = 0.3307 r_free = 0.3307 target = 0.044612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.036098 restraints weight = 740893.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.036504 restraints weight = 458704.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.036533 restraints weight = 361168.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.036648 restraints weight = 286864.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.036805 restraints weight = 245701.673| |-----------------------------------------------------------------------------| r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 45510 Z= 0.118 Angle : 0.593 13.529 61816 Z= 0.304 Chirality : 0.040 0.316 7116 Planarity : 0.004 0.079 7722 Dihedral : 11.481 179.024 6471 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.39 % Favored : 94.57 % Rotamer: Outliers : 0.02 % Allowed : 1.70 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.12), residues: 5452 helix: 1.05 (0.09), residues: 3218 sheet: -1.50 (0.32), residues: 251 loop : -1.57 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2538 TYR 0.016 0.001 TYR A2572 PHE 0.022 0.001 PHE B 436 TRP 0.011 0.001 TRP A1039 HIS 0.011 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (45510) covalent geometry : angle 0.59339 / 0.30 (61816) hydrogen bonds : bond 0.03422 / 2.30 ( 2464) hydrogen bonds : angle 4.70292 / 3.38 ( 7242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 317 time to evaluate : 1.883 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8017 (mpp) cc_final: 0.7725 (mpp) REVERT: A 208 MET cc_start: 0.9459 (pmm) cc_final: 0.9211 (pmm) REVERT: A 251 PHE cc_start: 0.9277 (t80) cc_final: 0.9053 (t80) REVERT: A 342 MET cc_start: 0.9072 (ppp) cc_final: 0.8821 (ppp) REVERT: A 384 MET cc_start: 0.9613 (ptp) cc_final: 0.9395 (ptp) REVERT: A 441 MET cc_start: 0.9224 (mmt) cc_final: 0.8841 (mmp) REVERT: A 465 PHE cc_start: 0.9073 (t80) cc_final: 0.8760 (t80) REVERT: A 541 MET cc_start: 0.8452 (ptp) cc_final: 0.7865 (ptp) REVERT: A 649 PHE cc_start: 0.9262 (t80) cc_final: 0.8786 (t80) REVERT: A 879 MET cc_start: 0.9115 (mmp) cc_final: 0.8627 (mpp) REVERT: A 880 MET cc_start: 0.8497 (ptp) cc_final: 0.8023 (ptt) REVERT: A 937 MET cc_start: 0.9456 (ptp) cc_final: 0.9223 (ptm) REVERT: A 1270 PHE cc_start: 0.9300 (m-10) cc_final: 0.8997 (m-80) REVERT: A 1297 PHE cc_start: 0.9269 (m-10) cc_final: 0.9062 (m-80) REVERT: A 1342 MET cc_start: 0.9680 (mtm) cc_final: 0.9388 (mtp) REVERT: A 1600 MET cc_start: 0.9037 (mmp) cc_final: 0.8664 (mmm) REVERT: A 1871 MET cc_start: 0.8615 (mmp) cc_final: 0.8060 (mmm) REVERT: A 1877 LEU cc_start: 0.9767 (mt) cc_final: 0.9305 (mt) REVERT: A 1881 TYR cc_start: 0.8474 (m-80) cc_final: 0.8002 (m-80) REVERT: A 2094 MET cc_start: 0.8669 (ptt) cc_final: 0.8125 (ppp) REVERT: A 2220 MET cc_start: 0.9225 (ptp) cc_final: 0.8729 (ppp) REVERT: A 2374 LEU cc_start: 0.9444 (mt) cc_final: 0.9229 (pp) REVERT: A 2419 ASP cc_start: 0.9699 (t70) cc_final: 0.9481 (t0) REVERT: A 2442 MET cc_start: 0.9031 (tpt) cc_final: 0.8707 (tmm) REVERT: A 2809 PHE cc_start: 0.9592 (t80) cc_final: 0.9350 (t80) REVERT: A 2820 MET cc_start: 0.8911 (tmm) cc_final: 0.8685 (tmm) REVERT: A 2840 PHE cc_start: 0.9527 (m-80) cc_final: 0.9308 (m-80) REVERT: A 2936 TYR cc_start: 0.9528 (m-80) cc_final: 0.9285 (m-10) REVERT: A 2943 PHE cc_start: 0.9322 (m-80) cc_final: 0.8953 (m-80) REVERT: A 3044 MET cc_start: 0.9298 (mmt) cc_final: 0.8843 (mmm) REVERT: A 3173 MET cc_start: 0.9508 (mmp) cc_final: 0.9188 (mmm) REVERT: A 3240 MET cc_start: 0.9324 (mmp) cc_final: 0.8924 (mmp) REVERT: A 3414 MET cc_start: 0.9283 (mmt) cc_final: 0.8926 (mmp) REVERT: A 3694 PHE cc_start: 0.8620 (p90) cc_final: 0.8205 (p90) REVERT: A 3796 MET cc_start: 0.9100 (mmp) cc_final: 0.8680 (mmm) REVERT: B 87 PHE cc_start: 0.9088 (m-80) cc_final: 0.8702 (m-80) REVERT: B 345 LEU cc_start: 0.9692 (mp) cc_final: 0.9308 (tp) REVERT: B 348 MET cc_start: 0.8623 (mmp) cc_final: 0.7430 (mmm) REVERT: B 363 ARG cc_start: 0.8734 (ttp-110) cc_final: 0.8528 (ttp-110) REVERT: B 382 PHE cc_start: 0.9600 (m-80) cc_final: 0.9193 (m-80) REVERT: B 446 MET cc_start: 0.8455 (tpp) cc_final: 0.8245 (tpp) REVERT: C 14 MET cc_start: 0.7026 (ppp) cc_final: 0.6736 (ppp) REVERT: C 84 MET cc_start: 0.9594 (ppp) cc_final: 0.9292 (ppp) REVERT: C 115 MET cc_start: 0.8964 (ppp) cc_final: 0.8753 (ppp) REVERT: C 345 PHE cc_start: 0.8931 (m-80) cc_final: 0.8688 (m-80) REVERT: C 389 MET cc_start: 0.7016 (tpt) cc_final: 0.5891 (tpt) REVERT: C 461 MET cc_start: 0.9087 (tpt) cc_final: 0.8778 (tpp) REVERT: H 59 MET cc_start: 0.9308 (mmm) cc_final: 0.9089 (mmm) REVERT: J 667 MET cc_start: 0.7813 (ppp) cc_final: 0.7304 (ppp) REVERT: J 746 MET cc_start: 0.9153 (tpt) cc_final: 0.8881 (tpp) outliers start: 1 outliers final: 0 residues processed: 318 average time/residue: 0.2611 time to fit residues: 142.0281 Evaluate side-chains 261 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 83 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 312 optimal weight: 5.9990 chunk 320 optimal weight: 0.9980 chunk 474 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 518 optimal weight: 20.0000 chunk 172 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 chunk 338 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN ** A1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 718 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 = 0.3305 r_free = 0.3305 target = 0.044451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.036040 restraints weight = 741350.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.036333 restraints weight = 446802.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.036539 restraints weight = 360611.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.036736 restraints weight = 263332.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.036807 restraints weight = 244869.885| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 45510 Z= 0.118 Angle : 0.589 11.592 61816 Z= 0.302 Chirality : 0.040 0.239 7116 Planarity : 0.004 0.061 7722 Dihedral : 11.423 179.333 6471 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.47 % Favored : 94.50 % Rotamer: Outliers : 0.02 % Allowed : 1.16 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.12), residues: 5452 helix: 1.10 (0.09), residues: 3219 sheet: -1.49 (0.31), residues: 256 loop : -1.56 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 363 TYR 0.017 0.001 TYR A3828 PHE 0.059 0.001 PHE A3768 TRP 0.015 0.001 TRP J 738 HIS 0.019 0.001 HIS A1772 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (45510) covalent geometry : angle 0.58869 / 0.30 (61816) hydrogen bonds : bond 0.03324 / 2.22 ( 2464) hydrogen bonds : angle 4.63190 / 3.33 ( 7242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 1.910 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: 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: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8044 (mpp) cc_final: 0.7743 (mpp) REVERT: A 208 MET cc_start: 0.9548 (pmm) cc_final: 0.9346 (pmm) REVERT: A 251 PHE cc_start: 0.9231 (t80) cc_final: 0.9009 (t80) REVERT: A 342 MET cc_start: 0.9078 (ppp) cc_final: 0.8822 (ppp) REVERT: A 441 MET cc_start: 0.9218 (mmt) cc_final: 0.8827 (mmp) REVERT: A 465 PHE cc_start: 0.9117 (t80) cc_final: 0.8844 (t80) REVERT: A 541 MET cc_start: 0.8475 (ptp) cc_final: 0.7909 (ptp) REVERT: A 634 LEU cc_start: 0.9540 (tp) cc_final: 0.9238 (mp) REVERT: A 649 PHE cc_start: 0.9285 (t80) cc_final: 0.8852 (t80) REVERT: A 732 PHE cc_start: 0.9295 (t80) cc_final: 0.8772 (t80) REVERT: A 762 TYR cc_start: 0.8987 (t80) cc_final: 0.8784 (t80) REVERT: A 879 MET cc_start: 0.9087 (mmp) cc_final: 0.8605 (mpp) REVERT: A 880 MET cc_start: 0.8513 (ptp) cc_final: 0.8004 (ptt) REVERT: A 937 MET cc_start: 0.9431 (ptp) cc_final: 0.9201 (ptm) REVERT: A 1270 PHE cc_start: 0.9304 (m-10) cc_final: 0.8989 (m-80) REVERT: A 1297 PHE cc_start: 0.9285 (m-10) cc_final: 0.9073 (m-80) REVERT: A 1342 MET cc_start: 0.9676 (mtm) cc_final: 0.9381 (mtp) REVERT: A 1600 MET cc_start: 0.9062 (mmp) cc_final: 0.8615 (mmm) REVERT: A 1871 MET cc_start: 0.8560 (mmp) cc_final: 0.8013 (mmm) REVERT: A 1877 LEU cc_start: 0.9762 (mt) cc_final: 0.9315 (mt) REVERT: A 1881 TYR cc_start: 0.8442 (m-80) cc_final: 0.8011 (m-80) REVERT: A 2094 MET cc_start: 0.8657 (ptt) cc_final: 0.7983 (ppp) REVERT: A 2220 MET cc_start: 0.9241 (ptp) cc_final: 0.8823 (ppp) REVERT: A 2442 MET cc_start: 0.9067 (tpt) cc_final: 0.8741 (tmm) REVERT: A 2809 PHE cc_start: 0.9595 (t80) cc_final: 0.9363 (t80) REVERT: A 2820 MET cc_start: 0.8919 (tmm) cc_final: 0.8712 (tmm) REVERT: A 2840 PHE cc_start: 0.9523 (m-80) cc_final: 0.9298 (m-80) REVERT: A 2936 TYR cc_start: 0.9537 (m-80) cc_final: 0.9276 (m-10) REVERT: A 2943 PHE cc_start: 0.9306 (m-80) cc_final: 0.8913 (m-80) REVERT: A 3044 MET cc_start: 0.9319 (mmt) cc_final: 0.8912 (mmm) REVERT: A 3173 MET cc_start: 0.9502 (mmp) cc_final: 0.9181 (mmm) REVERT: A 3240 MET cc_start: 0.9356 (mmp) cc_final: 0.8989 (mmp) REVERT: A 3414 MET cc_start: 0.9258 (mmt) cc_final: 0.8916 (mmp) REVERT: A 3694 PHE cc_start: 0.8637 (p90) cc_final: 0.8195 (p90) REVERT: A 3768 PHE cc_start: 0.9561 (m-80) cc_final: 0.9072 (m-80) REVERT: A 3796 MET cc_start: 0.9154 (mmp) cc_final: 0.8746 (mmm) REVERT: A 3967 PHE cc_start: 0.9333 (m-80) cc_final: 0.9042 (m-80) REVERT: B 87 PHE cc_start: 0.9077 (m-80) cc_final: 0.8683 (m-80) REVERT: B 167 MET cc_start: 0.7429 (tpt) cc_final: 0.7222 (tpt) REVERT: B 345 LEU cc_start: 0.9701 (mp) cc_final: 0.9301 (tp) REVERT: B 348 MET cc_start: 0.8629 (mmp) cc_final: 0.7405 (mmm) REVERT: C 14 MET cc_start: 0.7218 (ppp) cc_final: 0.6968 (ppp) REVERT: C 115 MET cc_start: 0.8988 (ppp) cc_final: 0.8777 (ppp) REVERT: C 345 PHE cc_start: 0.8919 (m-80) cc_final: 0.8716 (m-80) REVERT: C 389 MET cc_start: 0.7153 (tpt) cc_final: 0.6261 (tpt) REVERT: C 461 MET cc_start: 0.9105 (tpt) cc_final: 0.8770 (tpp) REVERT: G 159 MET cc_start: 0.9416 (ppp) cc_final: 0.9142 (ppp) REVERT: H 59 MET cc_start: 0.9226 (mmm) cc_final: 0.8980 (mmm) REVERT: H 61 MET cc_start: 0.8300 (ptt) cc_final: 0.8063 (ptt) REVERT: J 667 MET cc_start: 0.7838 (ppp) cc_final: 0.7284 (ppp) outliers start: 1 outliers final: 1 residues processed: 320 average time/residue: 0.2617 time to fit residues: 143.2351 Evaluate side-chains 263 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 451 optimal weight: 0.0050 chunk 150 optimal weight: 6.9990 chunk 57 optimal weight: 0.2980 chunk 205 optimal weight: 0.8980 chunk 269 optimal weight: 6.9990 chunk 527 optimal weight: 0.6980 chunk 194 optimal weight: 0.9990 chunk 431 optimal weight: 5.9990 chunk 322 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 252 optimal weight: 8.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN A1084 ASN ** A1115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN C 360 GLN ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 ASN H 141 ASN ** J 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.044825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.036296 restraints weight = 738595.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.036750 restraints weight = 449147.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.036705 restraints weight = 366345.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.036875 restraints weight = 296484.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.037024 restraints weight = 249881.064| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 45510 Z= 0.112 Angle : 0.584 12.990 61816 Z= 0.297 Chirality : 0.040 0.351 7116 Planarity : 0.004 0.062 7722 Dihedral : 11.371 179.758 6471 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.41 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.12), residues: 5452 helix: 1.13 (0.09), residues: 3219 sheet: -1.43 (0.31), residues: 264 loop : -1.54 (0.14), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A4041 TYR 0.016 0.001 TYR A2572 PHE 0.039 0.001 PHE A3768 TRP 0.017 0.001 TRP J 738 HIS 0.015 0.001 HIS A1772 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (45510) covalent geometry : angle 0.58416 / 0.30 (61816) hydrogen bonds : bond 0.03233 / 2.17 ( 2464) hydrogen bonds : angle 4.55690 / 3.28 ( 7242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 1.620 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.7910 (mpp) cc_final: 0.7637 (mpp) REVERT: A 208 MET cc_start: 0.9381 (pmm) cc_final: 0.9073 (pmm) REVERT: A 342 MET cc_start: 0.9088 (ppp) cc_final: 0.8820 (ppp) REVERT: A 441 MET cc_start: 0.9214 (mmt) cc_final: 0.8816 (mmp) REVERT: A 465 PHE cc_start: 0.9080 (t80) cc_final: 0.8807 (t80) REVERT: A 541 MET cc_start: 0.8671 (ptp) cc_final: 0.8173 (ptp) REVERT: A 634 LEU cc_start: 0.9494 (tp) cc_final: 0.9266 (mp) REVERT: A 649 PHE cc_start: 0.9277 (t80) cc_final: 0.8849 (t80) REVERT: A 879 MET cc_start: 0.9075 (mmp) cc_final: 0.8624 (mpp) REVERT: A 880 MET cc_start: 0.8467 (ptp) cc_final: 0.7936 (ptt) REVERT: A 937 MET cc_start: 0.9403 (ptp) cc_final: 0.9176 (ptm) REVERT: A 1270 PHE cc_start: 0.9283 (m-10) cc_final: 0.8964 (m-80) REVERT: A 1297 PHE cc_start: 0.9295 (m-10) cc_final: 0.9088 (m-80) REVERT: A 1342 MET cc_start: 0.9701 (mtm) cc_final: 0.9401 (mtp) REVERT: A 1646 LEU cc_start: 0.9775 (tt) cc_final: 0.9536 (tt) REVERT: A 1871 MET cc_start: 0.8586 (mmp) cc_final: 0.8025 (mmm) REVERT: A 1877 LEU cc_start: 0.9755 (mt) cc_final: 0.9304 (mt) REVERT: A 1881 TYR cc_start: 0.8386 (m-80) cc_final: 0.7926 (m-80) REVERT: A 2220 MET cc_start: 0.9243 (ptp) cc_final: 0.8820 (ppp) REVERT: A 2442 MET cc_start: 0.9047 (tpt) cc_final: 0.8724 (tmm) REVERT: A 2809 PHE cc_start: 0.9599 (t80) cc_final: 0.9380 (t80) REVERT: A 2820 MET cc_start: 0.8871 (tmm) cc_final: 0.8666 (tmm) REVERT: A 2840 PHE cc_start: 0.9548 (m-80) cc_final: 0.9316 (m-80) REVERT: A 2936 TYR cc_start: 0.9541 (m-80) cc_final: 0.9282 (m-80) REVERT: A 2943 PHE cc_start: 0.9297 (m-80) cc_final: 0.8895 (m-80) REVERT: A 3173 MET cc_start: 0.9483 (mmp) cc_final: 0.9138 (mmm) REVERT: A 3240 MET cc_start: 0.9344 (mmp) cc_final: 0.8978 (mmp) REVERT: A 3414 MET cc_start: 0.9251 (mmt) cc_final: 0.8934 (mmm) REVERT: A 3694 PHE cc_start: 0.8410 (p90) cc_final: 0.8004 (p90) REVERT: A 3768 PHE cc_start: 0.9550 (m-80) cc_final: 0.9166 (m-10) REVERT: A 3796 MET cc_start: 0.9191 (mmp) cc_final: 0.8785 (mmm) REVERT: B 87 PHE cc_start: 0.9083 (m-80) cc_final: 0.8681 (m-80) REVERT: B 167 MET cc_start: 0.7368 (tpt) cc_final: 0.7152 (tpt) REVERT: B 345 LEU cc_start: 0.9701 (mp) cc_final: 0.9347 (tp) REVERT: B 348 MET cc_start: 0.8538 (mmp) cc_final: 0.7311 (mmm) REVERT: C 14 MET cc_start: 0.6798 (ppp) cc_final: 0.6270 (ppp) REVERT: C 84 MET cc_start: 0.9577 (ppp) cc_final: 0.9243 (ppp) REVERT: C 115 MET cc_start: 0.8974 (ppp) cc_final: 0.8763 (ppp) REVERT: C 340 PHE cc_start: 0.9399 (t80) cc_final: 0.8779 (t80) REVERT: C 345 PHE cc_start: 0.8857 (m-80) cc_final: 0.8596 (m-80) REVERT: C 389 MET cc_start: 0.7114 (tpt) cc_final: 0.5748 (mmm) REVERT: C 461 MET cc_start: 0.9101 (tpt) cc_final: 0.8765 (tpp) REVERT: J 667 MET cc_start: 0.7801 (ppp) cc_final: 0.7228 (ppp) REVERT: J 746 MET cc_start: 0.9501 (tpt) cc_final: 0.9063 (tpp) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.2508 time to fit residues: 136.1811 Evaluate side-chains 266 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 66 optimal weight: 9.9990 chunk 162 optimal weight: 0.0570 chunk 345 optimal weight: 0.0980 chunk 105 optimal weight: 5.9990 chunk 431 optimal weight: 5.9990 chunk 334 optimal weight: 1.9990 chunk 320 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 chunk 535 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 255 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS A 278 HIS ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN ** A1115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1598 ASN A1687 HIS ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3697 ASN A3969 ASN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.045071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.036665 restraints weight = 732278.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.036974 restraints weight = 446045.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.036923 restraints weight = 345970.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.037180 restraints weight = 290336.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.037305 restraints weight = 240190.146| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 45510 Z= 0.112 Angle : 0.595 12.038 61816 Z= 0.302 Chirality : 0.040 0.332 7116 Planarity : 0.004 0.062 7722 Dihedral : 11.330 179.144 6471 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.17 % Favored : 94.81 % Rotamer: Outliers : 0.02 % Allowed : 0.45 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.12), residues: 5452 helix: 1.16 (0.09), residues: 3215 sheet: -1.36 (0.31), residues: 264 loop : -1.56 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A2425 TYR 0.015 0.001 TYR A2572 PHE 0.036 0.001 PHE A3768 TRP 0.013 0.001 TRP A2981 HIS 0.011 0.001 HIS A1772 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (45510) covalent geometry : angle 0.59491 / 0.30 (61816) hydrogen bonds : bond 0.03245 / 2.17 ( 2464) hydrogen bonds : angle 4.55516 / 3.28 ( 7242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 1.798 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 PHE cc_start: 0.8964 (m-80) cc_final: 0.8762 (m-80) REVERT: A 144 MET cc_start: 0.7882 (mpp) cc_final: 0.7604 (mpp) REVERT: A 208 MET cc_start: 0.9406 (pmm) cc_final: 0.9123 (pmm) REVERT: A 342 MET cc_start: 0.9102 (ppp) cc_final: 0.8832 (ppp) REVERT: A 384 MET cc_start: 0.9609 (ptp) cc_final: 0.9395 (ptp) REVERT: A 441 MET cc_start: 0.9201 (mmt) cc_final: 0.8806 (mmp) REVERT: A 465 PHE cc_start: 0.9062 (t80) cc_final: 0.8792 (t80) REVERT: A 541 MET cc_start: 0.8728 (ptp) cc_final: 0.8238 (ptp) REVERT: A 649 PHE cc_start: 0.9312 (t80) cc_final: 0.8889 (t80) REVERT: A 879 MET cc_start: 0.9085 (mmp) cc_final: 0.8654 (mpp) REVERT: A 880 MET cc_start: 0.8438 (ptp) cc_final: 0.7899 (ptt) REVERT: A 937 MET cc_start: 0.9373 (ptp) cc_final: 0.9147 (ptm) REVERT: A 1270 PHE cc_start: 0.9291 (m-10) cc_final: 0.8988 (m-80) REVERT: A 1297 PHE cc_start: 0.9254 (m-10) cc_final: 0.9034 (m-80) REVERT: A 1342 MET cc_start: 0.9706 (mtm) cc_final: 0.9401 (mtp) REVERT: A 1600 MET cc_start: 0.8798 (mmm) cc_final: 0.8388 (mmm) REVERT: A 1871 MET cc_start: 0.8641 (mmp) cc_final: 0.8059 (mmm) REVERT: A 1877 LEU cc_start: 0.9771 (mt) cc_final: 0.9294 (mt) REVERT: A 1881 TYR cc_start: 0.8342 (m-80) cc_final: 0.7903 (m-80) REVERT: A 2094 MET cc_start: 0.8597 (ptt) cc_final: 0.7897 (ppp) REVERT: A 2220 MET cc_start: 0.9257 (ptp) cc_final: 0.8918 (ppp) REVERT: A 2809 PHE cc_start: 0.9601 (t80) cc_final: 0.9388 (t80) REVERT: A 2820 MET cc_start: 0.8861 (tmm) cc_final: 0.8659 (tmm) REVERT: A 2840 PHE cc_start: 0.9551 (m-80) cc_final: 0.9311 (m-80) REVERT: A 2936 TYR cc_start: 0.9513 (m-80) cc_final: 0.9241 (m-80) REVERT: A 2943 PHE cc_start: 0.9291 (m-80) cc_final: 0.8866 (m-80) REVERT: A 3044 MET cc_start: 0.9116 (mmp) cc_final: 0.8861 (mmm) REVERT: A 3173 MET cc_start: 0.9495 (mmp) cc_final: 0.9159 (mmm) REVERT: A 3240 MET cc_start: 0.9282 (mmp) cc_final: 0.8955 (mmp) REVERT: A 3414 MET cc_start: 0.9217 (mmt) cc_final: 0.8864 (mmm) REVERT: A 3694 PHE cc_start: 0.8318 (p90) cc_final: 0.7924 (p90) REVERT: A 3768 PHE cc_start: 0.9537 (m-80) cc_final: 0.9127 (m-10) REVERT: A 3796 MET cc_start: 0.9215 (mmp) cc_final: 0.8821 (mmm) REVERT: B 87 PHE cc_start: 0.8875 (m-80) cc_final: 0.8536 (m-80) REVERT: B 167 MET cc_start: 0.7289 (tpt) cc_final: 0.7059 (tpt) REVERT: B 345 LEU cc_start: 0.9702 (mp) cc_final: 0.9350 (tp) REVERT: B 348 MET cc_start: 0.8510 (mmp) cc_final: 0.7282 (mmm) REVERT: C 14 MET cc_start: 0.6734 (ppp) cc_final: 0.6172 (ppp) REVERT: C 84 MET cc_start: 0.9559 (ppp) cc_final: 0.9258 (ppp) REVERT: C 115 MET cc_start: 0.8953 (ppp) cc_final: 0.8742 (ppp) REVERT: C 340 PHE cc_start: 0.9393 (t80) cc_final: 0.8766 (t80) REVERT: C 345 PHE cc_start: 0.8854 (m-80) cc_final: 0.8591 (m-80) REVERT: C 389 MET cc_start: 0.7067 (tpt) cc_final: 0.5678 (mmm) REVERT: C 461 MET cc_start: 0.9121 (tpt) cc_final: 0.8767 (tpp) REVERT: J 667 MET cc_start: 0.7751 (ppp) cc_final: 0.7158 (ppp) REVERT: J 746 MET cc_start: 0.9421 (tpt) cc_final: 0.9145 (tpp) outliers start: 1 outliers final: 1 residues processed: 321 average time/residue: 0.2448 time to fit residues: 133.7093 Evaluate side-chains 260 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 249 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 228 optimal weight: 0.4980 chunk 181 optimal weight: 0.0040 chunk 27 optimal weight: 0.9990 chunk 411 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 336 optimal weight: 6.9990 chunk 388 optimal weight: 0.4980 chunk 123 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS A 960 GLN ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN A1115 HIS A1146 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3697 ASN ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.045060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.036572 restraints weight = 735117.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.036960 restraints weight = 453048.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.037038 restraints weight = 359266.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.037292 restraints weight = 274544.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.037400 restraints weight = 239444.839| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 45510 Z= 0.109 Angle : 0.586 12.492 61816 Z= 0.298 Chirality : 0.040 0.312 7116 Planarity : 0.004 0.063 7722 Dihedral : 11.275 178.494 6471 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.12 % Favored : 94.86 % Rotamer: Outliers : 0.02 % Allowed : 0.35 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.12), residues: 5452 helix: 1.21 (0.09), residues: 3221 sheet: -1.28 (0.31), residues: 264 loop : -1.56 (0.14), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A4041 TYR 0.015 0.001 TYR A2572 PHE 0.031 0.001 PHE A3768 TRP 0.018 0.001 TRP A3179 HIS 0.010 0.001 HIS A1772 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (45510) covalent geometry : angle 0.58619 / 0.30 (61816) hydrogen bonds : bond 0.03157 / 2.12 ( 2464) hydrogen bonds : angle 4.48956 / 3.23 ( 7242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 318 time to evaluate : 1.392 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 PHE cc_start: 0.9003 (m-80) cc_final: 0.8729 (m-80) REVERT: A 144 MET cc_start: 0.7836 (mpp) cc_final: 0.7567 (mpp) REVERT: A 208 MET cc_start: 0.9427 (pmm) cc_final: 0.9130 (pmm) REVERT: A 342 MET cc_start: 0.9097 (ppp) cc_final: 0.8822 (ppp) REVERT: A 384 MET cc_start: 0.9605 (ptp) cc_final: 0.9393 (ptp) REVERT: A 441 MET cc_start: 0.9195 (mmt) cc_final: 0.8794 (mmp) REVERT: A 465 PHE cc_start: 0.9061 (t80) cc_final: 0.8789 (t80) REVERT: A 649 PHE cc_start: 0.9302 (t80) cc_final: 0.8894 (t80) REVERT: A 762 TYR cc_start: 0.8959 (t80) cc_final: 0.8749 (t80) REVERT: A 879 MET cc_start: 0.9088 (mmp) cc_final: 0.8697 (mpp) REVERT: A 880 MET cc_start: 0.8410 (ptp) cc_final: 0.7858 (ptt) REVERT: A 1270 PHE cc_start: 0.9286 (m-10) cc_final: 0.8981 (m-80) REVERT: A 1297 PHE cc_start: 0.9226 (m-10) cc_final: 0.9022 (m-80) REVERT: A 1342 MET cc_start: 0.9700 (mtm) cc_final: 0.9390 (mtp) REVERT: A 1369 MET cc_start: 0.7780 (ttt) cc_final: 0.7495 (ttt) REVERT: A 1600 MET cc_start: 0.8768 (mmm) cc_final: 0.8330 (mmm) REVERT: A 1871 MET cc_start: 0.8518 (mmp) cc_final: 0.8017 (mmm) REVERT: A 1877 LEU cc_start: 0.9777 (mt) cc_final: 0.9323 (mt) REVERT: A 1881 TYR cc_start: 0.8550 (m-80) cc_final: 0.8041 (m-80) REVERT: A 2094 MET cc_start: 0.8536 (ptt) cc_final: 0.7876 (ppp) REVERT: A 2220 MET cc_start: 0.9343 (ptp) cc_final: 0.8874 (ppp) REVERT: A 2442 MET cc_start: 0.9083 (tpt) cc_final: 0.8767 (tmm) REVERT: A 2809 PHE cc_start: 0.9585 (t80) cc_final: 0.9378 (t80) REVERT: A 2820 MET cc_start: 0.8926 (tmm) cc_final: 0.8725 (tmm) REVERT: A 2840 PHE cc_start: 0.9514 (m-80) cc_final: 0.9280 (m-80) REVERT: A 2943 PHE cc_start: 0.9267 (m-80) cc_final: 0.8879 (m-80) REVERT: A 3173 MET cc_start: 0.9471 (mmp) cc_final: 0.9119 (mmm) REVERT: A 3240 MET cc_start: 0.9288 (mmp) cc_final: 0.8965 (mmp) REVERT: A 3414 MET cc_start: 0.9184 (mmt) cc_final: 0.8810 (mmm) REVERT: A 3694 PHE cc_start: 0.8313 (p90) cc_final: 0.7916 (p90) REVERT: A 3768 PHE cc_start: 0.9538 (m-80) cc_final: 0.9108 (m-10) REVERT: A 3796 MET cc_start: 0.9230 (mmp) cc_final: 0.8839 (mmm) REVERT: B 87 PHE cc_start: 0.8819 (m-80) cc_final: 0.8544 (m-80) REVERT: B 345 LEU cc_start: 0.9702 (mp) cc_final: 0.9335 (tp) REVERT: B 348 MET cc_start: 0.8480 (mmp) cc_final: 0.7261 (mmm) REVERT: B 363 ARG cc_start: 0.9028 (ttm110) cc_final: 0.8693 (ttm110) REVERT: C 14 MET cc_start: 0.6727 (ppp) cc_final: 0.6165 (ppp) REVERT: C 84 MET cc_start: 0.9554 (ppp) cc_final: 0.9252 (ppp) REVERT: C 115 MET cc_start: 0.8969 (ppp) cc_final: 0.8757 (ppp) REVERT: C 340 PHE cc_start: 0.9382 (t80) cc_final: 0.8763 (t80) REVERT: C 345 PHE cc_start: 0.8850 (m-80) cc_final: 0.8606 (m-80) REVERT: C 389 MET cc_start: 0.7090 (tpt) cc_final: 0.5753 (mmm) REVERT: C 461 MET cc_start: 0.9097 (tpt) cc_final: 0.8729 (tpp) REVERT: H 59 MET cc_start: 0.9009 (mmp) cc_final: 0.8769 (mmm) REVERT: J 667 MET cc_start: 0.7759 (ppp) cc_final: 0.7165 (ppp) REVERT: J 746 MET cc_start: 0.9351 (tpt) cc_final: 0.9061 (tpp) outliers start: 1 outliers final: 0 residues processed: 319 average time/residue: 0.2235 time to fit residues: 120.9162 Evaluate side-chains 260 residues out of total 5019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 345 optimal weight: 0.0270 chunk 251 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 chunk 304 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 291 optimal weight: 1.9990 chunk 493 optimal weight: 30.0000 chunk 25 optimal weight: 0.9990 chunk 296 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS A1048 GLN A1146 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3697 ASN ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 718 HIS ** 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 = 0.3315 r_free = 0.3315 target = 0.044805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.035777 restraints weight = 737925.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.036142 restraints weight = 508771.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.036471 restraints weight = 379936.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.036755 restraints weight = 311236.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.037008 restraints weight = 261011.604| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 45510 Z= 0.110 Angle : 0.582 12.960 61816 Z= 0.296 Chirality : 0.040 0.304 7116 Planarity : 0.004 0.061 7722 Dihedral : 11.236 178.261 6471 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.02 % Allowed : 0.17 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.12), residues: 5452 helix: 1.27 (0.09), residues: 3210 sheet: -1.33 (0.31), residues: 275 loop : -1.51 (0.14), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3696 TYR 0.014 0.001 TYR A2572 PHE 0.030 0.001 PHE A3768 TRP 0.019 0.001 TRP A1039 HIS 0.009 0.001 HIS A1772 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (45510) covalent geometry : angle 0.58157 / 0.30 (61816) hydrogen bonds : bond 0.03136 / 2.10 ( 2464) hydrogen bonds : angle 4.45351 / 3.20 ( 7242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8272.87 seconds wall clock time: 144 minutes 9.42 seconds (8649.42 seconds total)