Starting phenix.real_space_refine on Tue Aug 26 04:14:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjl_60149/08_2025/8zjl_60149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjl_60149/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zjl_60149/08_2025/8zjl_60149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjl_60149/08_2025/8zjl_60149.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zjl_60149/08_2025/8zjl_60149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjl_60149/08_2025/8zjl_60149.map" } resolution = 4.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.49, per 1000 atoms: 0.23 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: 2.78 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.4 microseconds 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: 1.47 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: 7.97 Time building geometry restraints manager: 3.73 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.120 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.840 ------------------------------------------------------------------------------- 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 : 36.96 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.013 0.001 ARG B 870 TYR 0.024 0.002 TYR B1328 PHE 0.026 0.002 PHE E 795 TRP 0.020 0.003 TRP E 102 HIS 0.009 0.002 HIS B1097 Details of bonding type rmsd covalent geometry : bond 0.00527 (33556) covalent geometry : angle 0.80911 (45324) hydrogen bonds : bond 0.17939 ( 1693) hydrogen bonds : angle 7.50648 ( 4959) *********************** 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 : 1.340 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: 0.1915 time to fit residues: 55.7945 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 : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.0570 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 ASN 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 ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 ASN E 118 GLN E 130 GLN E 276 ASN E 334 HIS E 350 GLN 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** ** E 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1014 ASN E1203 ASN E1293 GLN E1401 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.051450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.030684 restraints weight = 296787.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.031277 restraints weight = 205311.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.031809 restraints weight = 163980.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.032099 restraints weight = 137401.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.032231 restraints weight = 123753.404| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 33556 Z= 0.187 Angle : 0.701 9.051 45324 Z= 0.370 Chirality : 0.045 0.162 5024 Planarity : 0.006 0.090 5796 Dihedral : 5.634 32.623 4394 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 24.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.41 % Allowed : 7.07 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.13), residues: 4022 helix: -0.41 (0.11), residues: 2032 sheet: -1.85 (0.24), residues: 456 loop : -1.40 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 870 TYR 0.025 0.002 TYR B1566 PHE 0.014 0.002 PHE E 712 TRP 0.021 0.002 TRP E 102 HIS 0.010 0.001 HIS B1056 Details of bonding type rmsd covalent geometry : bond 0.00393 (33556) covalent geometry : angle 0.70134 (45324) hydrogen bonds : bond 0.05072 ( 1693) hydrogen bonds : angle 6.05242 ( 4959) *********************** 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 178 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 306 MET cc_start: 0.0917 (tpt) cc_final: -0.0364 (ttt) REVERT: B 860 MET cc_start: 0.9258 (ptp) cc_final: 0.9031 (ptp) REVERT: B 929 MET cc_start: 0.8629 (mtt) cc_final: 0.8406 (mtp) REVERT: B 958 ILE cc_start: 0.9623 (pt) cc_final: 0.9302 (pt) REVERT: B 1007 MET cc_start: 0.9013 (tmm) cc_final: 0.8451 (tmm) REVERT: B 1011 MET cc_start: 0.9236 (mmp) cc_final: 0.8834 (mmm) REVERT: B 1105 MET cc_start: 0.8540 (ppp) cc_final: 0.7974 (ppp) REVERT: B 1313 MET cc_start: 0.7948 (ttm) cc_final: 0.7478 (tmm) REVERT: B 1560 MET cc_start: 0.7427 (pmm) cc_final: 0.7112 (pmm) REVERT: D 721 ASP cc_start: 0.7950 (t70) cc_final: 0.7596 (p0) REVERT: E 579 MET cc_start: 0.1365 (mtt) cc_final: 0.1120 (mtm) REVERT: E 929 MET cc_start: 0.8621 (mtt) cc_final: 0.8169 (mtm) REVERT: E 958 ILE cc_start: 0.9622 (pt) cc_final: 0.9284 (pt) REVERT: E 1007 MET cc_start: 0.9067 (tmm) cc_final: 0.8727 (tmm) REVERT: E 1105 MET cc_start: 0.8587 (ppp) cc_final: 0.7947 (ppp) outliers start: 15 outliers final: 1 residues processed: 178 average time/residue: 0.1811 time to fit residues: 55.8355 Evaluate side-chains 145 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 226 optimal weight: 9.9990 chunk 214 optimal weight: 0.9990 chunk 161 optimal weight: 0.0980 chunk 397 optimal weight: 5.9990 chunk 265 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 249 optimal weight: 40.0000 chunk 164 optimal weight: 0.9980 chunk 41 optimal weight: 20.0000 chunk 278 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN B 414 GLN ** 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** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 GLN 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** E1267 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.053058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.032089 restraints weight = 281633.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.032578 restraints weight = 196377.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.032967 restraints weight = 152338.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.033200 restraints weight = 128779.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.033489 restraints weight = 116759.206| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33556 Z= 0.136 Angle : 0.654 9.448 45324 Z= 0.339 Chirality : 0.044 0.226 5024 Planarity : 0.005 0.061 5796 Dihedral : 5.358 36.160 4394 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.11 % Allowed : 5.05 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.13), residues: 4022 helix: -0.07 (0.11), residues: 2024 sheet: -1.75 (0.24), residues: 450 loop : -1.33 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 931 TYR 0.020 0.002 TYR E 585 PHE 0.041 0.001 PHE B 795 TRP 0.034 0.002 TRP E1043 HIS 0.009 0.001 HIS D 660 Details of bonding type rmsd covalent geometry : bond 0.00289 (33556) covalent geometry : angle 0.65394 (45324) hydrogen bonds : bond 0.04426 ( 1693) hydrogen bonds : angle 5.67582 ( 4959) *********************** 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 175 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 171 time to evaluate : 1.203 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: 0.3295 (tpt) cc_final: 0.2265 (mmm) REVERT: B 306 MET cc_start: 0.0428 (tpt) cc_final: -0.1428 (ttt) REVERT: B 929 MET cc_start: 0.8689 (mtt) cc_final: 0.8332 (mtp) REVERT: B 958 ILE cc_start: 0.9626 (pt) cc_final: 0.9302 (pt) REVERT: B 1007 MET cc_start: 0.8983 (tmm) cc_final: 0.8584 (tmm) REVERT: B 1011 MET cc_start: 0.9165 (mmp) cc_final: 0.8946 (mmm) REVERT: B 1105 MET cc_start: 0.8426 (ppp) cc_final: 0.7858 (ppp) REVERT: B 1110 LEU cc_start: 0.9206 (mp) cc_final: 0.8978 (mp) REVERT: B 1313 MET cc_start: 0.7952 (ttm) cc_final: 0.7365 (tmm) REVERT: B 1482 MET cc_start: 0.8443 (mmm) cc_final: 0.8152 (mmt) REVERT: B 1560 MET cc_start: 0.7478 (pmm) cc_final: 0.7217 (pmm) REVERT: C 45 MET cc_start: 0.6542 (pmm) cc_final: 0.5787 (tmm) REVERT: D 721 ASP cc_start: 0.7925 (t70) cc_final: 0.7636 (p0) REVERT: E 243 MET cc_start: 0.4358 (ppp) cc_final: 0.3539 (ttp) REVERT: E 579 MET cc_start: 0.1224 (mtt) cc_final: 0.0954 (mtm) REVERT: E 958 ILE cc_start: 0.9600 (pt) cc_final: 0.9250 (pt) REVERT: E 1007 MET cc_start: 0.9118 (tmm) cc_final: 0.8605 (tmm) REVERT: E 1011 MET cc_start: 0.9239 (mmp) cc_final: 0.8829 (mmm) REVERT: E 1105 MET cc_start: 0.8302 (ppp) cc_final: 0.7969 (ppp) REVERT: E 1110 LEU cc_start: 0.9220 (mp) cc_final: 0.8997 (mp) REVERT: E 1482 MET cc_start: 0.8409 (mmp) cc_final: 0.7803 (mmm) outliers start: 4 outliers final: 1 residues processed: 174 average time/residue: 0.1948 time to fit residues: 56.8588 Evaluate side-chains 148 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 369 optimal weight: 0.9990 chunk 269 optimal weight: 30.0000 chunk 140 optimal weight: 0.9990 chunk 233 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 317 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 210 optimal weight: 0.7980 chunk 223 optimal weight: 4.9990 chunk 338 optimal weight: 0.8980 chunk 385 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** ** B1056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1267 HIS E 130 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** E1014 ASN ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.053205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.032267 restraints weight = 288194.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.032988 restraints weight = 215354.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.033463 restraints weight = 155666.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.033307 restraints weight = 149972.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.033341 restraints weight = 138411.030| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33556 Z= 0.126 Angle : 0.626 9.056 45324 Z= 0.323 Chirality : 0.043 0.194 5024 Planarity : 0.004 0.063 5796 Dihedral : 5.199 36.410 4394 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.08 % Allowed : 3.06 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.13), residues: 4022 helix: 0.10 (0.11), residues: 2026 sheet: -1.65 (0.24), residues: 458 loop : -1.25 (0.17), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 935 TYR 0.019 0.001 TYR E 585 PHE 0.042 0.001 PHE E 795 TRP 0.016 0.002 TRP E 102 HIS 0.006 0.001 HIS B 949 Details of bonding type rmsd covalent geometry : bond 0.00268 (33556) covalent geometry : angle 0.62597 (45324) hydrogen bonds : bond 0.04056 ( 1693) hydrogen bonds : angle 5.45946 ( 4959) *********************** 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 175 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 172 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4427 (tpt) cc_final: 0.3975 (mmm) REVERT: B 306 MET cc_start: -0.1067 (tpt) cc_final: -0.3355 (ttt) REVERT: B 929 MET cc_start: 0.8681 (mtt) cc_final: 0.8475 (mtp) REVERT: B 958 ILE cc_start: 0.9598 (pt) cc_final: 0.9280 (pt) REVERT: B 1007 MET cc_start: 0.8864 (tmm) cc_final: 0.8464 (tmm) REVERT: B 1313 MET cc_start: 0.7940 (ttm) cc_final: 0.7449 (tmm) REVERT: B 1324 LEU cc_start: 0.9288 (tp) cc_final: 0.9020 (tp) REVERT: B 1482 MET cc_start: 0.8439 (mmm) cc_final: 0.7813 (mmm) REVERT: B 1560 MET cc_start: 0.7444 (pmm) cc_final: 0.7203 (pmm) REVERT: D 721 ASP cc_start: 0.8024 (t70) cc_final: 0.7756 (p0) REVERT: E 243 MET cc_start: 0.4695 (ppp) cc_final: 0.3857 (ttp) REVERT: E 267 MET cc_start: 0.3999 (mmm) cc_final: 0.3603 (tmm) REVERT: E 306 MET cc_start: -0.2709 (tpt) cc_final: -0.5270 (ttp) REVERT: E 579 MET cc_start: 0.1094 (mtt) cc_final: 0.0807 (mtm) REVERT: E 958 ILE cc_start: 0.9595 (pt) cc_final: 0.9272 (pt) REVERT: E 987 MET cc_start: 0.9321 (tmm) cc_final: 0.9115 (tmm) REVERT: E 1007 MET cc_start: 0.9051 (tmm) cc_final: 0.8533 (tmm) REVERT: E 1011 MET cc_start: 0.9143 (mmp) cc_final: 0.8726 (mmm) REVERT: E 1105 MET cc_start: 0.8310 (ppp) cc_final: 0.8006 (ppp) outliers start: 3 outliers final: 1 residues processed: 174 average time/residue: 0.1832 time to fit residues: 53.1955 Evaluate side-chains 150 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 76 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 391 optimal weight: 5.9990 chunk 298 optimal weight: 0.8980 chunk 300 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 192 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 E 276 ASN E 376 ASN ** 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** E1014 ASN E1048 HIS ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.051512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.031522 restraints weight = 296491.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.031524 restraints weight = 225065.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.032002 restraints weight = 167039.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.032161 restraints weight = 134427.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.032161 restraints weight = 122259.138| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33556 Z= 0.186 Angle : 0.648 8.966 45324 Z= 0.341 Chirality : 0.044 0.195 5024 Planarity : 0.005 0.059 5796 Dihedral : 5.230 34.849 4394 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.08 % Allowed : 3.82 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.13), residues: 4022 helix: 0.11 (0.11), residues: 2024 sheet: -1.61 (0.24), residues: 458 loop : -1.23 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 683 TYR 0.019 0.002 TYR B 585 PHE 0.015 0.001 PHE E1462 TRP 0.017 0.002 TRP E 102 HIS 0.009 0.001 HIS B1056 Details of bonding type rmsd covalent geometry : bond 0.00392 (33556) covalent geometry : angle 0.64847 (45324) hydrogen bonds : bond 0.04164 ( 1693) hydrogen bonds : angle 5.50256 ( 4959) *********************** 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 162 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 159 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3684 (tpt) cc_final: 0.2899 (mmm) REVERT: B 306 MET cc_start: -0.1011 (tpt) cc_final: -0.3441 (ttt) REVERT: B 802 MET cc_start: 0.6939 (ptm) cc_final: 0.6213 (ppp) REVERT: B 958 ILE cc_start: 0.9619 (pt) cc_final: 0.9312 (pt) REVERT: B 1007 MET cc_start: 0.8910 (tmm) cc_final: 0.8310 (tmm) REVERT: B 1011 MET cc_start: 0.9190 (mmp) cc_final: 0.8772 (mmm) REVERT: B 1482 MET cc_start: 0.8481 (mmm) cc_final: 0.7910 (mmm) REVERT: B 1560 MET cc_start: 0.7477 (pmm) cc_final: 0.7246 (pmm) REVERT: C 45 MET cc_start: 0.6482 (pmm) cc_final: 0.5717 (tmm) REVERT: D 721 ASP cc_start: 0.8066 (t70) cc_final: 0.7764 (p0) REVERT: E 243 MET cc_start: 0.4893 (ppp) cc_final: 0.4105 (ttp) REVERT: E 267 MET cc_start: 0.4096 (mmm) cc_final: 0.3675 (tmm) REVERT: E 579 MET cc_start: 0.1097 (mtt) cc_final: 0.0827 (mtm) REVERT: E 958 ILE cc_start: 0.9633 (pt) cc_final: 0.9302 (pt) REVERT: E 987 MET cc_start: 0.9363 (tmm) cc_final: 0.9161 (tmm) REVERT: E 1007 MET cc_start: 0.9090 (tmm) cc_final: 0.8682 (tmm) REVERT: E 1011 MET cc_start: 0.9170 (mmp) cc_final: 0.8771 (mmm) REVERT: E 1105 MET cc_start: 0.8540 (ppp) cc_final: 0.8186 (ppp) REVERT: F 45 MET cc_start: 0.6526 (pmm) cc_final: 0.5603 (tmm) outliers start: 3 outliers final: 0 residues processed: 162 average time/residue: 0.1673 time to fit residues: 46.2896 Evaluate side-chains 141 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 335 optimal weight: 1.9990 chunk 251 optimal weight: 6.9990 chunk 344 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 334 optimal weight: 2.9990 chunk 313 optimal weight: 3.9990 chunk 191 optimal weight: 20.0000 chunk 165 optimal weight: 0.2980 chunk 358 optimal weight: 0.8980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 601 HIS ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 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 ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 HIS E 412 GLN ** 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** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.052593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.031684 restraints weight = 295064.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.032091 restraints weight = 206588.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.032518 restraints weight = 156249.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.032874 restraints weight = 130939.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.032986 restraints weight = 115167.317| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 33556 Z= 0.137 Angle : 0.636 10.177 45324 Z= 0.330 Chirality : 0.043 0.184 5024 Planarity : 0.005 0.065 5796 Dihedral : 5.157 35.897 4394 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.03 % Allowed : 2.32 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.13), residues: 4022 helix: 0.19 (0.11), residues: 2036 sheet: -1.54 (0.24), residues: 446 loop : -1.29 (0.17), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1121 TYR 0.017 0.001 TYR B 585 PHE 0.041 0.001 PHE B 795 TRP 0.015 0.002 TRP E 102 HIS 0.005 0.001 HIS E1056 Details of bonding type rmsd covalent geometry : bond 0.00298 (33556) covalent geometry : angle 0.63645 (45324) hydrogen bonds : bond 0.03957 ( 1693) hydrogen bonds : angle 5.40402 ( 4959) *********************** 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 165 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.2518 (tpt) cc_final: 0.1823 (mmm) REVERT: B 306 MET cc_start: 0.0144 (tpt) cc_final: -0.1620 (ttt) REVERT: B 802 MET cc_start: 0.6893 (ptm) cc_final: 0.6485 (ppp) REVERT: B 929 MET cc_start: 0.8534 (mtt) cc_final: 0.8330 (mtp) REVERT: B 958 ILE cc_start: 0.9607 (pt) cc_final: 0.9307 (pt) REVERT: B 1007 MET cc_start: 0.8983 (tmm) cc_final: 0.8409 (tmm) REVERT: B 1011 MET cc_start: 0.9125 (mmp) cc_final: 0.8741 (mmm) REVERT: B 1131 MET cc_start: 0.7732 (ptp) cc_final: 0.7481 (ptp) REVERT: B 1426 MET cc_start: 0.8415 (ttm) cc_final: 0.8101 (mtp) REVERT: B 1482 MET cc_start: 0.8437 (mmm) cc_final: 0.7849 (mmm) REVERT: B 1560 MET cc_start: 0.7373 (pmm) cc_final: 0.7020 (pmm) REVERT: D 721 ASP cc_start: 0.8064 (t70) cc_final: 0.7750 (p0) REVERT: E 243 MET cc_start: 0.4899 (ppp) cc_final: 0.4246 (ttp) REVERT: E 267 MET cc_start: 0.4127 (mmm) cc_final: 0.3773 (tmm) REVERT: E 579 MET cc_start: 0.0671 (mtt) cc_final: 0.0453 (mtm) REVERT: E 929 MET cc_start: 0.8626 (mtm) cc_final: 0.8289 (mtp) REVERT: E 958 ILE cc_start: 0.9632 (pt) cc_final: 0.9357 (pt) REVERT: E 964 MET cc_start: 0.7710 (mmm) cc_final: 0.6872 (mmm) REVERT: E 1007 MET cc_start: 0.9083 (tmm) cc_final: 0.8595 (tmm) REVERT: E 1011 MET cc_start: 0.9136 (mmp) cc_final: 0.8703 (mmm) REVERT: E 1105 MET cc_start: 0.8494 (ppp) cc_final: 0.7819 (ppp) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.1623 time to fit residues: 46.0820 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 : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 201 optimal weight: 0.7980 chunk 258 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 222 optimal weight: 0.8980 chunk 373 optimal weight: 0.8980 chunk 397 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 385 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** B1477 ASN ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1477 ASN ** 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 = 0.3625 r_free = 0.3625 target = 0.053155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.032199 restraints weight = 287307.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.032629 restraints weight = 203757.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.033124 restraints weight = 157617.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.033333 restraints weight = 131813.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.033660 restraints weight = 122390.710| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 33556 Z= 0.122 Angle : 0.633 9.383 45324 Z= 0.325 Chirality : 0.043 0.242 5024 Planarity : 0.004 0.063 5796 Dihedral : 5.041 37.165 4394 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.14), residues: 4022 helix: 0.33 (0.12), residues: 2022 sheet: -1.34 (0.25), residues: 442 loop : -1.23 (0.17), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 683 TYR 0.020 0.001 TYR E1291 PHE 0.033 0.001 PHE B 795 TRP 0.015 0.001 TRP E 102 HIS 0.003 0.001 HIS B 924 Details of bonding type rmsd covalent geometry : bond 0.00263 (33556) covalent geometry : angle 0.63272 (45324) hydrogen bonds : bond 0.03802 ( 1693) hydrogen bonds : angle 5.21840 ( 4959) *********************** 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 161 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.225 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: 0.2496 (tpt) cc_final: 0.1901 (mmm) REVERT: B 306 MET cc_start: -0.0202 (tpt) cc_final: -0.1366 (ttt) REVERT: B 802 MET cc_start: 0.6776 (ptm) cc_final: 0.6420 (ppp) REVERT: B 958 ILE cc_start: 0.9634 (pt) cc_final: 0.9367 (pt) REVERT: B 1007 MET cc_start: 0.9051 (tmm) cc_final: 0.8577 (tmm) REVERT: B 1011 MET cc_start: 0.9183 (mmp) cc_final: 0.8747 (mmm) REVERT: B 1131 MET cc_start: 0.7742 (ptp) cc_final: 0.7530 (ptp) REVERT: B 1324 LEU cc_start: 0.9293 (tp) cc_final: 0.9072 (tp) REVERT: B 1482 MET cc_start: 0.8401 (mmm) cc_final: 0.7806 (mmm) REVERT: B 1560 MET cc_start: 0.7361 (pmm) cc_final: 0.7106 (pmm) REVERT: C 45 MET cc_start: 0.6467 (pmm) cc_final: 0.5681 (tmm) REVERT: D 721 ASP cc_start: 0.8050 (t70) cc_final: 0.7740 (p0) REVERT: E 243 MET cc_start: 0.4794 (ppp) cc_final: 0.4119 (ttp) REVERT: E 306 MET cc_start: -0.1599 (tpt) cc_final: -0.3641 (ttt) REVERT: E 929 MET cc_start: 0.8446 (mtm) cc_final: 0.8220 (mtp) REVERT: E 958 ILE cc_start: 0.9623 (pt) cc_final: 0.9366 (pt) REVERT: E 987 MET cc_start: 0.9325 (tmm) cc_final: 0.9109 (tmm) REVERT: E 1007 MET cc_start: 0.9100 (tmm) cc_final: 0.8625 (tmm) REVERT: E 1011 MET cc_start: 0.9196 (mmp) cc_final: 0.8719 (mmm) REVERT: E 1482 MET cc_start: 0.8300 (mmp) cc_final: 0.7505 (mmm) REVERT: F 45 MET cc_start: 0.6359 (pmm) cc_final: 0.5464 (tmm) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1620 time to fit residues: 45.0319 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 : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 285 optimal weight: 9.9990 chunk 377 optimal weight: 0.4980 chunk 59 optimal weight: 6.9990 chunk 80 optimal weight: 0.0170 chunk 393 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 216 optimal weight: 0.8980 chunk 223 optimal weight: 2.9990 chunk 386 optimal weight: 0.3980 chunk 247 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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** ** 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 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 = 0.3630 r_free = 0.3630 target = 0.053429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.032272 restraints weight = 285619.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.032959 restraints weight = 196886.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.033413 restraints weight = 154881.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.033668 restraints weight = 131969.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.033882 restraints weight = 118777.903| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 33556 Z= 0.122 Angle : 0.630 9.310 45324 Z= 0.323 Chirality : 0.043 0.228 5024 Planarity : 0.004 0.080 5796 Dihedral : 4.977 37.523 4394 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.14), residues: 4022 helix: 0.41 (0.12), residues: 2020 sheet: -1.45 (0.24), residues: 456 loop : -1.22 (0.17), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 935 TYR 0.024 0.001 TYR E 572 PHE 0.017 0.001 PHE B 59 TRP 0.014 0.001 TRP E 102 HIS 0.003 0.001 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00263 (33556) covalent geometry : angle 0.62962 (45324) hydrogen bonds : bond 0.03788 ( 1693) hydrogen bonds : angle 5.13544 ( 4959) *********************** 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 164 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.2791 (tpt) cc_final: 0.2396 (mmm) REVERT: B 158 MET cc_start: 0.8951 (pmm) cc_final: 0.8715 (pmm) REVERT: B 306 MET cc_start: 0.0684 (tpt) cc_final: -0.0118 (ttt) REVERT: B 764 PHE cc_start: 0.9640 (m-80) cc_final: 0.9423 (m-80) REVERT: B 802 MET cc_start: 0.6934 (ptm) cc_final: 0.6644 (ppp) REVERT: B 905 LEU cc_start: 0.9489 (tp) cc_final: 0.9210 (pp) REVERT: B 929 MET cc_start: 0.8732 (mtt) cc_final: 0.8232 (mtp) REVERT: B 958 ILE cc_start: 0.9672 (pt) cc_final: 0.9403 (pt) REVERT: B 1007 MET cc_start: 0.9166 (tmm) cc_final: 0.8732 (tmm) REVERT: B 1011 MET cc_start: 0.9309 (mmp) cc_final: 0.8799 (mmm) REVERT: B 1105 MET cc_start: 0.9088 (tmm) cc_final: 0.8878 (tmm) REVERT: B 1313 MET cc_start: 0.8185 (ttm) cc_final: 0.7470 (tmm) REVERT: B 1324 LEU cc_start: 0.9258 (tp) cc_final: 0.8999 (tp) REVERT: B 1482 MET cc_start: 0.8477 (mmm) cc_final: 0.7867 (mmm) REVERT: B 1560 MET cc_start: 0.7413 (pmm) cc_final: 0.7127 (pmm) REVERT: C 45 MET cc_start: 0.6335 (pmm) cc_final: 0.5475 (tmm) REVERT: D 721 ASP cc_start: 0.7952 (t70) cc_final: 0.7642 (p0) REVERT: E 158 MET cc_start: 0.8978 (pmm) cc_final: 0.8720 (pmm) REVERT: E 243 MET cc_start: 0.4937 (ppp) cc_final: 0.4315 (ttp) REVERT: E 267 MET cc_start: 0.3928 (mmm) cc_final: 0.3716 (tmm) REVERT: E 306 MET cc_start: -0.1188 (tpt) cc_final: -0.2894 (ttt) REVERT: E 929 MET cc_start: 0.8701 (mtm) cc_final: 0.8394 (mtp) REVERT: E 958 ILE cc_start: 0.9664 (pt) cc_final: 0.9411 (pt) REVERT: E 964 MET cc_start: 0.8290 (mmp) cc_final: 0.7931 (mmm) REVERT: E 987 MET cc_start: 0.9379 (tmm) cc_final: 0.9153 (tmm) REVERT: E 1007 MET cc_start: 0.9171 (tmm) cc_final: 0.8688 (tmm) REVERT: E 1011 MET cc_start: 0.9295 (mmp) cc_final: 0.8758 (mmm) REVERT: E 1482 MET cc_start: 0.8396 (mmp) cc_final: 0.7568 (mmm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1803 time to fit residues: 50.9068 Evaluate side-chains 146 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 120 optimal weight: 6.9990 chunk 219 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 393 optimal weight: 3.9990 chunk 58 optimal weight: 0.1980 chunk 364 optimal weight: 2.9990 chunk 302 optimal weight: 9.9990 chunk 363 optimal weight: 3.9990 chunk 288 optimal weight: 9.9990 chunk 154 optimal weight: 0.4980 chunk 312 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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** ** 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 = 0.3612 r_free = 0.3612 target = 0.052166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.031816 restraints weight = 287643.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.032198 restraints weight = 220580.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.032596 restraints weight = 164617.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.032915 restraints weight = 138187.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.033119 restraints weight = 122898.344| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2985 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= 0.146 Angle : 0.651 13.048 45324 Z= 0.337 Chirality : 0.043 0.212 5024 Planarity : 0.005 0.062 5796 Dihedral : 5.008 36.021 4394 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.14), residues: 4022 helix: 0.42 (0.12), residues: 2008 sheet: -1.39 (0.24), residues: 458 loop : -1.20 (0.17), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 935 TYR 0.028 0.002 TYR E 572 PHE 0.034 0.001 PHE B 795 TRP 0.015 0.002 TRP E 102 HIS 0.005 0.001 HIS B1056 Details of bonding type rmsd covalent geometry : bond 0.00321 (33556) covalent geometry : angle 0.65103 (45324) hydrogen bonds : bond 0.03846 ( 1693) hydrogen bonds : angle 5.23911 ( 4959) *********************** 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 159 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 306 MET cc_start: -0.1001 (tpt) cc_final: -0.2288 (ttt) REVERT: B 593 MET cc_start: 0.3630 (ptp) cc_final: 0.2916 (tmm) REVERT: B 595 MET cc_start: 0.7056 (mmt) cc_final: 0.6840 (mmt) REVERT: B 764 PHE cc_start: 0.9618 (m-80) cc_final: 0.9415 (m-80) REVERT: B 929 MET cc_start: 0.8324 (mtt) cc_final: 0.7909 (mtt) REVERT: B 958 ILE cc_start: 0.9630 (pt) cc_final: 0.9364 (pt) REVERT: B 1007 MET cc_start: 0.9050 (tmm) cc_final: 0.8561 (tmm) REVERT: B 1011 MET cc_start: 0.9256 (mmp) cc_final: 0.8800 (mmm) REVERT: B 1105 MET cc_start: 0.9086 (tmm) cc_final: 0.8839 (tmm) REVERT: B 1131 MET cc_start: 0.7684 (ptp) cc_final: 0.7472 (ptp) REVERT: B 1313 MET cc_start: 0.8170 (ttm) cc_final: 0.7596 (tmm) REVERT: B 1324 LEU cc_start: 0.9306 (tp) cc_final: 0.8988 (tp) REVERT: B 1426 MET cc_start: 0.8508 (ttm) cc_final: 0.8242 (ttp) REVERT: B 1482 MET cc_start: 0.8452 (mmm) cc_final: 0.7873 (mmm) REVERT: B 1560 MET cc_start: 0.7426 (pmm) cc_final: 0.7158 (pmm) REVERT: E 243 MET cc_start: 0.4904 (ppp) cc_final: 0.4235 (ttp) REVERT: E 267 MET cc_start: 0.3986 (mmm) cc_final: 0.3688 (tmm) REVERT: E 306 MET cc_start: -0.2412 (tpt) cc_final: -0.4795 (ttt) REVERT: E 762 TYR cc_start: 0.8986 (m-80) cc_final: 0.8230 (m-10) REVERT: E 764 PHE cc_start: 0.9588 (m-80) cc_final: 0.9361 (m-80) REVERT: E 958 ILE cc_start: 0.9641 (pt) cc_final: 0.9378 (pt) REVERT: E 987 MET cc_start: 0.9365 (tmm) cc_final: 0.9146 (tmm) REVERT: E 1007 MET cc_start: 0.9062 (tmm) cc_final: 0.8659 (tmm) REVERT: E 1011 MET cc_start: 0.9249 (mmp) cc_final: 0.8851 (mmm) REVERT: E 1146 MET cc_start: 0.8811 (pmm) cc_final: 0.8603 (pmm) REVERT: E 1482 MET cc_start: 0.8460 (mmp) cc_final: 0.7614 (mmm) REVERT: F 45 MET cc_start: 0.6046 (pmm) cc_final: 0.5225 (tmm) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1559 time to fit residues: 42.8053 Evaluate side-chains 146 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 272 optimal weight: 50.0000 chunk 205 optimal weight: 0.9980 chunk 166 optimal weight: 10.0000 chunk 385 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 389 optimal weight: 0.8980 chunk 364 optimal weight: 2.9990 chunk 216 optimal weight: 0.0060 chunk 188 optimal weight: 20.0000 chunk 124 optimal weight: 0.9980 overall best weight: 1.1798 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.053166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.031702 restraints weight = 297433.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.032466 restraints weight = 199842.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.032797 restraints weight = 154121.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.033144 restraints weight = 135074.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.033381 restraints weight = 122872.314| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 33556 Z= 0.126 Angle : 0.653 11.042 45324 Z= 0.337 Chirality : 0.044 0.204 5024 Planarity : 0.004 0.066 5796 Dihedral : 4.964 36.942 4394 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.14), residues: 4022 helix: 0.42 (0.12), residues: 2036 sheet: -1.51 (0.24), residues: 448 loop : -1.23 (0.17), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 683 TYR 0.019 0.001 TYR E 585 PHE 0.031 0.001 PHE B 795 TRP 0.018 0.002 TRP E 98 HIS 0.003 0.001 HIS B1056 Details of bonding type rmsd covalent geometry : bond 0.00278 (33556) covalent geometry : angle 0.65333 (45324) hydrogen bonds : bond 0.03795 ( 1693) hydrogen bonds : angle 5.17953 ( 4959) ********************** 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 164 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 721 ASP cc_start: 0.7608 (t70) cc_final: 0.7337 (t0) REVERT: B 306 MET cc_start: 0.0383 (tpt) cc_final: -0.0393 (ttt) REVERT: B 593 MET cc_start: 0.3347 (ptp) cc_final: 0.2725 (tmm) REVERT: B 595 MET cc_start: 0.6996 (mmt) cc_final: 0.6778 (mmt) REVERT: B 762 TYR cc_start: 0.9037 (m-80) cc_final: 0.8302 (m-10) REVERT: B 764 PHE cc_start: 0.9660 (m-80) cc_final: 0.9453 (m-10) REVERT: B 929 MET cc_start: 0.8386 (mtt) cc_final: 0.7764 (mtt) REVERT: B 958 ILE cc_start: 0.9650 (pt) cc_final: 0.9378 (pt) REVERT: B 1007 MET cc_start: 0.9150 (tmm) cc_final: 0.8726 (tmm) REVERT: B 1011 MET cc_start: 0.9331 (mmp) cc_final: 0.8831 (mmm) REVERT: B 1105 MET cc_start: 0.9046 (tmm) cc_final: 0.8774 (tmm) REVERT: B 1131 MET cc_start: 0.7779 (ptp) cc_final: 0.7564 (ptp) REVERT: B 1313 MET cc_start: 0.8217 (ttm) cc_final: 0.7518 (tmm) REVERT: B 1324 LEU cc_start: 0.9295 (tp) cc_final: 0.9003 (tp) REVERT: B 1482 MET cc_start: 0.8486 (mmm) cc_final: 0.7878 (mmm) REVERT: B 1560 MET cc_start: 0.7516 (pmm) cc_final: 0.7225 (pmm) REVERT: C 45 MET cc_start: 0.6306 (pmm) cc_final: 0.5454 (tmm) REVERT: D 721 ASP cc_start: 0.7992 (t0) cc_final: 0.7716 (p0) REVERT: E 243 MET cc_start: 0.4987 (ppp) cc_final: 0.4387 (ttp) REVERT: E 306 MET cc_start: -0.1150 (tpt) cc_final: -0.2798 (ttt) REVERT: E 762 TYR cc_start: 0.9020 (m-80) cc_final: 0.8292 (m-10) REVERT: E 764 PHE cc_start: 0.9623 (m-80) cc_final: 0.9372 (m-80) REVERT: E 929 MET cc_start: 0.8110 (mtp) cc_final: 0.7857 (mtp) REVERT: E 958 ILE cc_start: 0.9660 (pt) cc_final: 0.9385 (pt) REVERT: E 987 MET cc_start: 0.9441 (tmm) cc_final: 0.9219 (tmm) REVERT: E 1007 MET cc_start: 0.9141 (tmm) cc_final: 0.8666 (tmm) REVERT: E 1011 MET cc_start: 0.9349 (mmp) cc_final: 0.8817 (mmm) REVERT: E 1482 MET cc_start: 0.8408 (mmp) cc_final: 0.7568 (mmm) REVERT: F 45 MET cc_start: 0.6194 (pmm) cc_final: 0.5291 (tmm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1675 time to fit residues: 47.1427 Evaluate side-chains 149 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 350 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 293 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 326 optimal weight: 5.9990 chunk 358 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 377 optimal weight: 0.0670 chunk 30 optimal weight: 0.9980 chunk 185 optimal weight: 0.7980 overall best weight: 0.9722 ------------------------------------------------------------------------------- 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** ** B1424 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 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.053213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.032374 restraints weight = 295578.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.032576 restraints weight = 212891.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.033074 restraints weight = 163103.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.033465 restraints weight = 133179.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.033690 restraints weight = 119923.054| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3283 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= 0.126 Angle : 0.652 15.715 45324 Z= 0.338 Chirality : 0.044 0.227 5024 Planarity : 0.004 0.067 5796 Dihedral : 4.896 37.640 4394 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.14), residues: 4022 helix: 0.41 (0.12), residues: 2042 sheet: -1.49 (0.25), residues: 420 loop : -1.24 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 683 TYR 0.019 0.001 TYR B 969 PHE 0.031 0.001 PHE B 795 TRP 0.026 0.002 TRP E 98 HIS 0.003 0.001 HIS B1056 Details of bonding type rmsd covalent geometry : bond 0.00275 (33556) covalent geometry : angle 0.65237 (45324) hydrogen bonds : bond 0.03764 ( 1693) hydrogen bonds : angle 5.16178 ( 4959) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6696.30 seconds wall clock time: 116 minutes 33.73 seconds (6993.73 seconds total)