Starting phenix.real_space_refine on Tue Aug 26 04:19:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zji_60146/08_2025/8zji_60146.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zji_60146/08_2025/8zji_60146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zji_60146/08_2025/8zji_60146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zji_60146/08_2025/8zji_60146.map" model { file = "/net/cci-nas-00/data/ceres_data/8zji_60146/08_2025/8zji_60146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zji_60146/08_2025/8zji_60146.cif" } resolution = 4.23 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 144 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: 7.50, per 1000 atoms: 0.23 Number of scatterers: 32858 At special positions: 0 Unit cell: (227.43, 166.25, 160.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 176 16.00 O 6092 8.00 N 5538 7.00 C 21052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 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: 172 helices and 24 sheets defined 55.5% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 530 through 540 Processing helix chain 'A' and resid 541 through 559 removed outlier: 3.646A pdb=" N LEU A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.767A pdb=" N ILE A 613 " --> pdb=" O VAL A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 622 No H-bonds generated for 'chain 'A' and resid 620 through 622' Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.602A pdb=" N VAL A 637 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 638 " --> pdb=" O LYS A 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 634 through 638' Processing helix chain 'A' and resid 658 through 673 Processing helix chain 'A' and resid 679 through 696 Processing helix chain 'B' and resid 84 through 107 removed outlier: 3.516A pdb=" N VAL B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 133 removed outlier: 4.070A pdb=" N SER B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 168 through 172 removed outlier: 4.187A pdb=" N ILE B 172 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 180 through 205 removed outlier: 4.431A pdb=" N LYS B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.760A pdb=" N GLY B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 276 Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 357 through 361 removed outlier: 3.641A pdb=" N ARG B 360 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 361 " --> pdb=" O ARG B 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 357 through 361' Processing helix chain 'B' and resid 378 through 389 removed outlier: 3.599A pdb=" N VAL B 382 " --> pdb=" O PRO B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 521 through 523 No H-bonds generated for 'chain 'B' and resid 521 through 523' Processing helix chain 'B' and resid 537 through 544 Processing helix chain 'B' and resid 575 through 581 Processing helix chain 'B' and resid 581 through 586 removed outlier: 3.557A pdb=" N LEU B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 605 removed outlier: 3.990A pdb=" N LYS B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN B 605 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 642 removed outlier: 3.699A pdb=" N LEU B 638 " --> pdb=" O ASN B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 648 No H-bonds generated for 'chain 'B' and resid 646 through 648' Processing helix chain 'B' and resid 649 through 658 removed outlier: 4.143A pdb=" N MET B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 666 removed outlier: 3.536A pdb=" N ILE B 665 " --> pdb=" O ASP B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 684 Processing helix chain 'B' and resid 686 through 705 removed outlier: 3.517A pdb=" N ASP B 690 " --> pdb=" O SER B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 711 No H-bonds generated for 'chain 'B' and resid 709 through 711' Processing helix chain 'B' and resid 712 through 723 Processing helix chain 'B' and resid 728 through 743 removed outlier: 3.691A pdb=" N LYS B 732 " --> pdb=" O LEU B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 759 removed outlier: 3.856A pdb=" N GLU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 779 removed outlier: 3.514A pdb=" N LEU B 763 " --> pdb=" O ALA B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 803 Processing helix chain 'B' and resid 805 through 808 removed outlier: 3.595A pdb=" N GLU B 808 " --> pdb=" O PRO B 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 805 through 808' Processing helix chain 'B' and resid 809 through 820 Processing helix chain 'B' and resid 820 through 830 removed outlier: 4.014A pdb=" N ILE B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASP B 826 " --> pdb=" O SER B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 846 Processing helix chain 'B' and resid 852 through 866 Processing helix chain 'B' and resid 874 through 889 Proline residue: B 880 - end of helix Processing helix chain 'B' and resid 895 through 897 No H-bonds generated for 'chain 'B' and resid 895 through 897' Processing helix chain 'B' and resid 898 through 915 Processing helix chain 'B' and resid 921 through 943 removed outlier: 6.386A pdb=" N ARG B 934 " --> pdb=" O GLU B 930 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ARG B 935 " --> pdb=" O ARG B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 964 removed outlier: 3.756A pdb=" N PHE B 953 " --> pdb=" O HIS B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 972 removed outlier: 4.130A pdb=" N TYR B 972 " --> pdb=" O HIS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 976 removed outlier: 4.034A pdb=" N PHE B 976 " --> pdb=" O ILE B 973 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 973 through 976' Processing helix chain 'B' and resid 978 through 998 removed outlier: 3.510A pdb=" N ILE B 982 " --> pdb=" O THR B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1033 Processing helix chain 'B' and resid 1034 through 1037 Processing helix chain 'B' and resid 1042 through 1054 Processing helix chain 'B' and resid 1065 through 1076 removed outlier: 3.855A pdb=" N ARG B1069 " --> pdb=" O SER B1065 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B1070 " --> pdb=" O GLN B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1095 removed outlier: 3.935A pdb=" N GLU B1082 " --> pdb=" O ASP B1078 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY B1095 " --> pdb=" O TRP B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1100 removed outlier: 4.238A pdb=" N ILE B1099 " --> pdb=" O PRO B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1101 through 1106 removed outlier: 3.807A pdb=" N MET B1105 " --> pdb=" O PHE B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1106 through 1114 removed outlier: 3.919A pdb=" N LEU B1110 " --> pdb=" O VAL B1106 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU B1111 " --> pdb=" O GLY B1107 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL B1112 " --> pdb=" O PRO B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1118 through 1139 Proline residue: B1126 - end of helix removed outlier: 3.704A pdb=" N PHE B1129 " --> pdb=" O ILE B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1161 Processing helix chain 'B' and resid 1165 through 1182 removed outlier: 3.636A pdb=" N LYS B1182 " --> pdb=" O GLU B1178 " (cutoff:3.500A) Processing helix chain 'B' and resid 1184 through 1215 Processing helix chain 'B' and resid 1216 through 1235 Processing helix chain 'B' and resid 1236 through 1254 Processing helix chain 'B' and resid 1256 through 1271 removed outlier: 4.029A pdb=" N LEU B1270 " --> pdb=" O LEU B1266 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B1271 " --> pdb=" O HIS B1267 " (cutoff:3.500A) Processing helix chain 'B' and resid 1292 through 1311 Processing helix chain 'B' and resid 1313 through 1332 removed outlier: 3.705A pdb=" N ALA B1317 " --> pdb=" O MET B1313 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU B1323 " --> pdb=" O LYS B1319 " (cutoff:3.500A) Processing helix chain 'B' and resid 1334 through 1355 removed outlier: 3.628A pdb=" N LEU B1338 " --> pdb=" O ASP B1334 " (cutoff:3.500A) Processing helix chain 'B' and resid 1390 through 1402 Processing helix chain 'B' and resid 1447 through 1457 removed outlier: 4.390A pdb=" N LEU B1451 " --> pdb=" O PRO B1447 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B1456 " --> pdb=" O ASN B1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 1513 through 1539 removed outlier: 3.561A pdb=" N ASP B1539 " --> pdb=" O GLN B1535 " (cutoff:3.500A) Processing helix chain 'B' and resid 1544 through 1556 Processing helix chain 'B' and resid 1561 through 1570 Processing helix chain 'B' and resid 1572 through 1579 removed outlier: 3.735A pdb=" N LEU B1576 " --> pdb=" O THR B1572 " (cutoff:3.500A) Processing helix chain 'B' and resid 1580 through 1584 removed outlier: 3.847A pdb=" N GLU B1584 " --> pdb=" O GLU B1581 " (cutoff:3.500A) Processing helix chain 'B' and resid 1585 through 1610 Proline residue: B1598 - end of helix Processing helix chain 'B' and resid 1614 through 1635 removed outlier: 4.179A pdb=" N LEU B1618 " --> pdb=" O GLN B1614 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 26 removed outlier: 3.836A pdb=" N LEU C 19 " --> pdb=" O ALA C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.915A pdb=" N ARG C 66 " --> pdb=" O ASP C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.748A pdb=" N SER C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 67 through 72' Processing helix chain 'C' and resid 86 through 96 Processing helix chain 'C' and resid 96 through 105 Processing helix chain 'C' and resid 116 through 121 removed outlier: 3.700A pdb=" N ASP C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.520A pdb=" N GLY C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 removed outlier: 4.369A pdb=" N VAL C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 177 " --> pdb=" O ILE C 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 540 Processing helix chain 'D' and resid 541 through 559 removed outlier: 3.647A pdb=" N LEU D 545 " --> pdb=" O GLN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 removed outlier: 3.768A pdb=" N ILE D 613 " --> pdb=" O VAL D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 622 No H-bonds generated for 'chain 'D' and resid 620 through 622' Processing helix chain 'D' and resid 634 through 638 removed outlier: 3.601A pdb=" N VAL D 637 " --> pdb=" O ASN D 634 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU D 638 " --> pdb=" O LYS D 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 634 through 638' Processing helix chain 'D' and resid 658 through 673 Processing helix chain 'D' and resid 679 through 696 Processing helix chain 'E' and resid 84 through 107 removed outlier: 3.516A pdb=" N VAL E 88 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 133 removed outlier: 4.071A pdb=" N SER E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 168 through 172 removed outlier: 4.186A pdb=" N ILE E 172 " --> pdb=" O ASN E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 177 Processing helix chain 'E' and resid 180 through 205 removed outlier: 4.431A pdb=" N LYS E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER E 203 " --> pdb=" O GLN E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 217 removed outlier: 3.760A pdb=" N GLY E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 276 Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 329 through 335 Processing helix chain 'E' and resid 357 through 361 removed outlier: 3.640A pdb=" N ARG E 360 " --> pdb=" O ILE E 357 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN E 361 " --> pdb=" O ARG E 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 357 through 361' Processing helix chain 'E' and resid 378 through 389 removed outlier: 3.599A pdb=" N VAL E 382 " --> pdb=" O PRO E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 417 Processing helix chain 'E' and resid 521 through 523 No H-bonds generated for 'chain 'E' and resid 521 through 523' Processing helix chain 'E' and resid 537 through 544 Processing helix chain 'E' and resid 575 through 581 Processing helix chain 'E' and resid 581 through 586 removed outlier: 3.557A pdb=" N LEU E 586 " --> pdb=" O ALA E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 591 through 605 removed outlier: 3.990A pdb=" N LYS E 604 " --> pdb=" O LEU E 600 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN E 605 " --> pdb=" O GLN E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 642 removed outlier: 3.699A pdb=" N LEU E 638 " --> pdb=" O ASN E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 648 No H-bonds generated for 'chain 'E' and resid 646 through 648' Processing helix chain 'E' and resid 649 through 658 removed outlier: 4.143A pdb=" N MET E 658 " --> pdb=" O LEU E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 661 through 666 removed outlier: 3.536A pdb=" N ILE E 665 " --> pdb=" O ASP E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 684 Processing helix chain 'E' and resid 686 through 705 removed outlier: 3.517A pdb=" N ASP E 690 " --> pdb=" O SER E 686 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 711 No H-bonds generated for 'chain 'E' and resid 709 through 711' Processing helix chain 'E' and resid 712 through 723 Processing helix chain 'E' and resid 728 through 743 removed outlier: 3.691A pdb=" N LYS E 732 " --> pdb=" O LEU E 728 " (cutoff:3.500A) Processing helix chain 'E' and resid 746 through 759 removed outlier: 3.856A pdb=" N GLU E 751 " --> pdb=" O SER E 747 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 759 through 779 removed outlier: 3.514A pdb=" N LEU E 763 " --> pdb=" O ALA E 759 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 803 Processing helix chain 'E' and resid 805 through 808 removed outlier: 3.596A pdb=" N GLU E 808 " --> pdb=" O PRO E 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 805 through 808' Processing helix chain 'E' and resid 809 through 820 Processing helix chain 'E' and resid 820 through 830 removed outlier: 4.014A pdb=" N ILE E 824 " --> pdb=" O LEU E 820 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN E 825 " --> pdb=" O PRO E 821 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ASP E 826 " --> pdb=" O SER E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 832 through 846 Processing helix chain 'E' and resid 852 through 866 Processing helix chain 'E' and resid 874 through 889 Proline residue: E 880 - end of helix Processing helix chain 'E' and resid 895 through 897 No H-bonds generated for 'chain 'E' and resid 895 through 897' Processing helix chain 'E' and resid 898 through 915 Processing helix chain 'E' and resid 921 through 943 removed outlier: 6.386A pdb=" N ARG E 934 " --> pdb=" O GLU E 930 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ARG E 935 " --> pdb=" O ARG E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 949 through 964 removed outlier: 3.756A pdb=" N PHE E 953 " --> pdb=" O HIS E 949 " (cutoff:3.500A) Processing helix chain 'E' and resid 965 through 972 removed outlier: 4.129A pdb=" N TYR E 972 " --> pdb=" O HIS E 968 " (cutoff:3.500A) Processing helix chain 'E' and resid 973 through 976 removed outlier: 4.033A pdb=" N PHE E 976 " --> pdb=" O ILE E 973 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 973 through 976' Processing helix chain 'E' and resid 978 through 998 removed outlier: 3.509A pdb=" N ILE E 982 " --> pdb=" O THR E 978 " (cutoff:3.500A) Processing helix chain 'E' and resid 1006 through 1033 Processing helix chain 'E' and resid 1034 through 1037 Processing helix chain 'E' and resid 1042 through 1054 Processing helix chain 'E' and resid 1065 through 1076 removed outlier: 3.855A pdb=" N ARG E1069 " --> pdb=" O SER E1065 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN E1070 " --> pdb=" O GLN E1066 " (cutoff:3.500A) Processing helix chain 'E' and resid 1078 through 1095 removed outlier: 3.936A pdb=" N GLU E1082 " --> pdb=" O ASP E1078 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY E1095 " --> pdb=" O TRP E1091 " (cutoff:3.500A) Processing helix chain 'E' and resid 1096 through 1100 removed outlier: 4.237A pdb=" N ILE E1099 " --> pdb=" O PRO E1096 " (cutoff:3.500A) Processing helix chain 'E' and resid 1101 through 1106 removed outlier: 3.807A pdb=" N MET E1105 " --> pdb=" O PHE E1101 " (cutoff:3.500A) Processing helix chain 'E' and resid 1106 through 1114 removed outlier: 3.918A pdb=" N LEU E1110 " --> pdb=" O VAL E1106 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU E1111 " --> pdb=" O GLY E1107 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL E1112 " --> pdb=" O PRO E1108 " (cutoff:3.500A) Processing helix chain 'E' and resid 1118 through 1139 Proline residue: E1126 - end of helix removed outlier: 3.703A pdb=" N PHE E1129 " --> pdb=" O ILE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1144 through 1161 Processing helix chain 'E' and resid 1165 through 1182 removed outlier: 3.635A pdb=" N LYS E1182 " --> pdb=" O GLU E1178 " (cutoff:3.500A) Processing helix chain 'E' and resid 1184 through 1215 Processing helix chain 'E' and resid 1216 through 1235 Processing helix chain 'E' and resid 1236 through 1254 Processing helix chain 'E' and resid 1256 through 1271 removed outlier: 4.029A pdb=" N LEU E1270 " --> pdb=" O LEU E1266 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU E1271 " --> pdb=" O HIS E1267 " (cutoff:3.500A) Processing helix chain 'E' and resid 1292 through 1311 Processing helix chain 'E' and resid 1313 through 1332 removed outlier: 3.705A pdb=" N ALA E1317 " --> pdb=" O MET E1313 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU E1323 " --> pdb=" O LYS E1319 " (cutoff:3.500A) Processing helix chain 'E' and resid 1334 through 1355 removed outlier: 3.627A pdb=" N LEU E1338 " --> pdb=" O ASP E1334 " (cutoff:3.500A) Processing helix chain 'E' and resid 1390 through 1402 Processing helix chain 'E' and resid 1447 through 1457 removed outlier: 4.390A pdb=" N LEU E1451 " --> pdb=" O PRO E1447 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA E1456 " --> pdb=" O ASN E1452 " (cutoff:3.500A) Processing helix chain 'E' and resid 1513 through 1539 removed outlier: 3.562A pdb=" N ASP E1539 " --> pdb=" O GLN E1535 " (cutoff:3.500A) Processing helix chain 'E' and resid 1544 through 1556 Processing helix chain 'E' and resid 1561 through 1570 Processing helix chain 'E' and resid 1572 through 1579 removed outlier: 3.735A pdb=" N LEU E1576 " --> pdb=" O THR E1572 " (cutoff:3.500A) Processing helix chain 'E' and resid 1580 through 1584 removed outlier: 3.848A pdb=" N GLU E1584 " --> pdb=" O GLU E1581 " (cutoff:3.500A) Processing helix chain 'E' and resid 1585 through 1610 Proline residue: E1598 - end of helix Processing helix chain 'E' and resid 1614 through 1635 removed outlier: 4.180A pdb=" N LEU E1618 " --> pdb=" O GLN E1614 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 26 removed outlier: 3.837A pdb=" N LEU F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 66 removed outlier: 3.915A pdb=" N ARG F 66 " --> pdb=" O ASP F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 72 removed outlier: 3.747A pdb=" N SER F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR F 72 " --> pdb=" O ARG F 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 67 through 72' Processing helix chain 'F' and resid 86 through 96 Processing helix chain 'F' and resid 96 through 105 Processing helix chain 'F' and resid 116 through 121 removed outlier: 3.701A pdb=" N ASP F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 138 through 150 removed outlier: 3.520A pdb=" N GLY F 142 " --> pdb=" O THR F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 177 removed outlier: 4.368A pdb=" N VAL F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU F 177 " --> pdb=" O ILE F 173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 561 through 563 Processing sheet with id=AA2, first strand: chain 'A' and resid 578 through 579 Processing sheet with id=AA3, first strand: chain 'A' and resid 616 through 618 Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.830A pdb=" N ILE B 37 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TYR B 48 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 46 " --> pdb=" O GLU B 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 344 through 347 removed outlier: 6.654A pdb=" N GLY B 398 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHE B 231 " --> pdb=" O GLY B 398 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TRP B 400 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N TYR B 222 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP B 283 " --> pdb=" O TYR B 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 252 through 253 Processing sheet with id=AA7, first strand: chain 'B' and resid 252 through 253 removed outlier: 6.575A pdb=" N LEU B 296 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL B 326 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N CYS B 298 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL B 324 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE B 300 " --> pdb=" O PHE B 322 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 484 through 485 removed outlier: 6.988A pdb=" N CYS B 508 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N HIS B 452 " --> pdb=" O CYS B 508 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU B 450 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR B 512 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL B 448 " --> pdb=" O THR B 512 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS B 514 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 446 " --> pdb=" O LYS B 514 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLN B 621 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLY B 453 " --> pdb=" O SER B 619 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N SER B 619 " --> pdb=" O GLY B 453 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B 565 " --> pdb=" O THR B 624 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 495 through 496 removed outlier: 3.541A pdb=" N ARG B 532 " --> pdb=" O GLU B 467 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1425 through 1430 Processing sheet with id=AB2, first strand: chain 'B' and resid 1432 through 1433 removed outlier: 6.669A pdb=" N GLN B1461 " --> pdb=" O TYR B1493 " (cutoff:3.500A) removed outlier: 10.897A pdb=" N TYR B1493 " --> pdb=" O GLN B1461 " (cutoff:3.500A) removed outlier: 11.789A pdb=" N ARG B1463 " --> pdb=" O THR B1491 " (cutoff:3.500A) removed outlier: 11.619A pdb=" N THR B1491 " --> pdb=" O ARG B1463 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 41 through 45 removed outlier: 6.936A pdb=" N CYS C 6 " --> pdb=" O TRP C 56 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LYS C 5 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU C 79 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL C 7 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N CYS C 81 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 9 " --> pdb=" O CYS C 81 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 111 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE C 110 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N LEU C 155 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU C 112 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 561 through 563 Processing sheet with id=AB5, first strand: chain 'D' and resid 578 through 579 Processing sheet with id=AB6, first strand: chain 'D' and resid 616 through 618 Processing sheet with id=AB7, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.830A pdb=" N ILE E 37 " --> pdb=" O TYR E 48 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N TYR E 48 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG E 46 " --> pdb=" O GLU E 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 344 through 347 removed outlier: 6.655A pdb=" N GLY E 398 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHE E 231 " --> pdb=" O GLY E 398 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP E 400 " --> pdb=" O LYS E 229 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TYR E 222 " --> pdb=" O ASP E 283 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP E 283 " --> pdb=" O TYR E 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 252 through 253 Processing sheet with id=AC1, first strand: chain 'E' and resid 252 through 253 removed outlier: 6.575A pdb=" N LEU E 296 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL E 326 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N CYS E 298 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL E 324 " --> pdb=" O CYS E 298 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE E 300 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 484 through 485 removed outlier: 6.987A pdb=" N CYS E 508 " --> pdb=" O HIS E 452 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N HIS E 452 " --> pdb=" O CYS E 508 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU E 450 " --> pdb=" O TYR E 510 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR E 512 " --> pdb=" O VAL E 448 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL E 448 " --> pdb=" O THR E 512 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS E 514 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE E 446 " --> pdb=" O LYS E 514 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLN E 621 " --> pdb=" O ILE E 451 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLY E 453 " --> pdb=" O SER E 619 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER E 619 " --> pdb=" O GLY E 453 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY E 565 " --> pdb=" O THR E 624 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 495 through 496 removed outlier: 3.541A pdb=" N ARG E 532 " --> pdb=" O GLU E 467 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 1425 through 1430 Processing sheet with id=AC5, first strand: chain 'E' and resid 1432 through 1433 removed outlier: 6.668A pdb=" N GLN E1461 " --> pdb=" O TYR E1493 " (cutoff:3.500A) removed outlier: 10.897A pdb=" N TYR E1493 " --> pdb=" O GLN E1461 " (cutoff:3.500A) removed outlier: 11.789A pdb=" N ARG E1463 " --> pdb=" O THR E1491 " (cutoff:3.500A) removed outlier: 11.619A pdb=" N THR E1491 " --> pdb=" O ARG E1463 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 41 through 45 removed outlier: 6.936A pdb=" N CYS F 6 " --> pdb=" O TRP F 56 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LYS F 5 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU F 79 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL F 7 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N CYS F 81 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL F 9 " --> pdb=" O CYS F 81 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 111 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE F 110 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N LEU F 155 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU F 112 " --> pdb=" O LEU F 155 " (cutoff:3.500A) 1669 hydrogen bonds defined for protein. 4833 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.54 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6877 1.33 - 1.45: 7367 1.45 - 1.57: 19018 1.57 - 1.69: 0 1.69 - 1.81: 294 Bond restraints: 33556 Sorted by residual: bond pdb=" CA PRO D 710 " pdb=" C PRO D 710 " ideal model delta sigma weight residual 1.514 1.498 0.016 5.50e-03 3.31e+04 8.79e+00 bond pdb=" CA PRO A 710 " pdb=" C PRO A 710 " ideal model delta sigma weight residual 1.514 1.498 0.016 5.50e-03 3.31e+04 8.43e+00 bond pdb=" CA VAL A 599 " pdb=" C VAL A 599 " ideal model delta sigma weight residual 1.522 1.506 0.016 7.10e-03 1.98e+04 5.19e+00 bond pdb=" CA VAL D 599 " pdb=" C VAL D 599 " ideal model delta sigma weight residual 1.522 1.506 0.016 7.10e-03 1.98e+04 5.18e+00 bond pdb=" CA ILE D 713 " pdb=" C ILE D 713 " ideal model delta sigma weight residual 1.524 1.544 -0.019 1.05e-02 9.07e+03 3.45e+00 ... (remaining 33551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 44480 2.48 - 4.96: 729 4.96 - 7.43: 100 7.43 - 9.91: 11 9.91 - 12.39: 4 Bond angle restraints: 45324 Sorted by residual: angle pdb=" C HIS E 971 " pdb=" N TYR E 972 " pdb=" CA TYR E 972 " ideal model delta sigma weight residual 122.58 113.00 9.58 2.07e+00 2.33e-01 2.14e+01 angle pdb=" C HIS B 971 " pdb=" N TYR B 972 " pdb=" CA TYR B 972 " ideal model delta sigma weight residual 122.58 113.05 9.53 2.07e+00 2.33e-01 2.12e+01 angle pdb=" CB MET B1009 " pdb=" CG MET B1009 " pdb=" SD MET B1009 " ideal model delta sigma weight residual 112.70 100.31 12.39 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CB MET E1009 " pdb=" CG MET E1009 " pdb=" SD MET E1009 " ideal model delta sigma weight residual 112.70 100.32 12.38 3.00e+00 1.11e-01 1.70e+01 angle pdb=" N VAL C 14 " pdb=" CA VAL C 14 " pdb=" C VAL C 14 " ideal model delta sigma weight residual 113.71 110.01 3.70 9.50e-01 1.11e+00 1.52e+01 ... (remaining 45319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 18284 17.96 - 35.92: 1862 35.92 - 53.88: 261 53.88 - 71.85: 43 71.85 - 89.81: 26 Dihedral angle restraints: 20476 sinusoidal: 8586 harmonic: 11890 Sorted by residual: dihedral pdb=" CA GLN D 541 " pdb=" C GLN D 541 " pdb=" N PRO D 542 " pdb=" CA PRO D 542 " ideal model delta harmonic sigma weight residual -180.00 -149.85 -30.15 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA GLN A 541 " pdb=" C GLN A 541 " pdb=" N PRO A 542 " pdb=" CA PRO A 542 " ideal model delta harmonic sigma weight residual 180.00 -149.85 -30.15 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA LEU E1576 " pdb=" C LEU E1576 " pdb=" N GLN E1577 " pdb=" CA GLN E1577 " ideal model delta harmonic sigma weight residual 180.00 151.97 28.03 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 20473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3772 0.050 - 0.100: 1003 0.100 - 0.150: 229 0.150 - 0.200: 12 0.200 - 0.250: 8 Chirality restraints: 5024 Sorted by residual: chirality pdb=" CG LEU B1338 " pdb=" CB LEU B1338 " pdb=" CD1 LEU B1338 " pdb=" CD2 LEU B1338 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CG LEU E1338 " pdb=" CB LEU E1338 " pdb=" CD1 LEU E1338 " pdb=" CD2 LEU E1338 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE E1353 " pdb=" CA ILE E1353 " pdb=" CG1 ILE E1353 " pdb=" CG2 ILE E1353 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 5021 not shown) Planarity restraints: 5796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B1107 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO B1108 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B1108 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B1108 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E1107 " 0.043 5.00e-02 4.00e+02 6.47e-02 6.69e+00 pdb=" N PRO E1108 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO E1108 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E1108 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B1527 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C GLU B1527 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU B1527 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG B1528 " -0.013 2.00e-02 2.50e+03 ... (remaining 5793 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 734 2.63 - 3.20: 35072 3.20 - 3.76: 57546 3.76 - 4.33: 78204 4.33 - 4.90: 117256 Nonbonded interactions: 288812 Sorted by model distance: nonbonded pdb=" O ASP E1275 " pdb=" OG1 THR E1292 " model vdw 2.061 3.040 nonbonded pdb=" O ASP B1275 " pdb=" OG1 THR B1292 " model vdw 2.061 3.040 nonbonded pdb=" O ALA E1260 " pdb=" OG1 THR E1263 " model vdw 2.071 3.040 nonbonded pdb=" O ALA B1260 " pdb=" OG1 THR B1263 " model vdw 2.072 3.040 nonbonded pdb=" OG1 THR B 49 " pdb=" OD1 ASN B 52 " model vdw 2.079 3.040 ... (remaining 288807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 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: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 33.230 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 33556 Z= 0.247 Angle : 0.803 12.391 45324 Z= 0.445 Chirality : 0.047 0.250 5024 Planarity : 0.004 0.065 5796 Dihedral : 14.183 89.807 12780 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 32.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z 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: -1.62 (0.13), residues: 4022 helix: -0.62 (0.11), residues: 1988 sheet: -1.49 (0.23), residues: 444 loop : -1.35 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG C 66 TYR 0.035 0.002 TYR B1388 PHE 0.029 0.002 PHE E1101 TRP 0.019 0.002 TRP A 575 HIS 0.020 0.002 HIS B 971 Details of bonding type rmsd covalent geometry : bond 0.00495 (33556) covalent geometry : angle 0.80253 (45324) hydrogen bonds : bond 0.17184 ( 1665) hydrogen bonds : angle 7.38686 ( 4833) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 ARG cc_start: 0.4777 (tpm170) cc_final: 0.4426 (tpm170) REVERT: B 1 MET cc_start: 0.0750 (mmm) cc_final: -0.0343 (mmm) REVERT: B 158 MET cc_start: 0.8494 (pmm) cc_final: 0.8236 (pmm) REVERT: B 192 LYS cc_start: 0.9176 (tptp) cc_final: 0.8823 (tppt) REVERT: B 668 PHE cc_start: 0.8942 (m-10) cc_final: 0.8688 (m-10) REVERT: B 957 MET cc_start: 0.9124 (ppp) cc_final: 0.8870 (ppp) REVERT: B 964 MET cc_start: 0.7639 (mmm) cc_final: 0.7257 (mmm) REVERT: B 1522 MET cc_start: 0.8024 (tpt) cc_final: 0.7394 (tpt) REVERT: C 6 CYS cc_start: 0.9088 (t) cc_final: 0.8805 (m) REVERT: D 726 CYS cc_start: 0.4584 (t) cc_final: 0.3659 (p) REVERT: E 1 MET cc_start: 0.0466 (mmm) cc_final: -0.0430 (mmm) REVERT: E 579 MET cc_start: 0.1738 (ttm) cc_final: 0.1442 (tpp) REVERT: E 658 MET cc_start: 0.6951 (ppp) cc_final: 0.6498 (ptp) REVERT: E 668 PHE cc_start: 0.8849 (m-10) cc_final: 0.8580 (m-80) REVERT: E 671 ASP cc_start: 0.9078 (m-30) cc_final: 0.8790 (t70) REVERT: E 787 PHE cc_start: 0.8867 (t80) cc_final: 0.8648 (t80) REVERT: E 802 MET cc_start: 0.8001 (ppp) cc_final: 0.7517 (ppp) REVERT: E 958 ILE cc_start: 0.9423 (pt) cc_final: 0.9064 (pt) REVERT: E 964 MET cc_start: 0.8183 (mmm) cc_final: 0.7954 (mmm) REVERT: E 1009 MET cc_start: 0.8866 (mmt) cc_final: 0.8464 (mmp) REVERT: E 1079 MET cc_start: 0.8956 (mtm) cc_final: 0.8717 (mtm) REVERT: E 1560 MET cc_start: 0.0610 (ppp) cc_final: -0.0252 (ttp) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2052 time to fit residues: 75.8571 Evaluate side-chains 154 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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: 6.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1014 ASN ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1531 ASN ** B1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 2 GLN C 103 HIS D 550 GLN D 554 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1014 ASN E1035 GLN ** E1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1093 ASN ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1531 ASN F 2 GLN F 103 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.055720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.035969 restraints weight = 263207.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.036861 restraints weight = 199808.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.037745 restraints weight = 146483.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.037286 restraints weight = 126270.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.037274 restraints weight = 123483.141| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 33556 Z= 0.275 Angle : 0.800 11.143 45324 Z= 0.419 Chirality : 0.047 0.291 5024 Planarity : 0.006 0.092 5796 Dihedral : 5.883 72.846 4394 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 27.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.44 % Allowed : 9.04 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -1.55 (0.13), residues: 4022 helix: -0.58 (0.11), residues: 1998 sheet: -1.49 (0.22), residues: 508 loop : -1.26 (0.17), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E1390 TYR 0.041 0.003 TYR B1388 PHE 0.027 0.003 PHE E 795 TRP 0.020 0.002 TRP D 575 HIS 0.017 0.002 HIS E 971 Details of bonding type rmsd covalent geometry : bond 0.00568 (33556) covalent geometry : angle 0.80002 (45324) hydrogen bonds : bond 0.05562 ( 1665) hydrogen bonds : angle 6.14268 ( 4833) *********************** 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 203 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 ARG cc_start: 0.4950 (tpm170) cc_final: 0.4589 (tpm170) REVERT: B 1 MET cc_start: 0.2934 (mmm) cc_final: 0.1672 (mmm) REVERT: B 158 MET cc_start: 0.8604 (pmm) cc_final: 0.8390 (pmm) REVERT: B 192 LYS cc_start: 0.9388 (tptp) cc_final: 0.9157 (tppt) REVERT: B 243 MET cc_start: -0.0778 (tpt) cc_final: -0.1324 (tpt) REVERT: B 490 TYR cc_start: 0.7390 (t80) cc_final: 0.6974 (t80) REVERT: B 668 PHE cc_start: 0.8906 (m-10) cc_final: 0.8664 (m-80) REVERT: B 860 MET cc_start: 0.9386 (pmm) cc_final: 0.9078 (pmm) REVERT: B 1009 MET cc_start: 0.8906 (mmt) cc_final: 0.8589 (mmt) REVERT: B 1011 MET cc_start: 0.9396 (mmp) cc_final: 0.9168 (mmm) REVERT: B 1243 TYR cc_start: 0.8395 (m-80) cc_final: 0.7741 (m-80) REVERT: B 1522 MET cc_start: 0.8742 (tpt) cc_final: 0.8157 (tpt) REVERT: C 6 CYS cc_start: 0.9164 (t) cc_final: 0.8916 (m) REVERT: D 692 MET cc_start: 0.8688 (mmp) cc_final: 0.8243 (mmm) REVERT: E 1 MET cc_start: 0.2340 (mmm) cc_final: 0.1493 (mmm) REVERT: E 658 MET cc_start: 0.7466 (ppp) cc_final: 0.7207 (ptp) REVERT: E 668 PHE cc_start: 0.8795 (m-10) cc_final: 0.8550 (m-80) REVERT: E 671 ASP cc_start: 0.8989 (m-30) cc_final: 0.8661 (t70) REVERT: E 787 PHE cc_start: 0.8865 (t80) cc_final: 0.8624 (t80) REVERT: E 795 PHE cc_start: 0.9553 (m-80) cc_final: 0.9349 (m-10) REVERT: E 802 MET cc_start: 0.7450 (ppp) cc_final: 0.6761 (ppp) REVERT: E 958 ILE cc_start: 0.9500 (pt) cc_final: 0.9036 (pt) REVERT: E 1011 MET cc_start: 0.9261 (mmp) cc_final: 0.9028 (mmm) REVERT: E 1243 TYR cc_start: 0.8510 (m-80) cc_final: 0.7846 (m-80) REVERT: E 1426 MET cc_start: 0.8592 (ptt) cc_final: 0.8367 (ptt) REVERT: E 1435 MET cc_start: 0.8572 (tpt) cc_final: 0.8360 (tpt) REVERT: E 1560 MET cc_start: 0.1542 (ppp) cc_final: 0.0753 (ttp) REVERT: E 1597 MET cc_start: 0.9224 (mmp) cc_final: 0.8539 (ttp) REVERT: F 2 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7490 (pp30) REVERT: F 45 MET cc_start: 0.8072 (tpt) cc_final: 0.7869 (tpt) outliers start: 16 outliers final: 7 residues processed: 203 average time/residue: 0.2079 time to fit residues: 72.3704 Evaluate side-chains 163 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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: 6.9990 chunk 214 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 397 optimal weight: 6.9990 chunk 265 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 249 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 chunk 41 optimal weight: 30.0000 chunk 278 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 HIS ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 HIS B 845 GLN ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 ASN B1460 GLN ** B1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1636 HIS ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 HIS ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 GLN ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1035 GLN ** E1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1351 ASN ** E1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1565 ASN F 103 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.057133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.035577 restraints weight = 275791.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.036496 restraints weight = 202481.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.036407 restraints weight = 156442.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.036644 restraints weight = 131126.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.036618 restraints weight = 122624.496| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33556 Z= 0.191 Angle : 0.709 11.593 45324 Z= 0.369 Chirality : 0.046 0.267 5024 Planarity : 0.005 0.074 5796 Dihedral : 5.697 74.159 4394 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.29 (0.13), residues: 4022 helix: -0.29 (0.11), residues: 2012 sheet: -1.50 (0.22), residues: 508 loop : -1.20 (0.17), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 534 TYR 0.031 0.002 TYR B1388 PHE 0.026 0.002 PHE B 777 TRP 0.022 0.002 TRP E 102 HIS 0.013 0.001 HIS B 971 Details of bonding type rmsd covalent geometry : bond 0.00411 (33556) covalent geometry : angle 0.70926 (45324) hydrogen bonds : bond 0.05010 ( 1665) hydrogen bonds : angle 5.79825 ( 4833) *********************** 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 200 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 197 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 ARG cc_start: 0.4973 (tpm170) cc_final: 0.4618 (tpm170) REVERT: B 1 MET cc_start: 0.3180 (mmm) cc_final: 0.1571 (mmm) REVERT: B 158 MET cc_start: 0.8759 (pmm) cc_final: 0.8456 (pmm) REVERT: B 192 LYS cc_start: 0.9381 (tptp) cc_final: 0.9118 (tppt) REVERT: B 243 MET cc_start: -0.1702 (tpt) cc_final: -0.1967 (tpt) REVERT: B 683 MET cc_start: 0.6898 (ppp) cc_final: 0.6696 (ppp) REVERT: B 958 ILE cc_start: 0.9553 (pt) cc_final: 0.9204 (pt) REVERT: B 971 HIS cc_start: 0.8405 (m-70) cc_final: 0.8182 (m-70) REVERT: B 1011 MET cc_start: 0.9336 (mmp) cc_final: 0.8934 (mmp) REVERT: B 1243 TYR cc_start: 0.8129 (m-80) cc_final: 0.7464 (m-80) REVERT: B 1522 MET cc_start: 0.8680 (tpt) cc_final: 0.8065 (tpt) REVERT: C 1 MET cc_start: 0.5295 (tpt) cc_final: 0.4961 (tpp) REVERT: C 6 CYS cc_start: 0.9115 (t) cc_final: 0.8898 (m) REVERT: C 45 MET cc_start: 0.8169 (tpt) cc_final: 0.7686 (tpt) REVERT: D 692 MET cc_start: 0.8627 (mmp) cc_final: 0.8199 (mmm) REVERT: E 1 MET cc_start: 0.2442 (mmm) cc_final: 0.1413 (mmm) REVERT: E 353 MET cc_start: 0.5589 (mpp) cc_final: 0.4717 (mpp) REVERT: E 579 MET cc_start: 0.0574 (ttm) cc_final: 0.0345 (tpp) REVERT: E 658 MET cc_start: 0.7430 (ppp) cc_final: 0.7124 (ptp) REVERT: E 668 PHE cc_start: 0.8658 (m-10) cc_final: 0.8447 (m-80) REVERT: E 958 ILE cc_start: 0.9522 (pt) cc_final: 0.9094 (pt) REVERT: E 1011 MET cc_start: 0.9257 (mmp) cc_final: 0.8885 (mmm) REVERT: E 1243 TYR cc_start: 0.8366 (m-80) cc_final: 0.7772 (m-80) REVERT: E 1435 MET cc_start: 0.8561 (tpt) cc_final: 0.8358 (tpt) REVERT: E 1522 MET cc_start: 0.9047 (mtp) cc_final: 0.8267 (tpt) REVERT: E 1560 MET cc_start: 0.1814 (ppp) cc_final: 0.0920 (ttp) REVERT: E 1597 MET cc_start: 0.9152 (mmp) cc_final: 0.8483 (ttp) REVERT: F 6 CYS cc_start: 0.9156 (t) cc_final: 0.8868 (m) REVERT: F 45 MET cc_start: 0.7987 (tpt) cc_final: 0.7761 (tpt) outliers start: 3 outliers final: 1 residues processed: 200 average time/residue: 0.2136 time to fit residues: 72.7737 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 : 1.408 ------------------------------------------------------------------------------- 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: 1.9990 chunk 269 optimal weight: 40.0000 chunk 140 optimal weight: 4.9990 chunk 233 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 317 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 210 optimal weight: 8.9990 chunk 223 optimal weight: 20.0000 chunk 338 optimal weight: 0.9980 chunk 385 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 HIS ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 HIS D 550 GLN ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1035 GLN ** E1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1203 ASN ** E1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN F 103 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.056931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.035280 restraints weight = 273927.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.035426 restraints weight = 198879.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.035938 restraints weight = 157463.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.036171 restraints weight = 135799.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.036409 restraints weight = 125882.746| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 33556 Z= 0.197 Angle : 0.707 10.495 45324 Z= 0.368 Chirality : 0.045 0.263 5024 Planarity : 0.005 0.072 5796 Dihedral : 5.619 72.668 4394 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 22.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.08 % Allowed : 5.46 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -1.19 (0.13), residues: 4022 helix: -0.17 (0.11), residues: 2006 sheet: -1.49 (0.22), residues: 498 loop : -1.21 (0.17), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 128 TYR 0.026 0.002 TYR B1328 PHE 0.022 0.002 PHE E 795 TRP 0.042 0.002 TRP B 643 HIS 0.008 0.001 HIS B 971 Details of bonding type rmsd covalent geometry : bond 0.00415 (33556) covalent geometry : angle 0.70710 (45324) hydrogen bonds : bond 0.04701 ( 1665) hydrogen bonds : angle 5.68836 ( 4833) *********************** 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 198 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 195 time to evaluate : 1.400 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: 0.2820 (mmm) cc_final: 0.1131 (mmm) REVERT: B 243 MET cc_start: -0.1693 (tpt) cc_final: -0.1961 (tpt) REVERT: B 353 MET cc_start: 0.5671 (mpp) cc_final: 0.4801 (mpp) REVERT: B 658 MET cc_start: 0.7169 (ppp) cc_final: 0.6748 (ptp) REVERT: B 668 PHE cc_start: 0.8805 (m-80) cc_final: 0.8338 (m-80) REVERT: B 683 MET cc_start: 0.6990 (ppp) cc_final: 0.6647 (ppp) REVERT: B 802 MET cc_start: 0.6748 (ppp) cc_final: 0.6453 (ppp) REVERT: B 958 ILE cc_start: 0.9540 (pt) cc_final: 0.9209 (pt) REVERT: B 971 HIS cc_start: 0.8415 (m-70) cc_final: 0.8138 (m-70) REVERT: B 1011 MET cc_start: 0.9392 (mmp) cc_final: 0.8989 (mmp) REVERT: B 1243 TYR cc_start: 0.8549 (m-80) cc_final: 0.7857 (m-80) REVERT: B 1522 MET cc_start: 0.8907 (tpt) cc_final: 0.8172 (tpt) REVERT: C 1 MET cc_start: 0.5706 (tpt) cc_final: 0.5206 (tpp) REVERT: C 6 CYS cc_start: 0.9122 (t) cc_final: 0.8883 (m) REVERT: D 692 MET cc_start: 0.8651 (mmp) cc_final: 0.8258 (mmm) REVERT: E 1 MET cc_start: 0.1827 (mmm) cc_final: 0.0282 (mmm) REVERT: E 579 MET cc_start: -0.0418 (ttm) cc_final: -0.0648 (tpp) REVERT: E 658 MET cc_start: 0.7563 (ppp) cc_final: 0.7312 (ptp) REVERT: E 668 PHE cc_start: 0.8710 (m-10) cc_final: 0.8497 (m-80) REVERT: E 762 TYR cc_start: 0.8647 (m-10) cc_final: 0.8195 (m-10) REVERT: E 958 ILE cc_start: 0.9526 (pt) cc_final: 0.9206 (pt) REVERT: E 1011 MET cc_start: 0.9319 (mmp) cc_final: 0.8915 (mmm) REVERT: E 1243 TYR cc_start: 0.8663 (m-80) cc_final: 0.8116 (m-80) REVERT: E 1313 MET cc_start: 0.8311 (mtp) cc_final: 0.8111 (ttt) REVERT: E 1435 MET cc_start: 0.8632 (tpt) cc_final: 0.8418 (tpt) REVERT: E 1597 MET cc_start: 0.9200 (mmp) cc_final: 0.8538 (ttp) REVERT: F 6 CYS cc_start: 0.9127 (t) cc_final: 0.8918 (m) REVERT: F 92 ASN cc_start: 0.9300 (t0) cc_final: 0.9091 (t0) outliers start: 3 outliers final: 1 residues processed: 198 average time/residue: 0.2102 time to fit residues: 71.2433 Evaluate side-chains 163 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 1.600 ------------------------------------------------------------------------------- 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: 3.9990 chunk 200 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 391 optimal weight: 0.8980 chunk 298 optimal weight: 3.9990 chunk 300 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 2 GLN C 92 ASN C 103 HIS ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 GLN ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 HIS ** E 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1035 GLN ** E1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1526 ASN F 103 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.057962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.036433 restraints weight = 274580.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.037009 restraints weight = 200298.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.036984 restraints weight = 162908.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.037169 restraints weight = 128681.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.037229 restraints weight = 119994.135| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33556 Z= 0.140 Angle : 0.671 8.800 45324 Z= 0.343 Chirality : 0.045 0.233 5024 Planarity : 0.005 0.068 5796 Dihedral : 5.449 73.005 4394 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.08 % Allowed : 3.03 % Favored : 96.89 % 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: -0.88 (0.13), residues: 4022 helix: 0.13 (0.11), residues: 1998 sheet: -1.49 (0.22), residues: 502 loop : -1.06 (0.17), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 534 TYR 0.022 0.002 TYR B1388 PHE 0.021 0.001 PHE E1372 TRP 0.020 0.001 TRP E 102 HIS 0.008 0.001 HIS F 103 Details of bonding type rmsd covalent geometry : bond 0.00307 (33556) covalent geometry : angle 0.67095 (45324) hydrogen bonds : bond 0.04281 ( 1665) hydrogen bonds : angle 5.44723 ( 4833) *********************** 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 195 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 192 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.2824 (mmm) cc_final: 0.1052 (mmm) REVERT: B 243 MET cc_start: -0.1709 (tpt) cc_final: -0.1973 (tpt) REVERT: B 353 MET cc_start: 0.5693 (mpp) cc_final: 0.4842 (mpp) REVERT: B 658 MET cc_start: 0.7384 (ppp) cc_final: 0.7046 (ptp) REVERT: B 668 PHE cc_start: 0.8740 (m-80) cc_final: 0.8394 (m-10) REVERT: B 683 MET cc_start: 0.7331 (ppp) cc_final: 0.6963 (ppp) REVERT: B 860 MET cc_start: 0.9369 (pmm) cc_final: 0.9015 (pmm) REVERT: B 958 ILE cc_start: 0.9488 (pt) cc_final: 0.9176 (pt) REVERT: B 971 HIS cc_start: 0.8356 (m-70) cc_final: 0.8097 (m-70) REVERT: B 1011 MET cc_start: 0.9418 (mmp) cc_final: 0.9203 (mmm) REVERT: B 1231 TYR cc_start: 0.8111 (m-10) cc_final: 0.7887 (m-80) REVERT: B 1243 TYR cc_start: 0.8529 (m-80) cc_final: 0.7802 (m-80) REVERT: B 1522 MET cc_start: 0.8909 (tpt) cc_final: 0.8141 (tpt) REVERT: C 2 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7587 (pp30) REVERT: C 6 CYS cc_start: 0.9095 (t) cc_final: 0.8879 (m) REVERT: C 92 ASN cc_start: 0.9139 (t0) cc_final: 0.8871 (t0) REVERT: E 1 MET cc_start: 0.2379 (mmm) cc_final: 0.1355 (mmm) REVERT: E 658 MET cc_start: 0.7639 (ppp) cc_final: 0.7337 (ptp) REVERT: E 668 PHE cc_start: 0.8676 (m-10) cc_final: 0.8460 (m-80) REVERT: E 958 ILE cc_start: 0.9500 (pt) cc_final: 0.9224 (pt) REVERT: E 1011 MET cc_start: 0.9360 (mmp) cc_final: 0.8936 (mmm) REVERT: E 1231 TYR cc_start: 0.8256 (m-10) cc_final: 0.8036 (m-80) REVERT: E 1243 TYR cc_start: 0.8646 (m-80) cc_final: 0.8056 (m-80) REVERT: E 1522 MET cc_start: 0.9101 (mtp) cc_final: 0.8762 (tpt) REVERT: E 1597 MET cc_start: 0.9140 (mmp) cc_final: 0.8413 (ttp) REVERT: F 6 CYS cc_start: 0.9105 (t) cc_final: 0.8874 (m) REVERT: F 45 MET cc_start: 0.7653 (tpt) cc_final: 0.7307 (tpt) REVERT: F 92 ASN cc_start: 0.9242 (t0) cc_final: 0.9021 (t0) outliers start: 3 outliers final: 0 residues processed: 195 average time/residue: 0.2117 time to fit residues: 71.4722 Evaluate side-chains 163 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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: 5.9990 chunk 251 optimal weight: 9.9990 chunk 344 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 186 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 chunk 334 optimal weight: 0.9980 chunk 313 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 358 optimal weight: 4.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 HIS ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN C 103 HIS ** D 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 HIS ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1035 GLN E1060 GLN ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.056548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.034869 restraints weight = 274966.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.035565 restraints weight = 194337.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.036004 restraints weight = 152693.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.036284 restraints weight = 133103.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.036483 restraints weight = 121799.358| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.004 0.068 33556 Z= 0.196 Angle : 0.706 8.876 45324 Z= 0.367 Chirality : 0.045 0.341 5024 Planarity : 0.005 0.078 5796 Dihedral : 5.525 71.248 4394 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 22.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -1.01 (0.13), residues: 4022 helix: -0.04 (0.11), residues: 2002 sheet: -1.48 (0.22), residues: 518 loop : -1.03 (0.17), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E1088 TYR 0.023 0.002 TYR A 588 PHE 0.018 0.002 PHE C 78 TRP 0.015 0.002 TRP E 102 HIS 0.006 0.001 HIS E 971 Details of bonding type rmsd covalent geometry : bond 0.00420 (33556) covalent geometry : angle 0.70552 (45324) hydrogen bonds : bond 0.04532 ( 1665) hydrogen bonds : angle 5.61249 ( 4833) *********************** 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 186 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.2856 (mmm) cc_final: 0.1265 (mmm) REVERT: B 243 MET cc_start: -0.1670 (tpt) cc_final: -0.1936 (tpt) REVERT: B 353 MET cc_start: 0.5644 (mpp) cc_final: 0.4749 (mpp) REVERT: B 658 MET cc_start: 0.7609 (ppp) cc_final: 0.7234 (ptp) REVERT: B 802 MET cc_start: 0.6746 (ppp) cc_final: 0.6538 (ppp) REVERT: B 958 ILE cc_start: 0.9514 (pt) cc_final: 0.9178 (pt) REVERT: B 1007 MET cc_start: 0.9001 (ppp) cc_final: 0.8722 (ppp) REVERT: B 1011 MET cc_start: 0.9461 (mmp) cc_final: 0.9013 (mmp) REVERT: B 1105 MET cc_start: 0.7801 (mmp) cc_final: 0.7359 (mmp) REVERT: B 1231 TYR cc_start: 0.8084 (m-10) cc_final: 0.7716 (m-80) REVERT: B 1243 TYR cc_start: 0.8629 (m-80) cc_final: 0.8110 (m-80) REVERT: B 1326 GLU cc_start: 0.8085 (pp20) cc_final: 0.7767 (pp20) REVERT: B 1522 MET cc_start: 0.8734 (tpt) cc_final: 0.8238 (tpt) REVERT: C 6 CYS cc_start: 0.9109 (t) cc_final: 0.8868 (m) REVERT: C 92 ASN cc_start: 0.9186 (t0) cc_final: 0.8928 (t0) REVERT: D 692 MET cc_start: 0.8796 (mmm) cc_final: 0.8492 (mmm) REVERT: E 1 MET cc_start: 0.2303 (mmm) cc_final: 0.0922 (mmm) REVERT: E 658 MET cc_start: 0.7703 (ppp) cc_final: 0.7367 (ptp) REVERT: E 668 PHE cc_start: 0.8684 (m-10) cc_final: 0.8482 (m-80) REVERT: E 762 TYR cc_start: 0.8667 (m-10) cc_final: 0.8254 (m-10) REVERT: E 958 ILE cc_start: 0.9508 (pt) cc_final: 0.9215 (pt) REVERT: E 1011 MET cc_start: 0.9337 (mmp) cc_final: 0.8914 (mmm) REVERT: E 1231 TYR cc_start: 0.8358 (m-10) cc_final: 0.8056 (m-10) REVERT: E 1243 TYR cc_start: 0.8766 (m-80) cc_final: 0.8172 (m-80) REVERT: E 1435 MET cc_start: 0.8673 (tpt) cc_final: 0.8411 (tpt) REVERT: E 1549 MET cc_start: 0.8892 (mmm) cc_final: 0.8100 (mmm) REVERT: E 1560 MET cc_start: 0.1289 (ttp) cc_final: 0.0307 (ttt) REVERT: E 1597 MET cc_start: 0.9184 (mmp) cc_final: 0.8550 (ttp) REVERT: F 6 CYS cc_start: 0.9110 (t) cc_final: 0.8884 (m) REVERT: F 45 MET cc_start: 0.7835 (tpt) cc_final: 0.7375 (tpt) REVERT: F 92 ASN cc_start: 0.9255 (t0) cc_final: 0.9034 (t0) outliers start: 2 outliers final: 0 residues processed: 186 average time/residue: 0.2081 time to fit residues: 66.5011 Evaluate side-chains 155 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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: 0.4980 chunk 258 optimal weight: 0.3980 chunk 199 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 222 optimal weight: 9.9990 chunk 373 optimal weight: 3.9990 chunk 397 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 385 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 HIS B 116 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 738 ASN ** B 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1022 ASN B1133 GLN ** B1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1565 ASN ** B1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 HIS ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.057746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.036231 restraints weight = 271306.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.036368 restraints weight = 197464.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.036854 restraints weight = 154617.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.037108 restraints weight = 132478.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.037344 restraints weight = 120656.824| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33556 Z= 0.137 Angle : 0.675 10.425 45324 Z= 0.345 Chirality : 0.044 0.273 5024 Planarity : 0.005 0.066 5796 Dihedral : 5.370 73.334 4394 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.03 % Allowed : 1.83 % Favored : 98.14 % 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: -0.82 (0.13), residues: 4022 helix: 0.15 (0.11), residues: 2008 sheet: -1.43 (0.22), residues: 510 loop : -1.01 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B1627 TYR 0.018 0.001 TYR B1388 PHE 0.016 0.001 PHE B1064 TRP 0.020 0.001 TRP E 102 HIS 0.013 0.001 HIS B 971 Details of bonding type rmsd covalent geometry : bond 0.00299 (33556) covalent geometry : angle 0.67523 (45324) hydrogen bonds : bond 0.04167 ( 1665) hydrogen bonds : angle 5.43639 ( 4833) *********************** 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 190 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 1.438 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: 0.2906 (mmm) cc_final: 0.1159 (mmm) REVERT: B 158 MET cc_start: 0.8876 (pmm) cc_final: 0.8667 (pmm) REVERT: B 353 MET cc_start: 0.5723 (mpp) cc_final: 0.4867 (mpp) REVERT: B 658 MET cc_start: 0.7632 (ppp) cc_final: 0.7256 (ptp) REVERT: B 802 MET cc_start: 0.6660 (ppp) cc_final: 0.6383 (ppp) REVERT: B 860 MET cc_start: 0.9321 (pmm) cc_final: 0.9036 (pmm) REVERT: B 958 ILE cc_start: 0.9450 (pt) cc_final: 0.9146 (pt) REVERT: B 964 MET cc_start: 0.7761 (mmm) cc_final: 0.7509 (mmm) REVERT: B 971 HIS cc_start: 0.8337 (m-70) cc_final: 0.8081 (m-70) REVERT: B 1007 MET cc_start: 0.8964 (ppp) cc_final: 0.8500 (ppp) REVERT: B 1011 MET cc_start: 0.9337 (mmp) cc_final: 0.8918 (mmp) REVERT: B 1231 TYR cc_start: 0.7900 (m-10) cc_final: 0.7570 (m-80) REVERT: B 1243 TYR cc_start: 0.8686 (m-80) cc_final: 0.8161 (m-80) REVERT: B 1313 MET cc_start: 0.8466 (mmm) cc_final: 0.8243 (tpp) REVERT: B 1326 GLU cc_start: 0.8042 (pp20) cc_final: 0.7698 (pp20) REVERT: B 1522 MET cc_start: 0.8547 (tpt) cc_final: 0.7958 (tpt) REVERT: B 1540 ARG cc_start: 0.7740 (tpt170) cc_final: 0.7492 (tpt90) REVERT: C 6 CYS cc_start: 0.9081 (t) cc_final: 0.8840 (m) REVERT: C 45 MET cc_start: 0.7349 (tpt) cc_final: 0.7024 (tpt) REVERT: C 92 ASN cc_start: 0.9132 (t0) cc_final: 0.8861 (t0) REVERT: D 692 MET cc_start: 0.8757 (mmm) cc_final: 0.8443 (mmm) REVERT: E 1 MET cc_start: 0.2444 (mmm) cc_final: 0.1491 (mmm) REVERT: E 658 MET cc_start: 0.7717 (ppp) cc_final: 0.7401 (ptp) REVERT: E 668 PHE cc_start: 0.8662 (m-10) cc_final: 0.8460 (m-80) REVERT: E 958 ILE cc_start: 0.9481 (pt) cc_final: 0.9236 (pt) REVERT: E 987 MET cc_start: 0.8714 (tmm) cc_final: 0.8442 (tmm) REVERT: E 1007 MET cc_start: 0.8981 (ppp) cc_final: 0.8641 (ppp) REVERT: E 1011 MET cc_start: 0.9251 (mmp) cc_final: 0.8746 (mmm) REVERT: E 1243 TYR cc_start: 0.8651 (m-80) cc_final: 0.8048 (m-80) REVERT: E 1278 CYS cc_start: 0.6311 (m) cc_final: 0.5624 (p) REVERT: E 1313 MET cc_start: 0.7982 (mtp) cc_final: 0.7692 (tpp) REVERT: E 1522 MET cc_start: 0.9131 (tpt) cc_final: 0.8802 (tpp) REVERT: E 1560 MET cc_start: 0.1301 (ttp) cc_final: 0.0489 (ttt) REVERT: E 1597 MET cc_start: 0.9040 (mmp) cc_final: 0.8371 (ttp) REVERT: F 45 MET cc_start: 0.7664 (tpt) cc_final: 0.7382 (tpt) REVERT: F 92 ASN cc_start: 0.9234 (t0) cc_final: 0.9005 (t0) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.1943 time to fit residues: 63.6233 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 : 1.376 ------------------------------------------------------------------------------- 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: 0.0970 chunk 377 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 393 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 386 optimal weight: 2.9990 chunk 247 optimal weight: 8.9990 chunk 261 optimal weight: 8.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1517 ASN ** B1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 HIS D 660 HIS ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.057635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.035465 restraints weight = 271485.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.036073 restraints weight = 192606.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.036654 restraints weight = 154005.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.036864 restraints weight = 134160.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.037240 restraints weight = 118048.201| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 33556 Z= 0.150 Angle : 0.676 9.098 45324 Z= 0.347 Chirality : 0.044 0.254 5024 Planarity : 0.005 0.095 5796 Dihedral : 5.324 72.461 4394 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -0.79 (0.13), residues: 4022 helix: 0.19 (0.11), residues: 1998 sheet: -1.39 (0.22), residues: 510 loop : -1.01 (0.17), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 66 TYR 0.024 0.002 TYR B1328 PHE 0.014 0.001 PHE C 90 TRP 0.021 0.002 TRP F 56 HIS 0.012 0.001 HIS B 971 Details of bonding type rmsd covalent geometry : bond 0.00328 (33556) covalent geometry : angle 0.67634 (45324) hydrogen bonds : bond 0.04169 ( 1665) hydrogen bonds : angle 5.44573 ( 4833) *********************** 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 183 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.094 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: 0.2851 (mmm) cc_final: 0.1238 (mmm) REVERT: B 353 MET cc_start: 0.6068 (mpp) cc_final: 0.5324 (mpp) REVERT: B 802 MET cc_start: 0.6701 (ppp) cc_final: 0.6451 (ppp) REVERT: B 958 ILE cc_start: 0.9472 (pt) cc_final: 0.9193 (pt) REVERT: B 971 HIS cc_start: 0.8541 (m-70) cc_final: 0.8203 (m-70) REVERT: B 1007 MET cc_start: 0.9042 (ppp) cc_final: 0.8463 (ppp) REVERT: B 1011 MET cc_start: 0.9419 (mmp) cc_final: 0.8911 (mmm) REVERT: B 1231 TYR cc_start: 0.8088 (m-10) cc_final: 0.7754 (m-80) REVERT: B 1243 TYR cc_start: 0.8752 (m-80) cc_final: 0.8179 (m-80) REVERT: B 1313 MET cc_start: 0.8559 (mmm) cc_final: 0.8318 (tpp) REVERT: B 1326 GLU cc_start: 0.8160 (pp20) cc_final: 0.7858 (pp20) REVERT: B 1522 MET cc_start: 0.8656 (tpt) cc_final: 0.8148 (tpt) REVERT: B 1540 ARG cc_start: 0.7750 (tpt170) cc_final: 0.7497 (tpt90) REVERT: C 6 CYS cc_start: 0.9094 (t) cc_final: 0.8854 (m) REVERT: C 45 MET cc_start: 0.7409 (tpt) cc_final: 0.7185 (tpt) REVERT: C 92 ASN cc_start: 0.9154 (t0) cc_final: 0.8885 (t0) REVERT: D 692 MET cc_start: 0.8731 (mmm) cc_final: 0.8478 (mmm) REVERT: E 1 MET cc_start: 0.2541 (mmm) cc_final: 0.0970 (mmm) REVERT: E 658 MET cc_start: 0.7684 (ppp) cc_final: 0.7392 (ptp) REVERT: E 668 PHE cc_start: 0.8663 (m-10) cc_final: 0.8462 (m-80) REVERT: E 958 ILE cc_start: 0.9508 (pt) cc_final: 0.9273 (pt) REVERT: E 987 MET cc_start: 0.8769 (tmm) cc_final: 0.8471 (tmm) REVERT: E 1009 MET cc_start: 0.8935 (mmt) cc_final: 0.8644 (mpp) REVERT: E 1011 MET cc_start: 0.9358 (mmp) cc_final: 0.8825 (mmp) REVERT: E 1243 TYR cc_start: 0.8690 (m-80) cc_final: 0.8083 (m-80) REVERT: E 1278 CYS cc_start: 0.6086 (m) cc_final: 0.5431 (p) REVERT: E 1313 MET cc_start: 0.8093 (mtp) cc_final: 0.7772 (tpp) REVERT: E 1522 MET cc_start: 0.9120 (tpt) cc_final: 0.8872 (tpp) REVERT: E 1560 MET cc_start: 0.1535 (ttp) cc_final: 0.0628 (ttt) REVERT: E 1597 MET cc_start: 0.9089 (mmp) cc_final: 0.8520 (mmm) REVERT: F 45 MET cc_start: 0.7715 (tpt) cc_final: 0.7448 (tpt) REVERT: F 92 ASN cc_start: 0.9246 (t0) cc_final: 0.9021 (t0) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1688 time to fit residues: 53.5429 Evaluate side-chains 158 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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: 4.9990 chunk 219 optimal weight: 10.0000 chunk 206 optimal weight: 0.9990 chunk 393 optimal weight: 0.2980 chunk 58 optimal weight: 7.9990 chunk 364 optimal weight: 0.9980 chunk 302 optimal weight: 0.8980 chunk 363 optimal weight: 0.9980 chunk 288 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 chunk 312 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 HIS ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 738 ASN ** E 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.057988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.036792 restraints weight = 262426.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.036913 restraints weight = 191542.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.037469 restraints weight = 152724.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.037723 restraints weight = 130464.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.037950 restraints weight = 119035.075| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33556 Z= 0.130 Angle : 0.679 9.724 45324 Z= 0.345 Chirality : 0.044 0.225 5024 Planarity : 0.005 0.059 5796 Dihedral : 5.172 72.749 4394 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -0.63 (0.13), residues: 4022 helix: 0.34 (0.12), residues: 2000 sheet: -1.30 (0.22), residues: 510 loop : -0.96 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 534 TYR 0.017 0.001 TYR E1231 PHE 0.011 0.001 PHE E 531 TRP 0.020 0.001 TRP E 102 HIS 0.010 0.001 HIS B 971 Details of bonding type rmsd covalent geometry : bond 0.00279 (33556) covalent geometry : angle 0.67941 (45324) hydrogen bonds : bond 0.04016 ( 1665) hydrogen bonds : angle 5.34153 ( 4833) *********************** 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 190 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.2600 (mmm) cc_final: 0.0972 (mmm) REVERT: B 158 MET cc_start: 0.8826 (pmm) cc_final: 0.8403 (pmm) REVERT: B 353 MET cc_start: 0.5499 (mpp) cc_final: 0.4515 (mpp) REVERT: B 802 MET cc_start: 0.6455 (ppp) cc_final: 0.6134 (ppp) REVERT: B 860 MET cc_start: 0.9256 (pmm) cc_final: 0.8951 (pmm) REVERT: B 929 MET cc_start: 0.7175 (ttt) cc_final: 0.6873 (ttt) REVERT: B 958 ILE cc_start: 0.9411 (pt) cc_final: 0.9146 (pt) REVERT: B 1011 MET cc_start: 0.9211 (mmp) cc_final: 0.8953 (mmp) REVERT: B 1231 TYR cc_start: 0.7745 (m-10) cc_final: 0.7468 (m-80) REVERT: B 1243 TYR cc_start: 0.8614 (m-80) cc_final: 0.8132 (m-80) REVERT: B 1326 GLU cc_start: 0.8104 (pp20) cc_final: 0.7769 (pp20) REVERT: B 1522 MET cc_start: 0.8501 (tpt) cc_final: 0.7863 (tpt) REVERT: B 1540 ARG cc_start: 0.7751 (tpt170) cc_final: 0.7497 (tpt90) REVERT: C 6 CYS cc_start: 0.9082 (t) cc_final: 0.8825 (m) REVERT: C 45 MET cc_start: 0.7359 (tpt) cc_final: 0.7150 (tpt) REVERT: C 91 GLU cc_start: 0.9274 (mp0) cc_final: 0.9017 (mp0) REVERT: C 92 ASN cc_start: 0.9160 (t0) cc_final: 0.8891 (t0) REVERT: D 692 MET cc_start: 0.8697 (mmm) cc_final: 0.8430 (mmm) REVERT: E 1 MET cc_start: 0.1542 (mmm) cc_final: 0.0542 (mmm) REVERT: E 658 MET cc_start: 0.7809 (ppp) cc_final: 0.7454 (ptp) REVERT: E 929 MET cc_start: 0.7929 (ttt) cc_final: 0.7453 (ttt) REVERT: E 958 ILE cc_start: 0.9441 (pt) cc_final: 0.9236 (pt) REVERT: E 964 MET cc_start: 0.8324 (mmm) cc_final: 0.7972 (mmm) REVERT: E 1007 MET cc_start: 0.8927 (ppp) cc_final: 0.8518 (ppp) REVERT: E 1011 MET cc_start: 0.9214 (mmp) cc_final: 0.8648 (mmm) REVERT: E 1243 TYR cc_start: 0.8379 (m-80) cc_final: 0.7888 (m-80) REVERT: E 1278 CYS cc_start: 0.6070 (m) cc_final: 0.5676 (p) REVERT: E 1560 MET cc_start: 0.1335 (ttp) cc_final: 0.0476 (ttt) REVERT: E 1597 MET cc_start: 0.8808 (mmp) cc_final: 0.8201 (mtp) REVERT: F 45 MET cc_start: 0.7521 (tpt) cc_final: 0.7260 (tpt) REVERT: F 92 ASN cc_start: 0.9201 (t0) cc_final: 0.8956 (t0) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1823 time to fit residues: 59.7588 Evaluate side-chains 160 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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: 30.0000 chunk 205 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 385 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 389 optimal weight: 0.6980 chunk 364 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 HIS ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1351 ASN ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1526 ASN ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.058016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.037124 restraints weight = 265560.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.037243 restraints weight = 206253.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.037529 restraints weight = 155975.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.037750 restraints weight = 133847.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.037750 restraints weight = 119432.626| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 33556 Z= 0.131 Angle : 0.677 10.242 45324 Z= 0.344 Chirality : 0.044 0.222 5024 Planarity : 0.005 0.120 5796 Dihedral : 5.086 71.069 4394 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.57 (0.13), residues: 4022 helix: 0.38 (0.12), residues: 1994 sheet: -1.22 (0.22), residues: 510 loop : -0.95 (0.17), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 534 TYR 0.017 0.001 TYR B1328 PHE 0.011 0.001 PHE E 529 TRP 0.018 0.001 TRP E 102 HIS 0.008 0.001 HIS C 103 Details of bonding type rmsd covalent geometry : bond 0.00287 (33556) covalent geometry : angle 0.67667 (45324) hydrogen bonds : bond 0.03990 ( 1665) hydrogen bonds : angle 5.31627 ( 4833) ********************** 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 190 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 678 MET cc_start: 0.8199 (pmm) cc_final: 0.7966 (pmm) REVERT: B 1 MET cc_start: 0.2605 (mmm) cc_final: 0.1036 (mmm) REVERT: B 158 MET cc_start: 0.8839 (pmm) cc_final: 0.8410 (pmm) REVERT: B 353 MET cc_start: 0.5414 (mpp) cc_final: 0.4378 (mpp) REVERT: B 802 MET cc_start: 0.6512 (ppp) cc_final: 0.6212 (ppp) REVERT: B 860 MET cc_start: 0.9211 (pmm) cc_final: 0.8968 (pmm) REVERT: B 958 ILE cc_start: 0.9426 (pt) cc_final: 0.9161 (pt) REVERT: B 1011 MET cc_start: 0.9296 (mmp) cc_final: 0.8965 (mmp) REVERT: B 1231 TYR cc_start: 0.7953 (m-10) cc_final: 0.7651 (m-80) REVERT: B 1243 TYR cc_start: 0.8676 (m-80) cc_final: 0.8139 (m-80) REVERT: B 1326 GLU cc_start: 0.8137 (pp20) cc_final: 0.7807 (pp20) REVERT: B 1522 MET cc_start: 0.8618 (tpt) cc_final: 0.7950 (tpt) REVERT: B 1540 ARG cc_start: 0.7767 (tpt170) cc_final: 0.7494 (tpt90) REVERT: C 6 CYS cc_start: 0.9146 (t) cc_final: 0.8889 (m) REVERT: C 45 MET cc_start: 0.7472 (tpt) cc_final: 0.7232 (tpt) REVERT: C 91 GLU cc_start: 0.9313 (mp0) cc_final: 0.9064 (mp0) REVERT: E 1 MET cc_start: 0.1959 (mmm) cc_final: 0.0428 (mmm) REVERT: E 658 MET cc_start: 0.7962 (ppp) cc_final: 0.7531 (ptp) REVERT: E 929 MET cc_start: 0.7904 (ttt) cc_final: 0.7152 (ttt) REVERT: E 964 MET cc_start: 0.8325 (mmm) cc_final: 0.7714 (tpp) REVERT: E 1011 MET cc_start: 0.9284 (mmp) cc_final: 0.9074 (mmp) REVERT: E 1243 TYR cc_start: 0.8548 (m-80) cc_final: 0.8042 (m-80) REVERT: E 1278 CYS cc_start: 0.6174 (m) cc_final: 0.5770 (p) REVERT: E 1597 MET cc_start: 0.9034 (mmp) cc_final: 0.8399 (mmm) REVERT: F 45 MET cc_start: 0.7766 (tpt) cc_final: 0.7496 (tpt) REVERT: F 92 ASN cc_start: 0.9213 (t0) cc_final: 0.8961 (t0) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1735 time to fit residues: 57.2503 Evaluate side-chains 158 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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: 0.9980 chunk 40 optimal weight: 0.8980 chunk 293 optimal weight: 4.9990 chunk 282 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 326 optimal weight: 5.9990 chunk 358 optimal weight: 6.9990 chunk 60 optimal weight: 0.0770 chunk 377 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1517 ASN ** B1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 ASN ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1022 ASN ** E1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1351 ASN ** E1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1526 ASN ** F 2 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 = 0.3760 r_free = 0.3760 target = 0.058318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.036565 restraints weight = 266222.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.037292 restraints weight = 191481.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.037883 restraints weight = 155802.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.038106 restraints weight = 133056.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.038296 restraints weight = 119824.278| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33556 Z= 0.125 Angle : 0.671 8.673 45324 Z= 0.340 Chirality : 0.044 0.201 5024 Planarity : 0.005 0.088 5796 Dihedral : 4.902 66.963 4394 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.50 (0.13), residues: 4022 helix: 0.43 (0.12), residues: 1998 sheet: -1.15 (0.22), residues: 516 loop : -0.93 (0.17), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 534 TYR 0.017 0.001 TYR E1231 PHE 0.011 0.001 PHE E 59 TRP 0.019 0.001 TRP E 102 HIS 0.010 0.001 HIS B 971 Details of bonding type rmsd covalent geometry : bond 0.00271 (33556) covalent geometry : angle 0.67055 (45324) hydrogen bonds : bond 0.03880 ( 1665) hydrogen bonds : angle 5.21412 ( 4833) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7426.37 seconds wall clock time: 129 minutes 12.56 seconds (7752.56 seconds total)