Starting phenix.real_space_refine on Fri May 30 07:40:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjm_60150/05_2025/8zjm_60150.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjm_60150/05_2025/8zjm_60150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zjm_60150/05_2025/8zjm_60150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjm_60150/05_2025/8zjm_60150.map" model { file = "/net/cci-nas-00/data/ceres_data/8zjm_60150/05_2025/8zjm_60150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjm_60150/05_2025/8zjm_60150.cif" } resolution = 4.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 176 5.16 5 C 21052 2.51 5 N 5538 2.21 5 O 6092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.54s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32858 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1608 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "B" Number of atoms: 13436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1642, 13436 Classifications: {'peptide': 1642} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1583} Chain: "C" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1385 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 165} Chain: "D" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1608 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "E" Number of atoms: 13436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1642, 13436 Classifications: {'peptide': 1642} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1583} Chain: "F" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1385 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 165} Time building chain proxies: 17.03, per 1000 atoms: 0.52 Number of scatterers: 32858 At special positions: 0 Unit cell: (272.65, 166.25, 154.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 176 16.00 O 6092 8.00 N 5538 7.00 C 21052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.44 Conformation dependent library (CDL) restraints added in 4.0 seconds 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7696 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 22 sheets defined 54.7% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 530 through 540 removed outlier: 3.588A pdb=" N ILE A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 559 removed outlier: 3.524A pdb=" N GLU A 546 " --> pdb=" O PRO A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 626 Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.861A pdb=" N VAL A 637 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 4.077A 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 698 Processing helix chain 'B' and resid 85 through 108 removed outlier: 3.879A pdb=" N VAL B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 131 Processing helix chain 'B' and resid 137 through 160 Processing helix chain 'B' and resid 168 through 172 removed outlier: 4.133A 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: 5.524A pdb=" N LYS B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.994A pdb=" N GLY B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.516A pdb=" N ILE B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 removed outlier: 3.839A pdb=" N ARG B 360 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 389 removed outlier: 3.660A 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 580 Processing helix chain 'B' and resid 581 through 586 Processing helix chain 'B' and resid 591 through 605 removed outlier: 3.756A pdb=" N LYS B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN B 605 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 642 removed outlier: 3.854A 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 657 removed outlier: 3.631A pdb=" N LYS B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 666 Processing helix chain 'B' and resid 668 through 683 Processing helix chain 'B' and resid 686 through 705 Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 728 through 743 Processing helix chain 'B' and resid 749 through 759 removed outlier: 3.915A pdb=" N ALA B 759 " --> pdb=" O ALA B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 778 Processing helix chain 'B' and resid 783 through 804 removed outlier: 4.002A pdb=" N ASN B 788 " --> pdb=" O GLY B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 820 Processing helix chain 'B' and resid 820 through 828 removed outlier: 4.193A pdb=" N ASN B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.630A 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 891 Proline residue: B 880 - end of helix removed outlier: 4.401A pdb=" N ASP B 891 " --> pdb=" O SER B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 915 removed outlier: 4.378A pdb=" N ASP B 898 " --> pdb=" O SER B 894 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLU B 900 " --> pdb=" O LYS B 896 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 943 removed outlier: 5.818A pdb=" N ARG B 934 " --> pdb=" O GLU B 930 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ARG B 935 " --> pdb=" O ARG B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 963 Processing helix chain 'B' and resid 965 through 973 removed outlier: 3.749A pdb=" N HIS B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR B 972 " --> pdb=" O HIS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 998 Processing helix chain 'B' and resid 1006 through 1032 Processing helix chain 'B' and resid 1041 through 1055 removed outlier: 4.328A pdb=" N ASN B1045 " --> pdb=" O GLN B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1063 Processing helix chain 'B' and resid 1065 through 1077 removed outlier: 4.001A pdb=" N ARG B1069 " --> pdb=" O SER B1065 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN B1070 " --> pdb=" O GLN B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1095 removed outlier: 3.620A pdb=" N GLU B1082 " --> pdb=" O ASP B1078 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B1095 " --> pdb=" O TRP B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1099 Processing helix chain 'B' and resid 1101 through 1115 removed outlier: 4.866A pdb=" N GLY B1107 " --> pdb=" O PRO B1103 " (cutoff:3.500A) Proline residue: B1108 - end of helix Processing helix chain 'B' and resid 1117 through 1139 removed outlier: 3.733A pdb=" N ARG B1121 " --> pdb=" O GLU B1117 " (cutoff:3.500A) Proline residue: B1126 - end of helix Processing helix chain 'B' and resid 1140 through 1142 No H-bonds generated for 'chain 'B' and resid 1140 through 1142' Processing helix chain 'B' and resid 1144 through 1162 Processing helix chain 'B' and resid 1165 through 1182 Processing helix chain 'B' and resid 1184 through 1212 Processing helix chain 'B' and resid 1217 through 1235 Processing helix chain 'B' and resid 1236 through 1254 Processing helix chain 'B' and resid 1256 through 1271 Processing helix chain 'B' and resid 1292 through 1311 Processing helix chain 'B' and resid 1313 through 1332 removed outlier: 4.648A pdb=" N GLU B1323 " --> pdb=" O LYS B1319 " (cutoff:3.500A) Processing helix chain 'B' and resid 1334 through 1355 Processing helix chain 'B' and resid 1390 through 1402 Processing helix chain 'B' and resid 1416 through 1421 removed outlier: 3.807A pdb=" N SER B1420 " --> pdb=" O GLU B1416 " (cutoff:3.500A) Processing helix chain 'B' and resid 1447 through 1455 removed outlier: 4.461A pdb=" N LEU B1451 " --> pdb=" O PRO B1447 " (cutoff:3.500A) Processing helix chain 'B' and resid 1513 through 1539 Processing helix chain 'B' and resid 1544 through 1556 removed outlier: 3.739A pdb=" N ASP B1556 " --> pdb=" O SER B1552 " (cutoff:3.500A) Processing helix chain 'B' and resid 1561 through 1570 Processing helix chain 'B' and resid 1572 through 1579 removed outlier: 3.863A pdb=" N LEU B1576 " --> pdb=" O THR B1572 " (cutoff:3.500A) Processing helix chain 'B' and resid 1580 through 1584 removed outlier: 3.573A pdb=" N GLN B1583 " --> pdb=" O PRO B1580 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU B1584 " --> pdb=" O GLU B1581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1580 through 1584' Processing helix chain 'B' and resid 1585 through 1610 Proline residue: B1598 - end of helix Processing helix chain 'B' and resid 1614 through 1636 removed outlier: 3.768A pdb=" N LEU B1618 " --> pdb=" O GLN B1614 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 26 removed outlier: 4.110A pdb=" N LEU C 19 " --> pdb=" O ALA C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 Processing helix 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 removed outlier: 3.643A pdb=" N VAL C 101 " --> pdb=" O TRP C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 removed outlier: 3.853A 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 Processing helix chain 'C' and resid 164 through 175 Processing helix chain 'D' and resid 531 through 540 removed outlier: 3.589A pdb=" N ILE D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 559 removed outlier: 3.524A pdb=" N GLU D 546 " --> pdb=" O PRO D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 626 Proline residue: D 623 - end of helix Processing helix chain 'D' and resid 634 through 638 removed outlier: 3.861A pdb=" N VAL D 637 " --> pdb=" O ASN D 634 " (cutoff:3.500A) removed outlier: 4.077A 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 698 Processing helix chain 'E' and resid 85 through 108 removed outlier: 3.878A pdb=" N VAL E 100 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 131 Processing helix chain 'E' and resid 137 through 160 Processing helix chain 'E' and resid 168 through 172 removed outlier: 4.133A 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: 5.524A pdb=" N LYS E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER E 203 " --> pdb=" O GLN E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 217 removed outlier: 3.993A pdb=" N GLY E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 291 Processing helix chain 'E' and resid 329 through 334 removed outlier: 3.516A pdb=" N ILE E 333 " --> pdb=" O ILE E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 361 removed outlier: 3.839A pdb=" N ARG E 360 " --> pdb=" O ILE E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 389 removed outlier: 3.659A 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 580 Processing helix chain 'E' and resid 581 through 586 Processing helix chain 'E' and resid 591 through 605 removed outlier: 3.756A pdb=" N LYS E 604 " --> pdb=" O LEU E 600 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN E 605 " --> pdb=" O GLN E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 642 removed outlier: 3.854A 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 657 removed outlier: 3.631A pdb=" N LYS E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 661 through 666 Processing helix chain 'E' and resid 668 through 683 Processing helix chain 'E' and resid 686 through 705 Processing helix chain 'E' and resid 712 through 722 Processing helix chain 'E' and resid 728 through 743 Processing helix chain 'E' and resid 749 through 759 removed outlier: 3.915A pdb=" N ALA E 759 " --> pdb=" O ALA E 755 " (cutoff:3.500A) Processing helix chain 'E' and resid 759 through 778 Processing helix chain 'E' and resid 783 through 804 removed outlier: 4.001A pdb=" N ASN E 788 " --> pdb=" O GLY E 784 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 820 Processing helix chain 'E' and resid 820 through 828 removed outlier: 4.192A pdb=" N ASN E 825 " --> pdb=" O PRO E 821 " (cutoff:3.500A) removed outlier: 4.630A 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 891 Proline residue: E 880 - end of helix removed outlier: 4.401A pdb=" N ASP E 891 " --> pdb=" O SER E 887 " (cutoff:3.500A) Processing helix chain 'E' and resid 894 through 915 removed outlier: 4.379A pdb=" N ASP E 898 " --> pdb=" O SER E 894 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLU E 900 " --> pdb=" O LYS E 896 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA E 901 " --> pdb=" O PRO E 897 " (cutoff:3.500A) Processing helix chain 'E' and resid 921 through 943 removed outlier: 5.818A pdb=" N ARG E 934 " --> pdb=" O GLU E 930 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ARG E 935 " --> pdb=" O ARG E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 949 through 963 Processing helix chain 'E' and resid 965 through 973 removed outlier: 3.749A pdb=" N HIS E 971 " --> pdb=" O SER E 967 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR E 972 " --> pdb=" O HIS E 968 " (cutoff:3.500A) Processing helix chain 'E' and resid 978 through 998 Processing helix chain 'E' and resid 1006 through 1032 Processing helix chain 'E' and resid 1041 through 1055 removed outlier: 4.328A pdb=" N ASN E1045 " --> pdb=" O GLN E1041 " (cutoff:3.500A) Processing helix chain 'E' and resid 1058 through 1063 Processing helix chain 'E' and resid 1065 through 1077 removed outlier: 4.000A pdb=" N ARG E1069 " --> pdb=" O SER E1065 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN E1070 " --> pdb=" O GLN E1066 " (cutoff:3.500A) Processing helix chain 'E' and resid 1078 through 1095 removed outlier: 3.619A pdb=" N GLU E1082 " --> pdb=" O ASP E1078 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY E1095 " --> pdb=" O TRP E1091 " (cutoff:3.500A) Processing helix chain 'E' and resid 1096 through 1099 Processing helix chain 'E' and resid 1101 through 1115 removed outlier: 4.867A pdb=" N GLY E1107 " --> pdb=" O PRO E1103 " (cutoff:3.500A) Proline residue: E1108 - end of helix Processing helix chain 'E' and resid 1117 through 1139 removed outlier: 3.733A pdb=" N ARG E1121 " --> pdb=" O GLU E1117 " (cutoff:3.500A) Proline residue: E1126 - end of helix Processing helix chain 'E' and resid 1140 through 1142 No H-bonds generated for 'chain 'E' and resid 1140 through 1142' Processing helix chain 'E' and resid 1144 through 1162 Processing helix chain 'E' and resid 1165 through 1182 Processing helix chain 'E' and resid 1184 through 1212 Processing helix chain 'E' and resid 1217 through 1235 Processing helix chain 'E' and resid 1236 through 1254 Processing helix chain 'E' and resid 1256 through 1271 Processing helix chain 'E' and resid 1292 through 1311 Processing helix chain 'E' and resid 1313 through 1332 removed outlier: 4.648A pdb=" N GLU E1323 " --> pdb=" O LYS E1319 " (cutoff:3.500A) Processing helix chain 'E' and resid 1334 through 1355 Processing helix chain 'E' and resid 1390 through 1402 Processing helix chain 'E' and resid 1416 through 1421 removed outlier: 3.807A pdb=" N SER E1420 " --> pdb=" O GLU E1416 " (cutoff:3.500A) Processing helix chain 'E' and resid 1447 through 1455 removed outlier: 4.461A pdb=" N LEU E1451 " --> pdb=" O PRO E1447 " (cutoff:3.500A) Processing helix chain 'E' and resid 1513 through 1539 Processing helix chain 'E' and resid 1544 through 1556 removed outlier: 3.738A pdb=" N ASP E1556 " --> pdb=" O SER E1552 " (cutoff:3.500A) Processing helix chain 'E' and resid 1561 through 1570 Processing helix chain 'E' and resid 1572 through 1579 removed outlier: 3.863A pdb=" N LEU E1576 " --> pdb=" O THR E1572 " (cutoff:3.500A) Processing helix chain 'E' and resid 1580 through 1584 removed outlier: 3.574A pdb=" N GLN E1583 " --> pdb=" O PRO E1580 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU E1584 " --> pdb=" O GLU E1581 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1580 through 1584' Processing helix chain 'E' and resid 1585 through 1610 Proline residue: E1598 - end of helix Processing helix chain 'E' and resid 1614 through 1636 removed outlier: 3.769A pdb=" N LEU E1618 " --> pdb=" O GLN E1614 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 26 removed outlier: 4.109A pdb=" N LEU F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 66 Processing helix 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 removed outlier: 3.643A pdb=" N VAL F 101 " --> pdb=" O TRP F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 121 removed outlier: 3.854A 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 Processing helix chain 'F' and resid 164 through 175 Processing sheet with id=AA1, first strand: chain 'A' and resid 561 through 562 Processing sheet with id=AA2, first strand: chain 'A' and resid 615 through 618 removed outlier: 3.587A pdb=" N ALA A 615 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 642 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 644 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR A 646 " --> pdb=" O CYS A 650 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N CYS A 650 " --> pdb=" O TYR A 646 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 40 removed outlier: 7.260A pdb=" N ARG B 46 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N MET B 40 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N TRP B 44 " --> pdb=" O MET B 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 252 through 253 removed outlier: 3.988A pdb=" N THR B 252 " --> pdb=" O ASP B 247 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B 247 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 252 through 253 removed outlier: 3.988A pdb=" N THR B 252 " --> pdb=" O ASP B 247 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B 247 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 296 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL B 326 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N CYS B 298 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL B 324 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE B 300 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 326 " --> pdb=" O PRO B 347 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASP B 328 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N PHE B 345 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY B 398 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N PHE B 231 " --> pdb=" O GLY B 398 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N TRP B 400 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TYR B 222 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP B 283 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN B 278 " --> pdb=" O ALA B 426 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA B 428 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 280 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 484 through 485 removed outlier: 6.708A pdb=" N CYS B 508 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS B 452 " --> pdb=" O CYS B 508 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU B 450 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR B 512 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 448 " --> pdb=" O THR B 512 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS B 514 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE B 446 " --> pdb=" O LYS B 514 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER B 516 " --> pdb=" O ASN B 444 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASN B 444 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU B 450 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA B 623 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 484 through 485 removed outlier: 6.708A pdb=" N CYS B 508 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS B 452 " --> pdb=" O CYS B 508 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU B 450 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR B 512 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 448 " --> pdb=" O THR B 512 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS B 514 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE B 446 " --> pdb=" O LYS B 514 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER B 516 " --> pdb=" O ASN B 444 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASN B 444 " --> pdb=" O SER B 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 495 through 496 removed outlier: 3.725A pdb=" N GLY B 548 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1362 through 1367 removed outlier: 3.822A pdb=" N TYR B1367 " --> pdb=" O LYS B1379 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS B1379 " --> pdb=" O TYR B1367 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE B1380 " --> pdb=" O VAL B1504 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLU B1503 " --> pdb=" O ALA B1492 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA B1492 " --> pdb=" O GLU B1503 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR B1490 " --> pdb=" O LYS B1505 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B1507 " --> pdb=" O THR B1488 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR B1488 " --> pdb=" O ILE B1507 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN B1460 " --> pdb=" O THR B1491 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1467 through 1469 Processing sheet with id=AB2, first strand: chain 'C' and resid 41 through 44 removed outlier: 3.507A pdb=" N VAL C 44 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 51 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLN C 2 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N GLY C 54 " --> pdb=" O GLN C 2 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE C 4 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TRP C 56 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS C 6 " --> pdb=" O TRP C 56 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR C 58 " --> pdb=" O CYS C 6 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL C 8 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 7 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE C 78 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL C 113 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE C 80 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR C 115 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE C 82 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE C 110 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU C 155 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU C 112 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 561 through 562 Processing sheet with id=AB4, first strand: chain 'D' and resid 615 through 618 removed outlier: 3.587A pdb=" N ALA D 615 " --> pdb=" O LEU D 645 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE D 642 " --> pdb=" O PHE D 654 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 644 " --> pdb=" O LEU D 652 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR D 646 " --> pdb=" O CYS D 650 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N CYS D 650 " --> pdb=" O TYR D 646 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 36 through 40 removed outlier: 7.261A pdb=" N ARG E 46 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N MET E 40 " --> pdb=" O TRP E 44 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N TRP E 44 " --> pdb=" O MET E 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 252 through 253 removed outlier: 3.988A pdb=" N THR E 252 " --> pdb=" O ASP E 247 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP E 247 " --> pdb=" O THR E 252 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 252 through 253 removed outlier: 3.988A pdb=" N THR E 252 " --> pdb=" O ASP E 247 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP E 247 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU E 296 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL E 326 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N CYS E 298 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL E 324 " --> pdb=" O CYS E 298 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE E 300 " --> pdb=" O PHE E 322 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL E 326 " --> pdb=" O PRO E 347 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASP E 328 " --> pdb=" O PHE E 345 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N PHE E 345 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY E 398 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N PHE E 231 " --> pdb=" O GLY E 398 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N TRP E 400 " --> pdb=" O LYS E 229 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N TYR E 222 " --> pdb=" O ASP E 283 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP E 283 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN E 278 " --> pdb=" O ALA E 426 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ALA E 428 " --> pdb=" O GLN E 278 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL E 280 " --> pdb=" O ALA E 428 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 484 through 485 removed outlier: 6.709A pdb=" N CYS E 508 " --> pdb=" O HIS E 452 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS E 452 " --> pdb=" O CYS E 508 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU E 450 " --> pdb=" O TYR E 510 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR E 512 " --> pdb=" O VAL E 448 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL E 448 " --> pdb=" O THR E 512 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS E 514 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE E 446 " --> pdb=" O LYS E 514 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER E 516 " --> pdb=" O ASN E 444 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASN E 444 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU E 450 " --> pdb=" O ALA E 623 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA E 623 " --> pdb=" O LEU E 450 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 484 through 485 removed outlier: 6.709A pdb=" N CYS E 508 " --> pdb=" O HIS E 452 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS E 452 " --> pdb=" O CYS E 508 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU E 450 " --> pdb=" O TYR E 510 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR E 512 " --> pdb=" O VAL E 448 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL E 448 " --> pdb=" O THR E 512 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS E 514 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE E 446 " --> pdb=" O LYS E 514 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER E 516 " --> pdb=" O ASN E 444 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASN E 444 " --> pdb=" O SER E 516 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 495 through 496 removed outlier: 3.725A pdb=" N GLY E 548 " --> pdb=" O PHE E 531 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 1362 through 1367 removed outlier: 3.823A pdb=" N TYR E1367 " --> pdb=" O LYS E1379 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS E1379 " --> pdb=" O TYR E1367 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE E1380 " --> pdb=" O VAL E1504 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLU E1503 " --> pdb=" O ALA E1492 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA E1492 " --> pdb=" O GLU E1503 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR E1490 " --> pdb=" O LYS E1505 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE E1507 " --> pdb=" O THR E1488 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR E1488 " --> pdb=" O ILE E1507 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLN E1460 " --> pdb=" O THR E1491 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 1467 through 1469 Processing sheet with id=AC4, first strand: chain 'F' and resid 41 through 44 removed outlier: 3.508A pdb=" N VAL F 44 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL F 51 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLN F 2 " --> pdb=" O ASN F 52 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY F 54 " --> pdb=" O GLN F 2 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE F 4 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TRP F 56 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS F 6 " --> pdb=" O TRP F 56 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR F 58 " --> pdb=" O CYS F 6 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL F 8 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL F 7 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE F 78 " --> pdb=" O ILE F 111 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL F 113 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE F 80 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR F 115 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE F 82 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE F 110 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU F 155 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU F 112 " --> pdb=" O LEU F 155 " (cutoff:3.500A) 1669 hydrogen bonds defined for protein. 4881 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.43 Time building geometry restraints manager: 9.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10552 1.34 - 1.46: 6166 1.46 - 1.58: 16544 1.58 - 1.70: 0 1.70 - 1.82: 294 Bond restraints: 33556 Sorted by residual: bond pdb=" C THR E1494 " pdb=" N PHE E1495 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.58e-02 4.01e+03 7.34e+00 bond pdb=" C THR B1494 " pdb=" N PHE B1495 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.58e-02 4.01e+03 7.00e+00 bond pdb=" CG1 ILE B 983 " pdb=" CD1 ILE B 983 " ideal model delta sigma weight residual 1.513 1.433 0.080 3.90e-02 6.57e+02 4.24e+00 bond pdb=" CG1 ILE E 983 " pdb=" CD1 ILE E 983 " ideal model delta sigma weight residual 1.513 1.433 0.080 3.90e-02 6.57e+02 4.19e+00 bond pdb=" C ASP B1443 " pdb=" N LYS B1444 " ideal model delta sigma weight residual 1.333 1.302 0.031 1.61e-02 3.86e+03 3.69e+00 ... (remaining 33551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 44057 2.39 - 4.77: 1083 4.77 - 7.16: 143 7.16 - 9.55: 33 9.55 - 11.94: 8 Bond angle restraints: 45324 Sorted by residual: angle pdb=" N VAL C 46 " pdb=" CA VAL C 46 " pdb=" C VAL C 46 " ideal model delta sigma weight residual 112.12 106.57 5.55 8.40e-01 1.42e+00 4.36e+01 angle pdb=" N VAL F 46 " pdb=" CA VAL F 46 " pdb=" C VAL F 46 " ideal model delta sigma weight residual 112.12 106.62 5.50 8.40e-01 1.42e+00 4.28e+01 angle pdb=" N PHE E1563 " pdb=" CA PHE E1563 " pdb=" C PHE E1563 " ideal model delta sigma weight residual 110.97 106.17 4.80 1.09e+00 8.42e-01 1.94e+01 angle pdb=" N PHE B1563 " pdb=" CA PHE B1563 " pdb=" C PHE B1563 " ideal model delta sigma weight residual 110.97 106.21 4.76 1.09e+00 8.42e-01 1.91e+01 angle pdb=" N VAL F 36 " pdb=" CA VAL F 36 " pdb=" C VAL F 36 " ideal model delta sigma weight residual 113.22 107.86 5.36 1.23e+00 6.61e-01 1.90e+01 ... (remaining 45319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 18393 18.00 - 36.00: 1788 36.00 - 54.00: 225 54.00 - 71.99: 44 71.99 - 89.99: 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 -141.03 -38.97 0 5.00e+00 4.00e-02 6.07e+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 -141.09 -38.91 0 5.00e+00 4.00e-02 6.06e+01 dihedral pdb=" CA GLN B1041 " pdb=" C GLN B1041 " pdb=" N LEU B1042 " pdb=" CA LEU B1042 " ideal model delta harmonic sigma weight residual 180.00 149.83 30.17 0 5.00e+00 4.00e-02 3.64e+01 ... (remaining 20473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4536 0.086 - 0.171: 466 0.171 - 0.257: 16 0.257 - 0.342: 4 0.342 - 0.428: 2 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 -2.16 -0.43 2.00e-01 2.50e+01 4.58e+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 -2.16 -0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CG LEU B 879 " pdb=" CB LEU B 879 " pdb=" CD1 LEU B 879 " pdb=" CD2 LEU B 879 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 5021 not shown) Planarity restraints: 5796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B1425 " 0.016 2.00e-02 2.50e+03 2.57e-02 1.32e+01 pdb=" CG TYR B1425 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR B1425 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR B1425 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B1425 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B1425 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B1425 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B1425 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E1425 " 0.016 2.00e-02 2.50e+03 2.56e-02 1.31e+01 pdb=" CG TYR E1425 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR E1425 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR E1425 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR E1425 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR E1425 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E1425 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E1425 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 896 " 0.045 5.00e-02 4.00e+02 6.76e-02 7.31e+00 pdb=" N PRO B 897 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 897 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 897 " 0.038 5.00e-02 4.00e+02 ... (remaining 5793 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 842 2.62 - 3.19: 36213 3.19 - 3.76: 60514 3.76 - 4.33: 84018 4.33 - 4.90: 122391 Nonbonded interactions: 303978 Sorted by model distance: nonbonded pdb=" OG1 THR E1521 " pdb=" OH TYR E1566 " model vdw 2.055 3.040 nonbonded pdb=" OG1 THR B1521 " pdb=" OH TYR B1566 " model vdw 2.055 3.040 nonbonded pdb=" OE1 GLU E 256 " pdb=" OH TYR E 447 " model vdw 2.064 3.040 nonbonded pdb=" O PRO D 711 " pdb=" OH TYR E 63 " model vdw 2.064 3.040 nonbonded pdb=" OE1 GLU B 256 " pdb=" OH TYR B 447 " model vdw 2.064 3.040 ... (remaining 303973 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'E' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'E' } Set refine NCS operators NCS operators will be refined. 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 71.500 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 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 : 0.006 0.080 33556 Z= 0.286 Angle : 0.921 11.937 45324 Z= 0.505 Chirality : 0.051 0.428 5024 Planarity : 0.005 0.068 5796 Dihedral : 14.084 89.994 12780 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 50.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.12), residues: 4022 helix: -1.34 (0.11), residues: 1980 sheet: -1.69 (0.24), residues: 422 loop : -1.97 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B1006 HIS 0.016 0.002 HIS B1179 PHE 0.030 0.003 PHE E1372 TYR 0.061 0.003 TYR B1425 ARG 0.017 0.001 ARG F 66 Details of bonding type rmsd hydrogen bonds : bond 0.20359 ( 1663) hydrogen bonds : angle 8.10160 ( 4881) covalent geometry : bond 0.00600 (33556) covalent geometry : angle 0.92090 (45324) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.215 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.2752 time to fit residues: 2.3614 Evaluate side-chains 4 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.212 Evaluate side-chains 7 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.195 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.2198 time to fit residues: 1.8866 Evaluate side-chains 5 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.158 Evaluate side-chains 80 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 TRP cc_start: 0.8975 (p-90) cc_final: 0.8361 (p-90) REVERT: B 1132 MET cc_start: 0.8056 (ppp) cc_final: 0.7853 (ppp) REVERT: B 1221 MET cc_start: 0.9483 (mpp) cc_final: 0.9270 (mpp) REVERT: B 1482 MET cc_start: 0.3487 (ptt) cc_final: 0.1295 (mmt) REVERT: B 1538 TRP cc_start: 0.7782 (m-90) cc_final: 0.7496 (m-90) REVERT: B 1585 LYS cc_start: 0.8595 (mppt) cc_final: 0.8254 (mttt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2284 time to fit residues: 29.4298 Evaluate side-chains 67 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 2.9990 chunk 303 optimal weight: 0.4980 chunk 168 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 204 optimal weight: 0.5980 chunk 161 optimal weight: 0.7980 chunk 313 optimal weight: 3.9990 chunk 121 optimal weight: 0.0060 chunk 190 optimal weight: 0.0770 chunk 233 optimal weight: 0.2980 chunk 363 optimal weight: 6.9990 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN ** B 187 HIS ** 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 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 GLN ** B 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 ASN B1097 HIS B1203 ASN ** B1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1517 ASN B1535 GLN ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.048521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.046806 restraints weight = 56053.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.046806 restraints weight = 55603.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.046806 restraints weight = 55603.358| |-----------------------------------------------------------------------------| r_work (final): 0.3543 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.055419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.046869 restraints weight = 19166.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.047552 restraints weight = 15948.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.048060 restraints weight = 13745.886| |-----------------------------------------------------------------------------| r_work (final): 0.3653 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.058423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.038802 restraints weight = 196117.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.038803 restraints weight = 153532.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.038981 restraints weight = 117302.010| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33556 Z= 0.174 Angle : 0.734 9.348 45324 Z= 0.384 Chirality : 0.047 0.202 5024 Planarity : 0.005 0.064 5796 Dihedral : 6.093 32.427 4394 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.16 % Allowed : 6.50 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.13), residues: 4022 helix: -0.59 (0.11), residues: 2062 sheet: -1.56 (0.25), residues: 422 loop : -1.67 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 56 HIS 0.011 0.002 HIS B1179 PHE 0.026 0.002 PHE E 529 TYR 0.028 0.002 TYR B1362 ARG 0.011 0.001 ARG E1345 Details of bonding type rmsd hydrogen bonds : bond 0.05131 ( 1663) hydrogen bonds : angle 6.51942 ( 4881) covalent geometry : bond 0.00356 (33556) covalent geometry : angle 0.73350 (45324) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.197 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1226 time to fit residues: 0.8532 Evaluate side-chains 4 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.203 Evaluate side-chains 6 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.163 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.2473 time to fit residues: 1.8128 Evaluate side-chains 6 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.154 Evaluate side-chains 92 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 TRP cc_start: 0.9174 (p-90) cc_final: 0.8637 (p-90) REVERT: B 802 MET cc_start: 0.8449 (ppp) cc_final: 0.8200 (ppp) REVERT: B 929 MET cc_start: 0.4577 (tmm) cc_final: 0.3675 (ttt) REVERT: B 957 MET cc_start: 0.9492 (pmm) cc_final: 0.9007 (pmm) REVERT: B 1212 MET cc_start: 0.9198 (mpp) cc_final: 0.8932 (mmm) REVERT: B 1231 TYR cc_start: 0.9070 (m-80) cc_final: 0.8860 (m-80) REVERT: B 1426 MET cc_start: 0.4546 (mtt) cc_final: 0.4084 (mtt) REVERT: B 1482 MET cc_start: 0.3532 (ptt) cc_final: 0.1825 (tpt) REVERT: B 1549 MET cc_start: 0.4187 (mmp) cc_final: 0.3982 (tpp) outliers start: 3 outliers final: 1 residues processed: 91 average time/residue: 0.2139 time to fit residues: 31.9549 Evaluate side-chains 71 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 282 optimal weight: 0.0040 chunk 263 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 73 optimal weight: 40.0000 chunk 271 optimal weight: 0.0070 chunk 318 optimal weight: 7.9990 chunk 128 optimal weight: 0.0870 chunk 338 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 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 576 ASN ** B 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.059609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.043197 restraints weight = 21480.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.043197 restraints weight = 23251.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.043197 restraints weight = 23251.564| |-----------------------------------------------------------------------------| r_work (final): 0.3430 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.055668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.048213 restraints weight = 20089.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.048653 restraints weight = 17613.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.048896 restraints weight = 15847.179| |-----------------------------------------------------------------------------| r_work (final): 0.3687 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.058559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.038803 restraints weight = 196565.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.039055 restraints weight = 154665.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.039055 restraints weight = 120846.867| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.226 33556 Z= 0.368 Angle : 1.148 20.948 45324 Z= 0.601 Chirality : 0.064 0.595 5024 Planarity : 0.011 0.155 5796 Dihedral : 6.227 31.681 4394 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 31.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.05 % Allowed : 4.21 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.13), residues: 4022 helix: -0.93 (0.10), residues: 2048 sheet: -1.65 (0.26), residues: 418 loop : -1.72 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.007 TRP A 665 HIS 0.037 0.004 HIS E 187 PHE 0.201 0.007 PHE E 869 TYR 0.117 0.007 TYR E 12 ARG 0.056 0.003 ARG B 854 Details of bonding type rmsd hydrogen bonds : bond 0.05433 ( 1663) hydrogen bonds : angle 6.77957 ( 4881) covalent geometry : bond 0.00873 (33556) covalent geometry : angle 1.14822 (45324) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7694 Ramachandran restraints generated. 3847 Oldfield, 0 Emsley, 3847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.179 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1165 time to fit residues: 0.8245 Evaluate side-chains 4 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.179 Evaluate side-chains 6 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.148 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.2588 time to fit residues: 1.8584 Evaluate side-chains 5 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.159 Evaluate side-chains 87 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 TRP cc_start: 0.9162 (p-90) cc_final: 0.8592 (p-90) REVERT: B 680 MET cc_start: -0.0686 (ptt) cc_final: -0.1015 (ptm) REVERT: B 929 MET cc_start: 0.3231 (tmm) cc_final: 0.2642 (ttp) REVERT: B 957 MET cc_start: 0.9379 (pmm) cc_final: 0.9089 (pmm) REVERT: B 1212 MET cc_start: 0.9130 (mpp) cc_final: 0.8917 (mmm) REVERT: B 1426 MET cc_start: 0.4565 (mtt) cc_final: 0.4060 (mtt) REVERT: B 1482 MET cc_start: 0.3678 (ptt) cc_final: 0.1963 (mmt) outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 0.2168 time to fit residues: 30.6228 Evaluate side-chains 67 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.6364 > 50: distance: 2 - 3: 9.390 distance: 3 - 4: 17.595 distance: 3 - 6: 7.254 distance: 4 - 5: 13.890 distance: 4 - 9: 12.429 distance: 6 - 7: 6.601 distance: 6 - 8: 6.708 distance: 9 - 10: 12.830 distance: 10 - 11: 49.028 distance: 11 - 12: 8.561 distance: 11 - 13: 21.837 distance: 13 - 14: 11.721 distance: 14 - 15: 12.498 distance: 14 - 17: 16.757 distance: 15 - 16: 15.013 distance: 15 - 22: 11.482 distance: 17 - 18: 3.331 distance: 18 - 19: 10.449 distance: 19 - 20: 5.047 distance: 22 - 23: 21.608 distance: 23 - 24: 16.014 distance: 23 - 26: 12.283 distance: 24 - 25: 8.866 distance: 24 - 30: 36.373 distance: 26 - 27: 22.962 distance: 27 - 28: 32.628 distance: 27 - 29: 30.254 distance: 30 - 31: 17.707 distance: 31 - 32: 14.786 distance: 31 - 34: 36.047 distance: 32 - 33: 14.223 distance: 32 - 36: 15.545 distance: 34 - 35: 27.789 distance: 36 - 37: 10.387 distance: 36 - 42: 23.180 distance: 37 - 38: 23.902 distance: 37 - 40: 27.356 distance: 38 - 39: 7.567 distance: 38 - 43: 11.122 distance: 39 - 61: 27.819 distance: 40 - 41: 4.350 distance: 41 - 42: 39.014 distance: 43 - 44: 7.856 distance: 44 - 45: 8.237 distance: 44 - 47: 6.957 distance: 45 - 46: 14.270 distance: 45 - 53: 5.078 distance: 48 - 49: 3.017 distance: 48 - 50: 4.851 distance: 50 - 52: 3.392 distance: 51 - 52: 3.232 distance: 53 - 54: 20.622 distance: 54 - 55: 8.973 distance: 54 - 57: 18.135 distance: 55 - 56: 38.146 distance: 55 - 61: 28.051 distance: 57 - 58: 16.608 distance: 58 - 59: 29.565 distance: 59 - 60: 22.172 distance: 61 - 62: 21.198 distance: 62 - 63: 18.062 distance: 62 - 65: 19.445 distance: 63 - 64: 12.997 distance: 63 - 70: 19.337 distance: 65 - 66: 23.067 distance: 66 - 67: 14.277 distance: 68 - 69: 7.340 distance: 70 - 71: 17.790 distance: 71 - 72: 9.940 distance: 71 - 74: 15.284 distance: 72 - 73: 17.040 distance: 74 - 75: 20.196 distance: 75 - 76: 9.276 distance: 76 - 77: 8.150 distance: 76 - 78: 8.271 distance: 79 - 80: 5.927 distance: 80 - 81: 14.051 distance: 80 - 83: 13.172 distance: 81 - 82: 13.982