Starting phenix.real_space_refine on Sat Jun 28 16:35:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zji_60146/06_2025/8zji_60146.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zji_60146/06_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_60146/06_2025/8zji_60146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zji_60146/06_2025/8zji_60146.map" model { file = "/net/cci-nas-00/data/ceres_data/8zji_60146/06_2025/8zji_60146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zji_60146/06_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): 1.41s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 20.57, per 1000 atoms: 0.63 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: 9.09 Conformation dependent library (CDL) restraints added in 4.4 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: 5.00 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: 15.36 Time building geometry restraints manager: 10.59 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: 0.17 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: 3.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.420 Check model and map are aligned: 0.280 Set scattering table: 0.360 Process input model: 78.860 Find NCS groups from input model: 0.640 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: 0.000 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.910 ------------------------------------------------------------------------------- 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 : 3.963 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: 0.4152 time to fit residues: 153.2344 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 : 3.933 ------------------------------------------------------------------------------- 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 ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.059533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.037912 restraints weight = 261765.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.037935 restraints weight = 196116.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.038174 restraints weight = 158051.279| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1400 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= 0.148 Angle : 0.692 11.597 45324 Z= 0.356 Chirality : 0.044 0.238 5024 Planarity : 0.005 0.067 5796 Dihedral : 5.454 77.458 4394 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.33 % Allowed : 6.42 % Favored : 93.26 % 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 0.018 0.001 HIS E1545 PHE 0.025 0.002 PHE B 777 TYR 0.036 0.002 TYR B1388 ARG 0.008 0.001 ARG E1390 Details of bonding type rmsd hydrogen bonds : bond 0.04753 ( 1665) hydrogen bonds : angle 5.66060 ( 4833) covalent geometry : bond 0.00316 (33556) covalent geometry : angle 0.69188 (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 : 4.265 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: 0.4691 (tpm170) cc_final: 0.4447 (tpm170) REVERT: B 1 MET cc_start: 0.2872 (mmm) cc_final: 0.1644 (mmm) REVERT: B 185 LYS cc_start: 0.9460 (ptmt) cc_final: 0.9161 (ptmm) REVERT: B 192 LYS cc_start: 0.9347 (tptp) cc_final: 0.9075 (tppt) REVERT: B 243 MET cc_start: -0.1169 (tpt) cc_final: -0.2019 (ttp) REVERT: B 683 MET cc_start: 0.7274 (ppp) cc_final: 0.7056 (ppp) REVERT: B 764 PHE cc_start: 0.9465 (m-80) cc_final: 0.9263 (m-80) REVERT: B 958 ILE cc_start: 0.9530 (pt) cc_final: 0.9121 (pt) REVERT: B 971 HIS cc_start: 0.8368 (m90) cc_final: 0.8142 (m-70) REVERT: B 1009 MET cc_start: 0.8762 (mmt) cc_final: 0.8521 (mmt) REVERT: B 1011 MET cc_start: 0.9286 (mmp) cc_final: 0.8898 (mmp) REVERT: B 1243 TYR cc_start: 0.8409 (m-80) cc_final: 0.7708 (m-80) REVERT: B 1522 MET cc_start: 0.8414 (tpt) cc_final: 0.7668 (tpt) REVERT: C 45 MET cc_start: 0.8308 (tpt) cc_final: 0.8008 (tpt) REVERT: D 692 MET cc_start: 0.8642 (mmp) cc_final: 0.8228 (mmm) REVERT: E 1 MET cc_start: 0.1853 (mmm) cc_final: 0.0794 (mmm) REVERT: E 353 MET cc_start: 0.5569 (mpp) cc_final: 0.4689 (mpp) REVERT: E 658 MET cc_start: 0.7103 (ppp) cc_final: 0.6879 (ptp) REVERT: E 668 PHE cc_start: 0.8793 (m-10) cc_final: 0.8556 (m-80) REVERT: E 671 ASP cc_start: 0.9045 (m-30) cc_final: 0.8776 (t0) REVERT: E 787 PHE cc_start: 0.8775 (t80) cc_final: 0.8514 (t80) REVERT: E 802 MET cc_start: 0.7688 (ppp) cc_final: 0.7150 (ppp) REVERT: E 958 ILE cc_start: 0.9484 (pt) cc_final: 0.9019 (pt) REVERT: E 964 MET cc_start: 0.8242 (mmm) cc_final: 0.8002 (mmm) REVERT: E 1009 MET cc_start: 0.8998 (mmt) cc_final: 0.8710 (mmt) REVERT: E 1011 MET cc_start: 0.9195 (mmp) cc_final: 0.8853 (mmm) REVERT: E 1560 MET cc_start: 0.0648 (ppp) cc_final: -0.0232 (ttp) REVERT: E 1597 MET cc_start: 0.9007 (mmp) cc_final: 0.8224 (ttp) REVERT: F 2 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7858 (pp30) REVERT: F 6 CYS cc_start: 0.9188 (t) cc_final: 0.8893 (m) REVERT: F 45 MET cc_start: 0.7997 (tpt) cc_final: 0.7648 (tpt) outliers start: 12 outliers final: 3 residues processed: 237 average time/residue: 0.4455 time to fit residues: 184.1861 Evaluate side-chains 170 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 166 time to evaluate : 4.158 ------------------------------------------------------------------------------- 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: 0.5980 chunk 306 optimal weight: 6.9990 chunk 286 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 80 optimal weight: 0.0870 chunk 116 optimal weight: 7.9990 chunk 374 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 316 optimal weight: 5.9990 chunk 387 optimal weight: 7.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 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** B1045 ASN B1133 GLN ** B1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1526 ASN B1565 ASN B1636 HIS ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 HIS ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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** E1565 ASN F 103 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.060006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.038253 restraints weight = 270404.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.039028 restraints weight = 197788.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.038849 restraints weight = 154734.715| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 33556 Z= 0.132 Angle : 0.658 12.254 45324 Z= 0.337 Chirality : 0.044 0.212 5024 Planarity : 0.005 0.062 5796 Dihedral : 5.275 75.857 4394 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.25 % Allowed : 3.96 % Favored : 95.79 % 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: -0.81 (0.13), residues: 4022 helix: 0.19 (0.11), residues: 2000 sheet: -1.29 (0.23), residues: 466 loop : -1.12 (0.17), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 102 HIS 0.013 0.001 HIS B1048 PHE 0.030 0.001 PHE E 798 TYR 0.025 0.002 TYR E 740 ARG 0.012 0.001 ARG B 534 Details of bonding type rmsd hydrogen bonds : bond 0.04459 ( 1665) hydrogen bonds : angle 5.40727 ( 4833) covalent geometry : bond 0.00283 (33556) covalent geometry : angle 0.65820 (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 233 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 224 time to evaluate : 3.690 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: 0.4561 (tpm170) cc_final: 0.4296 (tpm170) REVERT: B 1 MET cc_start: 0.2982 (mmm) cc_final: 0.1476 (mmm) REVERT: B 158 MET cc_start: 0.8591 (pmm) cc_final: 0.8328 (pmm) REVERT: B 185 LYS cc_start: 0.9374 (ptmt) cc_final: 0.9066 (ptmm) REVERT: B 192 LYS cc_start: 0.9322 (tptp) cc_final: 0.9065 (tppt) REVERT: B 243 MET cc_start: -0.1428 (tpt) cc_final: -0.2114 (ttp) REVERT: B 764 PHE cc_start: 0.9390 (m-80) cc_final: 0.9176 (m-80) REVERT: B 860 MET cc_start: 0.9254 (pmm) cc_final: 0.8955 (pmm) REVERT: B 958 ILE cc_start: 0.9438 (pt) cc_final: 0.9078 (pt) REVERT: B 971 HIS cc_start: 0.8228 (m90) cc_final: 0.8018 (m-70) REVERT: B 1011 MET cc_start: 0.8817 (mmp) cc_final: 0.8576 (mmm) REVERT: B 1243 TYR cc_start: 0.7901 (m-80) cc_final: 0.7306 (m-80) REVERT: B 1522 MET cc_start: 0.8333 (tpt) cc_final: 0.7546 (tpt) REVERT: C 45 MET cc_start: 0.8285 (tpt) cc_final: 0.8001 (tpt) REVERT: E 1 MET cc_start: 0.2195 (mmm) cc_final: 0.0996 (mmm) REVERT: E 658 MET cc_start: 0.7636 (ppp) cc_final: 0.7312 (ptp) REVERT: E 668 PHE cc_start: 0.8750 (m-10) cc_final: 0.8505 (m-80) REVERT: E 671 ASP cc_start: 0.9190 (m-30) cc_final: 0.8859 (t0) REVERT: E 802 MET cc_start: 0.7444 (ppp) cc_final: 0.6714 (ppp) REVERT: E 958 ILE cc_start: 0.9404 (pt) cc_final: 0.8989 (pt) REVERT: E 1011 MET cc_start: 0.8976 (mmp) cc_final: 0.8725 (mmm) REVERT: E 1090 MET cc_start: 0.8390 (tpt) cc_final: 0.8105 (tpt) REVERT: E 1522 MET cc_start: 0.8966 (mtp) cc_final: 0.8193 (tpt) REVERT: E 1538 TRP cc_start: 0.6741 (p-90) cc_final: 0.6313 (p-90) REVERT: F 6 CYS cc_start: 0.9125 (t) cc_final: 0.8826 (m) REVERT: F 45 MET cc_start: 0.7828 (tpt) cc_final: 0.7569 (tpt) outliers start: 9 outliers final: 2 residues processed: 233 average time/residue: 0.3985 time to fit residues: 159.0832 Evaluate side-chains 173 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 3.654 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 341 optimal weight: 3.9990 chunk 296 optimal weight: 5.9990 chunk 378 optimal weight: 0.7980 chunk 161 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 ** 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 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1022 ASN B1203 ASN B1460 GLN ** B1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1565 ASN ** B1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 HIS ** E 130 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.058452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.037641 restraints weight = 270119.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.038451 restraints weight = 203410.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.038822 restraints weight = 156718.516| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2173 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= 0.154 Angle : 0.658 10.887 45324 Z= 0.339 Chirality : 0.043 0.190 5024 Planarity : 0.005 0.061 5796 Dihedral : 5.200 70.989 4394 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.05 % Allowed : 4.21 % Favored : 95.74 % 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: -0.77 (0.13), residues: 4022 helix: 0.21 (0.11), residues: 2004 sheet: -1.31 (0.22), residues: 498 loop : -1.06 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 102 HIS 0.008 0.001 HIS F 103 PHE 0.020 0.002 PHE E 795 TYR 0.020 0.002 TYR B 972 ARG 0.010 0.001 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 1665) hydrogen bonds : angle 5.33866 ( 4833) covalent geometry : bond 0.00332 (33556) covalent geometry : angle 0.65802 (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 210 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 208 time to evaluate : 4.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 ARG cc_start: 0.4894 (tpm170) cc_final: 0.4602 (tpm170) REVERT: B 1 MET cc_start: 0.3296 (mmm) cc_final: 0.1838 (mmm) REVERT: B 158 MET cc_start: 0.8715 (pmm) cc_final: 0.8458 (pmm) REVERT: B 192 LYS cc_start: 0.9341 (tptp) cc_final: 0.9059 (tppt) REVERT: B 243 MET cc_start: -0.1590 (tpt) cc_final: -0.1907 (tpt) REVERT: B 668 PHE cc_start: 0.8778 (m-80) cc_final: 0.8370 (m-10) REVERT: B 764 PHE cc_start: 0.9467 (m-80) cc_final: 0.9266 (m-80) REVERT: B 802 MET cc_start: 0.6541 (ppp) cc_final: 0.6251 (ppp) REVERT: B 860 MET cc_start: 0.9353 (pmm) cc_final: 0.9000 (pmm) REVERT: B 958 ILE cc_start: 0.9559 (pt) cc_final: 0.9216 (pt) REVERT: B 1011 MET cc_start: 0.9503 (mmp) cc_final: 0.9300 (mmm) REVERT: B 1243 TYR cc_start: 0.8085 (m-80) cc_final: 0.7480 (m-80) REVERT: B 1522 MET cc_start: 0.8712 (tpt) cc_final: 0.7914 (tpt) REVERT: E 1 MET cc_start: 0.3059 (mmm) cc_final: 0.1899 (mmm) REVERT: E 353 MET cc_start: 0.5328 (mpp) cc_final: 0.4396 (mpp) REVERT: E 658 MET cc_start: 0.7637 (ppp) cc_final: 0.7303 (ptp) REVERT: E 668 PHE cc_start: 0.8745 (m-10) cc_final: 0.8457 (m-80) REVERT: E 671 ASP cc_start: 0.9096 (m-30) cc_final: 0.8724 (t0) REVERT: E 929 MET cc_start: 0.8015 (ttt) cc_final: 0.7665 (ttt) REVERT: E 958 ILE cc_start: 0.9501 (pt) cc_final: 0.9070 (pt) REVERT: E 964 MET cc_start: 0.8076 (mmm) cc_final: 0.7691 (tpp) REVERT: E 1011 MET cc_start: 0.9415 (mmp) cc_final: 0.9009 (mmm) REVERT: E 1243 TYR cc_start: 0.8588 (m-80) cc_final: 0.7949 (m-80) REVERT: F 6 CYS cc_start: 0.9145 (t) cc_final: 0.8859 (m) REVERT: F 45 MET cc_start: 0.7892 (tpt) cc_final: 0.7599 (tpt) outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.4280 time to fit residues: 153.9187 Evaluate side-chains 163 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 4.225 ------------------------------------------------------------------------------- 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: 0.9980 chunk 301 optimal weight: 4.9990 chunk 394 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 21 optimal weight: 0.0030 chunk 246 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 160 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- 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 65 HIS ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 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** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 2 GLN C 103 HIS ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 GLN ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 HIS ** 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** ** E1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3769 r_free = 0.3769 target = 0.058701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.037467 restraints weight = 265978.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.038128 restraints weight = 197615.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.038235 restraints weight = 154855.914| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2505 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= 0.139 Angle : 0.652 8.892 45324 Z= 0.331 Chirality : 0.044 0.172 5024 Planarity : 0.005 0.062 5796 Dihedral : 5.125 69.873 4394 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.16 % Allowed : 3.50 % Favored : 96.34 % 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: -0.71 (0.13), residues: 4022 helix: 0.31 (0.11), residues: 2006 sheet: -1.39 (0.22), residues: 516 loop : -1.05 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 102 HIS 0.008 0.001 HIS C 103 PHE 0.026 0.001 PHE E 798 TYR 0.019 0.002 TYR B1388 ARG 0.014 0.001 ARG B 534 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 1665) hydrogen bonds : angle 5.26806 ( 4833) covalent geometry : bond 0.00302 (33556) covalent geometry : angle 0.65212 (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 207 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 201 time to evaluate : 4.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 ARG cc_start: 0.4891 (tpm170) cc_final: 0.4582 (tpm170) REVERT: B 1 MET cc_start: 0.3059 (mmm) cc_final: 0.1649 (mmm) REVERT: B 192 LYS cc_start: 0.9376 (tptp) cc_final: 0.9091 (tppt) REVERT: B 658 MET cc_start: 0.7219 (ppp) cc_final: 0.6837 (ptp) REVERT: B 668 PHE cc_start: 0.8702 (m-80) cc_final: 0.8327 (m-10) REVERT: B 683 MET cc_start: 0.7285 (ppp) cc_final: 0.7075 (ppp) REVERT: B 764 PHE cc_start: 0.9479 (m-80) cc_final: 0.9274 (m-80) REVERT: B 958 ILE cc_start: 0.9539 (pt) cc_final: 0.9262 (pt) REVERT: B 1011 MET cc_start: 0.9437 (mmp) cc_final: 0.9130 (mmp) REVERT: B 1231 TYR cc_start: 0.7806 (m-10) cc_final: 0.7532 (m-80) REVERT: B 1243 TYR cc_start: 0.8096 (m-80) cc_final: 0.7427 (m-80) REVERT: B 1522 MET cc_start: 0.8767 (tpt) cc_final: 0.7982 (tpt) REVERT: C 45 MET cc_start: 0.8006 (tpt) cc_final: 0.7602 (tpt) REVERT: D 692 MET cc_start: 0.8041 (mmm) cc_final: 0.7767 (mmm) REVERT: E 1 MET cc_start: 0.1903 (mmm) cc_final: 0.0883 (mmm) REVERT: E 353 MET cc_start: 0.5596 (mpp) cc_final: 0.4699 (mpp) REVERT: E 658 MET cc_start: 0.7699 (ppp) cc_final: 0.7384 (ptp) REVERT: E 958 ILE cc_start: 0.9488 (pt) cc_final: 0.9081 (pt) REVERT: E 964 MET cc_start: 0.8062 (mmm) cc_final: 0.7799 (mmm) REVERT: E 1011 MET cc_start: 0.9436 (mmp) cc_final: 0.8996 (mmm) REVERT: E 1090 MET cc_start: 0.8523 (tpt) cc_final: 0.8271 (tpt) REVERT: E 1231 TYR cc_start: 0.8247 (m-10) cc_final: 0.8026 (m-10) REVERT: E 1243 TYR cc_start: 0.8589 (m-80) cc_final: 0.7852 (m-80) outliers start: 6 outliers final: 2 residues processed: 207 average time/residue: 0.4304 time to fit residues: 153.7309 Evaluate side-chains 163 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 3.764 ------------------------------------------------------------------------------- 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: 8.9990 chunk 167 optimal weight: 6.9990 chunk 316 optimal weight: 10.0000 chunk 303 optimal weight: 5.9990 chunk 358 optimal weight: 0.8980 chunk 338 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 397 optimal weight: 9.9990 chunk 115 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 264 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** B1022 ASN B1281 HIS ** B1424 GLN ** 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 ** 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** E1045 ASN ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1424 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.058852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.037622 restraints weight = 265212.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.038339 restraints weight = 198782.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.038204 restraints weight = 157430.498| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2770 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= 0.131 Angle : 0.646 8.302 45324 Z= 0.332 Chirality : 0.043 0.177 5024 Planarity : 0.004 0.061 5796 Dihedral : 5.047 68.951 4394 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.03 % Allowed : 2.46 % Favored : 97.52 % 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: -0.63 (0.13), residues: 4022 helix: 0.37 (0.11), residues: 1996 sheet: -1.32 (0.21), residues: 528 loop : -1.00 (0.17), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 102 HIS 0.008 0.001 HIS F 103 PHE 0.024 0.001 PHE E 798 TYR 0.017 0.001 TYR B 585 ARG 0.015 0.001 ARG E 534 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 1665) hydrogen bonds : angle 5.24397 ( 4833) covalent geometry : bond 0.00285 (33556) covalent geometry : angle 0.64612 (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 206 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 3.677 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: 0.4829 (tpm170) cc_final: 0.4570 (tpm170) REVERT: B 1 MET cc_start: 0.2869 (mmm) cc_final: 0.1697 (mmm) REVERT: B 158 MET cc_start: 0.8616 (pmm) cc_final: 0.8296 (pmm) REVERT: B 668 PHE cc_start: 0.8720 (m-80) cc_final: 0.8222 (m-80) REVERT: B 683 MET cc_start: 0.7220 (ppp) cc_final: 0.6978 (ppp) REVERT: B 764 PHE cc_start: 0.9473 (m-80) cc_final: 0.9269 (m-80) REVERT: B 802 MET cc_start: 0.6186 (ppp) cc_final: 0.5899 (ppp) REVERT: B 860 MET cc_start: 0.9338 (pmm) cc_final: 0.8972 (pmm) REVERT: B 958 ILE cc_start: 0.9505 (pt) cc_final: 0.9207 (pt) REVERT: B 971 HIS cc_start: 0.8333 (m90) cc_final: 0.7954 (m-70) REVERT: B 1011 MET cc_start: 0.9248 (mmp) cc_final: 0.9022 (mmp) REVERT: B 1231 TYR cc_start: 0.7743 (m-10) cc_final: 0.7479 (m-80) REVERT: B 1243 TYR cc_start: 0.8140 (m-80) cc_final: 0.7441 (m-80) REVERT: B 1522 MET cc_start: 0.8836 (tpt) cc_final: 0.8056 (tpt) REVERT: C 45 MET cc_start: 0.8030 (tpt) cc_final: 0.7714 (tpt) REVERT: E 1 MET cc_start: 0.1786 (mmm) cc_final: 0.0721 (mmm) REVERT: E 658 MET cc_start: 0.7745 (ppp) cc_final: 0.7399 (ptp) REVERT: E 958 ILE cc_start: 0.9467 (pt) cc_final: 0.9081 (pt) REVERT: E 1011 MET cc_start: 0.9375 (mmp) cc_final: 0.8904 (mmm) REVERT: E 1243 TYR cc_start: 0.8544 (m-80) cc_final: 0.7841 (m-80) REVERT: E 1597 MET cc_start: 0.9034 (mmp) cc_final: 0.8274 (ttp) REVERT: F 45 MET cc_start: 0.7582 (tpt) cc_final: 0.7290 (tpt) outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 0.4092 time to fit residues: 146.1706 Evaluate side-chains 164 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 3.696 ------------------------------------------------------------------------------- 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: 4.9990 chunk 215 optimal weight: 0.9990 chunk 228 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 325 optimal weight: 0.0870 chunk 51 optimal weight: 8.9990 chunk 201 optimal weight: 0.0770 chunk 43 optimal weight: 10.0000 chunk 329 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 ** 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** ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1636 HIS ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 416 ASN ** 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 ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.059486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.038232 restraints weight = 262119.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.038762 restraints weight = 197284.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.038674 restraints weight = 163101.288| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 33556 Z= 0.120 Angle : 0.647 8.558 45324 Z= 0.325 Chirality : 0.043 0.171 5024 Planarity : 0.005 0.063 5796 Dihedral : 4.961 68.201 4394 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: -0.48 (0.13), residues: 4022 helix: 0.51 (0.12), residues: 2004 sheet: -1.22 (0.21), residues: 528 loop : -0.98 (0.17), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 102 HIS 0.009 0.001 HIS F 103 PHE 0.026 0.001 PHE E 798 TYR 0.018 0.001 TYR B1289 ARG 0.013 0.001 ARG E 534 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 1665) hydrogen bonds : angle 5.08507 ( 4833) covalent geometry : bond 0.00257 (33556) covalent geometry : angle 0.64673 (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 211 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 4.296 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: 0.2796 (mmm) cc_final: 0.1359 (mmm) REVERT: B 158 MET cc_start: 0.8661 (pmm) cc_final: 0.8417 (pmm) REVERT: B 267 MET cc_start: 0.4752 (mmp) cc_final: 0.4375 (mmm) REVERT: B 668 PHE cc_start: 0.8694 (m-80) cc_final: 0.8176 (m-10) REVERT: B 683 MET cc_start: 0.7171 (ppp) cc_final: 0.6943 (ppp) REVERT: B 764 PHE cc_start: 0.9439 (m-80) cc_final: 0.9229 (m-80) REVERT: B 802 MET cc_start: 0.6107 (ppp) cc_final: 0.5767 (ppp) REVERT: B 860 MET cc_start: 0.9251 (pmm) cc_final: 0.8755 (pmm) REVERT: B 958 ILE cc_start: 0.9452 (pt) cc_final: 0.9177 (pt) REVERT: B 971 HIS cc_start: 0.8279 (m90) cc_final: 0.8009 (m-70) REVERT: B 1007 MET cc_start: 0.8887 (ppp) cc_final: 0.8474 (ppp) REVERT: B 1011 MET cc_start: 0.9174 (mmp) cc_final: 0.8900 (mmm) REVERT: B 1231 TYR cc_start: 0.7533 (m-10) cc_final: 0.7289 (m-80) REVERT: B 1243 TYR cc_start: 0.8262 (m-80) cc_final: 0.7699 (m-80) REVERT: B 1522 MET cc_start: 0.8775 (tpt) cc_final: 0.8031 (tpt) REVERT: E 1 MET cc_start: 0.1705 (mmm) cc_final: 0.0679 (mmm) REVERT: E 158 MET cc_start: 0.9006 (pmm) cc_final: 0.8802 (pmm) REVERT: E 658 MET cc_start: 0.7768 (ppp) cc_final: 0.7442 (ptp) REVERT: E 929 MET cc_start: 0.8106 (ttt) cc_final: 0.7735 (ttt) REVERT: E 958 ILE cc_start: 0.9430 (pt) cc_final: 0.9064 (pt) REVERT: E 964 MET cc_start: 0.7893 (mmm) cc_final: 0.7648 (tpp) REVERT: E 987 MET cc_start: 0.8461 (tmm) cc_final: 0.8208 (tmm) REVERT: E 1007 MET cc_start: 0.8867 (ppp) cc_final: 0.8412 (ppp) REVERT: E 1011 MET cc_start: 0.9269 (mmp) cc_final: 0.8668 (mmm) REVERT: E 1033 MET cc_start: 0.7547 (mmt) cc_final: 0.7220 (mtp) REVERT: E 1090 MET cc_start: 0.8487 (tpt) cc_final: 0.8269 (tpt) REVERT: E 1231 TYR cc_start: 0.8087 (m-10) cc_final: 0.7716 (m-80) REVERT: E 1243 TYR cc_start: 0.8514 (m-80) cc_final: 0.7878 (m-80) REVERT: E 1597 MET cc_start: 0.8922 (mmp) cc_final: 0.8180 (mtp) REVERT: F 45 MET cc_start: 0.7420 (tpt) cc_final: 0.7199 (tpt) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.4232 time to fit residues: 155.9003 Evaluate side-chains 170 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 4.269 ------------------------------------------------------------------------------- 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: 0.9990 chunk 135 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 334 optimal weight: 1.9990 chunk 357 optimal weight: 0.9980 chunk 322 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 293 optimal weight: 20.0000 chunk 161 optimal weight: 8.9990 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 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** B1281 HIS ** 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 416 ASN ** 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** E1093 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 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.058765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.037510 restraints weight = 273605.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.038396 restraints weight = 205295.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.038317 restraints weight = 156287.768| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3151 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= 0.133 Angle : 0.640 8.320 45324 Z= 0.326 Chirality : 0.043 0.169 5024 Planarity : 0.005 0.075 5796 Dihedral : 4.909 65.794 4394 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: -0.47 (0.13), residues: 4022 helix: 0.51 (0.12), residues: 2002 sheet: -1.22 (0.21), residues: 528 loop : -0.95 (0.17), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 102 HIS 0.009 0.001 HIS C 103 PHE 0.020 0.001 PHE E 798 TYR 0.016 0.001 TYR B1388 ARG 0.012 0.001 ARG C 66 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 1665) hydrogen bonds : angle 5.14952 ( 4833) covalent geometry : bond 0.00292 (33556) covalent geometry : angle 0.64002 (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 201 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 3.830 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: B 1 MET cc_start: 0.2990 (mmm) cc_final: 0.1953 (mmm) REVERT: B 158 MET cc_start: 0.8767 (pmm) cc_final: 0.8450 (pmm) REVERT: B 192 LYS cc_start: 0.9351 (tptp) cc_final: 0.9075 (tppt) REVERT: B 267 MET cc_start: 0.4815 (mmp) cc_final: 0.4454 (mmm) REVERT: B 668 PHE cc_start: 0.8672 (m-80) cc_final: 0.8166 (m-80) REVERT: B 683 MET cc_start: 0.7217 (ppp) cc_final: 0.6967 (ppp) REVERT: B 764 PHE cc_start: 0.9446 (m-80) cc_final: 0.9235 (m-80) REVERT: B 802 MET cc_start: 0.6117 (ppp) cc_final: 0.5750 (ppp) REVERT: B 958 ILE cc_start: 0.9450 (pt) cc_final: 0.9156 (pt) REVERT: B 971 HIS cc_start: 0.8471 (m90) cc_final: 0.8133 (m-70) REVERT: B 1011 MET cc_start: 0.9284 (mmp) cc_final: 0.8971 (mmp) REVERT: B 1231 TYR cc_start: 0.7520 (m-10) cc_final: 0.7245 (m-80) REVERT: B 1243 TYR cc_start: 0.8263 (m-80) cc_final: 0.7895 (m-80) REVERT: B 1522 MET cc_start: 0.8851 (tpt) cc_final: 0.8065 (tpt) REVERT: E 1 MET cc_start: 0.1729 (mmm) cc_final: 0.0676 (mmm) REVERT: E 658 MET cc_start: 0.7759 (ppp) cc_final: 0.7464 (ptp) REVERT: E 668 PHE cc_start: 0.8387 (m-80) cc_final: 0.7967 (m-80) REVERT: E 929 MET cc_start: 0.8189 (ttt) cc_final: 0.7752 (ttt) REVERT: E 958 ILE cc_start: 0.9426 (pt) cc_final: 0.9109 (pt) REVERT: E 1011 MET cc_start: 0.9279 (mmp) cc_final: 0.8896 (mmm) REVERT: E 1033 MET cc_start: 0.7649 (mmt) cc_final: 0.7411 (mtp) REVERT: E 1204 LEU cc_start: 0.9428 (mp) cc_final: 0.9050 (tt) REVERT: E 1243 TYR cc_start: 0.8553 (m-80) cc_final: 0.7945 (m-80) REVERT: E 1313 MET cc_start: 0.7858 (ppp) cc_final: 0.7619 (tmm) REVERT: E 1597 MET cc_start: 0.9009 (mmp) cc_final: 0.8305 (mtp) REVERT: F 45 MET cc_start: 0.7492 (tpt) cc_final: 0.7222 (tpt) REVERT: F 177 LEU cc_start: 0.7587 (mt) cc_final: 0.7348 (pp) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.4179 time to fit residues: 146.3621 Evaluate side-chains 171 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 4.145 ------------------------------------------------------------------------------- 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: 1.9990 chunk 62 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 291 optimal weight: 6.9990 chunk 357 optimal weight: 9.9990 chunk 364 optimal weight: 0.8980 chunk 175 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 203 optimal weight: 20.0000 chunk 367 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.058414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.037360 restraints weight = 265640.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.037578 restraints weight = 200079.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.037749 restraints weight = 167857.804| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3360 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= 0.139 Angle : 0.666 8.875 45324 Z= 0.340 Chirality : 0.044 0.255 5024 Planarity : 0.005 0.060 5796 Dihedral : 4.915 65.516 4394 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: -0.47 (0.13), residues: 4022 helix: 0.48 (0.12), residues: 2000 sheet: -1.19 (0.21), residues: 522 loop : -0.92 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 102 HIS 0.007 0.001 HIS F 103 PHE 0.021 0.001 PHE E 798 TYR 0.021 0.001 TYR D 576 ARG 0.010 0.001 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.03892 ( 1665) hydrogen bonds : angle 5.22271 ( 4833) covalent geometry : bond 0.00301 (33556) covalent geometry : angle 0.66595 (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 204 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 3.824 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: B 1 MET cc_start: 0.2958 (mmm) cc_final: 0.1533 (mmm) REVERT: B 267 MET cc_start: 0.4942 (mmp) cc_final: 0.4601 (mmm) REVERT: B 668 PHE cc_start: 0.8621 (m-80) cc_final: 0.8109 (m-80) REVERT: B 683 MET cc_start: 0.7143 (ppp) cc_final: 0.6892 (ppp) REVERT: B 764 PHE cc_start: 0.9444 (m-80) cc_final: 0.9241 (m-80) REVERT: B 802 MET cc_start: 0.6389 (ppp) cc_final: 0.6047 (ppp) REVERT: B 958 ILE cc_start: 0.9464 (pt) cc_final: 0.9201 (pt) REVERT: B 960 LEU cc_start: 0.9727 (tt) cc_final: 0.9497 (tp) REVERT: B 964 MET cc_start: 0.7744 (mmm) cc_final: 0.6926 (tpp) REVERT: B 1007 MET cc_start: 0.9016 (ppp) cc_final: 0.8566 (ppp) REVERT: B 1011 MET cc_start: 0.9300 (mmp) cc_final: 0.8917 (mmm) REVERT: B 1231 TYR cc_start: 0.7934 (m-10) cc_final: 0.7638 (m-80) REVERT: B 1243 TYR cc_start: 0.8357 (m-80) cc_final: 0.7872 (m-80) REVERT: B 1522 MET cc_start: 0.9016 (tpt) cc_final: 0.8259 (tpt) REVERT: C 45 MET cc_start: 0.7657 (tpt) cc_final: 0.7343 (tpt) REVERT: D 692 MET cc_start: 0.8645 (mmm) cc_final: 0.8353 (mmm) REVERT: E 1 MET cc_start: 0.1750 (mmm) cc_final: -0.0232 (mmm) REVERT: E 658 MET cc_start: 0.7787 (ppp) cc_final: 0.7453 (ptp) REVERT: E 668 PHE cc_start: 0.8495 (m-80) cc_final: 0.8028 (m-80) REVERT: E 958 ILE cc_start: 0.9451 (pt) cc_final: 0.9139 (pt) REVERT: E 1007 MET cc_start: 0.8955 (ppp) cc_final: 0.8515 (ppp) REVERT: E 1011 MET cc_start: 0.9286 (mmp) cc_final: 0.8864 (mmm) REVERT: E 1033 MET cc_start: 0.7710 (mmt) cc_final: 0.7438 (mmm) REVERT: E 1243 TYR cc_start: 0.8665 (m-80) cc_final: 0.8193 (m-80) REVERT: E 1282 LEU cc_start: 0.7234 (mp) cc_final: 0.6547 (pp) REVERT: E 1313 MET cc_start: 0.8062 (ppp) cc_final: 0.7568 (tmm) REVERT: E 1522 MET cc_start: 0.8959 (mtp) cc_final: 0.8694 (tpt) REVERT: E 1597 MET cc_start: 0.9123 (mmp) cc_final: 0.8497 (mtp) REVERT: F 45 MET cc_start: 0.7580 (tpt) cc_final: 0.7339 (tpt) REVERT: F 177 LEU cc_start: 0.7522 (mt) cc_final: 0.7311 (pp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.4223 time to fit residues: 147.6636 Evaluate side-chains 161 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 3.806 ------------------------------------------------------------------------------- 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: 20.0000 chunk 276 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 371 optimal weight: 0.8980 chunk 226 optimal weight: 0.0770 chunk 254 optimal weight: 0.0870 chunk 103 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 307 optimal weight: 1.9990 chunk 188 optimal weight: 9.9990 overall best weight: 0.7918 ------------------------------------------------------------------------------- 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** 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 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 = 0.3778 r_free = 0.3778 target = 0.059065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.038052 restraints weight = 263010.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.038215 restraints weight = 198280.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.038505 restraints weight = 159999.369| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3551 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= 0.127 Angle : 0.679 9.373 45324 Z= 0.345 Chirality : 0.044 0.205 5024 Planarity : 0.005 0.151 5796 Dihedral : 4.891 65.186 4394 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 0.53 (0.12), residues: 1996 sheet: -1.15 (0.21), residues: 522 loop : -0.92 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 102 HIS 0.010 0.001 HIS C 103 PHE 0.032 0.001 PHE E 798 TYR 0.042 0.001 TYR E1328 ARG 0.024 0.001 ARG B 935 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 1665) hydrogen bonds : angle 5.17672 ( 4833) covalent geometry : bond 0.00272 (33556) covalent geometry : angle 0.67910 (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 205 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 3.787 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: B 1 MET cc_start: 0.2816 (mmm) cc_final: 0.1382 (mmm) REVERT: B 158 MET cc_start: 0.8862 (pmm) cc_final: 0.8629 (pmm) REVERT: B 267 MET cc_start: 0.4941 (mmp) cc_final: 0.4599 (mmm) REVERT: B 668 PHE cc_start: 0.8718 (m-80) cc_final: 0.8181 (m-80) REVERT: B 683 MET cc_start: 0.7143 (ppp) cc_final: 0.6915 (ppp) REVERT: B 764 PHE cc_start: 0.9422 (m-80) cc_final: 0.9221 (m-80) REVERT: B 802 MET cc_start: 0.6304 (ppp) cc_final: 0.5939 (ppp) REVERT: B 958 ILE cc_start: 0.9422 (pt) cc_final: 0.9145 (pt) REVERT: B 971 HIS cc_start: 0.8941 (t-90) cc_final: 0.8698 (t-90) REVERT: B 1007 MET cc_start: 0.8927 (ppp) cc_final: 0.8395 (ppp) REVERT: B 1011 MET cc_start: 0.9302 (mmp) cc_final: 0.8934 (mmm) REVERT: B 1105 MET cc_start: 0.7417 (mmp) cc_final: 0.7095 (mmm) REVERT: B 1231 TYR cc_start: 0.7731 (m-10) cc_final: 0.7426 (m-80) REVERT: B 1243 TYR cc_start: 0.8399 (m-80) cc_final: 0.7985 (m-80) REVERT: B 1326 GLU cc_start: 0.7801 (pp20) cc_final: 0.7430 (pp20) REVERT: B 1522 MET cc_start: 0.8931 (tpt) cc_final: 0.8315 (tpt) REVERT: C 45 MET cc_start: 0.7377 (tpt) cc_final: 0.6891 (tpt) REVERT: D 692 MET cc_start: 0.8689 (mmm) cc_final: 0.8407 (mmm) REVERT: E 1 MET cc_start: 0.2006 (mmm) cc_final: -0.0029 (mmm) REVERT: E 658 MET cc_start: 0.7950 (ppp) cc_final: 0.7518 (ptp) REVERT: E 668 PHE cc_start: 0.8394 (m-80) cc_final: 0.7927 (m-80) REVERT: E 958 ILE cc_start: 0.9405 (pt) cc_final: 0.9088 (pt) REVERT: E 1007 MET cc_start: 0.8909 (ppp) cc_final: 0.8600 (ppp) REVERT: E 1011 MET cc_start: 0.9195 (mmp) cc_final: 0.8872 (mmm) REVERT: E 1243 TYR cc_start: 0.8556 (m-80) cc_final: 0.8159 (m-80) REVERT: E 1278 CYS cc_start: 0.5872 (m) cc_final: 0.5525 (p) REVERT: E 1313 MET cc_start: 0.8021 (ppp) cc_final: 0.7459 (tmm) REVERT: E 1522 MET cc_start: 0.8892 (mtp) cc_final: 0.8647 (tpt) REVERT: E 1597 MET cc_start: 0.9056 (mmp) cc_final: 0.8403 (mtp) REVERT: F 45 MET cc_start: 0.7404 (tpt) cc_final: 0.7170 (tpt) REVERT: F 177 LEU cc_start: 0.7547 (mt) cc_final: 0.7300 (pp) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.4063 time to fit residues: 143.6009 Evaluate side-chains 164 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 3.635 ------------------------------------------------------------------------------- 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: 8.9990 chunk 107 optimal weight: 1.9990 chunk 284 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 396 optimal weight: 7.9990 chunk 373 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 377 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 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** B1370 GLN ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1619 HIS ** 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** ** 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 = 0.3761 r_free = 0.3761 target = 0.058181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.036290 restraints weight = 265903.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.036900 restraints weight = 194376.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.037536 restraints weight = 158496.709| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33556 Z= 0.141 Angle : 0.674 9.838 45324 Z= 0.344 Chirality : 0.044 0.219 5024 Planarity : 0.005 0.101 5796 Dihedral : 4.893 64.541 4394 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -0.49 (0.13), residues: 4022 helix: 0.44 (0.12), residues: 2002 sheet: -1.21 (0.21), residues: 522 loop : -0.90 (0.17), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 56 HIS 0.008 0.001 HIS E1636 PHE 0.030 0.001 PHE E 798 TYR 0.044 0.002 TYR E1328 ARG 0.020 0.001 ARG B 534 Details of bonding type rmsd hydrogen bonds : bond 0.03897 ( 1665) hydrogen bonds : angle 5.22358 ( 4833) covalent geometry : bond 0.00306 (33556) covalent geometry : angle 0.67386 (45324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12372.41 seconds wall clock time: 215 minutes 6.96 seconds (12906.96 seconds total)