Starting phenix.real_space_refine on Sat Jun 28 16:03:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjl_60149/06_2025/8zjl_60149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjl_60149/06_2025/8zjl_60149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zjl_60149/06_2025/8zjl_60149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjl_60149/06_2025/8zjl_60149.map" model { file = "/net/cci-nas-00/data/ceres_data/8zjl_60149/06_2025/8zjl_60149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjl_60149/06_2025/8zjl_60149.cif" } resolution = 4.31 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 154 residue(s): 0.70s 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: 17.99, per 1000 atoms: 0.55 Number of scatterers: 32858 At special positions: 0 Unit cell: (242.06, 160.93, 156.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 176 16.00 O 6092 8.00 N 5538 7.00 C 21052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.46 Conformation dependent library (CDL) restraints added in 5.4 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: 162 helices and 20 sheets defined 55.1% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 530 through 540 Processing helix chain 'A' and resid 541 through 559 removed outlier: 3.580A pdb=" N LEU A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 627 Processing helix chain 'A' and resid 634 through 638 Processing helix chain 'A' and resid 658 through 673 Processing helix chain 'A' and resid 679 through 698 Processing helix chain 'B' and resid 84 through 107 removed outlier: 3.563A pdb=" N VAL B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 133 removed outlier: 3.896A 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: 4.155A pdb=" N ILE B 172 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 205 removed outlier: 4.551A pdb=" N LYS B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 270 through 275 removed outlier: 4.596A pdb=" N ASN B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) 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: 3.948A pdb=" N ARG B 360 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 3.951A 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: 3.608A 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 Processing helix chain 'B' and resid 591 through 605 removed outlier: 3.742A pdb=" N LYS B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 605 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 643 through 645 No H-bonds generated for 'chain 'B' and resid 643 through 645' Processing helix chain 'B' and resid 646 through 658 removed outlier: 4.258A pdb=" N LYS B 651 " --> pdb=" O SER B 647 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N HIS B 652 " --> pdb=" O GLN B 648 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 666 Processing helix chain 'B' and resid 668 through 683 removed outlier: 3.505A pdb=" N MET B 683 " --> pdb=" O ILE B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 705 Processing helix chain 'B' and resid 712 through 724 removed outlier: 3.665A pdb=" N PHE B 724 " --> pdb=" O ILE B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 743 removed outlier: 3.790A pdb=" N LYS B 732 " --> pdb=" O LEU B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 759 removed outlier: 4.080A pdb=" N GLU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 759 " --> pdb=" O ALA B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 779 Processing helix chain 'B' and resid 783 through 804 Processing helix chain 'B' and resid 805 through 808 removed outlier: 3.582A 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: 3.989A pdb=" N ILE B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASP B 826 " --> pdb=" O SER B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 846 removed outlier: 3.566A pdb=" N LEU B 836 " --> pdb=" O ASP B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 866 removed outlier: 3.552A pdb=" N SER B 866 " --> pdb=" O LYS B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 889 Proline residue: B 880 - end of helix Processing helix chain 'B' and resid 898 through 915 Processing helix chain 'B' and resid 921 through 943 removed outlier: 6.346A pdb=" N ARG B 934 " --> pdb=" O GLU B 930 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG B 935 " --> pdb=" O ARG B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 964 Processing helix chain 'B' and resid 965 through 972 removed outlier: 4.013A pdb=" N TYR B 972 " --> pdb=" O HIS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 998 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 1055 Processing helix chain 'B' and resid 1065 through 1076 removed outlier: 3.994A pdb=" N ARG B1069 " --> pdb=" O SER B1065 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN B1070 " --> pdb=" O GLN B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1095 removed outlier: 3.934A pdb=" N GLY B1095 " --> pdb=" O TRP B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1098 No H-bonds generated for 'chain 'B' and resid 1096 through 1098' Processing helix chain 'B' and resid 1101 through 1114 removed outlier: 5.141A pdb=" N GLY B1107 " --> pdb=" O PRO B1103 " (cutoff:3.500A) Proline residue: B1108 - end of helix removed outlier: 3.950A pdb=" N GLU B1111 " --> pdb=" O GLY B1107 " (cutoff:3.500A) removed outlier: 4.536A 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: 3.841A pdb=" N PHE B1129 " --> pdb=" O ILE B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1161 removed outlier: 3.615A pdb=" N GLU B1150 " --> pdb=" O MET B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1165 through 1183 removed outlier: 3.616A 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 1255 Processing helix chain 'B' and resid 1256 through 1270 removed outlier: 3.698A pdb=" N LEU B1270 " --> pdb=" O LEU B1266 " (cutoff:3.500A) Processing helix chain 'B' and resid 1292 through 1311 Processing helix chain 'B' and resid 1313 through 1332 removed outlier: 4.038A pdb=" N ALA B1317 " --> pdb=" O MET B1313 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU B1323 " --> pdb=" O LYS B1319 " (cutoff:3.500A) Processing helix chain 'B' and resid 1334 through 1355 Processing helix chain 'B' and resid 1390 through 1402 Processing helix chain 'B' and resid 1447 through 1455 removed outlier: 3.891A pdb=" N LEU B1451 " --> pdb=" O PRO B1447 " (cutoff:3.500A) Processing helix chain 'B' and resid 1477 through 1481 removed outlier: 3.773A pdb=" N THR B1481 " --> pdb=" O GLU B1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 1513 through 1539 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 Processing helix chain 'B' and resid 1580 through 1584 removed outlier: 3.834A 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: 4.015A pdb=" N LEU B1618 " --> pdb=" O GLN B1614 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 26 removed outlier: 3.694A pdb=" N LEU C 19 " --> pdb=" O ALA C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.744A pdb=" N SER C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) 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 122 removed outlier: 3.652A 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: 3.866A pdb=" N GLY C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 removed outlier: 4.020A pdb=" N VAL C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 540 Processing helix chain 'D' and resid 541 through 559 removed outlier: 3.580A pdb=" N LEU D 545 " --> pdb=" O GLN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 627 Processing helix chain 'D' and resid 634 through 638 Processing helix chain 'D' and resid 658 through 673 Processing helix chain 'D' and resid 679 through 698 Processing helix chain 'E' and resid 84 through 107 removed outlier: 3.564A pdb=" N VAL E 88 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 133 removed outlier: 3.896A 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: 4.155A pdb=" N ILE E 172 " --> pdb=" O ASN E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 205 removed outlier: 4.550A pdb=" N LYS E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER E 203 " --> pdb=" O GLN E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 217 Processing helix chain 'E' and resid 270 through 275 removed outlier: 4.597A pdb=" N ASN E 275 " --> pdb=" O ILE E 271 " (cutoff:3.500A) 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: 3.947A pdb=" N ARG E 360 " --> pdb=" O ILE E 357 " (cutoff:3.500A) removed outlier: 3.951A 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: 3.609A 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 Processing helix chain 'E' and resid 591 through 605 removed outlier: 3.742A pdb=" N LYS E 604 " --> pdb=" O LEU E 600 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN E 605 " --> pdb=" O GLN E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 642 Processing helix chain 'E' and resid 643 through 645 No H-bonds generated for 'chain 'E' and resid 643 through 645' Processing helix chain 'E' and resid 646 through 658 removed outlier: 4.259A pdb=" N LYS E 651 " --> pdb=" O SER E 647 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N HIS E 652 " --> pdb=" O GLN E 648 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET E 658 " --> pdb=" O LEU E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 661 through 666 Processing helix chain 'E' and resid 668 through 683 removed outlier: 3.504A pdb=" N MET E 683 " --> pdb=" O ILE E 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 686 through 705 Processing helix chain 'E' and resid 712 through 724 removed outlier: 3.665A pdb=" N PHE E 724 " --> pdb=" O ILE E 720 " (cutoff:3.500A) Processing helix chain 'E' and resid 728 through 743 removed outlier: 3.790A pdb=" N LYS E 732 " --> pdb=" O LEU E 728 " (cutoff:3.500A) Processing helix chain 'E' and resid 746 through 759 removed outlier: 4.080A pdb=" N GLU E 751 " --> pdb=" O SER E 747 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA E 759 " --> pdb=" O ALA E 755 " (cutoff:3.500A) Processing helix chain 'E' and resid 759 through 779 Processing helix chain 'E' and resid 783 through 804 Processing helix chain 'E' and resid 805 through 808 removed outlier: 3.582A 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: 3.988A pdb=" N ILE E 824 " --> pdb=" O LEU E 820 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN E 825 " --> pdb=" O PRO E 821 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASP E 826 " --> pdb=" O SER E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 832 through 846 removed outlier: 3.566A pdb=" N LEU E 836 " --> pdb=" O ASP E 832 " (cutoff:3.500A) Processing helix chain 'E' and resid 852 through 866 removed outlier: 3.551A pdb=" N SER E 866 " --> pdb=" O LYS E 862 " (cutoff:3.500A) Processing helix chain 'E' and resid 874 through 889 Proline residue: E 880 - end of helix Processing helix chain 'E' and resid 898 through 915 Processing helix chain 'E' and resid 921 through 943 removed outlier: 6.345A pdb=" N ARG E 934 " --> pdb=" O GLU E 930 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG E 935 " --> pdb=" O ARG E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 949 through 964 Processing helix chain 'E' and resid 965 through 972 removed outlier: 4.013A pdb=" N TYR E 972 " --> pdb=" O HIS E 968 " (cutoff:3.500A) Processing helix chain 'E' and resid 978 through 998 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 1055 Processing helix chain 'E' and resid 1065 through 1076 removed outlier: 3.995A pdb=" N ARG E1069 " --> pdb=" O SER E1065 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN E1070 " --> pdb=" O GLN E1066 " (cutoff:3.500A) Processing helix chain 'E' and resid 1078 through 1095 removed outlier: 3.935A pdb=" N GLY E1095 " --> pdb=" O TRP E1091 " (cutoff:3.500A) Processing helix chain 'E' and resid 1096 through 1098 No H-bonds generated for 'chain 'E' and resid 1096 through 1098' Processing helix chain 'E' and resid 1101 through 1114 removed outlier: 5.141A pdb=" N GLY E1107 " --> pdb=" O PRO E1103 " (cutoff:3.500A) Proline residue: E1108 - end of helix removed outlier: 3.950A pdb=" N GLU E1111 " --> pdb=" O GLY E1107 " (cutoff:3.500A) removed outlier: 4.535A 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: 3.841A pdb=" N PHE E1129 " --> pdb=" O ILE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1144 through 1161 removed outlier: 3.615A pdb=" N GLU E1150 " --> pdb=" O MET E1146 " (cutoff:3.500A) Processing helix chain 'E' and resid 1165 through 1183 removed outlier: 3.616A 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 1255 Processing helix chain 'E' and resid 1256 through 1270 removed outlier: 3.698A pdb=" N LEU E1270 " --> pdb=" O LEU E1266 " (cutoff:3.500A) Processing helix chain 'E' and resid 1292 through 1311 Processing helix chain 'E' and resid 1313 through 1332 removed outlier: 4.037A pdb=" N ALA E1317 " --> pdb=" O MET E1313 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU E1323 " --> pdb=" O LYS E1319 " (cutoff:3.500A) Processing helix chain 'E' and resid 1334 through 1355 Processing helix chain 'E' and resid 1390 through 1402 Processing helix chain 'E' and resid 1447 through 1455 removed outlier: 3.891A pdb=" N LEU E1451 " --> pdb=" O PRO E1447 " (cutoff:3.500A) Processing helix chain 'E' and resid 1477 through 1481 removed outlier: 3.773A pdb=" N THR E1481 " --> pdb=" O GLU E1478 " (cutoff:3.500A) Processing helix chain 'E' and resid 1513 through 1539 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 Processing helix chain 'E' and resid 1580 through 1584 removed outlier: 3.834A 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: 4.015A pdb=" N LEU E1618 " --> pdb=" O GLN E1614 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 26 removed outlier: 3.694A pdb=" N LEU F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 66 Processing helix chain 'F' and resid 67 through 72 removed outlier: 3.744A pdb=" N SER F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) 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 122 removed outlier: 3.653A 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: 3.866A pdb=" N GLY F 142 " --> pdb=" O THR F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 177 removed outlier: 4.021A pdb=" N VAL F 176 " --> pdb=" O ALA F 172 " (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 35 through 40 removed outlier: 3.939A pdb=" N ILE B 37 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR B 48 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 252 through 253 Processing sheet with id=AA6, first strand: chain 'B' and resid 252 through 253 removed outlier: 3.536A pdb=" N VAL B 301 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ARG B 302 " --> pdb=" O PRO B 321 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY B 304 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ARG B 319 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL B 326 " --> pdb=" O PRO B 347 " (cutoff:3.500A) removed outlier: 9.441A pdb=" N ASP B 328 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 10.856A pdb=" N PHE B 345 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY B 398 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N PHE B 231 " --> pdb=" O GLY B 398 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TRP B 400 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TYR B 222 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP B 283 " --> pdb=" O TYR B 222 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 484 through 485 removed outlier: 3.671A pdb=" N GLU B 511 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 451 " --> pdb=" O GLN B 621 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLN B 621 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLY B 453 " --> pdb=" O SER B 619 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER B 619 " --> pdb=" O GLY B 453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 495 through 496 removed outlier: 3.703A pdb=" N THR B 530 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY B 548 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1425 through 1430 removed outlier: 6.240A pdb=" N ILE B1380 " --> pdb=" O VAL B1504 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N PHE B1502 " --> pdb=" O THR B1494 " (cutoff:3.500A) removed outlier: 9.776A pdb=" N THR B1494 " --> pdb=" O PHE B1502 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N VAL B1504 " --> pdb=" O ALA B1492 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA B1492 " --> pdb=" O VAL B1504 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN B1460 " --> pdb=" O THR B1491 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 44 removed outlier: 7.161A pdb=" N CYS C 6 " --> pdb=" O TRP C 56 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LYS C 5 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU C 79 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL C 7 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N CYS C 81 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL C 9 " --> pdb=" O CYS C 81 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE C 111 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE C 110 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N LEU C 155 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU C 112 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 561 through 563 Processing sheet with id=AB3, first strand: chain 'D' and resid 578 through 579 Processing sheet with id=AB4, first strand: chain 'D' and resid 616 through 618 Processing sheet with id=AB5, first strand: chain 'E' and resid 35 through 40 removed outlier: 3.939A pdb=" N ILE E 37 " --> pdb=" O TYR E 48 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N TYR E 48 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 252 through 253 Processing sheet with id=AB7, first strand: chain 'E' and resid 252 through 253 removed outlier: 3.536A pdb=" N VAL E 301 " --> pdb=" O GLU E 240 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ARG E 302 " --> pdb=" O PRO E 321 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY E 304 " --> pdb=" O ARG E 319 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ARG E 319 " --> pdb=" O GLY E 304 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL E 326 " --> pdb=" O PRO E 347 " (cutoff:3.500A) removed outlier: 9.441A pdb=" N ASP E 328 " --> pdb=" O PHE E 345 " (cutoff:3.500A) removed outlier: 10.856A pdb=" N PHE E 345 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY E 398 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N PHE E 231 " --> pdb=" O GLY E 398 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TRP E 400 " --> pdb=" O LYS E 229 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TYR E 222 " --> pdb=" O ASP E 283 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP E 283 " --> pdb=" O TYR E 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 484 through 485 removed outlier: 3.671A pdb=" N GLU E 511 " --> pdb=" O LEU E 450 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE E 451 " --> pdb=" O GLN E 621 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLN E 621 " --> pdb=" O ILE E 451 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLY E 453 " --> pdb=" O SER E 619 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER E 619 " --> pdb=" O GLY E 453 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 495 through 496 removed outlier: 3.703A pdb=" N THR E 530 " --> pdb=" O THR E 469 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY E 548 " --> pdb=" O PHE E 531 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 1425 through 1430 removed outlier: 6.241A pdb=" N ILE E1380 " --> pdb=" O VAL E1504 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N PHE E1502 " --> pdb=" O THR E1494 " (cutoff:3.500A) removed outlier: 9.776A pdb=" N THR E1494 " --> pdb=" O PHE E1502 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N VAL E1504 " --> pdb=" O ALA E1492 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA E1492 " --> pdb=" O VAL E1504 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN E1460 " --> pdb=" O THR E1491 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 41 through 44 removed outlier: 7.161A pdb=" N CYS F 6 " --> pdb=" O TRP F 56 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYS F 5 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU F 79 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL F 7 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N CYS F 81 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL F 9 " --> pdb=" O CYS F 81 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE F 111 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE F 110 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N LEU F 155 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU F 112 " --> pdb=" O LEU F 155 " (cutoff:3.500A) 1697 hydrogen bonds defined for protein. 4959 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: 14.85 Time building geometry restraints manager: 9.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10627 1.34 - 1.46: 6867 1.46 - 1.58: 15768 1.58 - 1.70: 0 1.70 - 1.82: 294 Bond restraints: 33556 Sorted by residual: bond pdb=" CA LYS E1500 " pdb=" C LYS E1500 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.80e-02 3.09e+03 6.79e+00 bond pdb=" CA LYS B1500 " pdb=" C LYS B1500 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.80e-02 3.09e+03 6.59e+00 bond pdb=" CG MET B1011 " pdb=" SD MET B1011 " ideal model delta sigma weight residual 1.803 1.759 0.044 2.50e-02 1.60e+03 3.09e+00 bond pdb=" CG MET E1011 " pdb=" SD MET E1011 " ideal model delta sigma weight residual 1.803 1.761 0.042 2.50e-02 1.60e+03 2.89e+00 bond pdb=" CG1 ILE B1125 " pdb=" CD1 ILE B1125 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.47e+00 ... (remaining 33551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 44165 2.21 - 4.42: 999 4.42 - 6.64: 132 6.64 - 8.85: 20 8.85 - 11.06: 8 Bond angle restraints: 45324 Sorted by residual: angle pdb=" C ARG B 157 " pdb=" N MET B 158 " pdb=" CA MET B 158 " ideal model delta sigma weight residual 121.14 113.45 7.69 1.75e+00 3.27e-01 1.93e+01 angle pdb=" C ARG E 157 " pdb=" N MET E 158 " pdb=" CA MET E 158 " ideal model delta sigma weight residual 121.14 113.46 7.68 1.75e+00 3.27e-01 1.93e+01 angle pdb=" N MET E 929 " pdb=" CA MET E 929 " pdb=" CB MET E 929 " ideal model delta sigma weight residual 109.91 115.47 -5.56 1.46e+00 4.69e-01 1.45e+01 angle pdb=" N MET B 929 " pdb=" CA MET B 929 " pdb=" CB MET B 929 " ideal model delta sigma weight residual 109.91 115.43 -5.52 1.46e+00 4.69e-01 1.43e+01 angle pdb=" O ASP B 849 " pdb=" C ASP B 849 " pdb=" N ASN B 850 " ideal model delta sigma weight residual 122.59 117.81 4.78 1.33e+00 5.65e-01 1.29e+01 ... (remaining 45319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 18253 17.59 - 35.18: 1883 35.18 - 52.77: 283 52.77 - 70.36: 43 70.36 - 87.95: 14 Dihedral angle restraints: 20476 sinusoidal: 8586 harmonic: 11890 Sorted by residual: 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 -152.42 -27.58 0 5.00e+00 4.00e-02 3.04e+01 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 -152.42 -27.58 0 5.00e+00 4.00e-02 3.04e+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 180.00 155.16 24.84 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 20473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3696 0.048 - 0.097: 1073 0.097 - 0.145: 217 0.145 - 0.194: 26 0.194 - 0.242: 12 Chirality restraints: 5024 Sorted by residual: chirality pdb=" CB ILE F 80 " pdb=" CA ILE F 80 " pdb=" CG1 ILE F 80 " pdb=" CG2 ILE F 80 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB VAL C 9 " pdb=" CA VAL C 9 " pdb=" CG1 VAL C 9 " pdb=" CG2 VAL C 9 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE C 80 " pdb=" CA ILE C 80 " pdb=" CG1 ILE C 80 " pdb=" CG2 ILE C 80 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 5021 not shown) Planarity restraints: 5796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B1107 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO B1108 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B1108 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B1108 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E1107 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.94e+00 pdb=" N PRO E1108 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E1108 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E1108 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B1156 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C ASP B1156 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP B1156 " -0.013 2.00e-02 2.50e+03 pdb=" N GLN B1157 " -0.011 2.00e-02 2.50e+03 ... (remaining 5793 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 959 2.65 - 3.21: 37317 3.21 - 3.77: 58219 3.77 - 4.34: 79903 4.34 - 4.90: 117297 Nonbonded interactions: 293695 Sorted by model distance: nonbonded pdb=" NH2 ARG E1390 " pdb=" O TYR F 23 " model vdw 2.086 3.120 nonbonded pdb=" O TYR B 819 " pdb=" OG SER B 822 " model vdw 2.095 3.040 nonbonded pdb=" O TYR E 819 " pdb=" OG SER E 822 " model vdw 2.096 3.040 nonbonded pdb=" OG1 THR E 180 " pdb=" OE1 GLN E 962 " model vdw 2.116 3.040 nonbonded pdb=" ND2 ASN A 670 " pdb=" O ASP A 676 " model vdw 2.116 3.120 ... (remaining 293690 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: 0.16 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.310 Check model and map are aligned: 0.250 Set scattering table: 0.290 Process input model: 74.430 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 0.061 33556 Z= 0.261 Angle : 0.809 11.062 45324 Z= 0.448 Chirality : 0.047 0.242 5024 Planarity : 0.005 0.050 5796 Dihedral : 13.880 87.949 12780 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 37.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: -1.91 (0.13), residues: 4022 helix: -0.80 (0.11), residues: 1976 sheet: -1.95 (0.23), residues: 448 loop : -1.48 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP E 102 HIS 0.009 0.002 HIS B1097 PHE 0.026 0.002 PHE E 795 TYR 0.024 0.002 TYR B1328 ARG 0.013 0.001 ARG B 870 Details of bonding type rmsd hydrogen bonds : bond 0.17939 ( 1693) hydrogen bonds : angle 7.50648 ( 4959) covalent geometry : bond 0.00527 (33556) covalent geometry : angle 0.80911 (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 169 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 4.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 MET cc_start: 0.8893 (mpp) cc_final: 0.8617 (mpp) REVERT: B 198 ILE cc_start: 0.8296 (pt) cc_final: 0.8079 (tp) REVERT: B 306 MET cc_start: -0.1832 (tpt) cc_final: -0.4469 (ttt) REVERT: B 579 MET cc_start: -0.0147 (mtt) cc_final: -0.0477 (mtt) REVERT: B 958 ILE cc_start: 0.9592 (pt) cc_final: 0.9346 (pt) REVERT: B 1105 MET cc_start: 0.8783 (ppp) cc_final: 0.8204 (ppp) REVERT: B 1560 MET cc_start: 0.7186 (pmm) cc_final: 0.6867 (pmm) REVERT: D 721 ASP cc_start: 0.7838 (t70) cc_final: 0.7458 (p0) REVERT: E 120 MET cc_start: 0.9363 (mtm) cc_final: 0.9161 (mtm) REVERT: E 198 ILE cc_start: 0.8448 (pt) cc_final: 0.8215 (tp) REVERT: E 929 MET cc_start: 0.8821 (mtt) cc_final: 0.8311 (ptp) REVERT: E 958 ILE cc_start: 0.9607 (pt) cc_final: 0.9342 (pt) REVERT: E 1105 MET cc_start: 0.8783 (ppp) cc_final: 0.8295 (ppp) REVERT: F 171 GLU cc_start: 0.8991 (mp0) cc_final: 0.8758 (tp30) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.4344 time to fit residues: 127.4437 Evaluate side-chains 147 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 4.180 ------------------------------------------------------------------------------- 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: 10.0000 chunk 303 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 204 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 313 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 190 optimal weight: 8.9990 chunk 233 optimal weight: 2.9990 chunk 363 optimal weight: 0.0040 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 ASN B 65 HIS B 118 GLN B 130 GLN B 276 ASN B 334 HIS B 412 GLN B 444 ASN B 503 GLN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1014 ASN B1203 ASN B1293 GLN B1401 GLN D 554 ASN E 118 GLN E 276 ASN E 334 HIS E 412 GLN E 444 ASN ** E 526 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 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1014 ASN E1203 ASN E1293 GLN E1401 GLN ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.052666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.031789 restraints weight = 286624.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.032156 restraints weight = 198800.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.032475 restraints weight = 154175.355| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33556 Z= 0.148 Angle : 0.679 9.701 45324 Z= 0.355 Chirality : 0.045 0.166 5024 Planarity : 0.005 0.070 5796 Dihedral : 5.494 35.831 4394 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.35 % Allowed : 6.06 % Favored : 93.58 % 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: -1.31 (0.13), residues: 4022 helix: -0.18 (0.11), residues: 2020 sheet: -1.77 (0.24), residues: 456 loop : -1.35 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 575 HIS 0.007 0.001 HIS E1097 PHE 0.015 0.001 PHE E 712 TYR 0.028 0.002 TYR B1566 ARG 0.007 0.001 ARG E 870 Details of bonding type rmsd hydrogen bonds : bond 0.04765 ( 1693) hydrogen bonds : angle 5.88294 ( 4959) covalent geometry : bond 0.00310 (33556) covalent geometry : angle 0.67861 (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 177 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 3.748 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: B 306 MET cc_start: 0.0455 (tpt) cc_final: -0.0988 (ttt) REVERT: B 860 MET cc_start: 0.9181 (ptp) cc_final: 0.8944 (ptp) REVERT: B 929 MET cc_start: 0.8574 (mtt) cc_final: 0.8339 (mtp) REVERT: B 958 ILE cc_start: 0.9637 (pt) cc_final: 0.9302 (pt) REVERT: B 1007 MET cc_start: 0.8994 (tmm) cc_final: 0.8446 (tmm) REVERT: B 1011 MET cc_start: 0.9181 (mmp) cc_final: 0.8913 (mmm) REVERT: B 1105 MET cc_start: 0.8420 (ppp) cc_final: 0.7861 (ppp) REVERT: B 1313 MET cc_start: 0.7898 (ttm) cc_final: 0.7316 (tmm) REVERT: B 1560 MET cc_start: 0.7458 (pmm) cc_final: 0.7229 (pmm) REVERT: D 721 ASP cc_start: 0.7957 (t70) cc_final: 0.7649 (p0) REVERT: E 579 MET cc_start: 0.1289 (mtt) cc_final: 0.1034 (mtm) REVERT: E 929 MET cc_start: 0.8648 (mtt) cc_final: 0.7976 (mtm) REVERT: E 958 ILE cc_start: 0.9596 (pt) cc_final: 0.9247 (pt) REVERT: E 987 MET cc_start: 0.9359 (tmm) cc_final: 0.9146 (tmm) REVERT: E 1007 MET cc_start: 0.9110 (tmm) cc_final: 0.8744 (tmm) REVERT: E 1105 MET cc_start: 0.8508 (ppp) cc_final: 0.8003 (ppp) outliers start: 13 outliers final: 0 residues processed: 177 average time/residue: 0.4249 time to fit residues: 129.3259 Evaluate side-chains 145 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 4.198 ------------------------------------------------------------------------------- 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: 0.0970 chunk 306 optimal weight: 0.8980 chunk 286 optimal weight: 5.9990 chunk 47 optimal weight: 30.0000 chunk 80 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 374 optimal weight: 8.9990 chunk 298 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 316 optimal weight: 9.9990 chunk 387 optimal weight: 1.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 HIS B 130 GLN B 414 GLN B 485 HIS ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1267 HIS ** D 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 GLN E 485 HIS E 503 GLN ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1014 ASN E1267 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.052289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.031593 restraints weight = 290531.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.031917 restraints weight = 208751.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.032294 restraints weight = 159387.925| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33556 Z= 0.148 Angle : 0.640 8.460 45324 Z= 0.335 Chirality : 0.044 0.173 5024 Planarity : 0.005 0.059 5796 Dihedral : 5.302 36.292 4394 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.14 % Allowed : 5.41 % Favored : 94.46 % 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: -1.16 (0.13), residues: 4022 helix: -0.04 (0.11), residues: 2026 sheet: -1.73 (0.24), residues: 450 loop : -1.29 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 102 HIS 0.006 0.001 HIS E1048 PHE 0.010 0.001 PHE E 712 TYR 0.021 0.002 TYR E 585 ARG 0.010 0.001 ARG B 931 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 1693) hydrogen bonds : angle 5.65746 ( 4959) covalent geometry : bond 0.00315 (33556) covalent geometry : angle 0.64001 (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 172 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 167 time to evaluate : 4.122 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: 0.3490 (tpt) cc_final: 0.2528 (mmm) REVERT: B 306 MET cc_start: 0.0155 (tpt) cc_final: -0.1362 (ttt) REVERT: B 929 MET cc_start: 0.8733 (mtt) cc_final: 0.8373 (mtp) REVERT: B 958 ILE cc_start: 0.9623 (pt) cc_final: 0.9301 (pt) REVERT: B 1007 MET cc_start: 0.8984 (tmm) cc_final: 0.8647 (tmm) REVERT: B 1560 MET cc_start: 0.7506 (pmm) cc_final: 0.7241 (pmm) REVERT: C 45 MET cc_start: 0.6546 (pmm) cc_final: 0.5788 (tmm) REVERT: D 721 ASP cc_start: 0.7971 (t70) cc_final: 0.7682 (p0) REVERT: E 243 MET cc_start: 0.4477 (ppp) cc_final: 0.3633 (ttp) REVERT: E 579 MET cc_start: 0.1573 (mtt) cc_final: 0.1308 (mtm) REVERT: E 958 ILE cc_start: 0.9599 (pt) cc_final: 0.9252 (pt) REVERT: E 1007 MET cc_start: 0.9115 (tmm) cc_final: 0.8606 (tmm) REVERT: E 1011 MET cc_start: 0.9184 (mmp) cc_final: 0.8850 (mmm) REVERT: E 1105 MET cc_start: 0.8628 (ppp) cc_final: 0.7976 (ppp) REVERT: E 1482 MET cc_start: 0.8337 (mmp) cc_final: 0.7596 (mmm) outliers start: 5 outliers final: 2 residues processed: 172 average time/residue: 0.4663 time to fit residues: 134.5509 Evaluate side-chains 148 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 4.041 ------------------------------------------------------------------------------- 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: 4.9990 chunk 248 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 341 optimal weight: 1.9990 chunk 296 optimal weight: 10.0000 chunk 378 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1014 ASN ** B1056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1251 HIS ** 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 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.052772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.031857 restraints weight = 292238.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.032220 restraints weight = 208343.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.032703 restraints weight = 158887.476| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33556 Z= 0.136 Angle : 0.631 8.392 45324 Z= 0.326 Chirality : 0.043 0.209 5024 Planarity : 0.004 0.062 5796 Dihedral : 5.222 37.296 4394 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.05 % Allowed : 3.41 % Favored : 96.53 % 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: -1.01 (0.13), residues: 4022 helix: 0.09 (0.11), residues: 2030 sheet: -1.67 (0.24), residues: 458 loop : -1.22 (0.17), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E1043 HIS 0.005 0.001 HIS B1056 PHE 0.040 0.001 PHE E 795 TYR 0.019 0.001 TYR E 585 ARG 0.008 0.001 ARG D 683 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 1693) hydrogen bonds : angle 5.50132 ( 4959) covalent geometry : bond 0.00295 (33556) covalent geometry : angle 0.63088 (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 172 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 3.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3650 (tpt) cc_final: 0.2727 (mmm) REVERT: B 306 MET cc_start: -0.0236 (tpt) cc_final: -0.2250 (ttt) REVERT: B 929 MET cc_start: 0.8624 (mtt) cc_final: 0.8418 (mtp) REVERT: B 958 ILE cc_start: 0.9632 (pt) cc_final: 0.9318 (pt) REVERT: B 1007 MET cc_start: 0.8980 (tmm) cc_final: 0.8583 (tmm) REVERT: B 1011 MET cc_start: 0.9204 (mmp) cc_final: 0.8911 (mmm) REVERT: B 1105 MET cc_start: 0.9121 (tmm) cc_final: 0.8894 (tmm) REVERT: B 1313 MET cc_start: 0.7965 (ttm) cc_final: 0.7456 (tmm) REVERT: B 1324 LEU cc_start: 0.9311 (tp) cc_final: 0.9038 (tp) REVERT: B 1482 MET cc_start: 0.8481 (mmm) cc_final: 0.7867 (mmm) REVERT: B 1560 MET cc_start: 0.7443 (pmm) cc_final: 0.7192 (pmm) REVERT: D 721 ASP cc_start: 0.7870 (t70) cc_final: 0.7577 (p0) REVERT: E 243 MET cc_start: 0.4721 (ppp) cc_final: 0.3818 (ttp) REVERT: E 267 MET cc_start: 0.3971 (mmm) cc_final: 0.3594 (tmm) REVERT: E 306 MET cc_start: -0.2085 (tpt) cc_final: -0.4644 (ttp) REVERT: E 579 MET cc_start: 0.0916 (mtt) cc_final: 0.0646 (mtm) REVERT: E 958 ILE cc_start: 0.9623 (pt) cc_final: 0.9280 (pt) REVERT: E 987 MET cc_start: 0.9343 (tmm) cc_final: 0.9129 (tmm) REVERT: E 1007 MET cc_start: 0.9142 (tmm) cc_final: 0.8729 (tmm) REVERT: E 1011 MET cc_start: 0.9194 (mmp) cc_final: 0.8874 (mmm) REVERT: E 1105 MET cc_start: 0.8627 (ppp) cc_final: 0.7964 (ppp) outliers start: 2 outliers final: 0 residues processed: 172 average time/residue: 0.4390 time to fit residues: 127.3446 Evaluate side-chains 148 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 3.802 ------------------------------------------------------------------------------- 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: 4.9990 chunk 301 optimal weight: 5.9990 chunk 394 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 246 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 160 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 78 optimal weight: 30.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN B 376 ASN B 412 GLN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 ASN E 412 GLN ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 968 HIS ** 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 = 0.3598 r_free = 0.3598 target = 0.051873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.031530 restraints weight = 292407.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.031852 restraints weight = 202549.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.032202 restraints weight = 156004.046| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33556 Z= 0.157 Angle : 0.627 8.756 45324 Z= 0.329 Chirality : 0.043 0.172 5024 Planarity : 0.005 0.062 5796 Dihedral : 5.174 36.281 4394 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.11 % Allowed : 3.30 % Favored : 96.59 % 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: 0.16 (0.11), residues: 2026 sheet: -1.55 (0.25), residues: 442 loop : -1.29 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E1043 HIS 0.007 0.001 HIS B1056 PHE 0.011 0.001 PHE F 78 TYR 0.019 0.001 TYR B 585 ARG 0.017 0.001 ARG E 935 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 1693) hydrogen bonds : angle 5.43168 ( 4959) covalent geometry : bond 0.00333 (33556) covalent geometry : angle 0.62662 (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 165 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 161 time to evaluate : 4.033 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: 0.3804 (tpt) cc_final: 0.3010 (mmm) REVERT: B 306 MET cc_start: 0.0219 (tpt) cc_final: -0.1678 (ttt) REVERT: B 958 ILE cc_start: 0.9607 (pt) cc_final: 0.9295 (pt) REVERT: B 960 LEU cc_start: 0.9702 (tt) cc_final: 0.9486 (tt) REVERT: B 1007 MET cc_start: 0.8981 (tmm) cc_final: 0.8429 (tmm) REVERT: B 1011 MET cc_start: 0.9080 (mmp) cc_final: 0.8753 (mmm) REVERT: B 1105 MET cc_start: 0.9063 (tmm) cc_final: 0.8819 (tmm) REVERT: B 1482 MET cc_start: 0.8492 (mmm) cc_final: 0.7913 (mmm) REVERT: B 1560 MET cc_start: 0.7482 (pmm) cc_final: 0.7242 (pmm) REVERT: C 45 MET cc_start: 0.6479 (pmm) cc_final: 0.5699 (tmm) REVERT: D 721 ASP cc_start: 0.8053 (t70) cc_final: 0.7751 (p0) REVERT: E 243 MET cc_start: 0.4894 (ppp) cc_final: 0.4190 (ttp) REVERT: E 267 MET cc_start: 0.4024 (mmm) cc_final: 0.3650 (tmm) REVERT: E 579 MET cc_start: 0.0973 (mtt) cc_final: 0.0735 (mtm) REVERT: E 958 ILE cc_start: 0.9622 (pt) cc_final: 0.9293 (pt) REVERT: E 987 MET cc_start: 0.9339 (tmm) cc_final: 0.9139 (tmm) REVERT: E 1007 MET cc_start: 0.9098 (tmm) cc_final: 0.8530 (tmm) REVERT: E 1011 MET cc_start: 0.9140 (mmp) cc_final: 0.8731 (mmm) REVERT: E 1105 MET cc_start: 0.8633 (ppp) cc_final: 0.7991 (ppp) REVERT: F 45 MET cc_start: 0.6537 (pmm) cc_final: 0.5621 (tmm) outliers start: 4 outliers final: 0 residues processed: 165 average time/residue: 0.4217 time to fit residues: 120.2408 Evaluate side-chains 142 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 4.222 ------------------------------------------------------------------------------- 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: 2.9990 chunk 167 optimal weight: 4.9990 chunk 316 optimal weight: 7.9990 chunk 303 optimal weight: 2.9990 chunk 358 optimal weight: 3.9990 chunk 338 optimal weight: 2.9990 chunk 141 optimal weight: 0.5980 chunk 397 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 264 optimal weight: 20.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 550 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1048 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 = 0.3595 r_free = 0.3595 target = 0.051708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.031287 restraints weight = 294673.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 84)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.031657 restraints weight = 216729.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.032103 restraints weight = 162851.127| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 33556 Z= 0.161 Angle : 0.642 8.490 45324 Z= 0.334 Chirality : 0.044 0.211 5024 Planarity : 0.004 0.062 5796 Dihedral : 5.199 35.615 4394 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: 0.16 (0.11), residues: 2020 sheet: -1.52 (0.25), residues: 442 loop : -1.29 (0.17), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 102 HIS 0.007 0.001 HIS B1056 PHE 0.021 0.001 PHE E 59 TYR 0.018 0.001 TYR B 585 ARG 0.007 0.001 ARG B1627 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 1693) hydrogen bonds : angle 5.43592 ( 4959) covalent geometry : bond 0.00345 (33556) covalent geometry : angle 0.64191 (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 163 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 4.226 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: B 306 MET cc_start: -0.0119 (tpt) cc_final: -0.2090 (ttt) REVERT: B 802 MET cc_start: 0.6665 (ptm) cc_final: 0.5837 (ppp) REVERT: B 958 ILE cc_start: 0.9613 (pt) cc_final: 0.9310 (pt) REVERT: B 1007 MET cc_start: 0.8964 (tmm) cc_final: 0.8361 (tmm) REVERT: B 1011 MET cc_start: 0.9112 (mmp) cc_final: 0.8755 (mmm) REVERT: B 1426 MET cc_start: 0.8513 (ttm) cc_final: 0.8269 (ttm) REVERT: B 1482 MET cc_start: 0.8517 (mmm) cc_final: 0.7923 (mmm) REVERT: B 1560 MET cc_start: 0.7418 (pmm) cc_final: 0.7035 (pmm) REVERT: E 243 MET cc_start: 0.4856 (ppp) cc_final: 0.4133 (ttp) REVERT: E 267 MET cc_start: 0.4269 (mmm) cc_final: 0.3891 (tmm) REVERT: E 579 MET cc_start: 0.0915 (mtt) cc_final: 0.0674 (mtm) REVERT: E 958 ILE cc_start: 0.9626 (pt) cc_final: 0.9301 (pt) REVERT: E 1007 MET cc_start: 0.9108 (tmm) cc_final: 0.8544 (tmm) REVERT: E 1011 MET cc_start: 0.9134 (mmp) cc_final: 0.8756 (mmm) REVERT: E 1105 MET cc_start: 0.8656 (ppp) cc_final: 0.7995 (ppp) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.4340 time to fit residues: 122.8901 Evaluate side-chains 143 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 3.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 258 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 228 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 325 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 329 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 HIS ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 926 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 = 0.3615 r_free = 0.3615 target = 0.052645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.031732 restraints weight = 293424.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.032061 restraints weight = 206448.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.032594 restraints weight = 160089.496| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 33556 Z= 0.129 Angle : 0.638 9.393 45324 Z= 0.330 Chirality : 0.044 0.226 5024 Planarity : 0.005 0.069 5796 Dihedral : 5.107 36.560 4394 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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 (0.14), residues: 4022 helix: 0.27 (0.12), residues: 2022 sheet: -1.40 (0.25), residues: 442 loop : -1.23 (0.17), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 102 HIS 0.011 0.001 HIS E 968 PHE 0.041 0.001 PHE E 795 TYR 0.018 0.001 TYR E1289 ARG 0.011 0.001 ARG E 935 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 1693) hydrogen bonds : angle 5.32419 ( 4959) covalent geometry : bond 0.00281 (33556) covalent geometry : angle 0.63839 (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 166 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 4.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.2534 (tpt) cc_final: 0.1805 (mmm) REVERT: B 306 MET cc_start: 0.0130 (tpt) cc_final: -0.1605 (ttt) REVERT: B 802 MET cc_start: 0.6726 (ptm) cc_final: 0.5963 (ppp) REVERT: B 929 MET cc_start: 0.8187 (mtp) cc_final: 0.7902 (mtp) REVERT: B 958 ILE cc_start: 0.9604 (pt) cc_final: 0.9299 (pt) REVERT: B 1007 MET cc_start: 0.8982 (tmm) cc_final: 0.8398 (tmm) REVERT: B 1011 MET cc_start: 0.9159 (mmp) cc_final: 0.8753 (mmm) REVERT: B 1482 MET cc_start: 0.8474 (mmm) cc_final: 0.7885 (mmm) REVERT: B 1560 MET cc_start: 0.7362 (pmm) cc_final: 0.7042 (pmm) REVERT: C 45 MET cc_start: 0.6220 (pmm) cc_final: 0.5431 (tmm) REVERT: D 721 ASP cc_start: 0.8000 (t0) cc_final: 0.7708 (p0) REVERT: E 243 MET cc_start: 0.4907 (ppp) cc_final: 0.4230 (ttp) REVERT: E 267 MET cc_start: 0.4056 (mmm) cc_final: 0.3699 (tmm) REVERT: E 306 MET cc_start: -0.1309 (tpt) cc_final: -0.3448 (ttt) REVERT: E 802 MET cc_start: 0.6904 (ptm) cc_final: 0.6452 (ppp) REVERT: E 958 ILE cc_start: 0.9651 (pt) cc_final: 0.9392 (pt) REVERT: E 987 MET cc_start: 0.9359 (tmm) cc_final: 0.9124 (tmm) REVERT: E 1007 MET cc_start: 0.9112 (tmm) cc_final: 0.8517 (tmm) REVERT: E 1009 MET cc_start: 0.8950 (ptm) cc_final: 0.8599 (ptm) REVERT: E 1011 MET cc_start: 0.9182 (mmp) cc_final: 0.8746 (mmm) REVERT: E 1482 MET cc_start: 0.8390 (mmp) cc_final: 0.7606 (mmm) REVERT: F 45 MET cc_start: 0.6425 (pmm) cc_final: 0.5532 (tmm) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.4135 time to fit residues: 119.1260 Evaluate side-chains 143 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 3.709 ------------------------------------------------------------------------------- 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: 4.9990 chunk 206 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 334 optimal weight: 0.7980 chunk 357 optimal weight: 0.0270 chunk 322 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 293 optimal weight: 20.0000 chunk 161 optimal weight: 1.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 576 ASN ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.052731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.031774 restraints weight = 295366.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.032251 restraints weight = 209098.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.032702 restraints weight = 159551.378| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 33556 Z= 0.129 Angle : 0.635 9.359 45324 Z= 0.329 Chirality : 0.043 0.231 5024 Planarity : 0.004 0.062 5796 Dihedral : 5.070 36.354 4394 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: -0.76 (0.14), residues: 4022 helix: 0.31 (0.12), residues: 2022 sheet: -1.31 (0.25), residues: 442 loop : -1.23 (0.17), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 102 HIS 0.014 0.001 HIS E 968 PHE 0.016 0.001 PHE B1308 TYR 0.023 0.001 TYR E 572 ARG 0.014 0.001 ARG B1627 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 1693) hydrogen bonds : angle 5.27780 ( 4959) covalent geometry : bond 0.00282 (33556) covalent geometry : angle 0.63543 (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 163 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 4.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3092 (tpt) cc_final: 0.2401 (mmm) REVERT: B 158 MET cc_start: 0.8906 (pmm) cc_final: 0.8608 (pmm) REVERT: B 306 MET cc_start: -0.0710 (tpt) cc_final: -0.2744 (ttt) REVERT: B 958 ILE cc_start: 0.9618 (pt) cc_final: 0.9359 (pt) REVERT: B 1007 MET cc_start: 0.8945 (tmm) cc_final: 0.8381 (tmm) REVERT: B 1011 MET cc_start: 0.9129 (mmp) cc_final: 0.8730 (mmm) REVERT: B 1105 MET cc_start: 0.9016 (tmm) cc_final: 0.8765 (tmm) REVERT: B 1313 MET cc_start: 0.8072 (ttm) cc_final: 0.7601 (tmm) REVERT: B 1324 LEU cc_start: 0.9249 (tp) cc_final: 0.8974 (tp) REVERT: B 1426 MET cc_start: 0.8517 (ttm) cc_final: 0.8302 (ttp) REVERT: B 1482 MET cc_start: 0.8415 (mmm) cc_final: 0.7842 (mmm) REVERT: B 1560 MET cc_start: 0.7360 (pmm) cc_final: 0.7092 (pmm) REVERT: C 45 MET cc_start: 0.6442 (pmm) cc_final: 0.5725 (tmm) REVERT: E 243 MET cc_start: 0.4946 (ppp) cc_final: 0.4278 (ttp) REVERT: E 306 MET cc_start: -0.2100 (tpt) cc_final: -0.4418 (ttt) REVERT: E 802 MET cc_start: 0.6685 (ptm) cc_final: 0.6185 (ppp) REVERT: E 929 MET cc_start: 0.8745 (mtm) cc_final: 0.8410 (mtp) REVERT: E 958 ILE cc_start: 0.9631 (pt) cc_final: 0.9379 (pt) REVERT: E 987 MET cc_start: 0.9339 (tmm) cc_final: 0.9114 (tmm) REVERT: E 1007 MET cc_start: 0.9088 (tmm) cc_final: 0.8527 (tmm) REVERT: E 1011 MET cc_start: 0.9147 (mmp) cc_final: 0.8733 (mmm) REVERT: E 1482 MET cc_start: 0.8327 (mmp) cc_final: 0.7529 (mmm) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.4392 time to fit residues: 123.0338 Evaluate side-chains 144 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 3.985 ------------------------------------------------------------------------------- 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: 8.9990 chunk 62 optimal weight: 0.8980 chunk 285 optimal weight: 1.9990 chunk 291 optimal weight: 10.0000 chunk 357 optimal weight: 7.9990 chunk 364 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 203 optimal weight: 5.9990 chunk 367 optimal weight: 8.9990 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 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.052642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.032043 restraints weight = 288301.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.032458 restraints weight = 224611.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.032795 restraints weight = 163509.189| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 33556 Z= 0.129 Angle : 0.646 10.266 45324 Z= 0.334 Chirality : 0.043 0.213 5024 Planarity : 0.004 0.064 5796 Dihedral : 5.016 36.347 4394 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: -0.73 (0.14), residues: 4022 helix: 0.34 (0.12), residues: 2012 sheet: -1.49 (0.25), residues: 442 loop : -1.16 (0.17), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 102 HIS 0.010 0.001 HIS E 968 PHE 0.030 0.001 PHE B 795 TYR 0.020 0.001 TYR E 585 ARG 0.011 0.001 ARG D 683 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 1693) hydrogen bonds : angle 5.27867 ( 4959) covalent geometry : bond 0.00283 (33556) covalent geometry : angle 0.64643 (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 161 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 3.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.2806 (tpt) cc_final: 0.1654 (mmm) REVERT: B 120 MET cc_start: 0.9114 (mtm) cc_final: 0.8813 (mmm) REVERT: B 306 MET cc_start: -0.0852 (tpt) cc_final: -0.2508 (ttt) REVERT: B 764 PHE cc_start: 0.9619 (m-80) cc_final: 0.9415 (m-80) REVERT: B 958 ILE cc_start: 0.9633 (pt) cc_final: 0.9364 (pt) REVERT: B 1007 MET cc_start: 0.9078 (tmm) cc_final: 0.8580 (tmm) REVERT: B 1011 MET cc_start: 0.9192 (mmp) cc_final: 0.8732 (mmm) REVERT: B 1105 MET cc_start: 0.9047 (tmm) cc_final: 0.8777 (tmm) REVERT: B 1313 MET cc_start: 0.8160 (ttm) cc_final: 0.7598 (tmm) REVERT: B 1408 MET cc_start: 0.8433 (mpp) cc_final: 0.8226 (mpp) REVERT: B 1426 MET cc_start: 0.8525 (ttm) cc_final: 0.7950 (ttp) REVERT: B 1482 MET cc_start: 0.8497 (mmm) cc_final: 0.7906 (mmm) REVERT: B 1560 MET cc_start: 0.7513 (pmm) cc_final: 0.7203 (pmm) REVERT: C 45 MET cc_start: 0.6512 (pmm) cc_final: 0.5777 (tmm) REVERT: E 158 MET cc_start: 0.9002 (pmm) cc_final: 0.8720 (pmm) REVERT: E 243 MET cc_start: 0.4877 (ppp) cc_final: 0.4168 (ttp) REVERT: E 267 MET cc_start: 0.4018 (mmm) cc_final: 0.3722 (tmm) REVERT: E 306 MET cc_start: -0.2165 (tpt) cc_final: -0.4508 (ttt) REVERT: E 802 MET cc_start: 0.6586 (ptm) cc_final: 0.6030 (ppp) REVERT: E 929 MET cc_start: 0.8706 (mtm) cc_final: 0.8316 (mtp) REVERT: E 958 ILE cc_start: 0.9622 (pt) cc_final: 0.9379 (pt) REVERT: E 987 MET cc_start: 0.9380 (tmm) cc_final: 0.9152 (tmm) REVERT: E 1007 MET cc_start: 0.9052 (tmm) cc_final: 0.8558 (tmm) REVERT: E 1009 MET cc_start: 0.8967 (ptm) cc_final: 0.8751 (ppp) REVERT: E 1011 MET cc_start: 0.9189 (mmp) cc_final: 0.8728 (mmm) REVERT: E 1146 MET cc_start: 0.8811 (pmm) cc_final: 0.8609 (pmm) REVERT: E 1482 MET cc_start: 0.8394 (mmp) cc_final: 0.7567 (mmm) REVERT: E 1597 MET cc_start: 0.8800 (mmp) cc_final: 0.8007 (mmm) REVERT: F 45 MET cc_start: 0.6109 (pmm) cc_final: 0.5257 (tmm) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.4189 time to fit residues: 116.9146 Evaluate side-chains 143 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 3.630 ------------------------------------------------------------------------------- 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: 6.9990 chunk 276 optimal weight: 30.0000 chunk 107 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 chunk 371 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 254 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 307 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 ASN ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1093 ASN ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** 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 = 0.3620 r_free = 0.3620 target = 0.052920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.031933 restraints weight = 297685.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.032254 restraints weight = 208525.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.032776 restraints weight = 157379.794| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 33556 Z= 0.132 Angle : 0.661 10.275 45324 Z= 0.343 Chirality : 0.044 0.203 5024 Planarity : 0.005 0.138 5796 Dihedral : 5.022 36.383 4394 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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 (0.14), residues: 4022 helix: 0.37 (0.12), residues: 2008 sheet: -1.47 (0.25), residues: 444 loop : -1.16 (0.17), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 102 HIS 0.008 0.001 HIS E 968 PHE 0.018 0.001 PHE B 59 TYR 0.019 0.001 TYR E 585 ARG 0.019 0.001 ARG B 935 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 1693) hydrogen bonds : angle 5.24707 ( 4959) covalent geometry : bond 0.00290 (33556) covalent geometry : angle 0.66106 (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 157 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 4.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.9151 (mtm) cc_final: 0.8863 (mmm) REVERT: B 306 MET cc_start: -0.0139 (tpt) cc_final: -0.1023 (ttt) REVERT: B 764 PHE cc_start: 0.9662 (m-80) cc_final: 0.9439 (m-80) REVERT: B 929 MET cc_start: 0.8476 (mtt) cc_final: 0.8186 (mtt) REVERT: B 958 ILE cc_start: 0.9668 (pt) cc_final: 0.9400 (pt) REVERT: B 1007 MET cc_start: 0.9154 (tmm) cc_final: 0.8703 (tmm) REVERT: B 1011 MET cc_start: 0.9322 (mmp) cc_final: 0.8806 (mmm) REVERT: B 1105 MET cc_start: 0.9032 (tmm) cc_final: 0.8758 (tmm) REVERT: B 1313 MET cc_start: 0.8240 (ttm) cc_final: 0.7530 (tmm) REVERT: B 1426 MET cc_start: 0.8647 (ttm) cc_final: 0.8236 (ttp) REVERT: B 1482 MET cc_start: 0.8518 (mmm) cc_final: 0.7926 (mmm) REVERT: B 1560 MET cc_start: 0.7588 (pmm) cc_final: 0.7288 (pmm) REVERT: E 243 MET cc_start: 0.4983 (ppp) cc_final: 0.4370 (ttp) REVERT: E 267 MET cc_start: 0.3959 (mmm) cc_final: 0.3695 (tmm) REVERT: E 306 MET cc_start: -0.1225 (tpt) cc_final: -0.2998 (ttt) REVERT: E 802 MET cc_start: 0.6765 (ptm) cc_final: 0.6210 (ppp) REVERT: E 929 MET cc_start: 0.8655 (mtm) cc_final: 0.8319 (mtp) REVERT: E 958 ILE cc_start: 0.9658 (pt) cc_final: 0.9402 (pt) REVERT: E 964 MET cc_start: 0.8365 (mmp) cc_final: 0.7791 (mmm) REVERT: E 987 MET cc_start: 0.9422 (tmm) cc_final: 0.9185 (tmm) REVERT: E 1007 MET cc_start: 0.9104 (tmm) cc_final: 0.8578 (tmm) REVERT: E 1009 MET cc_start: 0.9059 (ptm) cc_final: 0.8770 (ppp) REVERT: E 1011 MET cc_start: 0.9305 (mmp) cc_final: 0.8787 (mmm) REVERT: E 1482 MET cc_start: 0.8440 (mmp) cc_final: 0.7604 (mmm) REVERT: E 1597 MET cc_start: 0.8857 (mmp) cc_final: 0.8087 (mmm) REVERT: F 45 MET cc_start: 0.6250 (pmm) cc_final: 0.5332 (tmm) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.4517 time to fit residues: 124.3858 Evaluate side-chains 143 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 3.970 ------------------------------------------------------------------------------- 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: 0.8980 chunk 107 optimal weight: 1.9990 chunk 284 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 121 optimal weight: 0.1980 chunk 396 optimal weight: 6.9990 chunk 373 optimal weight: 0.1980 chunk 93 optimal weight: 0.0870 chunk 377 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1477 ASN ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1477 ASN ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3638 r_free = 0.3638 target = 0.053575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.032548 restraints weight = 290102.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.032856 restraints weight = 207863.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.033329 restraints weight = 158684.771| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 33556 Z= 0.123 Angle : 0.651 10.366 45324 Z= 0.335 Chirality : 0.043 0.188 5024 Planarity : 0.004 0.099 5796 Dihedral : 4.889 37.357 4394 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % 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 : 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: -0.69 (0.14), residues: 4022 helix: 0.39 (0.12), residues: 2042 sheet: -1.42 (0.26), residues: 414 loop : -1.21 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E1043 HIS 0.005 0.001 HIS E 968 PHE 0.024 0.001 PHE B 795 TYR 0.022 0.001 TYR B 969 ARG 0.015 0.001 ARG B 935 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 1693) hydrogen bonds : angle 5.13504 ( 4959) covalent geometry : bond 0.00264 (33556) covalent geometry : angle 0.65112 (45324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13286.02 seconds wall clock time: 231 minutes 7.46 seconds (13867.46 seconds total)