Starting phenix.real_space_refine on Fri May 30 07:43:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zji_60146/05_2025/8zji_60146.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zji_60146/05_2025/8zji_60146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zji_60146/05_2025/8zji_60146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zji_60146/05_2025/8zji_60146.map" model { file = "/net/cci-nas-00/data/ceres_data/8zji_60146/05_2025/8zji_60146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zji_60146/05_2025/8zji_60146.cif" } resolution = 4.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 176 5.16 5 C 21052 2.51 5 N 5538 2.21 5 O 6092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.90s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32858 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1608 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "B" Number of atoms: 13436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1642, 13436 Classifications: {'peptide': 1642} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1583} Chain: "C" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1385 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 165} Chain: "D" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1608 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "E" Number of atoms: 13436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1642, 13436 Classifications: {'peptide': 1642} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1583} Chain: "F" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1385 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 165} Time building chain proxies: 17.83, per 1000 atoms: 0.54 Number of scatterers: 32858 At special positions: 0 Unit cell: (227.43, 166.25, 160.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 176 16.00 O 6092 8.00 N 5538 7.00 C 21052 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: 8.89 Conformation dependent library (CDL) restraints added in 4.6 seconds 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7696 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 24 sheets defined 55.5% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.37 Creating SS restraints... Processing helix chain 'A' and resid 530 through 540 Processing helix chain 'A' and resid 541 through 559 removed outlier: 3.646A pdb=" N LEU A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.767A pdb=" N ILE A 613 " --> pdb=" O VAL A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 622 No H-bonds generated for 'chain 'A' and resid 620 through 622' Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.602A pdb=" N VAL A 637 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 638 " --> pdb=" O LYS A 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 634 through 638' Processing helix chain 'A' and resid 658 through 673 Processing helix chain 'A' and resid 679 through 696 Processing helix chain 'B' and resid 84 through 107 removed outlier: 3.516A pdb=" N VAL B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 133 removed outlier: 4.070A pdb=" N SER B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 168 through 172 removed outlier: 4.187A pdb=" N ILE B 172 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 180 through 205 removed outlier: 4.431A pdb=" N LYS B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.760A pdb=" N GLY B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 276 Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 357 through 361 removed outlier: 3.641A pdb=" N ARG B 360 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 361 " --> pdb=" O ARG B 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 357 through 361' Processing helix chain 'B' and resid 378 through 389 removed outlier: 3.599A pdb=" N VAL B 382 " --> pdb=" O PRO B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 521 through 523 No H-bonds generated for 'chain 'B' and resid 521 through 523' Processing helix chain 'B' and resid 537 through 544 Processing helix chain 'B' and resid 575 through 581 Processing helix chain 'B' and resid 581 through 586 removed outlier: 3.557A pdb=" N LEU B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 605 removed outlier: 3.990A pdb=" N LYS B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN B 605 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 642 removed outlier: 3.699A pdb=" N LEU B 638 " --> pdb=" O ASN B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 648 No H-bonds generated for 'chain 'B' and resid 646 through 648' Processing helix chain 'B' and resid 649 through 658 removed outlier: 4.143A pdb=" N MET B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 666 removed outlier: 3.536A pdb=" N ILE B 665 " --> pdb=" O ASP B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 684 Processing helix chain 'B' and resid 686 through 705 removed outlier: 3.517A pdb=" N ASP B 690 " --> pdb=" O SER B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 711 No H-bonds generated for 'chain 'B' and resid 709 through 711' Processing helix chain 'B' and resid 712 through 723 Processing helix chain 'B' and resid 728 through 743 removed outlier: 3.691A pdb=" N LYS B 732 " --> pdb=" O LEU B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 759 removed outlier: 3.856A pdb=" N GLU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 779 removed outlier: 3.514A pdb=" N LEU B 763 " --> pdb=" O ALA B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 803 Processing helix chain 'B' and resid 805 through 808 removed outlier: 3.595A pdb=" N GLU B 808 " --> pdb=" O PRO B 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 805 through 808' Processing helix chain 'B' and resid 809 through 820 Processing helix chain 'B' and resid 820 through 830 removed outlier: 4.014A pdb=" N ILE B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASP B 826 " --> pdb=" O SER B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 846 Processing helix chain 'B' and resid 852 through 866 Processing helix chain 'B' and resid 874 through 889 Proline residue: B 880 - end of helix Processing helix chain 'B' and resid 895 through 897 No H-bonds generated for 'chain 'B' and resid 895 through 897' Processing helix chain 'B' and resid 898 through 915 Processing helix chain 'B' and resid 921 through 943 removed outlier: 6.386A pdb=" N ARG B 934 " --> pdb=" O GLU B 930 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ARG B 935 " --> pdb=" O ARG B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 964 removed outlier: 3.756A pdb=" N PHE B 953 " --> pdb=" O HIS B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 972 removed outlier: 4.130A pdb=" N TYR B 972 " --> pdb=" O HIS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 976 removed outlier: 4.034A pdb=" N PHE B 976 " --> pdb=" O ILE B 973 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 973 through 976' Processing helix chain 'B' and resid 978 through 998 removed outlier: 3.510A pdb=" N ILE B 982 " --> pdb=" O THR B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1033 Processing helix chain 'B' and resid 1034 through 1037 Processing helix chain 'B' and resid 1042 through 1054 Processing helix chain 'B' and resid 1065 through 1076 removed outlier: 3.855A pdb=" N ARG B1069 " --> pdb=" O SER B1065 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B1070 " --> pdb=" O GLN B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1095 removed outlier: 3.935A pdb=" N GLU B1082 " --> pdb=" O ASP B1078 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY B1095 " --> pdb=" O TRP B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1100 removed outlier: 4.238A pdb=" N ILE B1099 " --> pdb=" O PRO B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1101 through 1106 removed outlier: 3.807A pdb=" N MET B1105 " --> pdb=" O PHE B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1106 through 1114 removed outlier: 3.919A pdb=" N LEU B1110 " --> pdb=" O VAL B1106 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU B1111 " --> pdb=" O GLY B1107 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL B1112 " --> pdb=" O PRO B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1118 through 1139 Proline residue: B1126 - end of helix removed outlier: 3.704A pdb=" N PHE B1129 " --> pdb=" O ILE B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1161 Processing helix chain 'B' and resid 1165 through 1182 removed outlier: 3.636A pdb=" N LYS B1182 " --> pdb=" O GLU B1178 " (cutoff:3.500A) Processing helix chain 'B' and resid 1184 through 1215 Processing helix chain 'B' and resid 1216 through 1235 Processing helix chain 'B' and resid 1236 through 1254 Processing helix chain 'B' and resid 1256 through 1271 removed outlier: 4.029A pdb=" N LEU B1270 " --> pdb=" O LEU B1266 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B1271 " --> pdb=" O HIS B1267 " (cutoff:3.500A) Processing helix chain 'B' and resid 1292 through 1311 Processing helix chain 'B' and resid 1313 through 1332 removed outlier: 3.705A pdb=" N ALA B1317 " --> pdb=" O MET B1313 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU B1323 " --> pdb=" O LYS B1319 " (cutoff:3.500A) Processing helix chain 'B' and resid 1334 through 1355 removed outlier: 3.628A pdb=" N LEU B1338 " --> pdb=" O ASP B1334 " (cutoff:3.500A) Processing helix chain 'B' and resid 1390 through 1402 Processing helix chain 'B' and resid 1447 through 1457 removed outlier: 4.390A pdb=" N LEU B1451 " --> pdb=" O PRO B1447 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B1456 " --> pdb=" O ASN B1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 1513 through 1539 removed outlier: 3.561A pdb=" N ASP B1539 " --> pdb=" O GLN B1535 " (cutoff:3.500A) Processing helix chain 'B' and resid 1544 through 1556 Processing helix chain 'B' and resid 1561 through 1570 Processing helix chain 'B' and resid 1572 through 1579 removed outlier: 3.735A pdb=" N LEU B1576 " --> pdb=" O THR B1572 " (cutoff:3.500A) Processing helix chain 'B' and resid 1580 through 1584 removed outlier: 3.847A pdb=" N GLU B1584 " --> pdb=" O GLU B1581 " (cutoff:3.500A) Processing helix chain 'B' and resid 1585 through 1610 Proline residue: B1598 - end of helix Processing helix chain 'B' and resid 1614 through 1635 removed outlier: 4.179A pdb=" N LEU B1618 " --> pdb=" O GLN B1614 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 26 removed outlier: 3.836A pdb=" N LEU C 19 " --> pdb=" O ALA C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.915A pdb=" N ARG C 66 " --> pdb=" O ASP C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.748A pdb=" N SER C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 67 through 72' Processing helix chain 'C' and resid 86 through 96 Processing helix chain 'C' and resid 96 through 105 Processing helix chain 'C' and resid 116 through 121 removed outlier: 3.700A pdb=" N ASP C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.520A pdb=" N GLY C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 removed outlier: 4.369A pdb=" N VAL C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 177 " --> pdb=" O ILE C 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 540 Processing helix chain 'D' and resid 541 through 559 removed outlier: 3.647A pdb=" N LEU D 545 " --> pdb=" O GLN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 removed outlier: 3.768A pdb=" N ILE D 613 " --> pdb=" O VAL D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 622 No H-bonds generated for 'chain 'D' and resid 620 through 622' Processing helix chain 'D' and resid 634 through 638 removed outlier: 3.601A pdb=" N VAL D 637 " --> pdb=" O ASN D 634 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU D 638 " --> pdb=" O LYS D 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 634 through 638' Processing helix chain 'D' and resid 658 through 673 Processing helix chain 'D' and resid 679 through 696 Processing helix chain 'E' and resid 84 through 107 removed outlier: 3.516A pdb=" N VAL E 88 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 133 removed outlier: 4.071A pdb=" N SER E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 168 through 172 removed outlier: 4.186A pdb=" N ILE E 172 " --> pdb=" O ASN E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 177 Processing helix chain 'E' and resid 180 through 205 removed outlier: 4.431A pdb=" N LYS E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER E 203 " --> pdb=" O GLN E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 217 removed outlier: 3.760A pdb=" N GLY E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 276 Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 329 through 335 Processing helix chain 'E' and resid 357 through 361 removed outlier: 3.640A pdb=" N ARG E 360 " --> pdb=" O ILE E 357 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN E 361 " --> pdb=" O ARG E 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 357 through 361' Processing helix chain 'E' and resid 378 through 389 removed outlier: 3.599A pdb=" N VAL E 382 " --> pdb=" O PRO E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 417 Processing helix chain 'E' and resid 521 through 523 No H-bonds generated for 'chain 'E' and resid 521 through 523' Processing helix chain 'E' and resid 537 through 544 Processing helix chain 'E' and resid 575 through 581 Processing helix chain 'E' and resid 581 through 586 removed outlier: 3.557A pdb=" N LEU E 586 " --> pdb=" O ALA E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 591 through 605 removed outlier: 3.990A pdb=" N LYS E 604 " --> pdb=" O LEU E 600 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN E 605 " --> pdb=" O GLN E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 642 removed outlier: 3.699A pdb=" N LEU E 638 " --> pdb=" O ASN E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 648 No H-bonds generated for 'chain 'E' and resid 646 through 648' Processing helix chain 'E' and resid 649 through 658 removed outlier: 4.143A pdb=" N MET E 658 " --> pdb=" O LEU E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 661 through 666 removed outlier: 3.536A pdb=" N ILE E 665 " --> pdb=" O ASP E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 684 Processing helix chain 'E' and resid 686 through 705 removed outlier: 3.517A pdb=" N ASP E 690 " --> pdb=" O SER E 686 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 711 No H-bonds generated for 'chain 'E' and resid 709 through 711' Processing helix chain 'E' and resid 712 through 723 Processing helix chain 'E' and resid 728 through 743 removed outlier: 3.691A pdb=" N LYS E 732 " --> pdb=" O LEU E 728 " (cutoff:3.500A) Processing helix chain 'E' and resid 746 through 759 removed outlier: 3.856A pdb=" N GLU E 751 " --> pdb=" O SER E 747 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 759 through 779 removed outlier: 3.514A pdb=" N LEU E 763 " --> pdb=" O ALA E 759 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 803 Processing helix chain 'E' and resid 805 through 808 removed outlier: 3.596A pdb=" N GLU E 808 " --> pdb=" O PRO E 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 805 through 808' Processing helix chain 'E' and resid 809 through 820 Processing helix chain 'E' and resid 820 through 830 removed outlier: 4.014A pdb=" N ILE E 824 " --> pdb=" O LEU E 820 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN E 825 " --> pdb=" O PRO E 821 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ASP E 826 " --> pdb=" O SER E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 832 through 846 Processing helix chain 'E' and resid 852 through 866 Processing helix chain 'E' and resid 874 through 889 Proline residue: E 880 - end of helix Processing helix chain 'E' and resid 895 through 897 No H-bonds generated for 'chain 'E' and resid 895 through 897' Processing helix chain 'E' and resid 898 through 915 Processing helix chain 'E' and resid 921 through 943 removed outlier: 6.386A pdb=" N ARG E 934 " --> pdb=" O GLU E 930 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ARG E 935 " --> pdb=" O ARG E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 949 through 964 removed outlier: 3.756A pdb=" N PHE E 953 " --> pdb=" O HIS E 949 " (cutoff:3.500A) Processing helix chain 'E' and resid 965 through 972 removed outlier: 4.129A pdb=" N TYR E 972 " --> pdb=" O HIS E 968 " (cutoff:3.500A) Processing helix chain 'E' and resid 973 through 976 removed outlier: 4.033A pdb=" N PHE E 976 " --> pdb=" O ILE E 973 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 973 through 976' Processing helix chain 'E' and resid 978 through 998 removed outlier: 3.509A pdb=" N ILE E 982 " --> pdb=" O THR E 978 " (cutoff:3.500A) Processing helix chain 'E' and resid 1006 through 1033 Processing helix chain 'E' and resid 1034 through 1037 Processing helix chain 'E' and resid 1042 through 1054 Processing helix chain 'E' and resid 1065 through 1076 removed outlier: 3.855A pdb=" N ARG E1069 " --> pdb=" O SER E1065 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN E1070 " --> pdb=" O GLN E1066 " (cutoff:3.500A) Processing helix chain 'E' and resid 1078 through 1095 removed outlier: 3.936A pdb=" N GLU E1082 " --> pdb=" O ASP E1078 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY E1095 " --> pdb=" O TRP E1091 " (cutoff:3.500A) Processing helix chain 'E' and resid 1096 through 1100 removed outlier: 4.237A pdb=" N ILE E1099 " --> pdb=" O PRO E1096 " (cutoff:3.500A) Processing helix chain 'E' and resid 1101 through 1106 removed outlier: 3.807A pdb=" N MET E1105 " --> pdb=" O PHE E1101 " (cutoff:3.500A) Processing helix chain 'E' and resid 1106 through 1114 removed outlier: 3.918A pdb=" N LEU E1110 " --> pdb=" O VAL E1106 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU E1111 " --> pdb=" O GLY E1107 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL E1112 " --> pdb=" O PRO E1108 " (cutoff:3.500A) Processing helix chain 'E' and resid 1118 through 1139 Proline residue: E1126 - end of helix removed outlier: 3.703A pdb=" N PHE E1129 " --> pdb=" O ILE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1144 through 1161 Processing helix chain 'E' and resid 1165 through 1182 removed outlier: 3.635A pdb=" N LYS E1182 " --> pdb=" O GLU E1178 " (cutoff:3.500A) Processing helix chain 'E' and resid 1184 through 1215 Processing helix chain 'E' and resid 1216 through 1235 Processing helix chain 'E' and resid 1236 through 1254 Processing helix chain 'E' and resid 1256 through 1271 removed outlier: 4.029A pdb=" N LEU E1270 " --> pdb=" O LEU E1266 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU E1271 " --> pdb=" O HIS E1267 " (cutoff:3.500A) Processing helix chain 'E' and resid 1292 through 1311 Processing helix chain 'E' and resid 1313 through 1332 removed outlier: 3.705A pdb=" N ALA E1317 " --> pdb=" O MET E1313 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU E1323 " --> pdb=" O LYS E1319 " (cutoff:3.500A) Processing helix chain 'E' and resid 1334 through 1355 removed outlier: 3.627A pdb=" N LEU E1338 " --> pdb=" O ASP E1334 " (cutoff:3.500A) Processing helix chain 'E' and resid 1390 through 1402 Processing helix chain 'E' and resid 1447 through 1457 removed outlier: 4.390A pdb=" N LEU E1451 " --> pdb=" O PRO E1447 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA E1456 " --> pdb=" O ASN E1452 " (cutoff:3.500A) Processing helix chain 'E' and resid 1513 through 1539 removed outlier: 3.562A pdb=" N ASP E1539 " --> pdb=" O GLN E1535 " (cutoff:3.500A) Processing helix chain 'E' and resid 1544 through 1556 Processing helix chain 'E' and resid 1561 through 1570 Processing helix chain 'E' and resid 1572 through 1579 removed outlier: 3.735A pdb=" N LEU E1576 " --> pdb=" O THR E1572 " (cutoff:3.500A) Processing helix chain 'E' and resid 1580 through 1584 removed outlier: 3.848A pdb=" N GLU E1584 " --> pdb=" O GLU E1581 " (cutoff:3.500A) Processing helix chain 'E' and resid 1585 through 1610 Proline residue: E1598 - end of helix Processing helix chain 'E' and resid 1614 through 1635 removed outlier: 4.180A pdb=" N LEU E1618 " --> pdb=" O GLN E1614 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 26 removed outlier: 3.837A pdb=" N LEU F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 66 removed outlier: 3.915A pdb=" N ARG F 66 " --> pdb=" O ASP F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 72 removed outlier: 3.747A pdb=" N SER F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR F 72 " --> pdb=" O ARG F 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 67 through 72' Processing helix chain 'F' and resid 86 through 96 Processing helix chain 'F' and resid 96 through 105 Processing helix chain 'F' and resid 116 through 121 removed outlier: 3.701A pdb=" N ASP F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 138 through 150 removed outlier: 3.520A pdb=" N GLY F 142 " --> pdb=" O THR F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 177 removed outlier: 4.368A pdb=" N VAL F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU F 177 " --> pdb=" O ILE F 173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 561 through 563 Processing sheet with id=AA2, first strand: chain 'A' and resid 578 through 579 Processing sheet with id=AA3, first strand: chain 'A' and resid 616 through 618 Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.830A pdb=" N ILE B 37 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TYR B 48 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 46 " --> pdb=" O GLU B 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 344 through 347 removed outlier: 6.654A pdb=" N GLY B 398 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHE B 231 " --> pdb=" O GLY B 398 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TRP B 400 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N TYR B 222 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP B 283 " --> pdb=" O TYR B 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 252 through 253 Processing sheet with id=AA7, first strand: chain 'B' and resid 252 through 253 removed outlier: 6.575A pdb=" N LEU B 296 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL B 326 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N CYS B 298 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL B 324 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE B 300 " --> pdb=" O PHE B 322 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 484 through 485 removed outlier: 6.988A pdb=" N CYS B 508 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N HIS B 452 " --> pdb=" O CYS B 508 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU B 450 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR B 512 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL B 448 " --> pdb=" O THR B 512 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS B 514 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 446 " --> pdb=" O LYS B 514 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLN B 621 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLY B 453 " --> pdb=" O SER B 619 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N SER B 619 " --> pdb=" O GLY B 453 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B 565 " --> pdb=" O THR B 624 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 495 through 496 removed outlier: 3.541A pdb=" N ARG B 532 " --> pdb=" O GLU B 467 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1425 through 1430 Processing sheet with id=AB2, first strand: chain 'B' and resid 1432 through 1433 removed outlier: 6.669A pdb=" N GLN B1461 " --> pdb=" O TYR B1493 " (cutoff:3.500A) removed outlier: 10.897A pdb=" N TYR B1493 " --> pdb=" O GLN B1461 " (cutoff:3.500A) removed outlier: 11.789A pdb=" N ARG B1463 " --> pdb=" O THR B1491 " (cutoff:3.500A) removed outlier: 11.619A pdb=" N THR B1491 " --> pdb=" O ARG B1463 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 41 through 45 removed outlier: 6.936A pdb=" N CYS C 6 " --> pdb=" O TRP C 56 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LYS C 5 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU C 79 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL C 7 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N CYS C 81 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 9 " --> pdb=" O CYS C 81 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 111 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE C 110 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N LEU C 155 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU C 112 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 561 through 563 Processing sheet with id=AB5, first strand: chain 'D' and resid 578 through 579 Processing sheet with id=AB6, first strand: chain 'D' and resid 616 through 618 Processing sheet with id=AB7, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.830A pdb=" N ILE E 37 " --> pdb=" O TYR E 48 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N TYR E 48 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG E 46 " --> pdb=" O GLU E 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 344 through 347 removed outlier: 6.655A pdb=" N GLY E 398 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHE E 231 " --> pdb=" O GLY E 398 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP E 400 " --> pdb=" O LYS E 229 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TYR E 222 " --> pdb=" O ASP E 283 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP E 283 " --> pdb=" O TYR E 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 252 through 253 Processing sheet with id=AC1, first strand: chain 'E' and resid 252 through 253 removed outlier: 6.575A pdb=" N LEU E 296 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL E 326 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N CYS E 298 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL E 324 " --> pdb=" O CYS E 298 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE E 300 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 484 through 485 removed outlier: 6.987A pdb=" N CYS E 508 " --> pdb=" O HIS E 452 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N HIS E 452 " --> pdb=" O CYS E 508 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU E 450 " --> pdb=" O TYR E 510 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR E 512 " --> pdb=" O VAL E 448 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL E 448 " --> pdb=" O THR E 512 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS E 514 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE E 446 " --> pdb=" O LYS E 514 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLN E 621 " --> pdb=" O ILE E 451 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLY E 453 " --> pdb=" O SER E 619 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER E 619 " --> pdb=" O GLY E 453 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY E 565 " --> pdb=" O THR E 624 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 495 through 496 removed outlier: 3.541A pdb=" N ARG E 532 " --> pdb=" O GLU E 467 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 1425 through 1430 Processing sheet with id=AC5, first strand: chain 'E' and resid 1432 through 1433 removed outlier: 6.668A pdb=" N GLN E1461 " --> pdb=" O TYR E1493 " (cutoff:3.500A) removed outlier: 10.897A pdb=" N TYR E1493 " --> pdb=" O GLN E1461 " (cutoff:3.500A) removed outlier: 11.789A pdb=" N ARG E1463 " --> pdb=" O THR E1491 " (cutoff:3.500A) removed outlier: 11.619A pdb=" N THR E1491 " --> pdb=" O ARG E1463 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 41 through 45 removed outlier: 6.936A pdb=" N CYS F 6 " --> pdb=" O TRP F 56 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LYS F 5 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU F 79 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL F 7 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N CYS F 81 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL F 9 " --> pdb=" O CYS F 81 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 111 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE F 110 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N LEU F 155 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU F 112 " --> pdb=" O LEU F 155 " (cutoff:3.500A) 1669 hydrogen bonds defined for protein. 4833 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: 15.43 Time building geometry restraints manager: 10.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6877 1.33 - 1.45: 7367 1.45 - 1.57: 19018 1.57 - 1.69: 0 1.69 - 1.81: 294 Bond restraints: 33556 Sorted by residual: bond pdb=" CA PRO D 710 " pdb=" C PRO D 710 " ideal model delta sigma weight residual 1.514 1.498 0.016 5.50e-03 3.31e+04 8.79e+00 bond pdb=" CA PRO A 710 " pdb=" C PRO A 710 " ideal model delta sigma weight residual 1.514 1.498 0.016 5.50e-03 3.31e+04 8.43e+00 bond pdb=" CA VAL A 599 " pdb=" C VAL A 599 " ideal model delta sigma weight residual 1.522 1.506 0.016 7.10e-03 1.98e+04 5.19e+00 bond pdb=" CA VAL D 599 " pdb=" C VAL D 599 " ideal model delta sigma weight residual 1.522 1.506 0.016 7.10e-03 1.98e+04 5.18e+00 bond pdb=" CA ILE D 713 " pdb=" C ILE D 713 " ideal model delta sigma weight residual 1.524 1.544 -0.019 1.05e-02 9.07e+03 3.45e+00 ... (remaining 33551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 44480 2.48 - 4.96: 729 4.96 - 7.43: 100 7.43 - 9.91: 11 9.91 - 12.39: 4 Bond angle restraints: 45324 Sorted by residual: angle pdb=" C HIS E 971 " pdb=" N TYR E 972 " pdb=" CA TYR E 972 " ideal model delta sigma weight residual 122.58 113.00 9.58 2.07e+00 2.33e-01 2.14e+01 angle pdb=" C HIS B 971 " pdb=" N TYR B 972 " pdb=" CA TYR B 972 " ideal model delta sigma weight residual 122.58 113.05 9.53 2.07e+00 2.33e-01 2.12e+01 angle pdb=" CB MET B1009 " pdb=" CG MET B1009 " pdb=" SD MET B1009 " ideal model delta sigma weight residual 112.70 100.31 12.39 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CB MET E1009 " pdb=" CG MET E1009 " pdb=" SD MET E1009 " ideal model delta sigma weight residual 112.70 100.32 12.38 3.00e+00 1.11e-01 1.70e+01 angle pdb=" N VAL C 14 " pdb=" CA VAL C 14 " pdb=" C VAL C 14 " ideal model delta sigma weight residual 113.71 110.01 3.70 9.50e-01 1.11e+00 1.52e+01 ... (remaining 45319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 18284 17.96 - 35.92: 1862 35.92 - 53.88: 261 53.88 - 71.85: 43 71.85 - 89.81: 26 Dihedral angle restraints: 20476 sinusoidal: 8586 harmonic: 11890 Sorted by residual: dihedral pdb=" CA GLN D 541 " pdb=" C GLN D 541 " pdb=" N PRO D 542 " pdb=" CA PRO D 542 " ideal model delta harmonic sigma weight residual -180.00 -149.85 -30.15 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA GLN A 541 " pdb=" C GLN A 541 " pdb=" N PRO A 542 " pdb=" CA PRO A 542 " ideal model delta harmonic sigma weight residual 180.00 -149.85 -30.15 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA LEU E1576 " pdb=" C LEU E1576 " pdb=" N GLN E1577 " pdb=" CA GLN E1577 " ideal model delta harmonic sigma weight residual 180.00 151.97 28.03 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 20473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3772 0.050 - 0.100: 1003 0.100 - 0.150: 229 0.150 - 0.200: 12 0.200 - 0.250: 8 Chirality restraints: 5024 Sorted by residual: chirality pdb=" CG LEU B1338 " pdb=" CB LEU B1338 " pdb=" CD1 LEU B1338 " pdb=" CD2 LEU B1338 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CG LEU E1338 " pdb=" CB LEU E1338 " pdb=" CD1 LEU E1338 " pdb=" CD2 LEU E1338 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE E1353 " pdb=" CA ILE E1353 " pdb=" CG1 ILE E1353 " pdb=" CG2 ILE E1353 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 5021 not shown) Planarity restraints: 5796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B1107 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO B1108 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B1108 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B1108 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E1107 " 0.043 5.00e-02 4.00e+02 6.47e-02 6.69e+00 pdb=" N PRO E1108 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO E1108 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E1108 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B1527 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C GLU B1527 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU B1527 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG B1528 " -0.013 2.00e-02 2.50e+03 ... (remaining 5793 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 734 2.63 - 3.20: 35072 3.20 - 3.76: 57546 3.76 - 4.33: 78204 4.33 - 4.90: 117256 Nonbonded interactions: 288812 Sorted by model distance: nonbonded pdb=" O ASP E1275 " pdb=" OG1 THR E1292 " model vdw 2.061 3.040 nonbonded pdb=" O ASP B1275 " pdb=" OG1 THR B1292 " model vdw 2.061 3.040 nonbonded pdb=" O ALA E1260 " pdb=" OG1 THR E1263 " model vdw 2.071 3.040 nonbonded pdb=" O ALA B1260 " pdb=" OG1 THR B1263 " model vdw 2.072 3.040 nonbonded pdb=" OG1 THR B 49 " pdb=" OD1 ASN B 52 " model vdw 2.079 3.040 ... (remaining 288807 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.230 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 74.570 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.160 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 : 0.005 0.063 33556 Z= 0.247 Angle : 0.803 12.391 45324 Z= 0.445 Chirality : 0.047 0.250 5024 Planarity : 0.004 0.065 5796 Dihedral : 14.183 89.807 12780 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 32.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.13), residues: 4022 helix: -0.62 (0.11), residues: 1988 sheet: -1.49 (0.23), residues: 444 loop : -1.35 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 575 HIS 0.020 0.002 HIS B 971 PHE 0.029 0.002 PHE E1101 TYR 0.035 0.002 TYR B1388 ARG 0.024 0.001 ARG C 66 Details of bonding type rmsd hydrogen bonds : bond 0.17184 ( 1665) hydrogen bonds : angle 7.38686 ( 4833) covalent geometry : bond 0.00495 (33556) covalent geometry : angle 0.80253 (45324) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 3.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 ARG cc_start: 0.4777 (tpm170) cc_final: 0.4426 (tpm170) REVERT: B 1 MET cc_start: 0.0750 (mmm) cc_final: -0.0343 (mmm) REVERT: B 158 MET cc_start: 0.8494 (pmm) cc_final: 0.8236 (pmm) REVERT: B 192 LYS cc_start: 0.9176 (tptp) cc_final: 0.8823 (tppt) REVERT: B 668 PHE cc_start: 0.8942 (m-10) cc_final: 0.8688 (m-10) REVERT: B 957 MET cc_start: 0.9124 (ppp) cc_final: 0.8870 (ppp) REVERT: B 964 MET cc_start: 0.7639 (mmm) cc_final: 0.7257 (mmm) REVERT: B 1522 MET cc_start: 0.8024 (tpt) cc_final: 0.7394 (tpt) REVERT: C 6 CYS cc_start: 0.9088 (t) cc_final: 0.8805 (m) REVERT: D 726 CYS cc_start: 0.4584 (t) cc_final: 0.3659 (p) REVERT: E 1 MET cc_start: 0.0466 (mmm) cc_final: -0.0430 (mmm) REVERT: E 579 MET cc_start: 0.1738 (ttm) cc_final: 0.1442 (tpp) REVERT: E 658 MET cc_start: 0.6951 (ppp) cc_final: 0.6498 (ptp) REVERT: E 668 PHE cc_start: 0.8849 (m-10) cc_final: 0.8580 (m-80) REVERT: E 671 ASP cc_start: 0.9078 (m-30) cc_final: 0.8790 (t70) REVERT: E 787 PHE cc_start: 0.8867 (t80) cc_final: 0.8648 (t80) REVERT: E 802 MET cc_start: 0.8001 (ppp) cc_final: 0.7517 (ppp) REVERT: E 958 ILE cc_start: 0.9423 (pt) cc_final: 0.9064 (pt) REVERT: E 964 MET cc_start: 0.8183 (mmm) cc_final: 0.7954 (mmm) REVERT: E 1009 MET cc_start: 0.8866 (mmt) cc_final: 0.8464 (mmp) REVERT: E 1079 MET cc_start: 0.8956 (mtm) cc_final: 0.8717 (mtm) REVERT: E 1560 MET cc_start: 0.0610 (ppp) cc_final: -0.0252 (ttp) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.4215 time to fit residues: 154.7209 Evaluate side-chains 154 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 3.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 3.9990 chunk 303 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 204 optimal weight: 0.9990 chunk 161 optimal weight: 9.9990 chunk 313 optimal weight: 0.0570 chunk 121 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 363 optimal weight: 0.6980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 ASN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1014 ASN ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1531 ASN C 2 GLN C 103 HIS D 554 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1035 GLN ** E1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1093 ASN ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1531 ASN F 2 GLN F 103 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.059530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.037900 restraints weight = 262278.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.037970 restraints weight = 196834.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.038217 restraints weight = 157750.827| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33556 Z= 0.146 Angle : 0.691 11.678 45324 Z= 0.355 Chirality : 0.044 0.238 5024 Planarity : 0.005 0.067 5796 Dihedral : 5.455 77.451 4394 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.33 % Allowed : 6.36 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.13), residues: 4022 helix: -0.01 (0.11), residues: 2002 sheet: -1.37 (0.23), residues: 462 loop : -1.05 (0.17), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 102 HIS 0.013 0.001 HIS E1545 PHE 0.025 0.002 PHE E 795 TYR 0.035 0.002 TYR B1388 ARG 0.008 0.001 ARG E1390 Details of bonding type rmsd hydrogen bonds : bond 0.04757 ( 1665) hydrogen bonds : angle 5.66285 ( 4833) covalent geometry : bond 0.00312 (33556) covalent geometry : angle 0.69065 (45324) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 225 time to evaluate : 3.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 ARG cc_start: 0.4692 (tpm170) cc_final: 0.4450 (tpm170) REVERT: B 1 MET cc_start: 0.2891 (mmm) cc_final: 0.1678 (mmm) REVERT: B 185 LYS cc_start: 0.9451 (ptmt) cc_final: 0.9152 (ptmm) REVERT: B 192 LYS cc_start: 0.9344 (tptp) cc_final: 0.9071 (tppt) REVERT: B 243 MET cc_start: -0.1172 (tpt) cc_final: -0.2021 (ttp) REVERT: B 683 MET cc_start: 0.7291 (ppp) cc_final: 0.7076 (ppp) REVERT: B 764 PHE cc_start: 0.9461 (m-80) cc_final: 0.9259 (m-80) REVERT: B 958 ILE cc_start: 0.9525 (pt) cc_final: 0.9117 (pt) REVERT: B 971 HIS cc_start: 0.8361 (m90) cc_final: 0.8140 (m-70) REVERT: B 1009 MET cc_start: 0.8717 (mmt) cc_final: 0.8443 (mmt) REVERT: B 1011 MET cc_start: 0.9270 (mmp) cc_final: 0.8890 (mmp) REVERT: B 1243 TYR cc_start: 0.8407 (m-80) cc_final: 0.7706 (m-80) REVERT: B 1522 MET cc_start: 0.8418 (tpt) cc_final: 0.7672 (tpt) REVERT: C 45 MET cc_start: 0.8307 (tpt) cc_final: 0.7896 (tpt) REVERT: D 692 MET cc_start: 0.8641 (mmp) cc_final: 0.8228 (mmm) REVERT: E 1 MET cc_start: 0.1872 (mmm) cc_final: 0.0821 (mmm) REVERT: E 353 MET cc_start: 0.5564 (mpp) cc_final: 0.4681 (mpp) REVERT: E 658 MET cc_start: 0.7102 (ppp) cc_final: 0.6876 (ptp) REVERT: E 668 PHE cc_start: 0.8793 (m-10) cc_final: 0.8557 (m-80) REVERT: E 671 ASP cc_start: 0.9045 (m-30) cc_final: 0.8777 (t0) REVERT: E 787 PHE cc_start: 0.8776 (t80) cc_final: 0.8515 (t80) REVERT: E 802 MET cc_start: 0.7683 (ppp) cc_final: 0.7144 (ppp) REVERT: E 958 ILE cc_start: 0.9482 (pt) cc_final: 0.9018 (pt) REVERT: E 964 MET cc_start: 0.8237 (mmm) cc_final: 0.7993 (mmm) REVERT: E 1009 MET cc_start: 0.8994 (mmt) cc_final: 0.8713 (mmt) REVERT: E 1011 MET cc_start: 0.9190 (mmp) cc_final: 0.8850 (mmm) REVERT: E 1560 MET cc_start: 0.0646 (ppp) cc_final: -0.0236 (ttp) REVERT: E 1597 MET cc_start: 0.9011 (mmp) cc_final: 0.8223 (ttp) REVERT: F 2 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7857 (pp30) REVERT: F 6 CYS cc_start: 0.9189 (t) cc_final: 0.8895 (m) REVERT: F 45 MET cc_start: 0.7996 (tpt) cc_final: 0.7648 (tpt) outliers start: 12 outliers final: 3 residues processed: 237 average time/residue: 0.4152 time to fit residues: 169.6264 Evaluate side-chains 171 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 167 time to evaluate : 4.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 386 optimal weight: 6.9990 chunk 306 optimal weight: 7.9990 chunk 286 optimal weight: 5.9990 chunk 47 optimal weight: 0.2980 chunk 80 optimal weight: 0.0050 chunk 116 optimal weight: 5.9990 chunk 374 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 316 optimal weight: 2.9990 chunk 387 optimal weight: 9.9990 overall best weight: 1.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 HIS ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1133 GLN ** B1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1526 ASN B1636 HIS ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 HIS E 109 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1014 ASN E1035 GLN ** E1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1203 ASN ** E1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.059327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.038276 restraints weight = 266561.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.038268 restraints weight = 192917.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.038715 restraints weight = 165966.726| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33556 Z= 0.137 Angle : 0.657 11.865 45324 Z= 0.338 Chirality : 0.044 0.224 5024 Planarity : 0.005 0.061 5796 Dihedral : 5.286 74.727 4394 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.22 % Allowed : 4.37 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.13), residues: 4022 helix: 0.15 (0.11), residues: 2004 sheet: -1.33 (0.22), residues: 468 loop : -1.09 (0.17), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 102 HIS 0.012 0.001 HIS B1048 PHE 0.028 0.001 PHE B 777 TYR 0.024 0.002 TYR B1388 ARG 0.011 0.001 ARG B 534 Details of bonding type rmsd hydrogen bonds : bond 0.04483 ( 1665) hydrogen bonds : angle 5.42986 ( 4833) covalent geometry : bond 0.00293 (33556) covalent geometry : angle 0.65701 (45324) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 219 time to evaluate : 3.755 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: A 570 ARG cc_start: 0.4702 (tpm170) cc_final: 0.4451 (tpm170) REVERT: B 1 MET cc_start: 0.3118 (mmm) cc_final: 0.1654 (mmm) REVERT: B 158 MET cc_start: 0.8605 (pmm) cc_final: 0.8328 (pmm) REVERT: B 185 LYS cc_start: 0.9443 (ptmt) cc_final: 0.9143 (ptmm) REVERT: B 192 LYS cc_start: 0.9347 (tptp) cc_final: 0.9092 (tppt) REVERT: B 243 MET cc_start: -0.1300 (tpt) cc_final: -0.1664 (tpt) REVERT: B 306 MET cc_start: -0.3817 (ttm) cc_final: -0.4022 (ttt) REVERT: B 683 MET cc_start: 0.7288 (ppp) cc_final: 0.7080 (ppp) REVERT: B 764 PHE cc_start: 0.9420 (m-80) cc_final: 0.9219 (m-80) REVERT: B 845 GLN cc_start: 0.8908 (mm110) cc_final: 0.8690 (mm-40) REVERT: B 860 MET cc_start: 0.9379 (pmm) cc_final: 0.9034 (pmm) REVERT: B 958 ILE cc_start: 0.9504 (pt) cc_final: 0.9140 (pt) REVERT: B 971 HIS cc_start: 0.8365 (m90) cc_final: 0.8120 (m-70) REVERT: B 1011 MET cc_start: 0.9126 (mmp) cc_final: 0.8900 (mmm) REVERT: B 1243 TYR cc_start: 0.8088 (m-80) cc_final: 0.7428 (m-80) REVERT: B 1304 ILE cc_start: 0.9061 (mt) cc_final: 0.8851 (mt) REVERT: B 1522 MET cc_start: 0.8514 (tpt) cc_final: 0.7685 (tpt) REVERT: C 45 MET cc_start: 0.8300 (tpt) cc_final: 0.8080 (tpt) REVERT: E 1 MET cc_start: 0.2338 (mmm) cc_final: 0.1149 (mmm) REVERT: E 658 MET cc_start: 0.7653 (ppp) cc_final: 0.7317 (ptp) REVERT: E 668 PHE cc_start: 0.8720 (m-10) cc_final: 0.8476 (m-80) REVERT: E 671 ASP cc_start: 0.9197 (m-30) cc_final: 0.8868 (t0) REVERT: E 802 MET cc_start: 0.7524 (ppp) cc_final: 0.6800 (ppp) REVERT: E 958 ILE cc_start: 0.9481 (pt) cc_final: 0.9054 (pt) REVERT: E 1011 MET cc_start: 0.9273 (mmp) cc_final: 0.8915 (mmm) REVERT: E 1090 MET cc_start: 0.8482 (tpt) cc_final: 0.8193 (tpt) REVERT: E 1243 TYR cc_start: 0.8371 (m-80) cc_final: 0.7771 (m-80) REVERT: E 1522 MET cc_start: 0.9045 (mtp) cc_final: 0.8299 (tpt) REVERT: E 1538 TRP cc_start: 0.6812 (p-90) cc_final: 0.6389 (p-90) REVERT: F 6 CYS cc_start: 0.9171 (t) cc_final: 0.8890 (m) REVERT: F 45 MET cc_start: 0.8007 (tpt) cc_final: 0.7705 (tpt) outliers start: 8 outliers final: 2 residues processed: 227 average time/residue: 0.4009 time to fit residues: 155.8382 Evaluate side-chains 171 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 169 time to evaluate : 3.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 108 optimal weight: 0.0770 chunk 100 optimal weight: 5.9990 chunk 341 optimal weight: 2.9990 chunk 296 optimal weight: 5.9990 chunk 378 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN B 278 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1022 ASN ** B1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 ASN B1460 GLN ** B1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 HIS ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 GLN ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1022 ASN E1035 GLN ** E1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.058568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.037688 restraints weight = 268327.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.038352 restraints weight = 201970.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.039221 restraints weight = 156427.706| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33556 Z= 0.148 Angle : 0.654 9.204 45324 Z= 0.336 Chirality : 0.044 0.187 5024 Planarity : 0.005 0.061 5796 Dihedral : 5.204 70.766 4394 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 4022 helix: 0.22 (0.11), residues: 2006 sheet: -1.32 (0.22), residues: 498 loop : -1.07 (0.17), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 102 HIS 0.008 0.001 HIS F 103 PHE 0.019 0.001 PHE E 795 TYR 0.020 0.002 TYR B1388 ARG 0.011 0.001 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 1665) hydrogen bonds : angle 5.33513 ( 4833) covalent geometry : bond 0.00320 (33556) covalent geometry : angle 0.65407 (45324) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 205 time to evaluate : 3.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 ARG cc_start: 0.4896 (tpm170) cc_final: 0.4588 (tpm170) REVERT: B 1 MET cc_start: 0.3070 (mmm) cc_final: 0.1521 (mmm) REVERT: B 158 MET cc_start: 0.8716 (pmm) cc_final: 0.8473 (pmm) REVERT: B 192 LYS cc_start: 0.9330 (tptp) cc_final: 0.9062 (tppt) REVERT: B 243 MET cc_start: -0.1595 (tpt) cc_final: -0.1905 (tpt) REVERT: B 658 MET cc_start: 0.7128 (ppp) cc_final: 0.6729 (ptp) REVERT: B 668 PHE cc_start: 0.8765 (m-80) cc_final: 0.8349 (m-10) REVERT: B 764 PHE cc_start: 0.9482 (m-80) cc_final: 0.9278 (m-80) REVERT: B 860 MET cc_start: 0.9420 (pmm) cc_final: 0.9007 (pmm) REVERT: B 958 ILE cc_start: 0.9573 (pt) cc_final: 0.9241 (pt) REVERT: B 1007 MET cc_start: 0.9359 (ppp) cc_final: 0.9126 (ppp) REVERT: B 1011 MET cc_start: 0.9580 (mmp) cc_final: 0.9308 (mmm) REVERT: B 1243 TYR cc_start: 0.8071 (m-80) cc_final: 0.7465 (m-80) REVERT: B 1522 MET cc_start: 0.8766 (tpt) cc_final: 0.7952 (tpt) REVERT: E 1 MET cc_start: 0.2779 (mmm) cc_final: 0.1555 (mmm) REVERT: E 658 MET cc_start: 0.7642 (ppp) cc_final: 0.7316 (ptp) REVERT: E 668 PHE cc_start: 0.8737 (m-10) cc_final: 0.8478 (m-80) REVERT: E 929 MET cc_start: 0.8151 (ttt) cc_final: 0.7903 (ttt) REVERT: E 958 ILE cc_start: 0.9501 (pt) cc_final: 0.9063 (pt) REVERT: E 964 MET cc_start: 0.8065 (mmm) cc_final: 0.7688 (tpp) REVERT: E 1011 MET cc_start: 0.9458 (mmp) cc_final: 0.9048 (mmm) REVERT: E 1243 TYR cc_start: 0.8628 (m-80) cc_final: 0.8023 (m-80) REVERT: E 1597 MET cc_start: 0.9129 (mmp) cc_final: 0.8412 (ttp) REVERT: F 6 CYS cc_start: 0.9121 (t) cc_final: 0.8823 (m) REVERT: F 45 MET cc_start: 0.7865 (tpt) cc_final: 0.7567 (tpt) outliers start: 3 outliers final: 1 residues processed: 208 average time/residue: 0.4031 time to fit residues: 144.6106 Evaluate side-chains 164 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 3.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 343 optimal weight: 0.6980 chunk 301 optimal weight: 3.9990 chunk 394 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 246 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1281 HIS C 2 GLN C 103 HIS ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 HIS ** E 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1045 ASN ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1526 ASN F 103 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.059183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.037866 restraints weight = 263321.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.038379 restraints weight = 197935.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.038425 restraints weight = 161879.313| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33556 Z= 0.130 Angle : 0.646 8.432 45324 Z= 0.327 Chirality : 0.043 0.163 5024 Planarity : 0.005 0.065 5796 Dihedral : 5.104 69.922 4394 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.22 % Allowed : 3.22 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 4022 helix: 0.38 (0.11), residues: 2000 sheet: -1.35 (0.22), residues: 516 loop : -1.06 (0.17), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 102 HIS 0.015 0.001 HIS B 971 PHE 0.027 0.001 PHE E 798 TYR 0.019 0.001 TYR B1388 ARG 0.016 0.001 ARG B 534 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 1665) hydrogen bonds : angle 5.22746 ( 4833) covalent geometry : bond 0.00278 (33556) covalent geometry : angle 0.64578 (45324) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 3.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 ARG cc_start: 0.4891 (tpm170) cc_final: 0.4574 (tpm170) REVERT: B 1 MET cc_start: 0.2906 (mmm) cc_final: 0.1680 (mmm) REVERT: B 668 PHE cc_start: 0.8710 (m-80) cc_final: 0.8282 (m-10) REVERT: B 764 PHE cc_start: 0.9451 (m-80) cc_final: 0.9242 (m-80) REVERT: B 860 MET cc_start: 0.9337 (pmm) cc_final: 0.9029 (pmm) REVERT: B 929 MET cc_start: 0.7655 (ttt) cc_final: 0.7252 (ttt) REVERT: B 958 ILE cc_start: 0.9521 (pt) cc_final: 0.9251 (pt) REVERT: B 964 MET cc_start: 0.7772 (mmm) cc_final: 0.7156 (tpp) REVERT: B 971 HIS cc_start: 0.8266 (m-70) cc_final: 0.7982 (m90) REVERT: B 1011 MET cc_start: 0.9342 (mmp) cc_final: 0.9072 (mmp) REVERT: B 1231 TYR cc_start: 0.7764 (m-10) cc_final: 0.7506 (m-80) REVERT: B 1243 TYR cc_start: 0.8108 (m-80) cc_final: 0.7435 (m-80) REVERT: B 1522 MET cc_start: 0.8708 (tpt) cc_final: 0.7922 (tpt) REVERT: C 45 MET cc_start: 0.7961 (tpt) cc_final: 0.7566 (tpt) REVERT: D 692 MET cc_start: 0.7973 (mmm) cc_final: 0.7717 (mmm) REVERT: E 1 MET cc_start: 0.1821 (mmm) cc_final: 0.0786 (mmm) REVERT: E 353 MET cc_start: 0.5756 (mpp) cc_final: 0.4991 (mpp) REVERT: E 658 MET cc_start: 0.7716 (ppp) cc_final: 0.7421 (ptp) REVERT: E 958 ILE cc_start: 0.9477 (pt) cc_final: 0.9083 (pt) REVERT: E 964 MET cc_start: 0.7952 (mmm) cc_final: 0.7725 (mmm) REVERT: E 1011 MET cc_start: 0.9440 (mmp) cc_final: 0.9002 (mmm) REVERT: E 1090 MET cc_start: 0.8598 (tpt) cc_final: 0.8349 (tpt) REVERT: E 1231 TYR cc_start: 0.8204 (m-10) cc_final: 0.7881 (m-10) REVERT: E 1243 TYR cc_start: 0.8598 (m-80) cc_final: 0.7867 (m-80) REVERT: E 1597 MET cc_start: 0.9043 (mmp) cc_final: 0.8269 (ttp) outliers start: 8 outliers final: 3 residues processed: 211 average time/residue: 0.4064 time to fit residues: 147.0178 Evaluate side-chains 165 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 162 time to evaluate : 3.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 130 optimal weight: 0.0470 chunk 167 optimal weight: 6.9990 chunk 316 optimal weight: 7.9990 chunk 303 optimal weight: 7.9990 chunk 358 optimal weight: 0.9980 chunk 338 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 397 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 264 optimal weight: 20.0000 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1022 ASN ** B1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 HIS ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS ** F 141 GLN ** 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 = 0.3784 r_free = 0.3784 target = 0.059389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.038085 restraints weight = 262893.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.038860 restraints weight = 197976.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.038682 restraints weight = 154057.093| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33556 Z= 0.125 Angle : 0.647 9.071 45324 Z= 0.330 Chirality : 0.043 0.175 5024 Planarity : 0.004 0.062 5796 Dihedral : 4.989 68.399 4394 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 4022 helix: 0.45 (0.11), residues: 1996 sheet: -1.29 (0.21), residues: 528 loop : -0.98 (0.17), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 102 HIS 0.010 0.001 HIS B 971 PHE 0.011 0.001 PHE C 90 TYR 0.016 0.001 TYR B 585 ARG 0.013 0.000 ARG E 534 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 1665) hydrogen bonds : angle 5.18273 ( 4833) covalent geometry : bond 0.00270 (33556) covalent geometry : angle 0.64664 (45324) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 3.803 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: B 1 MET cc_start: 0.2996 (mmm) cc_final: 0.1831 (mmm) REVERT: B 158 MET cc_start: 0.8611 (pmm) cc_final: 0.8277 (pmm) REVERT: B 668 PHE cc_start: 0.8702 (m-80) cc_final: 0.8277 (m-10) REVERT: B 764 PHE cc_start: 0.9488 (m-80) cc_final: 0.9286 (m-80) REVERT: B 958 ILE cc_start: 0.9496 (pt) cc_final: 0.9208 (pt) REVERT: B 1007 MET cc_start: 0.8974 (ppp) cc_final: 0.8577 (ppp) REVERT: B 1011 MET cc_start: 0.9209 (mmp) cc_final: 0.8911 (mmm) REVERT: B 1231 TYR cc_start: 0.7694 (m-10) cc_final: 0.7442 (m-80) REVERT: B 1243 TYR cc_start: 0.8243 (m-80) cc_final: 0.7639 (m-80) REVERT: B 1522 MET cc_start: 0.8844 (tpt) cc_final: 0.8063 (tpt) REVERT: C 45 MET cc_start: 0.8072 (tpt) cc_final: 0.7655 (tpt) REVERT: E 1 MET cc_start: 0.1992 (mmm) cc_final: 0.0922 (mmm) REVERT: E 658 MET cc_start: 0.7733 (ppp) cc_final: 0.7384 (ptp) REVERT: E 958 ILE cc_start: 0.9466 (pt) cc_final: 0.9083 (pt) REVERT: E 1011 MET cc_start: 0.9377 (mmp) cc_final: 0.8986 (mmm) REVERT: E 1243 TYR cc_start: 0.8696 (m-80) cc_final: 0.7995 (m-80) REVERT: E 1597 MET cc_start: 0.9013 (mmp) cc_final: 0.8348 (mtp) REVERT: F 45 MET cc_start: 0.7691 (tpt) cc_final: 0.7319 (tpt) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.4395 time to fit residues: 156.7963 Evaluate side-chains 168 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 3.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 258 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 228 optimal weight: 0.9980 chunk 145 optimal weight: 0.5980 chunk 325 optimal weight: 0.2980 chunk 51 optimal weight: 6.9990 chunk 201 optimal weight: 0.0370 chunk 43 optimal weight: 7.9990 chunk 329 optimal weight: 8.9990 chunk 35 optimal weight: 0.1980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1133 GLN ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1517 ASN E1526 ASN E1565 ASN F 103 HIS ** F 141 GLN ** 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 = 0.3794 r_free = 0.3794 target = 0.059822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.038371 restraints weight = 268359.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.039594 restraints weight = 204861.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.039135 restraints weight = 149214.319| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33556 Z= 0.120 Angle : 0.637 8.111 45324 Z= 0.321 Chirality : 0.043 0.163 5024 Planarity : 0.005 0.069 5796 Dihedral : 4.916 67.073 4394 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.13), residues: 4022 helix: 0.54 (0.12), residues: 1998 sheet: -1.15 (0.21), residues: 528 loop : -0.93 (0.17), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 102 HIS 0.009 0.001 HIS F 103 PHE 0.029 0.001 PHE E 798 TYR 0.016 0.001 TYR B 585 ARG 0.011 0.000 ARG E 534 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 1665) hydrogen bonds : angle 5.05702 ( 4833) covalent geometry : bond 0.00257 (33556) covalent geometry : angle 0.63663 (45324) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 3.987 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: B 1 MET cc_start: 0.3503 (mmm) cc_final: 0.2250 (mmm) REVERT: B 158 MET cc_start: 0.8667 (pmm) cc_final: 0.8361 (pmm) REVERT: B 267 MET cc_start: 0.4791 (mmp) cc_final: 0.4408 (mmm) REVERT: B 668 PHE cc_start: 0.8689 (m-80) cc_final: 0.8284 (m-10) REVERT: B 764 PHE cc_start: 0.9455 (m-80) cc_final: 0.9251 (m-80) REVERT: B 860 MET cc_start: 0.9272 (pmm) cc_final: 0.8757 (pmm) REVERT: B 958 ILE cc_start: 0.9432 (pt) cc_final: 0.9197 (pt) REVERT: B 1231 TYR cc_start: 0.7530 (m-10) cc_final: 0.7301 (m-80) REVERT: B 1243 TYR cc_start: 0.8315 (m-80) cc_final: 0.7755 (m-80) REVERT: B 1408 MET cc_start: 0.6918 (pmm) cc_final: 0.6597 (pmm) REVERT: B 1522 MET cc_start: 0.8846 (tpt) cc_final: 0.8048 (tpt) REVERT: E 1 MET cc_start: 0.2586 (mmm) cc_final: 0.1650 (mmm) REVERT: E 158 MET cc_start: 0.9016 (pmm) cc_final: 0.8807 (pmm) REVERT: E 658 MET cc_start: 0.7690 (ppp) cc_final: 0.7342 (ptp) REVERT: E 929 MET cc_start: 0.8152 (ttt) cc_final: 0.7709 (ttt) REVERT: E 958 ILE cc_start: 0.9364 (pt) cc_final: 0.9032 (pt) REVERT: E 964 MET cc_start: 0.7876 (mmm) cc_final: 0.7631 (tpp) REVERT: E 987 MET cc_start: 0.8420 (tmm) cc_final: 0.8154 (tmm) REVERT: E 1007 MET cc_start: 0.9021 (ppp) cc_final: 0.8616 (ppp) REVERT: E 1011 MET cc_start: 0.9158 (mmp) cc_final: 0.8769 (mmm) REVERT: E 1090 MET cc_start: 0.8311 (tpt) cc_final: 0.8041 (tpt) REVERT: E 1243 TYR cc_start: 0.8629 (m-80) cc_final: 0.7921 (m-80) REVERT: E 1522 MET cc_start: 0.8585 (ttt) cc_final: 0.7748 (tpt) REVERT: E 1597 MET cc_start: 0.8953 (mmp) cc_final: 0.8209 (mtp) REVERT: F 45 MET cc_start: 0.7465 (tpt) cc_final: 0.7251 (tpt) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.4051 time to fit residues: 149.2519 Evaluate side-chains 167 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 3.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 117 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 334 optimal weight: 0.9980 chunk 357 optimal weight: 10.0000 chunk 322 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 293 optimal weight: 20.0000 chunk 161 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 HIS ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.058934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.037835 restraints weight = 272576.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.037504 restraints weight = 199391.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.037818 restraints weight = 187725.568| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 33556 Z= 0.132 Angle : 0.639 8.010 45324 Z= 0.324 Chirality : 0.043 0.183 5024 Planarity : 0.005 0.059 5796 Dihedral : 4.886 64.926 4394 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.13), residues: 4022 helix: 0.53 (0.12), residues: 2002 sheet: -1.17 (0.21), residues: 528 loop : -0.96 (0.17), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 102 HIS 0.014 0.001 HIS B 971 PHE 0.022 0.001 PHE E 798 TYR 0.016 0.001 TYR E1231 ARG 0.014 0.001 ARG F 66 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 1665) hydrogen bonds : angle 5.11976 ( 4833) covalent geometry : bond 0.00287 (33556) covalent geometry : angle 0.63897 (45324) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 3.955 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: B 1 MET cc_start: 0.3124 (mmm) cc_final: 0.1830 (mmm) REVERT: B 158 MET cc_start: 0.8768 (pmm) cc_final: 0.8441 (pmm) REVERT: B 267 MET cc_start: 0.4811 (mmp) cc_final: 0.4475 (mmm) REVERT: B 668 PHE cc_start: 0.8698 (m-80) cc_final: 0.8194 (m-80) REVERT: B 683 MET cc_start: 0.7203 (ppp) cc_final: 0.6984 (ppp) REVERT: B 764 PHE cc_start: 0.9485 (m-80) cc_final: 0.9276 (m-80) REVERT: B 929 MET cc_start: 0.7653 (ttt) cc_final: 0.7365 (ttt) REVERT: B 958 ILE cc_start: 0.9419 (pt) cc_final: 0.9154 (pt) REVERT: B 1007 MET cc_start: 0.8804 (ppp) cc_final: 0.8438 (ppp) REVERT: B 1011 MET cc_start: 0.9076 (mmp) cc_final: 0.8760 (mmm) REVERT: B 1231 TYR cc_start: 0.7500 (m-10) cc_final: 0.7245 (m-80) REVERT: B 1243 TYR cc_start: 0.8235 (m-80) cc_final: 0.7889 (m-80) REVERT: B 1408 MET cc_start: 0.6991 (pmm) cc_final: 0.6762 (pmm) REVERT: B 1522 MET cc_start: 0.8937 (tpt) cc_final: 0.8185 (tpt) REVERT: E 1 MET cc_start: 0.1886 (mmm) cc_final: 0.0850 (mmm) REVERT: E 658 MET cc_start: 0.7805 (ppp) cc_final: 0.7524 (ptp) REVERT: E 668 PHE cc_start: 0.8397 (m-80) cc_final: 0.7966 (m-80) REVERT: E 929 MET cc_start: 0.8134 (ttt) cc_final: 0.7708 (ttt) REVERT: E 958 ILE cc_start: 0.9381 (pt) cc_final: 0.9082 (pt) REVERT: E 1011 MET cc_start: 0.9049 (mmp) cc_final: 0.8803 (mmm) REVERT: E 1243 TYR cc_start: 0.8437 (m-80) cc_final: 0.7913 (m-80) REVERT: E 1522 MET cc_start: 0.8595 (ttt) cc_final: 0.7769 (tpt) REVERT: E 1560 MET cc_start: 0.2419 (ttt) cc_final: 0.2031 (ttt) REVERT: E 1597 MET cc_start: 0.9030 (mmp) cc_final: 0.8382 (mtp) REVERT: F 45 MET cc_start: 0.7369 (tpt) cc_final: 0.7115 (tpt) REVERT: F 177 LEU cc_start: 0.7589 (mt) cc_final: 0.7387 (pp) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.4053 time to fit residues: 145.6343 Evaluate side-chains 169 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 3.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 24 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 285 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 357 optimal weight: 10.0000 chunk 364 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 chunk 83 optimal weight: 0.0470 chunk 57 optimal weight: 7.9990 chunk 203 optimal weight: 20.0000 chunk 367 optimal weight: 10.0000 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1022 ASN ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.059241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.038390 restraints weight = 271673.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.038948 restraints weight = 213726.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.039981 restraints weight = 155474.467| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33556 Z= 0.126 Angle : 0.663 10.265 45324 Z= 0.336 Chirality : 0.044 0.248 5024 Planarity : 0.005 0.074 5796 Dihedral : 4.873 64.492 4394 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.13), residues: 4022 helix: 0.53 (0.12), residues: 2000 sheet: -1.12 (0.21), residues: 528 loop : -0.93 (0.17), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 102 HIS 0.014 0.001 HIS B 971 PHE 0.025 0.001 PHE E 798 TYR 0.044 0.001 TYR B1328 ARG 0.014 0.001 ARG A 697 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 1665) hydrogen bonds : angle 5.14841 ( 4833) covalent geometry : bond 0.00273 (33556) covalent geometry : angle 0.66317 (45324) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 3.796 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: B 1 MET cc_start: 0.3278 (mmm) cc_final: 0.2057 (mmm) REVERT: B 158 MET cc_start: 0.8580 (pmm) cc_final: 0.7980 (pmm) REVERT: B 192 LYS cc_start: 0.9379 (tptp) cc_final: 0.9142 (tppt) REVERT: B 267 MET cc_start: 0.4957 (mmp) cc_final: 0.4623 (mmm) REVERT: B 668 PHE cc_start: 0.8735 (m-80) cc_final: 0.8186 (m-80) REVERT: B 764 PHE cc_start: 0.9517 (m-80) cc_final: 0.9315 (m-80) REVERT: B 860 MET cc_start: 0.9407 (pmm) cc_final: 0.8952 (pmm) REVERT: B 958 ILE cc_start: 0.9453 (pt) cc_final: 0.9169 (pt) REVERT: B 971 HIS cc_start: 0.8431 (m-70) cc_final: 0.8105 (m90) REVERT: B 1007 MET cc_start: 0.9138 (ppp) cc_final: 0.8651 (ppp) REVERT: B 1011 MET cc_start: 0.9272 (mmp) cc_final: 0.8786 (mmm) REVERT: B 1231 TYR cc_start: 0.7602 (m-10) cc_final: 0.7346 (m-80) REVERT: B 1243 TYR cc_start: 0.8379 (m-80) cc_final: 0.7937 (m-80) REVERT: B 1522 MET cc_start: 0.9060 (tpt) cc_final: 0.8248 (tpt) REVERT: B 1636 HIS cc_start: 0.7416 (t70) cc_final: 0.7199 (t-170) REVERT: C 45 MET cc_start: 0.7635 (tpt) cc_final: 0.7329 (tpt) REVERT: D 692 MET cc_start: 0.8524 (mmm) cc_final: 0.8278 (mmm) REVERT: E 1 MET cc_start: 0.1839 (mmm) cc_final: -0.0151 (mmm) REVERT: E 658 MET cc_start: 0.7723 (ppp) cc_final: 0.7307 (ptp) REVERT: E 668 PHE cc_start: 0.8445 (m-80) cc_final: 0.8028 (m-80) REVERT: E 958 ILE cc_start: 0.9418 (pt) cc_final: 0.9116 (pt) REVERT: E 964 MET cc_start: 0.7578 (tpp) cc_final: 0.7152 (tpp) REVERT: E 1007 MET cc_start: 0.8924 (ppp) cc_final: 0.8650 (ppp) REVERT: E 1011 MET cc_start: 0.9063 (mmp) cc_final: 0.8705 (mmm) REVERT: E 1033 MET cc_start: 0.8160 (mmm) cc_final: 0.7501 (mmm) REVERT: E 1090 MET cc_start: 0.8316 (tpt) cc_final: 0.8094 (tpt) REVERT: E 1243 TYR cc_start: 0.8454 (m-80) cc_final: 0.7902 (m-80) REVERT: E 1522 MET cc_start: 0.8701 (ttt) cc_final: 0.7946 (tpt) REVERT: E 1560 MET cc_start: 0.2487 (ttt) cc_final: 0.2283 (ttt) REVERT: E 1597 MET cc_start: 0.8963 (mmp) cc_final: 0.8339 (mtp) REVERT: F 45 MET cc_start: 0.7437 (tpt) cc_final: 0.7153 (tpt) REVERT: F 177 LEU cc_start: 0.7586 (mt) cc_final: 0.7375 (pp) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.3973 time to fit residues: 143.1136 Evaluate side-chains 167 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 3.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 269 optimal weight: 40.0000 chunk 276 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 371 optimal weight: 2.9990 chunk 226 optimal weight: 0.6980 chunk 254 optimal weight: 0.4980 chunk 103 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 chunk 307 optimal weight: 1.9990 chunk 188 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1022 ASN ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 HIS ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.059572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.038152 restraints weight = 269967.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.039364 restraints weight = 199859.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.039196 restraints weight = 133233.351| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33556 Z= 0.124 Angle : 0.670 11.884 45324 Z= 0.339 Chirality : 0.044 0.206 5024 Planarity : 0.005 0.139 5796 Dihedral : 4.838 63.296 4394 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 4022 helix: 0.55 (0.12), residues: 2000 sheet: -1.08 (0.21), residues: 528 loop : -0.92 (0.17), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 102 HIS 0.012 0.001 HIS B 971 PHE 0.025 0.001 PHE E 798 TYR 0.042 0.001 TYR B1328 ARG 0.023 0.001 ARG E 935 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 1665) hydrogen bonds : angle 5.11076 ( 4833) covalent geometry : bond 0.00265 (33556) covalent geometry : angle 0.67027 (45324) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 3.925 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: B 1 MET cc_start: 0.3555 (mmm) cc_final: 0.2410 (mmm) REVERT: B 158 MET cc_start: 0.8771 (pmm) cc_final: 0.8518 (pmm) REVERT: B 267 MET cc_start: 0.5027 (mmp) cc_final: 0.4691 (mmm) REVERT: B 353 MET cc_start: 0.5193 (mpp) cc_final: 0.4571 (mtt) REVERT: B 668 PHE cc_start: 0.8740 (m-80) cc_final: 0.8219 (m-80) REVERT: B 764 PHE cc_start: 0.9461 (m-80) cc_final: 0.9258 (m-80) REVERT: B 860 MET cc_start: 0.9273 (pmm) cc_final: 0.8847 (pmm) REVERT: B 958 ILE cc_start: 0.9433 (pt) cc_final: 0.9123 (pt) REVERT: B 964 MET cc_start: 0.6907 (tpp) cc_final: 0.6551 (tpp) REVERT: B 1007 MET cc_start: 0.8959 (ppp) cc_final: 0.8696 (ppp) REVERT: B 1231 TYR cc_start: 0.7762 (m-10) cc_final: 0.7519 (m-80) REVERT: B 1243 TYR cc_start: 0.8487 (m-80) cc_final: 0.8047 (m-80) REVERT: B 1522 MET cc_start: 0.8952 (tpt) cc_final: 0.8123 (tpt) REVERT: C 45 MET cc_start: 0.7532 (tpt) cc_final: 0.7074 (tpt) REVERT: D 692 MET cc_start: 0.8600 (mmm) cc_final: 0.8313 (mmm) REVERT: E 1 MET cc_start: 0.2694 (mmm) cc_final: 0.0630 (mmm) REVERT: E 658 MET cc_start: 0.7832 (ppp) cc_final: 0.7419 (ptp) REVERT: E 668 PHE cc_start: 0.8436 (m-80) cc_final: 0.8048 (m-80) REVERT: E 958 ILE cc_start: 0.9368 (pt) cc_final: 0.9058 (pt) REVERT: E 964 MET cc_start: 0.7506 (tpp) cc_final: 0.7178 (tpp) REVERT: E 1007 MET cc_start: 0.8950 (ppp) cc_final: 0.8658 (ppp) REVERT: E 1011 MET cc_start: 0.9228 (mmp) cc_final: 0.8907 (mmm) REVERT: E 1033 MET cc_start: 0.8201 (mmm) cc_final: 0.7653 (mmm) REVERT: E 1243 TYR cc_start: 0.8504 (m-80) cc_final: 0.7967 (m-80) REVERT: E 1560 MET cc_start: 0.2864 (ttt) cc_final: 0.2649 (ttt) REVERT: E 1597 MET cc_start: 0.8912 (mmp) cc_final: 0.8226 (mtp) REVERT: F 45 MET cc_start: 0.7413 (tpt) cc_final: 0.7197 (tpt) REVERT: F 177 LEU cc_start: 0.7659 (mt) cc_final: 0.7431 (pp) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.4201 time to fit residues: 153.2566 Evaluate side-chains 165 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 4.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 173 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 284 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 396 optimal weight: 10.0000 chunk 373 optimal weight: 0.1980 chunk 93 optimal weight: 9.9990 chunk 377 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.059146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.037185 restraints weight = 264251.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.037925 restraints weight = 193142.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.038368 restraints weight = 155909.317| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33556 Z= 0.126 Angle : 0.655 10.793 45324 Z= 0.332 Chirality : 0.043 0.217 5024 Planarity : 0.005 0.100 5796 Dihedral : 4.797 62.171 4394 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.13), residues: 4022 helix: 0.56 (0.12), residues: 1998 sheet: -1.06 (0.21), residues: 522 loop : -0.89 (0.17), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 102 HIS 0.011 0.001 HIS B 971 PHE 0.020 0.001 PHE E 798 TYR 0.038 0.001 TYR B1328 ARG 0.021 0.001 ARG B 534 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 1665) hydrogen bonds : angle 5.08914 ( 4833) covalent geometry : bond 0.00275 (33556) covalent geometry : angle 0.65493 (45324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12061.66 seconds wall clock time: 212 minutes 2.30 seconds (12722.30 seconds total)