Starting phenix.real_space_refine on Fri May 30 07:34:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjj_60147/05_2025/8zjj_60147.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjj_60147/05_2025/8zjj_60147.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/8zjj_60147/05_2025/8zjj_60147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjj_60147/05_2025/8zjj_60147.map" model { file = "/net/cci-nas-00/data/ceres_data/8zjj_60147/05_2025/8zjj_60147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjj_60147/05_2025/8zjj_60147.cif" } resolution = 4.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 176 5.16 5 C 21052 2.51 5 N 5538 2.21 5 O 6092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 149 residue(s): 0.61s 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: 17.52, per 1000 atoms: 0.53 Number of scatterers: 32858 At special positions: 0 Unit cell: (238.07, 160.93, 158.27, 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: 8.61 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: 166 helices and 22 sheets defined 54.9% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 530 through 540 removed outlier: 3.561A pdb=" N ILE A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 559 removed outlier: 3.870A pdb=" N LEU A 545 " --> pdb=" O GLN A 541 " (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 639 removed outlier: 3.778A pdb=" N LEU A 638 " --> pdb=" O LYS A 635 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLU A 639 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 673 Processing helix chain 'A' and resid 679 through 698 Processing helix chain 'B' and resid 84 through 107 removed outlier: 3.585A pdb=" N VAL B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 133 removed outlier: 4.043A 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: 4.040A 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: 4.242A pdb=" N LYS B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 218 removed outlier: 3.794A pdb=" N THR B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 276 Processing helix chain 'B' and resid 285 through 290 removed outlier: 3.644A pdb=" N ILE B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 357 through 361 removed outlier: 3.851A pdb=" N ARG B 360 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 3.577A 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 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 591 through 605 removed outlier: 3.653A pdb=" N LYS B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN B 605 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 642 removed outlier: 3.973A 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: 4.562A pdb=" N MET B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 666 Processing helix chain 'B' and resid 668 through 684 Processing helix chain 'B' and resid 686 through 705 removed outlier: 3.508A 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 722 Processing helix chain 'B' and resid 728 through 743 removed outlier: 3.687A pdb=" N LYS B 732 " --> pdb=" O LEU B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 759 removed outlier: 4.073A pdb=" N GLU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 779 Processing helix chain 'B' and resid 783 through 804 removed outlier: 3.855A pdb=" N ARG B 804 " --> pdb=" O MET B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 808 No H-bonds generated for 'chain 'B' and resid 806 through 808' Processing helix chain 'B' and resid 809 through 830 Proline residue: B 821 - end of helix removed outlier: 4.044A pdb=" N ILE B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASN B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 5.446A 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 865 Processing helix chain 'B' and resid 874 through 889 Proline residue: B 880 - end of helix Processing helix chain 'B' and resid 898 through 915 Processing helix chain 'B' and resid 921 through 943 removed outlier: 5.929A pdb=" N ARG B 934 " --> pdb=" O GLU B 930 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ARG B 935 " --> pdb=" O ARG B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 964 removed outlier: 3.785A pdb=" N PHE B 953 " --> pdb=" O HIS B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 972 removed outlier: 3.962A pdb=" N TYR B 972 " --> pdb=" O HIS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 998 Processing helix chain 'B' and resid 1006 through 1033 Processing helix chain 'B' and resid 1042 through 1054 Processing helix chain 'B' and resid 1058 through 1064 Processing helix chain 'B' and resid 1065 through 1076 removed outlier: 3.901A pdb=" N ARG B1069 " --> pdb=" O SER B1065 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN B1070 " --> pdb=" O GLN B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1095 removed outlier: 3.881A pdb=" N GLU B1082 " --> pdb=" O ASP B1078 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY B1095 " --> pdb=" O TRP B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1100 removed outlier: 4.312A pdb=" N ILE B1099 " --> pdb=" O PRO B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1101 through 1106 removed outlier: 3.882A pdb=" N MET B1105 " --> pdb=" O PHE B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1106 through 1114 removed outlier: 3.851A pdb=" N LEU B1110 " --> pdb=" O VAL B1106 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU B1111 " --> pdb=" O GLY B1107 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL B1112 " --> pdb=" O PRO B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1118 through 1125 Processing helix chain 'B' and resid 1125 through 1139 removed outlier: 3.774A 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 1183 removed outlier: 3.786A pdb=" N LYS B1182 " --> pdb=" O GLU B1178 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS B1183 " --> pdb=" O HIS B1179 " (cutoff:3.500A) Processing helix chain 'B' and resid 1184 through 1215 removed outlier: 3.530A pdb=" N GLU B1215 " --> pdb=" O ILE B1211 " (cutoff:3.500A) Processing helix chain 'B' and resid 1216 through 1235 Processing helix chain 'B' and resid 1236 through 1255 Processing helix chain 'B' and resid 1256 through 1271 removed outlier: 3.652A pdb=" N LEU B1270 " --> pdb=" O LEU B1266 " (cutoff:3.500A) removed outlier: 4.006A 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 1331 removed outlier: 3.641A pdb=" N ALA B1317 " --> pdb=" O MET B1313 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B1323 " --> pdb=" O LYS B1319 " (cutoff:3.500A) Processing helix chain 'B' and resid 1334 through 1355 removed outlier: 3.560A pdb=" N ALA B1355 " --> pdb=" O ASN B1351 " (cutoff:3.500A) Processing helix chain 'B' and resid 1390 through 1401 Processing helix chain 'B' and resid 1416 through 1420 Processing helix chain 'B' and resid 1447 through 1457 removed outlier: 4.243A pdb=" N LEU B1451 " --> pdb=" O PRO B1447 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA B1456 " --> pdb=" O ASN B1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 1513 through 1539 removed outlier: 3.639A 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 1574 through 1579 Processing helix chain 'B' and resid 1580 through 1584 removed outlier: 3.533A pdb=" N GLN B1583 " --> pdb=" O PRO B1580 " (cutoff:3.500A) removed outlier: 3.962A 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 1611 Proline residue: B1598 - end of helix Processing helix chain 'B' and resid 1614 through 1635 removed outlier: 4.119A pdb=" N LEU B1618 " --> pdb=" O GLN B1614 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 26 removed outlier: 3.737A pdb=" N LEU C 19 " --> pdb=" O ALA C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.631A pdb=" N ARG C 66 " --> pdb=" O ASP C 63 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 116 through 121 removed outlier: 4.110A 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: 3.800A pdb=" N GLY C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 removed outlier: 4.108A pdb=" N VAL C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 540 removed outlier: 3.562A pdb=" N ILE D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 559 removed outlier: 3.871A pdb=" N LEU D 545 " --> pdb=" O GLN D 541 " (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 639 removed outlier: 3.778A pdb=" N LEU D 638 " --> pdb=" O LYS D 635 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLU D 639 " --> pdb=" O GLU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 673 Processing helix chain 'D' and resid 679 through 698 Processing helix chain 'E' and resid 84 through 107 removed outlier: 3.585A pdb=" N VAL E 88 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 133 removed outlier: 4.043A 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: 4.041A 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: 4.242A pdb=" N LYS E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER E 203 " --> pdb=" O GLN E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 218 removed outlier: 3.794A pdb=" N THR E 218 " --> pdb=" O SER E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 276 Processing helix chain 'E' and resid 285 through 290 removed outlier: 3.643A pdb=" N ILE E 290 " --> pdb=" O SER E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 334 Processing helix chain 'E' and resid 357 through 361 removed outlier: 3.852A pdb=" N ARG E 360 " --> pdb=" O ILE E 357 " (cutoff:3.500A) removed outlier: 3.577A 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 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 591 through 605 removed outlier: 3.653A pdb=" N LYS E 604 " --> pdb=" O LEU E 600 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN E 605 " --> pdb=" O GLN E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 642 removed outlier: 3.973A 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: 4.562A pdb=" N MET E 658 " --> pdb=" O LEU E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 661 through 666 Processing helix chain 'E' and resid 668 through 684 Processing helix chain 'E' and resid 686 through 705 removed outlier: 3.508A 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 722 Processing helix chain 'E' and resid 728 through 743 removed outlier: 3.687A pdb=" N LYS E 732 " --> pdb=" O LEU E 728 " (cutoff:3.500A) Processing helix chain 'E' and resid 746 through 759 removed outlier: 4.073A pdb=" N GLU E 751 " --> pdb=" O SER E 747 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 759 through 779 Processing helix chain 'E' and resid 783 through 804 removed outlier: 3.855A pdb=" N ARG E 804 " --> pdb=" O MET E 800 " (cutoff:3.500A) Processing helix chain 'E' and resid 806 through 808 No H-bonds generated for 'chain 'E' and resid 806 through 808' Processing helix chain 'E' and resid 809 through 830 Proline residue: E 821 - end of helix removed outlier: 4.044A pdb=" N ILE E 824 " --> pdb=" O LEU E 820 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASN E 825 " --> pdb=" O PRO E 821 " (cutoff:3.500A) removed outlier: 5.447A 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 865 Processing helix chain 'E' and resid 874 through 889 Proline residue: E 880 - end of helix Processing helix chain 'E' and resid 898 through 915 Processing helix chain 'E' and resid 921 through 943 removed outlier: 5.930A pdb=" N ARG E 934 " --> pdb=" O GLU E 930 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ARG E 935 " --> pdb=" O ARG E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 949 through 964 removed outlier: 3.785A pdb=" N PHE E 953 " --> pdb=" O HIS E 949 " (cutoff:3.500A) Processing helix chain 'E' and resid 965 through 972 removed outlier: 3.963A pdb=" N TYR E 972 " --> pdb=" O HIS E 968 " (cutoff:3.500A) Processing helix chain 'E' and resid 978 through 998 Processing helix chain 'E' and resid 1006 through 1033 Processing helix chain 'E' and resid 1042 through 1054 Processing helix chain 'E' and resid 1058 through 1064 Processing helix chain 'E' and resid 1065 through 1076 removed outlier: 3.902A pdb=" N ARG E1069 " --> pdb=" O SER E1065 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN E1070 " --> pdb=" O GLN E1066 " (cutoff:3.500A) Processing helix chain 'E' and resid 1078 through 1095 removed outlier: 3.881A pdb=" N GLU E1082 " --> pdb=" O ASP E1078 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY E1095 " --> pdb=" O TRP E1091 " (cutoff:3.500A) Processing helix chain 'E' and resid 1096 through 1100 removed outlier: 4.312A pdb=" N ILE E1099 " --> pdb=" O PRO E1096 " (cutoff:3.500A) Processing helix chain 'E' and resid 1101 through 1106 removed outlier: 3.882A pdb=" N MET E1105 " --> pdb=" O PHE E1101 " (cutoff:3.500A) Processing helix chain 'E' and resid 1106 through 1114 removed outlier: 3.850A pdb=" N LEU E1110 " --> pdb=" O VAL E1106 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU E1111 " --> pdb=" O GLY E1107 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL E1112 " --> pdb=" O PRO E1108 " (cutoff:3.500A) Processing helix chain 'E' and resid 1118 through 1125 Processing helix chain 'E' and resid 1125 through 1139 removed outlier: 3.774A 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 1183 removed outlier: 3.785A pdb=" N LYS E1182 " --> pdb=" O GLU E1178 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS E1183 " --> pdb=" O HIS E1179 " (cutoff:3.500A) Processing helix chain 'E' and resid 1184 through 1215 removed outlier: 3.530A pdb=" N GLU E1215 " --> pdb=" O ILE E1211 " (cutoff:3.500A) Processing helix chain 'E' and resid 1216 through 1235 Processing helix chain 'E' and resid 1236 through 1255 Processing helix chain 'E' and resid 1256 through 1271 removed outlier: 3.652A pdb=" N LEU E1270 " --> pdb=" O LEU E1266 " (cutoff:3.500A) removed outlier: 4.005A 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 1331 removed outlier: 3.641A pdb=" N ALA E1317 " --> pdb=" O MET E1313 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU E1323 " --> pdb=" O LYS E1319 " (cutoff:3.500A) Processing helix chain 'E' and resid 1334 through 1355 removed outlier: 3.561A pdb=" N ALA E1355 " --> pdb=" O ASN E1351 " (cutoff:3.500A) Processing helix chain 'E' and resid 1390 through 1401 Processing helix chain 'E' and resid 1416 through 1420 Processing helix chain 'E' and resid 1447 through 1457 removed outlier: 4.243A pdb=" N LEU E1451 " --> pdb=" O PRO E1447 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA E1456 " --> pdb=" O ASN E1452 " (cutoff:3.500A) Processing helix chain 'E' and resid 1513 through 1539 removed outlier: 3.640A 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 1574 through 1579 Processing helix chain 'E' and resid 1580 through 1584 removed outlier: 3.534A pdb=" N GLN E1583 " --> pdb=" O PRO E1580 " (cutoff:3.500A) removed outlier: 3.961A 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 1611 Proline residue: E1598 - end of helix Processing helix chain 'E' and resid 1614 through 1635 removed outlier: 4.119A pdb=" N LEU E1618 " --> pdb=" O GLN E1614 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 26 removed outlier: 3.738A pdb=" N LEU F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 66 removed outlier: 3.631A pdb=" N ARG F 66 " --> pdb=" O ASP F 63 " (cutoff:3.500A) 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 Processing helix chain 'F' and resid 116 through 121 removed outlier: 4.110A 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: 3.800A pdb=" N GLY F 142 " --> pdb=" O THR F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 177 removed outlier: 4.108A pdb=" N VAL F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 561 through 563 Processing sheet with id=AA2, first strand: chain 'A' and resid 578 through 579 Processing sheet with id=AA3, first strand: chain 'A' and resid 616 through 618 removed outlier: 3.507A pdb=" N ILE A 644 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.839A pdb=" N ILE B 37 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N TYR B 48 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 344 through 347 removed outlier: 3.538A pdb=" N LEU B 399 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY B 398 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N PHE B 231 " --> pdb=" O GLY B 398 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP B 400 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR B 222 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLN B 278 " --> pdb=" O ALA B 426 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA B 428 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL B 280 " --> pdb=" O ALA B 428 " (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: 3.514A pdb=" N ASP B 238 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU B 296 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL B 326 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N CYS B 298 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL B 324 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE B 300 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 349 " --> pdb=" O VAL B 324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 484 through 485 removed outlier: 7.289A pdb=" N CYS B 508 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N HIS B 452 " --> pdb=" O CYS B 508 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU B 450 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR B 512 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL B 448 " --> pdb=" O THR B 512 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LYS B 514 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE B 446 " --> pdb=" O LYS B 514 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE B 446 " --> pdb=" O CYS B 627 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N CYS B 627 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL B 448 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU B 625 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU B 450 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA B 623 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS B 452 " --> pdb=" O GLN B 621 " (cutoff:3.500A) removed outlier: 3.687A 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 Processing sheet with id=AB1, first strand: chain 'B' and resid 1362 through 1368 removed outlier: 6.008A pdb=" N ILE B1380 " --> pdb=" O VAL B1504 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N PHE B1502 " --> pdb=" O THR B1494 " (cutoff:3.500A) removed outlier: 9.365A pdb=" N THR B1494 " --> pdb=" O PHE B1502 " (cutoff:3.500A) removed outlier: 9.604A pdb=" N VAL B1504 " --> pdb=" O ALA B1492 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ALA B1492 " --> pdb=" O VAL B1504 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B1491 " --> pdb=" O GLN B1460 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLN B1460 " --> pdb=" O THR B1491 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR B1362 " --> pdb=" O VAL B1431 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 41 through 45 removed outlier: 6.350A pdb=" N ILE C 4 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TRP C 56 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N CYS C 6 " --> pdb=" O TRP C 56 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N VAL C 77 " --> pdb=" O ALA C 3 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LYS C 5 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU C 79 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL C 7 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N CYS C 81 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C 111 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE C 110 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N LEU C 155 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 6.165A 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 563 Processing sheet with id=AB4, first strand: chain 'D' and resid 578 through 579 Processing sheet with id=AB5, first strand: chain 'D' and resid 616 through 618 removed outlier: 3.507A pdb=" N ILE D 644 " --> pdb=" O LEU D 652 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.839A pdb=" N ILE E 37 " --> pdb=" O TYR E 48 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N TYR E 48 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 344 through 347 removed outlier: 3.537A pdb=" N LEU E 399 " --> pdb=" O ILE E 346 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY E 398 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N PHE E 231 " --> pdb=" O GLY E 398 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP E 400 " --> pdb=" O LYS E 229 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N TYR E 222 " --> pdb=" O ASP E 283 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLN E 278 " --> pdb=" O ALA E 426 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ALA E 428 " --> pdb=" O GLN E 278 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL E 280 " --> pdb=" O ALA E 428 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 252 through 253 Processing sheet with id=AB9, first strand: chain 'E' and resid 252 through 253 removed outlier: 3.514A pdb=" N ASP E 238 " --> pdb=" O VAL E 303 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU E 296 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL E 326 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N CYS E 298 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL E 324 " --> pdb=" O CYS E 298 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE E 300 " --> pdb=" O PHE E 322 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN E 349 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 484 through 485 removed outlier: 7.290A pdb=" N CYS E 508 " --> pdb=" O HIS E 452 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N HIS E 452 " --> pdb=" O CYS E 508 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU E 450 " --> pdb=" O TYR E 510 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR E 512 " --> pdb=" O VAL E 448 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL E 448 " --> pdb=" O THR E 512 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LYS E 514 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE E 446 " --> pdb=" O LYS E 514 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE E 446 " --> pdb=" O CYS E 627 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N CYS E 627 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL E 448 " --> pdb=" O LEU E 625 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU E 625 " --> pdb=" O VAL E 448 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU E 450 " --> pdb=" O ALA E 623 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA E 623 " --> pdb=" O LEU E 450 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS E 452 " --> pdb=" O GLN E 621 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY E 565 " --> pdb=" O THR E 624 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 495 through 496 Processing sheet with id=AC3, first strand: chain 'E' and resid 1362 through 1368 removed outlier: 6.008A pdb=" N ILE E1380 " --> pdb=" O VAL E1504 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N PHE E1502 " --> pdb=" O THR E1494 " (cutoff:3.500A) removed outlier: 9.365A pdb=" N THR E1494 " --> pdb=" O PHE E1502 " (cutoff:3.500A) removed outlier: 9.604A pdb=" N VAL E1504 " --> pdb=" O ALA E1492 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA E1492 " --> pdb=" O VAL E1504 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR E1491 " --> pdb=" O GLN E1460 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLN E1460 " --> pdb=" O THR E1491 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR E1362 " --> pdb=" O VAL E1431 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 41 through 45 removed outlier: 6.350A pdb=" N ILE F 4 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TRP F 56 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N CYS F 6 " --> pdb=" O TRP F 56 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N VAL F 77 " --> pdb=" O ALA F 3 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LYS F 5 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU F 79 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL F 7 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N CYS F 81 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE F 111 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE F 110 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LEU F 155 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU F 112 " --> pdb=" O LEU F 155 " (cutoff:3.500A) 1677 hydrogen bonds defined for protein. 4863 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: 13.26 Time building geometry restraints manager: 9.99 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: 10070 1.33 - 1.45: 5004 1.45 - 1.57: 18188 1.57 - 1.69: 0 1.69 - 1.81: 294 Bond restraints: 33556 Sorted by residual: bond pdb=" CA TYR C 64 " pdb=" C TYR C 64 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.34e-02 5.57e+03 1.12e+01 bond pdb=" CA TYR F 64 " pdb=" C TYR F 64 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.34e-02 5.57e+03 1.07e+01 bond pdb=" CA SER B1139 " pdb=" C SER B1139 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.34e-02 5.57e+03 3.88e+00 bond pdb=" CG1 ILE B1125 " pdb=" CD1 ILE B1125 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.80e+00 bond pdb=" CG1 ILE E1125 " pdb=" CD1 ILE E1125 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.80e+00 ... (remaining 33551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 44302 2.20 - 4.40: 892 4.40 - 6.59: 111 6.59 - 8.79: 11 8.79 - 10.99: 8 Bond angle restraints: 45324 Sorted by residual: angle pdb=" N GLU E1523 " pdb=" CA GLU E1523 " pdb=" CB GLU E1523 " ideal model delta sigma weight residual 110.01 115.68 -5.67 1.45e+00 4.76e-01 1.53e+01 angle pdb=" N GLU B1523 " pdb=" CA GLU B1523 " pdb=" CB GLU B1523 " ideal model delta sigma weight residual 110.01 115.65 -5.64 1.45e+00 4.76e-01 1.51e+01 angle pdb=" N ILE B 16 " pdb=" CA ILE B 16 " pdb=" C ILE B 16 " ideal model delta sigma weight residual 111.62 108.68 2.94 7.90e-01 1.60e+00 1.39e+01 angle pdb=" N ILE E 16 " pdb=" CA ILE E 16 " pdb=" C ILE E 16 " ideal model delta sigma weight residual 111.62 108.68 2.94 7.90e-01 1.60e+00 1.39e+01 angle pdb=" CB MET B 120 " pdb=" CG MET B 120 " pdb=" SD MET B 120 " ideal model delta sigma weight residual 112.70 123.69 -10.99 3.00e+00 1.11e-01 1.34e+01 ... (remaining 45319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 18122 17.24 - 34.48: 1984 34.48 - 51.73: 288 51.73 - 68.97: 56 68.97 - 86.21: 26 Dihedral angle restraints: 20476 sinusoidal: 8586 harmonic: 11890 Sorted by residual: dihedral pdb=" CA GLN A 541 " pdb=" C GLN A 541 " pdb=" N PRO A 542 " pdb=" CA PRO A 542 " ideal model delta harmonic sigma weight residual 180.00 -149.32 -30.68 0 5.00e+00 4.00e-02 3.76e+01 dihedral pdb=" CA GLN D 541 " pdb=" C GLN D 541 " pdb=" N PRO D 542 " pdb=" CA PRO D 542 " ideal model delta harmonic sigma weight residual -180.00 -149.33 -30.67 0 5.00e+00 4.00e-02 3.76e+01 dihedral pdb=" CA PHE B1402 " pdb=" C PHE B1402 " pdb=" N PRO B1403 " pdb=" CA PRO B1403 " ideal model delta harmonic sigma weight residual 180.00 157.50 22.50 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 20473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3533 0.043 - 0.086: 1124 0.086 - 0.129: 318 0.129 - 0.172: 43 0.172 - 0.215: 6 Chirality restraints: 5024 Sorted by residual: chirality pdb=" CB ILE F 137 " pdb=" CA ILE F 137 " pdb=" CG1 ILE F 137 " pdb=" CG2 ILE F 137 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE C 137 " pdb=" CA ILE C 137 " pdb=" CG1 ILE C 137 " pdb=" CG2 ILE C 137 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+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 -2.38 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 5021 not shown) Planarity restraints: 5796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 98 " -0.015 2.00e-02 2.50e+03 1.51e-02 5.71e+00 pdb=" CG TRP B 98 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 98 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 98 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 98 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 98 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 98 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 98 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 98 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 98 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 98 " -0.014 2.00e-02 2.50e+03 1.51e-02 5.67e+00 pdb=" CG TRP E 98 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP E 98 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP E 98 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 98 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP E 98 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 98 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 98 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 98 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 98 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E1107 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO E1108 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO E1108 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E1108 " 0.029 5.00e-02 4.00e+02 ... (remaining 5793 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 626 2.58 - 3.16: 32164 3.16 - 3.74: 57064 3.74 - 4.32: 78289 4.32 - 4.90: 118325 Nonbonded interactions: 286468 Sorted by model distance: nonbonded pdb=" OG1 THR B 49 " pdb=" OD1 ASN B 52 " model vdw 2.005 3.040 nonbonded pdb=" OG1 THR E 49 " pdb=" OD1 ASN E 52 " model vdw 2.006 3.040 nonbonded pdb=" OD2 ASP D 667 " pdb=" OG SER D 679 " model vdw 2.027 3.040 nonbonded pdb=" OD2 ASP A 667 " pdb=" OG SER A 679 " model vdw 2.028 3.040 nonbonded pdb=" OD1 ASN B1526 " pdb=" NE2 GLN B1596 " model vdw 2.070 3.120 ... (remaining 286463 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 1.330 Check model and map are aligned: 0.250 Set scattering table: 0.260 Process input model: 70.050 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.140 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 0.076 33556 Z= 0.230 Angle : 0.762 10.988 45324 Z= 0.426 Chirality : 0.045 0.215 5024 Planarity : 0.004 0.053 5796 Dihedral : 14.085 86.211 12780 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 29.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 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: -1.29 (0.13), residues: 4022 helix: -0.17 (0.11), residues: 1944 sheet: -1.27 (0.22), residues: 496 loop : -1.44 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 98 HIS 0.006 0.001 HIS B1056 PHE 0.029 0.002 PHE E 798 TYR 0.030 0.002 TYR B1566 ARG 0.017 0.001 ARG B1252 Details of bonding type rmsd hydrogen bonds : bond 0.17628 ( 1673) hydrogen bonds : angle 7.37825 ( 4863) covalent geometry : bond 0.00463 (33556) covalent geometry : angle 0.76243 (45324) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 3.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 ARG cc_start: 0.4838 (ttp80) cc_final: 0.4602 (tmm160) REVERT: B 120 MET cc_start: 0.8553 (mpp) cc_final: 0.8323 (mpp) REVERT: B 579 MET cc_start: -0.0950 (tpt) cc_final: -0.1366 (tpt) REVERT: B 764 PHE cc_start: 0.9732 (m-80) cc_final: 0.9375 (m-80) REVERT: B 957 MET cc_start: 0.9239 (ppp) cc_final: 0.8896 (ppp) REVERT: B 958 ILE cc_start: 0.9594 (pt) cc_final: 0.9379 (pt) REVERT: B 1158 GLU cc_start: 0.8841 (mp0) cc_final: 0.8626 (mp0) REVERT: B 1356 MET cc_start: 0.8099 (ppp) cc_final: 0.7663 (ppp) REVERT: B 1522 MET cc_start: 0.9336 (tpt) cc_final: 0.8874 (tpt) REVERT: B 1549 MET cc_start: 0.8819 (mmm) cc_final: 0.8246 (mmm) REVERT: D 625 MET cc_start: 0.2334 (mmm) cc_final: 0.1607 (tpp) REVERT: D 692 MET cc_start: 0.8743 (mmm) cc_final: 0.8479 (mmm) REVERT: E 12 TYR cc_start: 0.8097 (m-10) cc_final: 0.7674 (m-10) REVERT: E 764 PHE cc_start: 0.9724 (m-80) cc_final: 0.9362 (m-80) REVERT: E 957 MET cc_start: 0.9218 (ppp) cc_final: 0.8924 (ppp) REVERT: E 958 ILE cc_start: 0.9576 (pt) cc_final: 0.9326 (pt) REVERT: E 1146 MET cc_start: 0.8588 (mpp) cc_final: 0.8387 (pmm) REVERT: E 1158 GLU cc_start: 0.8818 (mp0) cc_final: 0.8537 (mp0) REVERT: E 1522 MET cc_start: 0.9206 (tpt) cc_final: 0.8562 (tpt) REVERT: E 1560 MET cc_start: 0.8094 (pmm) cc_final: 0.7786 (pmm) REVERT: E 1597 MET cc_start: 0.8593 (mpp) cc_final: 0.8322 (ptp) REVERT: F 92 ASN cc_start: 0.9108 (t0) cc_final: 0.8888 (t0) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.4073 time to fit residues: 135.6030 Evaluate side-chains 152 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 4.119 ------------------------------------------------------------------------------- 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: 7.9990 chunk 303 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 204 optimal weight: 0.1980 chunk 161 optimal weight: 0.8980 chunk 313 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 190 optimal weight: 9.9990 chunk 233 optimal weight: 0.6980 chunk 363 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 ASN A 582 ASN ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 885 GLN B 926 GLN B1401 GLN ** B1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 2 GLN ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 ASN ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN E 305 HIS ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 885 GLN E 926 GLN E1401 GLN ** E1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 2 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.060000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.037169 restraints weight = 309255.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.038213 restraints weight = 199874.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.038713 restraints weight = 148410.496| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 33556 Z= 0.144 Angle : 0.657 11.568 45324 Z= 0.342 Chirality : 0.043 0.195 5024 Planarity : 0.005 0.059 5796 Dihedral : 5.500 88.431 4394 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.27 % Allowed : 5.71 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 4022 helix: 0.27 (0.11), residues: 1978 sheet: -1.35 (0.22), residues: 506 loop : -1.32 (0.17), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 102 HIS 0.006 0.001 HIS B 899 PHE 0.021 0.002 PHE B 798 TYR 0.022 0.002 TYR B1566 ARG 0.006 0.001 ARG E1252 Details of bonding type rmsd hydrogen bonds : bond 0.04949 ( 1673) hydrogen bonds : angle 5.88864 ( 4863) covalent geometry : bond 0.00304 (33556) covalent geometry : angle 0.65689 (45324) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 200 time to evaluate : 4.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 MET cc_start: 0.8719 (mmt) cc_final: 0.8518 (mmp) REVERT: B 120 MET cc_start: 0.8799 (mpp) cc_final: 0.8556 (mmt) REVERT: B 764 PHE cc_start: 0.9773 (m-80) cc_final: 0.9374 (m-80) REVERT: B 957 MET cc_start: 0.9362 (ppp) cc_final: 0.9078 (ppp) REVERT: B 958 ILE cc_start: 0.9685 (pt) cc_final: 0.9426 (pt) REVERT: B 1007 MET cc_start: 0.8978 (tmm) cc_final: 0.8645 (tmm) REVERT: B 1132 MET cc_start: 0.8681 (ppp) cc_final: 0.8281 (ppp) REVERT: B 1352 ILE cc_start: 0.8503 (mm) cc_final: 0.8303 (mm) REVERT: B 1356 MET cc_start: 0.8067 (ppp) cc_final: 0.7662 (ppp) REVERT: B 1482 MET cc_start: 0.8069 (mmm) cc_final: 0.7854 (mmm) REVERT: B 1522 MET cc_start: 0.9384 (tpt) cc_final: 0.8948 (tpp) REVERT: B 1549 MET cc_start: 0.9071 (mmm) cc_final: 0.8625 (tpp) REVERT: D 625 MET cc_start: 0.2426 (mmm) cc_final: 0.1629 (tpp) REVERT: D 692 MET cc_start: 0.8791 (mmt) cc_final: 0.8565 (mmm) REVERT: E 1 MET cc_start: 0.0470 (tpp) cc_final: 0.0074 (mmm) REVERT: E 764 PHE cc_start: 0.9735 (m-80) cc_final: 0.9392 (m-80) REVERT: E 795 PHE cc_start: 0.9462 (m-80) cc_final: 0.9193 (m-80) REVERT: E 957 MET cc_start: 0.9256 (ppp) cc_final: 0.8941 (ppp) REVERT: E 958 ILE cc_start: 0.9651 (pt) cc_final: 0.9399 (pt) REVERT: E 964 MET cc_start: 0.7533 (mtm) cc_final: 0.7118 (mtp) REVERT: E 1007 MET cc_start: 0.8863 (tmm) cc_final: 0.8594 (tmm) REVERT: E 1426 MET cc_start: 0.8425 (ppp) cc_final: 0.7840 (tmm) REVERT: E 1522 MET cc_start: 0.9202 (tpt) cc_final: 0.8565 (tpt) REVERT: E 1523 GLU cc_start: 0.9362 (OUTLIER) cc_final: 0.9003 (pp20) REVERT: F 92 ASN cc_start: 0.9156 (t0) cc_final: 0.8822 (t0) outliers start: 10 outliers final: 2 residues processed: 210 average time/residue: 0.4318 time to fit residues: 152.9900 Evaluate side-chains 161 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 158 time to evaluate : 3.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 386 optimal weight: 9.9990 chunk 306 optimal weight: 1.9990 chunk 286 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 80 optimal weight: 30.0000 chunk 116 optimal weight: 4.9990 chunk 374 optimal weight: 0.0670 chunk 298 optimal weight: 3.9990 chunk 61 optimal weight: 0.0270 chunk 316 optimal weight: 20.0000 chunk 387 optimal weight: 10.0000 overall best weight: 1.6182 ------------------------------------------------------------------------------- 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 414 GLN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 HIS E 414 GLN ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1517 ASN ** E1596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.059930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.037833 restraints weight = 311051.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.038255 restraints weight = 193858.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.038698 restraints weight = 141961.076| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33556 Z= 0.144 Angle : 0.636 10.768 45324 Z= 0.328 Chirality : 0.043 0.179 5024 Planarity : 0.004 0.060 5796 Dihedral : 5.373 89.788 4394 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 4022 helix: 0.37 (0.11), residues: 1970 sheet: -1.31 (0.23), residues: 470 loop : -1.30 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 102 HIS 0.009 0.001 HIS E1048 PHE 0.015 0.001 PHE B1129 TYR 0.018 0.001 TYR E1575 ARG 0.005 0.001 ARG E 935 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 1673) hydrogen bonds : angle 5.62814 ( 4863) covalent geometry : bond 0.00309 (33556) covalent geometry : angle 0.63561 (45324) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 195 time to evaluate : 3.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3836 (mmm) cc_final: 0.3402 (mmm) REVERT: B 120 MET cc_start: 0.8815 (mpp) cc_final: 0.8611 (mmt) REVERT: B 157 ARG cc_start: 0.8977 (tpm170) cc_final: 0.8777 (ttp80) REVERT: B 764 PHE cc_start: 0.9745 (m-80) cc_final: 0.9352 (m-80) REVERT: B 943 MET cc_start: 0.6969 (ttt) cc_final: 0.6396 (ttt) REVERT: B 957 MET cc_start: 0.9359 (ppp) cc_final: 0.9082 (ppp) REVERT: B 958 ILE cc_start: 0.9696 (pt) cc_final: 0.9416 (pt) REVERT: B 964 MET cc_start: 0.7825 (mtm) cc_final: 0.7542 (mtp) REVERT: B 1007 MET cc_start: 0.8963 (tmm) cc_final: 0.8636 (tmm) REVERT: B 1356 MET cc_start: 0.8047 (ppp) cc_final: 0.7627 (ppp) REVERT: B 1432 LYS cc_start: 0.9232 (mmmt) cc_final: 0.8939 (mtmm) REVERT: B 1482 MET cc_start: 0.7969 (mmm) cc_final: 0.7734 (mmm) REVERT: B 1522 MET cc_start: 0.9373 (tpt) cc_final: 0.8912 (tpp) REVERT: D 625 MET cc_start: 0.2368 (mmm) cc_final: 0.1465 (tpp) REVERT: E 1 MET cc_start: 0.0750 (tpp) cc_final: 0.0337 (mmm) REVERT: E 764 PHE cc_start: 0.9736 (m-80) cc_final: 0.9511 (m-80) REVERT: E 957 MET cc_start: 0.9246 (ppp) cc_final: 0.8919 (ppp) REVERT: E 958 ILE cc_start: 0.9663 (pt) cc_final: 0.9389 (pt) REVERT: E 964 MET cc_start: 0.7716 (mtm) cc_final: 0.7229 (mtp) REVERT: E 1007 MET cc_start: 0.8879 (tmm) cc_final: 0.8614 (tmm) REVERT: E 1426 MET cc_start: 0.8243 (ppp) cc_final: 0.7932 (tmm) REVERT: E 1432 LYS cc_start: 0.9228 (mmmt) cc_final: 0.8909 (mtmm) REVERT: E 1522 MET cc_start: 0.9219 (tpt) cc_final: 0.8683 (tpt) REVERT: E 1549 MET cc_start: 0.8954 (mmm) cc_final: 0.8704 (mmm) REVERT: F 145 MET cc_start: 0.8235 (tpt) cc_final: 0.8020 (tpt) outliers start: 3 outliers final: 0 residues processed: 198 average time/residue: 0.4373 time to fit residues: 146.6773 Evaluate side-chains 156 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 3.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 341 optimal weight: 1.9990 chunk 296 optimal weight: 9.9990 chunk 378 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 ASN B1517 ASN ** B1596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 HIS ** E 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 908 ASN E1044 ASN ** E1596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.059678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.036856 restraints weight = 311090.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.037792 restraints weight = 196391.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.038498 restraints weight = 146350.770| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33556 Z= 0.149 Angle : 0.639 10.657 45324 Z= 0.330 Chirality : 0.043 0.173 5024 Planarity : 0.004 0.061 5796 Dihedral : 5.316 89.390 4394 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.05 % Allowed : 5.02 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 4022 helix: 0.42 (0.11), residues: 1970 sheet: -1.28 (0.23), residues: 474 loop : -1.33 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 102 HIS 0.006 0.001 HIS E1048 PHE 0.016 0.002 PHE E1333 TYR 0.023 0.002 TYR B1231 ARG 0.013 0.001 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04280 ( 1673) hydrogen bonds : angle 5.47289 ( 4863) covalent geometry : bond 0.00320 (33556) covalent geometry : angle 0.63931 (45324) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 3.629 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: A 678 MET cc_start: 0.8837 (pmm) cc_final: 0.8611 (pmm) REVERT: B 1 MET cc_start: 0.3866 (mmm) cc_final: 0.3539 (mmm) REVERT: B 120 MET cc_start: 0.8811 (mpp) cc_final: 0.8599 (mmt) REVERT: B 267 MET cc_start: 0.6529 (mmt) cc_final: 0.6310 (ttt) REVERT: B 764 PHE cc_start: 0.9761 (m-80) cc_final: 0.9411 (m-80) REVERT: B 860 MET cc_start: 0.9332 (ptp) cc_final: 0.9117 (ptm) REVERT: B 943 MET cc_start: 0.6984 (ttt) cc_final: 0.6516 (ttt) REVERT: B 957 MET cc_start: 0.9313 (ppp) cc_final: 0.8945 (ppp) REVERT: B 958 ILE cc_start: 0.9668 (pt) cc_final: 0.9439 (pt) REVERT: B 964 MET cc_start: 0.7798 (mtm) cc_final: 0.7436 (mtp) REVERT: B 1007 MET cc_start: 0.8993 (tmm) cc_final: 0.8714 (tmm) REVERT: B 1212 MET cc_start: 0.8804 (mpp) cc_final: 0.8501 (ppp) REVERT: B 1356 MET cc_start: 0.7890 (ppp) cc_final: 0.7581 (ppp) REVERT: B 1432 LYS cc_start: 0.9217 (mmmt) cc_final: 0.8927 (mtmm) REVERT: B 1482 MET cc_start: 0.7997 (mmm) cc_final: 0.7735 (mmm) REVERT: B 1522 MET cc_start: 0.9305 (tpt) cc_final: 0.8888 (tpp) REVERT: B 1549 MET cc_start: 0.9163 (mmm) cc_final: 0.8849 (tpt) REVERT: C 145 MET cc_start: 0.8175 (tpt) cc_final: 0.7920 (tpt) REVERT: D 625 MET cc_start: 0.2199 (mmm) cc_final: 0.1300 (tpp) REVERT: D 692 MET cc_start: 0.8707 (mmp) cc_final: 0.8479 (mmt) REVERT: E 1 MET cc_start: 0.0787 (tpp) cc_final: 0.0527 (mmm) REVERT: E 764 PHE cc_start: 0.9749 (m-80) cc_final: 0.9358 (m-10) REVERT: E 943 MET cc_start: 0.6704 (ttt) cc_final: 0.6105 (ttt) REVERT: E 957 MET cc_start: 0.9213 (ppp) cc_final: 0.8925 (ppp) REVERT: E 958 ILE cc_start: 0.9661 (pt) cc_final: 0.9389 (pt) REVERT: E 964 MET cc_start: 0.7630 (mtm) cc_final: 0.7093 (mtp) REVERT: E 1007 MET cc_start: 0.8907 (tmm) cc_final: 0.8664 (tmm) REVERT: E 1426 MET cc_start: 0.8293 (ppp) cc_final: 0.7925 (tmm) REVERT: E 1432 LYS cc_start: 0.9250 (mmmt) cc_final: 0.8911 (mtmm) REVERT: E 1522 MET cc_start: 0.9257 (tpt) cc_final: 0.8741 (tpp) REVERT: E 1549 MET cc_start: 0.8807 (mmm) cc_final: 0.7588 (mmm) REVERT: E 1560 MET cc_start: 0.7847 (pmm) cc_final: 0.7385 (pmm) outliers start: 2 outliers final: 0 residues processed: 185 average time/residue: 0.4198 time to fit residues: 132.5552 Evaluate side-chains 146 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 3.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) 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 368, 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 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) 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/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients 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: 58.3227 > 50: distance: 12 - 158: 14.566 distance: 15 - 155: 25.353 distance: 75 - 79: 7.852 distance: 79 - 80: 3.691 distance: 80 - 81: 12.940 distance: 80 - 83: 4.591 distance: 81 - 82: 4.076 distance: 81 - 88: 19.137 distance: 83 - 84: 7.024 distance: 84 - 85: 5.766 distance: 85 - 86: 7.573 distance: 85 - 87: 3.619 distance: 88 - 89: 11.910 distance: 89 - 90: 7.994 distance: 89 - 92: 4.741 distance: 90 - 96: 9.894 distance: 92 - 93: 9.234 distance: 92 - 94: 8.808 distance: 93 - 95: 16.047 distance: 96 - 97: 9.551 distance: 97 - 98: 12.091 distance: 97 - 100: 8.925 distance: 98 - 99: 13.972 distance: 98 - 105: 19.008 distance: 100 - 101: 21.526 distance: 101 - 102: 19.363 distance: 102 - 103: 22.299 distance: 102 - 104: 14.384 distance: 105 - 106: 11.845 distance: 106 - 107: 14.662 distance: 106 - 109: 17.743 distance: 107 - 108: 21.762 distance: 107 - 114: 10.140 distance: 108 - 130: 32.468 distance: 109 - 110: 9.591 distance: 110 - 111: 8.186 distance: 111 - 112: 14.741 distance: 112 - 113: 10.705 distance: 114 - 115: 8.084 distance: 115 - 116: 6.383 distance: 115 - 118: 18.567 distance: 116 - 117: 6.111 distance: 116 - 122: 8.839 distance: 118 - 119: 9.336 distance: 119 - 120: 8.716 distance: 119 - 121: 16.959 distance: 122 - 123: 12.065 distance: 123 - 124: 15.229 distance: 123 - 126: 8.345 distance: 124 - 125: 9.939 distance: 124 - 130: 39.719 distance: 126 - 127: 16.740 distance: 127 - 128: 6.214 distance: 127 - 129: 8.845 distance: 130 - 131: 18.834 distance: 131 - 132: 23.168 distance: 131 - 134: 13.988 distance: 132 - 133: 6.928 distance: 132 - 138: 31.794 distance: 134 - 135: 13.923 distance: 135 - 136: 14.427 distance: 135 - 137: 15.493 distance: 138 - 139: 32.823 distance: 139 - 140: 14.803 distance: 139 - 142: 11.213 distance: 140 - 141: 25.383 distance: 140 - 146: 14.022 distance: 142 - 143: 12.295 distance: 143 - 144: 47.819 distance: 143 - 145: 36.695 distance: 146 - 147: 15.261 distance: 147 - 148: 12.707 distance: 147 - 150: 29.855 distance: 148 - 149: 21.173 distance: 148 - 155: 9.511 distance: 150 - 151: 36.023 distance: 151 - 152: 8.927 distance: 152 - 153: 20.629 distance: 152 - 154: 20.171 distance: 155 - 156: 10.905 distance: 156 - 157: 25.054 distance: 156 - 159: 25.586 distance: 157 - 158: 11.696 distance: 157 - 160: 7.954