Starting phenix.real_space_refine on Mon Nov 18 18:36:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4z_35189/11_2024/8i4z_35189_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4z_35189/11_2024/8i4z_35189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4z_35189/11_2024/8i4z_35189.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4z_35189/11_2024/8i4z_35189.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4z_35189/11_2024/8i4z_35189_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4z_35189/11_2024/8i4z_35189_trim.cif" } resolution = 3.97 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= 0.001 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: 5 Type Number sf(0) Gaussians S 46 5.16 5 C 15345 2.51 5 N 4563 2.21 5 O 4675 1.98 5 H 24348 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 290 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 48977 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 24479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1687, 24479 Classifications: {'peptide': 1687} Link IDs: {'PTRANS': 122, 'TRANS': 1564} Chain: "B" Number of atoms: 24479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1687, 24479 Classifications: {'peptide': 1687} Link IDs: {'PTRANS': 122, 'TRANS': 1564} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'ONF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 22.35, per 1000 atoms: 0.46 Number of scatterers: 48977 At special positions: 0 Unit cell: (200.25, 167.32, 128.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 O 4675 8.00 N 4563 7.00 C 15345 6.00 H 24348 1.00 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: 12.25 Conformation dependent library (CDL) restraints added in 4.0 seconds 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5896 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 19 sheets defined 44.5% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.32 Creating SS restraints... Processing helix chain 'A' and resid 51 through 61 Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.717A pdb=" N LEU A 81 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 101 removed outlier: 4.154A pdb=" N PHE A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 111 through 129 removed outlier: 3.623A pdb=" N TRP A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 removed outlier: 3.727A pdb=" N ARG A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 160 through 165 removed outlier: 4.466A pdb=" N ASP A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 172 Processing helix chain 'A' and resid 174 through 185 removed outlier: 4.164A pdb=" N GLY A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 213 Processing helix chain 'A' and resid 230 through 239 Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 376 through 392 removed outlier: 3.915A pdb=" N GLY A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 412 removed outlier: 4.036A pdb=" N SER A 411 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 3.560A pdb=" N LEU A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 removed outlier: 3.714A pdb=" N THR A 504 " --> pdb=" O HIS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 533 Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 566 through 576 Proline residue: A 572 - end of helix Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.607A pdb=" N ALA A 581 " --> pdb=" O GLY A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 601 removed outlier: 4.096A pdb=" N ALA A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU A 599 " --> pdb=" O HIS A 595 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 610 removed outlier: 3.884A pdb=" N ALA A 606 " --> pdb=" O PRO A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 Processing helix chain 'A' and resid 619 through 640 Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.903A pdb=" N ALA A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 685 removed outlier: 3.807A pdb=" N ARG A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 707 removed outlier: 3.683A pdb=" N SER A 705 " --> pdb=" O ARG A 701 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 711 Processing helix chain 'A' and resid 729 through 744 removed outlier: 3.529A pdb=" N ARG A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 775 removed outlier: 3.527A pdb=" N GLU A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 772 " --> pdb=" O GLU A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 800 removed outlier: 4.339A pdb=" N ARG A 800 " --> pdb=" O PRO A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 811 removed outlier: 3.815A pdb=" N TRP A 805 " --> pdb=" O SER A 801 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 807 " --> pdb=" O GLU A 803 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N HIS A 808 " --> pdb=" O HIS A 804 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU A 809 " --> pdb=" O TRP A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 825 Processing helix chain 'A' and resid 839 through 848 Processing helix chain 'A' and resid 868 through 884 removed outlier: 3.558A pdb=" N ALA A 872 " --> pdb=" O PRO A 868 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 873 " --> pdb=" O PRO A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 893 removed outlier: 4.266A pdb=" N GLN A 891 " --> pdb=" O ASP A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 960 removed outlier: 4.162A pdb=" N ALA A 957 " --> pdb=" O PRO A 953 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY A 958 " --> pdb=" O GLY A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 985 removed outlier: 3.505A pdb=" N LEU A 976 " --> pdb=" O ALA A 972 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1065 Processing helix chain 'A' and resid 1073 through 1083 removed outlier: 3.539A pdb=" N TRP A1082 " --> pdb=" O TYR A1078 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A1083 " --> pdb=" O ARG A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1093 Processing helix chain 'A' and resid 1123 through 1138 removed outlier: 3.559A pdb=" N SER A1138 " --> pdb=" O LEU A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1197 Processing helix chain 'A' and resid 1200 through 1204 removed outlier: 4.149A pdb=" N GLY A1203 " --> pdb=" O GLU A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1255 removed outlier: 3.510A pdb=" N PHE A1255 " --> pdb=" O GLU A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1296 removed outlier: 4.063A pdb=" N VAL A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1313 removed outlier: 3.553A pdb=" N ALA A1311 " --> pdb=" O ALA A1308 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG A1312 " --> pdb=" O GLY A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1344 removed outlier: 3.774A pdb=" N GLY A1330 " --> pdb=" O CYS A1326 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG A1331 " --> pdb=" O ARG A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1345 through 1347 No H-bonds generated for 'chain 'A' and resid 1345 through 1347' Processing helix chain 'A' and resid 1367 through 1369 No H-bonds generated for 'chain 'A' and resid 1367 through 1369' Processing helix chain 'A' and resid 1370 through 1384 removed outlier: 4.086A pdb=" N THR A1374 " --> pdb=" O GLN A1370 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP A1382 " --> pdb=" O THR A1378 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS A1384 " --> pdb=" O LEU A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1412 removed outlier: 3.587A pdb=" N LEU A1406 " --> pdb=" O THR A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1444 removed outlier: 3.651A pdb=" N GLU A1442 " --> pdb=" O ALA A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1472 Processing helix chain 'A' and resid 1481 through 1486 removed outlier: 3.954A pdb=" N GLU A1485 " --> pdb=" O ALA A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1496 Processing helix chain 'A' and resid 1512 through 1524 Processing helix chain 'A' and resid 1544 through 1548 Processing helix chain 'A' and resid 1549 through 1574 removed outlier: 4.951A pdb=" N ALA A1558 " --> pdb=" O GLY A1554 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLY A1563 " --> pdb=" O GLY A1559 " (cutoff:3.500A) Proline residue: A1564 - end of helix Processing helix chain 'A' and resid 1590 through 1592 No H-bonds generated for 'chain 'A' and resid 1590 through 1592' Processing helix chain 'A' and resid 1598 through 1618 Processing helix chain 'A' and resid 1630 through 1634 Processing helix chain 'A' and resid 1639 through 1648 removed outlier: 3.659A pdb=" N VAL A1643 " --> pdb=" O GLU A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1654 through 1663 Processing helix chain 'A' and resid 1664 through 1668 removed outlier: 4.451A pdb=" N ALA A1667 " --> pdb=" O PRO A1664 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1691 Processing helix chain 'A' and resid 1715 through 1719 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.976A pdb=" N LEU B 81 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 110 Processing helix chain 'B' and resid 111 through 128 removed outlier: 3.506A pdb=" N ARG B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.601A pdb=" N ARG B 136 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 160 through 165 removed outlier: 4.017A pdb=" N ASP B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 174 through 184 removed outlier: 4.015A pdb=" N GLY B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 213 Processing helix chain 'B' and resid 230 through 239 removed outlier: 3.590A pdb=" N ARG B 239 " --> pdb=" O ASP B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 302 through 319 removed outlier: 3.761A pdb=" N ARG B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 349 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 376 through 392 Processing helix chain 'B' and resid 408 through 412 removed outlier: 4.456A pdb=" N SER B 411 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 493 removed outlier: 3.812A pdb=" N LEU B 479 " --> pdb=" O SER B 475 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA B 488 " --> pdb=" O GLU B 484 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR B 489 " --> pdb=" O ARG B 485 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 506 removed outlier: 3.794A pdb=" N HIS B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR B 504 " --> pdb=" O HIS B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 532 Processing helix chain 'B' and resid 557 through 563 Processing helix chain 'B' and resid 564 through 569 Processing helix chain 'B' and resid 569 through 582 removed outlier: 3.722A pdb=" N GLY B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU B 580 " --> pdb=" O ARG B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 598 removed outlier: 3.908A pdb=" N ALA B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU B 591 " --> pdb=" O GLU B 587 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 609 removed outlier: 4.223A pdb=" N ARG B 605 " --> pdb=" O GLY B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 617 Processing helix chain 'B' and resid 619 through 640 Processing helix chain 'B' and resid 652 through 661 removed outlier: 3.549A pdb=" N ALA B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 685 removed outlier: 3.721A pdb=" N ALA B 671 " --> pdb=" O ALA B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 707 removed outlier: 3.693A pdb=" N ALA B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 711 Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 758 through 774 removed outlier: 3.599A pdb=" N ARG B 770 " --> pdb=" O LEU B 766 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ALA B 771 " --> pdb=" O ALA B 767 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 772 " --> pdb=" O GLU B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 800 Processing helix chain 'B' and resid 801 through 807 removed outlier: 3.783A pdb=" N TRP B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 825 Processing helix chain 'B' and resid 839 through 848 Processing helix chain 'B' and resid 868 through 884 removed outlier: 4.111A pdb=" N ALA B 872 " --> pdb=" O PRO B 868 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU B 873 " --> pdb=" O PRO B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 894 removed outlier: 3.828A pdb=" N PHE B 893 " --> pdb=" O TRP B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 960 Processing helix chain 'B' and resid 971 through 984 Processing helix chain 'B' and resid 985 through 987 No H-bonds generated for 'chain 'B' and resid 985 through 987' Processing helix chain 'B' and resid 1061 through 1065 Processing helix chain 'B' and resid 1073 through 1083 Processing helix chain 'B' and resid 1090 through 1093 Processing helix chain 'B' and resid 1120 through 1122 No H-bonds generated for 'chain 'B' and resid 1120 through 1122' Processing helix chain 'B' and resid 1123 through 1138 removed outlier: 3.501A pdb=" N ALA B1131 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B1138 " --> pdb=" O LEU B1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 1193 through 1197 Processing helix chain 'B' and resid 1241 through 1255 Processing helix chain 'B' and resid 1282 through 1296 removed outlier: 3.593A pdb=" N VAL B1286 " --> pdb=" O ASP B1282 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU B1292 " --> pdb=" O LYS B1288 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B1293 " --> pdb=" O THR B1289 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B1294 " --> pdb=" O PHE B1290 " (cutoff:3.500A) Processing helix chain 'B' and resid 1308 through 1310 No H-bonds generated for 'chain 'B' and resid 1308 through 1310' Processing helix chain 'B' and resid 1311 through 1317 Processing helix chain 'B' and resid 1320 through 1344 removed outlier: 3.734A pdb=" N GLU B1342 " --> pdb=" O GLY B1338 " (cutoff:3.500A) Processing helix chain 'B' and resid 1345 through 1347 No H-bonds generated for 'chain 'B' and resid 1345 through 1347' Processing helix chain 'B' and resid 1367 through 1369 No H-bonds generated for 'chain 'B' and resid 1367 through 1369' Processing helix chain 'B' and resid 1370 through 1382 removed outlier: 4.124A pdb=" N THR B1374 " --> pdb=" O GLN B1370 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP B1382 " --> pdb=" O THR B1378 " (cutoff:3.500A) Processing helix chain 'B' and resid 1402 through 1412 removed outlier: 3.551A pdb=" N ARG B1412 " --> pdb=" O GLY B1408 " (cutoff:3.500A) Processing helix chain 'B' and resid 1438 through 1444 Processing helix chain 'B' and resid 1458 through 1472 removed outlier: 3.592A pdb=" N ALA B1464 " --> pdb=" O ARG B1460 " (cutoff:3.500A) Processing helix chain 'B' and resid 1481 through 1486 removed outlier: 3.702A pdb=" N GLU B1485 " --> pdb=" O ALA B1482 " (cutoff:3.500A) Processing helix chain 'B' and resid 1489 through 1496 Processing helix chain 'B' and resid 1512 through 1518 Processing helix chain 'B' and resid 1520 through 1525 Processing helix chain 'B' and resid 1551 through 1574 removed outlier: 3.755A pdb=" N ALA B1555 " --> pdb=" O ALA B1551 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA B1558 " --> pdb=" O GLY B1554 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLY B1563 " --> pdb=" O GLY B1559 " (cutoff:3.500A) Proline residue: B1564 - end of helix Processing helix chain 'B' and resid 1590 through 1592 No H-bonds generated for 'chain 'B' and resid 1590 through 1592' Processing helix chain 'B' and resid 1598 through 1618 removed outlier: 3.677A pdb=" N ARG B1613 " --> pdb=" O THR B1609 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B1618 " --> pdb=" O HIS B1614 " (cutoff:3.500A) Processing helix chain 'B' and resid 1630 through 1634 Processing helix chain 'B' and resid 1639 through 1649 Processing helix chain 'B' and resid 1654 through 1663 Processing helix chain 'B' and resid 1683 through 1690 removed outlier: 3.730A pdb=" N THR B1689 " --> pdb=" O ASP B1685 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 414 through 416 removed outlier: 3.687A pdb=" N ALA A 328 " --> pdb=" O ARG A 431 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 435 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN A 443 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE A 291 " --> pdb=" O ASN A 443 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N HIS A 445 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR A 289 " --> pdb=" O HIS A 445 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE A 447 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA A 284 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU A 268 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE A 41 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N MET A 266 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N CYS A 43 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA A 264 " --> pdb=" O CYS A 43 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N VAL A 191 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL A 142 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL A 193 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA A 144 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N VAL B 191 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL B 142 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL B 193 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA B 144 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA B 264 " --> pdb=" O CYS B 43 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N CYS B 43 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N MET B 266 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE B 41 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU B 268 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA B 284 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 447 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR B 289 " --> pdb=" O HIS B 445 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N HIS B 445 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE B 291 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN B 443 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS B 436 " --> pdb=" O GLY B 444 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 328 " --> pdb=" O ARG B 431 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA3, first strand: chain 'A' and resid 393 through 394 Processing sheet with id=AA4, first strand: chain 'A' and resid 467 through 473 removed outlier: 3.527A pdb=" N GLY A 517 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 785 through 787 removed outlier: 6.418A pdb=" N THR A 647 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A 646 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 860 " --> pdb=" O LEU A 830 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 713 through 717 removed outlier: 6.507A pdb=" N VAL A 725 " --> pdb=" O ALA A 716 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 935 through 936 removed outlier: 5.821A pdb=" N GLY A1032 " --> pdb=" O GLU A1042 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU A1042 " --> pdb=" O GLY A1032 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY A1045 " --> pdb=" O ILE A 997 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE A 997 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 993 " --> pdb=" O VAL A1049 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP A1149 " --> pdb=" O GLY A 996 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG A 998 " --> pdb=" O SER A1147 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER A1147 " --> pdb=" O ARG A 998 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A1148 " --> pdb=" O LEU A1191 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A1191 " --> pdb=" O VAL A1148 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU A1185 " --> pdb=" O SER A1154 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ALA A1173 " --> pdb=" O GLY A1190 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A1161 " --> pdb=" O VAL A1109 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A1097 " --> pdb=" O LEU A1108 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A1098 " --> pdb=" O LEU A1072 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 968 through 969 removed outlier: 3.729A pdb=" N GLN A 962 " --> pdb=" O VAL A 969 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1274 through 1276 removed outlier: 9.144A pdb=" N GLU A1274 " --> pdb=" O ALA A1259 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA A1261 " --> pdb=" O GLU A1274 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL A1276 " --> pdb=" O ALA A1261 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA A1263 " --> pdb=" O VAL A1276 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP A1235 " --> pdb=" O VAL A1260 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU A1262 " --> pdb=" O TRP A1235 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL A1237 " --> pdb=" O LEU A1262 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLY A1264 " --> pdb=" O VAL A1237 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N SER A1239 " --> pdb=" O GLY A1264 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER A1234 " --> pdb=" O VAL A1300 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A1302 " --> pdb=" O SER A1234 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA A1301 " --> pdb=" O ARG A1349 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N VAL A1351 " --> pdb=" O ALA A1301 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A1303 " --> pdb=" O VAL A1351 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N CYS A1353 " --> pdb=" O LEU A1303 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL A1305 " --> pdb=" O CYS A1353 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ALA A1355 " --> pdb=" O VAL A1305 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE A1350 " --> pdb=" O ALA A1390 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL A1392 " --> pdb=" O ILE A1350 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A1352 " --> pdb=" O VAL A1392 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU A1394 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER A1354 " --> pdb=" O LEU A1394 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N CYS A1389 " --> pdb=" O GLY A1417 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LEU A1419 " --> pdb=" O CYS A1389 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLN A1391 " --> pdb=" O LEU A1419 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL A1421 " --> pdb=" O GLN A1391 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP A1393 " --> pdb=" O VAL A1421 " (cutoff:3.500A) removed outlier: 15.490A pdb=" N ALA A1416 " --> pdb=" O LEU A1431 " (cutoff:3.500A) removed outlier: 11.027A pdb=" N LEU A1431 " --> pdb=" O ALA A1416 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ARG A1418 " --> pdb=" O ALA A1429 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A1422 " --> pdb=" O ARG A1425 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A1676 " --> pdb=" O VAL A1214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1502 through 1505 removed outlier: 7.497A pdb=" N THR A1451 " --> pdb=" O ARG A1531 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A1533 " --> pdb=" O THR A1451 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU A1453 " --> pdb=" O VAL A1533 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU A1535 " --> pdb=" O LEU A1453 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA A1455 " --> pdb=" O LEU A1535 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG A1531 " --> pdb=" O PHE A1582 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N VAL A1584 " --> pdb=" O ARG A1531 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A1533 " --> pdb=" O VAL A1584 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N SER A1586 " --> pdb=" O VAL A1533 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N LEU A1535 " --> pdb=" O SER A1586 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N SER A1588 " --> pdb=" O LEU A1535 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE A1583 " --> pdb=" O VAL A1623 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA A1625 " --> pdb=" O PHE A1583 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU A1585 " --> pdb=" O ALA A1625 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TRP A1627 " --> pdb=" O LEU A1585 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR A1587 " --> pdb=" O TRP A1627 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 94 through 95 Processing sheet with id=AB3, first strand: chain 'B' and resid 393 through 394 removed outlier: 3.553A pdb=" N GLU B 421 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 467 through 473 removed outlier: 3.696A pdb=" N GLY B 517 " --> pdb=" O VAL B 467 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 785 through 787 removed outlier: 6.540A pdb=" N THR B 647 " --> pdb=" O LEU B 786 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR B 550 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N LEU B 648 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 552 " --> pdb=" O LEU B 648 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N HIS B 650 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE B 554 " --> pdb=" O HIS B 650 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 713 through 720 removed outlier: 6.638A pdb=" N VAL B 725 " --> pdb=" O ALA B 716 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL B 718 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N THR B 723 " --> pdb=" O VAL B 718 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 935 through 936 removed outlier: 3.907A pdb=" N THR B 935 " --> pdb=" O THR B 948 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR B 948 " --> pdb=" O THR B 935 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N GLY B1032 " --> pdb=" O GLU B1042 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1042 " --> pdb=" O GLY B1032 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLY B1045 " --> pdb=" O ILE B 997 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE B 997 " --> pdb=" O GLY B1045 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP B1149 " --> pdb=" O GLY B 996 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG B 998 " --> pdb=" O SER B1147 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER B1147 " --> pdb=" O ARG B 998 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B1148 " --> pdb=" O LEU B1191 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B1191 " --> pdb=" O VAL B1148 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU B1185 " --> pdb=" O SER B1154 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG B1184 " --> pdb=" O SER B1179 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N SER B1179 " --> pdb=" O ARG B1184 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ALA B1173 " --> pdb=" O GLY B1190 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA B1172 " --> pdb=" O GLY B1168 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY B1168 " --> pdb=" O ALA B1172 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B1097 " --> pdb=" O LEU B1108 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL B1098 " --> pdb=" O LEU B1072 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA B1070 " --> pdb=" O LEU B1100 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 967 through 969 removed outlier: 3.730A pdb=" N GLN B 962 " --> pdb=" O VAL B 969 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1274 through 1276 removed outlier: 9.170A pdb=" N GLU B1274 " --> pdb=" O ALA B1259 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA B1261 " --> pdb=" O GLU B1274 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL B1276 " --> pdb=" O ALA B1261 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA B1263 " --> pdb=" O VAL B1276 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP B1235 " --> pdb=" O VAL B1260 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU B1262 " --> pdb=" O TRP B1235 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B1237 " --> pdb=" O LEU B1262 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N GLY B1264 " --> pdb=" O VAL B1237 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N SER B1239 " --> pdb=" O GLY B1264 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N SER B1234 " --> pdb=" O ALA B1301 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU B1303 " --> pdb=" O SER B1234 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B1236 " --> pdb=" O LEU B1303 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL B1305 " --> pdb=" O LEU B1236 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE B1238 " --> pdb=" O VAL B1305 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA B1301 " --> pdb=" O ARG B1349 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N VAL B1351 " --> pdb=" O ALA B1301 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU B1303 " --> pdb=" O VAL B1351 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N CYS B1353 " --> pdb=" O LEU B1303 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL B1305 " --> pdb=" O CYS B1353 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA B1355 " --> pdb=" O VAL B1305 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE B1350 " --> pdb=" O ALA B1390 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL B1392 " --> pdb=" O ILE B1350 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B1352 " --> pdb=" O VAL B1392 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B1394 " --> pdb=" O LEU B1352 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER B1354 " --> pdb=" O LEU B1394 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N CYS B1389 " --> pdb=" O GLY B1417 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N LEU B1419 " --> pdb=" O CYS B1389 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLN B1391 " --> pdb=" O LEU B1419 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL B1421 " --> pdb=" O GLN B1391 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP B1393 " --> pdb=" O VAL B1421 " (cutoff:3.500A) removed outlier: 15.326A pdb=" N ALA B1416 " --> pdb=" O LEU B1431 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N LEU B1431 " --> pdb=" O ALA B1416 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG B1418 " --> pdb=" O ALA B1429 " (cutoff:3.500A) removed outlier: 10.957A pdb=" N ALA B1677 " --> pdb=" O VAL B1622 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA B1624 " --> pdb=" O ALA B1677 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU B1679 " --> pdb=" O ALA B1624 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA B1626 " --> pdb=" O LEU B1679 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ARG B1681 " --> pdb=" O ALA B1626 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE B1583 " --> pdb=" O VAL B1623 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA B1625 " --> pdb=" O PHE B1583 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU B1585 " --> pdb=" O ALA B1625 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TRP B1627 " --> pdb=" O LEU B1585 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR B1587 " --> pdb=" O TRP B1627 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE B1582 " --> pdb=" O ARG B1531 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR B1451 " --> pdb=" O ARG B1531 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL B1533 " --> pdb=" O THR B1451 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B1453 " --> pdb=" O VAL B1533 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU B1535 " --> pdb=" O LEU B1453 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA B1455 " --> pdb=" O LEU B1535 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR B1452 " --> pdb=" O VAL B1478 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA B1480 " --> pdb=" O TYR B1452 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B1454 " --> pdb=" O ALA B1480 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1274 through 1276 removed outlier: 9.170A pdb=" N GLU B1274 " --> pdb=" O ALA B1259 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA B1261 " --> pdb=" O GLU B1274 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL B1276 " --> pdb=" O ALA B1261 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA B1263 " --> pdb=" O VAL B1276 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP B1235 " --> pdb=" O VAL B1260 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU B1262 " --> pdb=" O TRP B1235 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B1237 " --> pdb=" O LEU B1262 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N GLY B1264 " --> pdb=" O VAL B1237 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N SER B1239 " --> pdb=" O GLY B1264 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N SER B1234 " --> pdb=" O ALA B1301 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU B1303 " --> pdb=" O SER B1234 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B1236 " --> pdb=" O LEU B1303 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL B1305 " --> pdb=" O LEU B1236 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE B1238 " --> pdb=" O VAL B1305 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA B1301 " --> pdb=" O ARG B1349 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N VAL B1351 " --> pdb=" O ALA B1301 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU B1303 " --> pdb=" O VAL B1351 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N CYS B1353 " --> pdb=" O LEU B1303 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL B1305 " --> pdb=" O CYS B1353 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA B1355 " --> pdb=" O VAL B1305 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE B1350 " --> pdb=" O ALA B1390 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL B1392 " --> pdb=" O ILE B1350 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B1352 " --> pdb=" O VAL B1392 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B1394 " --> pdb=" O LEU B1352 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER B1354 " --> pdb=" O LEU B1394 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N CYS B1389 " --> pdb=" O GLY B1417 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N LEU B1419 " --> pdb=" O CYS B1389 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLN B1391 " --> pdb=" O LEU B1419 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL B1421 " --> pdb=" O GLN B1391 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP B1393 " --> pdb=" O VAL B1421 " (cutoff:3.500A) removed outlier: 15.326A pdb=" N ALA B1416 " --> pdb=" O LEU B1431 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N LEU B1431 " --> pdb=" O ALA B1416 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG B1418 " --> pdb=" O ALA B1429 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG B1681 " --> pdb=" O TYR B1651 " (cutoff:3.500A) 1156 hydrogen bonds defined for protein. 3210 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: 24.55 Time building geometry restraints manager: 14.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 24324 1.12 - 1.29: 4348 1.29 - 1.47: 8879 1.47 - 1.64: 11888 1.64 - 1.82: 68 Bond restraints: 49507 Sorted by residual: bond pdb=" N THR B1144 " pdb=" H THR B1144 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N GLY A 319 " pdb=" H GLY A 319 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" NH1 ARG A 867 " pdb="HH11 ARG A 867 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CD2 HIS A 881 " pdb=" HD2 HIS A 881 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N THR A1299 " pdb=" H THR A1299 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 49502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 75778 2.65 - 5.30: 10739 5.30 - 7.95: 3014 7.95 - 10.61: 61 10.61 - 13.26: 24 Bond angle restraints: 89616 Sorted by residual: angle pdb=" CA ASP B 64 " pdb=" CB ASP B 64 " pdb=" CG ASP B 64 " ideal model delta sigma weight residual 112.60 118.85 -6.25 1.00e+00 1.00e+00 3.91e+01 angle pdb=" N PRO A 928 " pdb=" CA PRO A 928 " pdb=" C PRO A 928 " ideal model delta sigma weight residual 110.70 117.87 -7.17 1.22e+00 6.72e-01 3.46e+01 angle pdb=" CA PHE A 960 " pdb=" CB PHE A 960 " pdb=" CG PHE A 960 " ideal model delta sigma weight residual 113.80 119.40 -5.60 1.00e+00 1.00e+00 3.14e+01 angle pdb=" CB HIS A 930 " pdb=" CG HIS A 930 " pdb=" CD2 HIS A 930 " ideal model delta sigma weight residual 131.20 123.97 7.23 1.30e+00 5.92e-01 3.10e+01 angle pdb=" CA PHE B 947 " pdb=" CB PHE B 947 " pdb=" CG PHE B 947 " ideal model delta sigma weight residual 113.80 119.27 -5.47 1.00e+00 1.00e+00 2.99e+01 ... (remaining 89611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 21242 18.00 - 35.99: 1233 35.99 - 53.99: 611 53.99 - 71.99: 198 71.99 - 89.98: 22 Dihedral angle restraints: 23306 sinusoidal: 12954 harmonic: 10352 Sorted by residual: dihedral pdb=" CA ARG A 545 " pdb=" C ARG A 545 " pdb=" N ALA A 546 " pdb=" CA ALA A 546 " ideal model delta harmonic sigma weight residual -180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA LEU B1413 " pdb=" C LEU B1413 " pdb=" N PRO B1414 " pdb=" CA PRO B1414 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA LYS A 249 " pdb=" C LYS A 249 " pdb=" N SER A 250 " pdb=" CA SER A 250 " ideal model delta harmonic sigma weight residual 180.00 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 23303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2504 0.087 - 0.175: 1125 0.175 - 0.262: 199 0.262 - 0.349: 30 0.349 - 0.436: 10 Chirality restraints: 3868 Sorted by residual: chirality pdb=" CA GLN B 33 " pdb=" N GLN B 33 " pdb=" C GLN B 33 " pdb=" CB GLN B 33 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA VAL B 862 " pdb=" N VAL B 862 " pdb=" C VAL B 862 " pdb=" CB VAL B 862 " both_signs ideal model delta sigma weight residual False 2.44 2.01 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CA ASP B1222 " pdb=" N ASP B1222 " pdb=" C ASP B1222 " pdb=" CB ASP B1222 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 3865 not shown) Planarity restraints: 7781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 75 " -0.194 2.00e-02 2.50e+03 8.05e-02 2.59e+02 pdb=" CG TRP B 75 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP B 75 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 75 " 0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP B 75 " 0.076 2.00e-02 2.50e+03 pdb=" CE2 TRP B 75 " 0.039 2.00e-02 2.50e+03 pdb=" CE3 TRP B 75 " 0.080 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 75 " -0.024 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 75 " 0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP B 75 " -0.044 2.00e-02 2.50e+03 pdb=" HD1 TRP B 75 " -0.052 2.00e-02 2.50e+03 pdb=" HE1 TRP B 75 " 0.112 2.00e-02 2.50e+03 pdb=" HE3 TRP B 75 " 0.099 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 75 " -0.076 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 75 " 0.021 2.00e-02 2.50e+03 pdb=" HH2 TRP B 75 " -0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1337 " -0.282 9.50e-02 1.11e+02 1.41e-01 2.57e+02 pdb=" NE ARG B1337 " -0.116 2.00e-02 2.50e+03 pdb=" CZ ARG B1337 " -0.063 2.00e-02 2.50e+03 pdb=" NH1 ARG B1337 " -0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG B1337 " -0.025 2.00e-02 2.50e+03 pdb="HH11 ARG B1337 " 0.184 2.00e-02 2.50e+03 pdb="HH12 ARG B1337 " -0.047 2.00e-02 2.50e+03 pdb="HH21 ARG B1337 " 0.193 2.00e-02 2.50e+03 pdb="HH22 ARG B1337 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1337 " 0.279 9.50e-02 1.11e+02 1.38e-01 2.39e+02 pdb=" NE ARG A1337 " 0.089 2.00e-02 2.50e+03 pdb=" CZ ARG A1337 " 0.074 2.00e-02 2.50e+03 pdb=" NH1 ARG A1337 " 0.063 2.00e-02 2.50e+03 pdb=" NH2 ARG A1337 " 0.053 2.00e-02 2.50e+03 pdb="HH11 ARG A1337 " -0.191 2.00e-02 2.50e+03 pdb="HH12 ARG A1337 " 0.039 2.00e-02 2.50e+03 pdb="HH21 ARG A1337 " -0.180 2.00e-02 2.50e+03 pdb="HH22 ARG A1337 " 0.040 2.00e-02 2.50e+03 ... (remaining 7778 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 3496 2.19 - 2.79: 86479 2.79 - 3.40: 135567 3.40 - 4.00: 178409 4.00 - 4.60: 261670 Nonbonded interactions: 665621 Sorted by model distance: nonbonded pdb=" HG SER B 665 " pdb=" OD2 ASP B 668 " model vdw 1.591 2.450 nonbonded pdb=" HG SER B1591 " pdb=" OD2 ASP B1605 " model vdw 1.592 2.450 nonbonded pdb=" OD1 ASP B 408 " pdb=" HG SER B 410 " model vdw 1.598 2.450 nonbonded pdb=" HG SER A1591 " pdb=" OD2 ASP A1605 " model vdw 1.608 2.450 nonbonded pdb=" OE1 GLU B 654 " pdb=" HG SER B 787 " model vdw 1.611 2.450 ... (remaining 665616 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 33 through 1719) selection = chain 'B' } 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: 2.950 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: 0.860 Extract box with map and model: 1.910 Check model and map are aligned: 0.340 Set scattering table: 0.420 Process input model: 104.780 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 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 : 0.012 0.046 25159 Z= 0.835 Angle : 1.806 8.674 34354 Z= 1.217 Chirality : 0.096 0.436 3868 Planarity : 0.016 0.171 4653 Dihedral : 12.609 89.982 9052 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 0.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 0.74 % Allowed : 2.73 % Favored : 96.53 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % 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: -0.79 (0.13), residues: 3370 helix: -0.89 (0.13), residues: 1214 sheet: 1.02 (0.24), residues: 446 loop : -0.57 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.134 0.020 TRP A1099 HIS 0.018 0.003 HIS A1461 PHE 0.085 0.013 PHE A 778 TYR 0.133 0.022 TYR B1651 ARG 0.014 0.001 ARG B 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 484 time to evaluate : 3.567 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: 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: 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: A 56 TRP cc_start: 0.8641 (t-100) cc_final: 0.8221 (t-100) REVERT: A 704 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7842 (tt) REVERT: A 873 LEU cc_start: 0.8682 (tp) cc_final: 0.8472 (tp) REVERT: A 1103 ASP cc_start: 0.8043 (p0) cc_final: 0.7809 (p0) REVERT: A 1459 THR cc_start: 0.8561 (p) cc_final: 0.8290 (t) REVERT: B 330 GLU cc_start: 0.8882 (tp30) cc_final: 0.8673 (tm-30) REVERT: B 595 HIS cc_start: 0.7478 (m90) cc_final: 0.7136 (m-70) REVERT: B 789 VAL cc_start: 0.9000 (t) cc_final: 0.8797 (p) REVERT: B 1029 PHE cc_start: 0.6765 (m-80) cc_final: 0.6515 (m-10) REVERT: B 1605 ASP cc_start: 0.7223 (m-30) cc_final: 0.6957 (m-30) REVERT: B 1639 GLU cc_start: 0.0792 (tt0) cc_final: -0.0549 (tt0) outliers start: 18 outliers final: 5 residues processed: 499 average time/residue: 1.1604 time to fit residues: 827.7718 Evaluate side-chains 202 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 196 time to evaluate : 3.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 1637 SER Chi-restraints excluded: chain B residue 1146 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 196 optimal weight: 0.8980 chunk 305 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 183 GLN A 374 GLN A 482 GLN A 963 GLN A1189 GLN B 33 GLN B 399 HIS ** B 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1409 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25159 Z= 0.261 Angle : 0.716 7.362 34354 Z= 0.387 Chirality : 0.044 0.152 3868 Planarity : 0.007 0.064 4653 Dihedral : 6.451 64.936 3720 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.46 % Favored : 97.51 % Rotamer: Outliers : 1.57 % Allowed : 7.89 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.14), residues: 3370 helix: 0.09 (0.14), residues: 1256 sheet: 0.55 (0.22), residues: 524 loop : -0.74 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 423 HIS 0.008 0.002 HIS A 634 PHE 0.015 0.002 PHE B 947 TYR 0.018 0.002 TYR A 151 ARG 0.007 0.001 ARG B 605 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 3.626 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: 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 274 ASP cc_start: 0.8025 (m-30) cc_final: 0.7732 (t0) REVERT: A 330 GLU cc_start: 0.8504 (tp30) cc_final: 0.8135 (tm-30) REVERT: A 704 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7867 (tt) REVERT: A 1459 THR cc_start: 0.8654 (p) cc_final: 0.8250 (t) REVERT: B 1605 ASP cc_start: 0.7368 (m-30) cc_final: 0.7087 (m-30) REVERT: B 1639 GLU cc_start: 0.0432 (tt0) cc_final: 0.0115 (tt0) REVERT: B 1717 ASN cc_start: 0.2045 (p0) cc_final: 0.1590 (m110) outliers start: 38 outliers final: 24 residues processed: 232 average time/residue: 0.9452 time to fit residues: 338.9702 Evaluate side-chains 175 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 3.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1286 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 399 HIS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 1249 CYS Chi-restraints excluded: chain B residue 1300 VAL Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1577 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 chunk 330 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 303 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 245 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 33 GLN B 399 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25159 Z= 0.227 Angle : 0.610 10.772 34354 Z= 0.318 Chirality : 0.042 0.155 3868 Planarity : 0.006 0.056 4653 Dihedral : 5.691 56.023 3716 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.09 % Favored : 96.88 % Rotamer: Outliers : 1.12 % Allowed : 8.68 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.14), residues: 3370 helix: 0.52 (0.14), residues: 1284 sheet: 0.37 (0.21), residues: 560 loop : -0.83 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1124 HIS 0.029 0.001 HIS B 399 PHE 0.017 0.001 PHE A1582 TYR 0.014 0.002 TYR A 151 ARG 0.005 0.001 ARG A1164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 3.996 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: 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 330 GLU cc_start: 0.8385 (tp30) cc_final: 0.8160 (tm-30) REVERT: A 704 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7849 (tt) REVERT: A 1459 THR cc_start: 0.8510 (p) cc_final: 0.8173 (t) REVERT: B 33 GLN cc_start: 0.3358 (OUTLIER) cc_final: 0.3145 (pm20) REVERT: B 1605 ASP cc_start: 0.7190 (m-30) cc_final: 0.6834 (m-30) REVERT: B 1639 GLU cc_start: 0.0446 (tt0) cc_final: 0.0148 (tt0) REVERT: B 1717 ASN cc_start: 0.2404 (p0) cc_final: 0.1899 (m-40) outliers start: 27 outliers final: 18 residues processed: 191 average time/residue: 0.8857 time to fit residues: 263.6543 Evaluate side-chains 155 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 3.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1286 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1501 GLU Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 1018 GLU Chi-restraints excluded: chain B residue 1249 CYS Chi-restraints excluded: chain B residue 1323 ASP Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1577 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 2.9990 chunk 229 optimal weight: 0.7980 chunk 158 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 205 optimal weight: 0.0060 chunk 306 optimal weight: 3.9990 chunk 324 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 290 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1167 HIS B 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 25159 Z= 0.261 Angle : 0.585 7.557 34354 Z= 0.303 Chirality : 0.042 0.155 3868 Planarity : 0.005 0.071 4653 Dihedral : 5.378 56.026 3715 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.62 % Rotamer: Outliers : 1.40 % Allowed : 8.72 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.14), residues: 3370 helix: 0.71 (0.14), residues: 1288 sheet: 0.16 (0.21), residues: 590 loop : -0.91 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1124 HIS 0.005 0.001 HIS A1692 PHE 0.013 0.001 PHE A 95 TYR 0.012 0.001 TYR A 151 ARG 0.008 0.000 ARG A1328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 3.911 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 704 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7888 (tt) REVERT: A 1459 THR cc_start: 0.8593 (p) cc_final: 0.8219 (t) REVERT: B 800 ARG cc_start: 0.6842 (mtt90) cc_final: 0.6601 (mpt180) REVERT: B 1323 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7197 (t70) REVERT: B 1605 ASP cc_start: 0.7178 (m-30) cc_final: 0.6851 (m-30) REVERT: B 1639 GLU cc_start: 0.0391 (tt0) cc_final: -0.0033 (tt0) REVERT: B 1717 ASN cc_start: 0.2733 (p0) cc_final: 0.2036 (m110) outliers start: 34 outliers final: 22 residues processed: 171 average time/residue: 0.9662 time to fit residues: 252.1510 Evaluate side-chains 153 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 3.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1167 HIS Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1501 GLU Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1635 ASP Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 1249 CYS Chi-restraints excluded: chain B residue 1323 ASP Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1577 THR Chi-restraints excluded: chain B residue 1705 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 8.9990 chunk 184 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 291 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25159 Z= 0.238 Angle : 0.563 6.953 34354 Z= 0.291 Chirality : 0.041 0.155 3868 Planarity : 0.005 0.059 4653 Dihedral : 5.089 55.635 3715 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.57 % Allowed : 9.09 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.14), residues: 3370 helix: 0.84 (0.14), residues: 1300 sheet: 0.15 (0.21), residues: 572 loop : -0.97 (0.15), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1124 HIS 0.020 0.001 HIS A1167 PHE 0.020 0.001 PHE B 251 TYR 0.018 0.002 TYR B 579 ARG 0.006 0.000 ARG A1166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 3.777 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: A 330 GLU cc_start: 0.8272 (tm-30) cc_final: 0.8013 (tm-30) REVERT: A 389 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7708 (mp) REVERT: A 704 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7864 (tt) REVERT: A 1459 THR cc_start: 0.8599 (p) cc_final: 0.8237 (t) REVERT: A 1547 GLU cc_start: 0.7295 (mp0) cc_final: 0.7048 (tt0) REVERT: B 294 ASP cc_start: 0.7973 (p0) cc_final: 0.7708 (p0) REVERT: B 1018 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7208 (tm-30) REVERT: B 1323 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7121 (t70) REVERT: B 1605 ASP cc_start: 0.7157 (m-30) cc_final: 0.6831 (m-30) REVERT: B 1639 GLU cc_start: 0.0319 (tt0) cc_final: -0.0142 (tt0) REVERT: B 1717 ASN cc_start: 0.2922 (p0) cc_final: 0.2211 (m-40) outliers start: 38 outliers final: 24 residues processed: 160 average time/residue: 0.8966 time to fit residues: 223.4322 Evaluate side-chains 142 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 3.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1439 ASP Chi-restraints excluded: chain A residue 1501 GLU Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 1018 GLU Chi-restraints excluded: chain B residue 1249 CYS Chi-restraints excluded: chain B residue 1323 ASP Chi-restraints excluded: chain B residue 1505 HIS Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1577 THR Chi-restraints excluded: chain B residue 1705 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 6.9990 chunk 292 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 325 optimal weight: 5.9990 chunk 269 optimal weight: 4.9990 chunk 150 optimal weight: 0.0470 chunk 27 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 overall best weight: 1.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 374 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25159 Z= 0.236 Angle : 0.551 7.163 34354 Z= 0.282 Chirality : 0.041 0.156 3868 Planarity : 0.005 0.057 4653 Dihedral : 4.926 55.393 3715 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 1.61 % Allowed : 9.55 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.14), residues: 3370 helix: 0.94 (0.15), residues: 1292 sheet: 0.06 (0.21), residues: 572 loop : -1.00 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1124 HIS 0.006 0.001 HIS A1167 PHE 0.013 0.001 PHE A 95 TYR 0.018 0.001 TYR B 579 ARG 0.007 0.000 ARG B 609 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 3.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8090 (tm-30) REVERT: A 704 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7841 (tt) REVERT: A 1251 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7738 (tp30) REVERT: A 1459 THR cc_start: 0.8581 (p) cc_final: 0.8235 (t) REVERT: A 1547 GLU cc_start: 0.7299 (mp0) cc_final: 0.7012 (tt0) REVERT: B 294 ASP cc_start: 0.8007 (p0) cc_final: 0.7668 (p0) REVERT: B 424 ARG cc_start: 0.7573 (tpp-160) cc_final: 0.7267 (mtp85) REVERT: B 807 ASP cc_start: 0.7565 (m-30) cc_final: 0.7131 (t0) REVERT: B 1018 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7256 (tm-30) REVERT: B 1323 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7175 (t0) REVERT: B 1605 ASP cc_start: 0.7130 (m-30) cc_final: 0.6823 (m-30) REVERT: B 1639 GLU cc_start: 0.0263 (tt0) cc_final: -0.0089 (tt0) REVERT: B 1717 ASN cc_start: 0.2905 (p0) cc_final: 0.2168 (m-40) outliers start: 39 outliers final: 26 residues processed: 160 average time/residue: 0.8824 time to fit residues: 224.7708 Evaluate side-chains 141 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1167 HIS Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1439 ASP Chi-restraints excluded: chain A residue 1501 GLU Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 761 ASP Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1018 GLU Chi-restraints excluded: chain B residue 1249 CYS Chi-restraints excluded: chain B residue 1323 ASP Chi-restraints excluded: chain B residue 1505 HIS Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1577 THR Chi-restraints excluded: chain B residue 1705 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 237 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 273 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 323 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 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 881 HIS B 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25159 Z= 0.282 Angle : 0.573 7.416 34354 Z= 0.294 Chirality : 0.042 0.154 3868 Planarity : 0.005 0.072 4653 Dihedral : 4.994 59.234 3715 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.43 % Rotamer: Outliers : 1.74 % Allowed : 9.71 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.14), residues: 3370 helix: 0.91 (0.15), residues: 1282 sheet: -0.11 (0.21), residues: 574 loop : -1.10 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1124 HIS 0.005 0.001 HIS A1692 PHE 0.015 0.001 PHE A 95 TYR 0.011 0.002 TYR B1706 ARG 0.008 0.000 ARG A1518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 GLU cc_start: 0.8658 (pt0) cc_final: 0.8284 (pt0) REVERT: A 330 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8107 (tm-30) REVERT: A 389 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7730 (mp) REVERT: A 704 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7832 (tt) REVERT: A 1251 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7772 (tp30) REVERT: B 294 ASP cc_start: 0.8045 (p0) cc_final: 0.7764 (p0) REVERT: B 424 ARG cc_start: 0.7653 (tpp-160) cc_final: 0.7309 (mtp85) REVERT: B 807 ASP cc_start: 0.7537 (m-30) cc_final: 0.7254 (t0) REVERT: B 1018 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7303 (tm-30) REVERT: B 1323 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7214 (t0) REVERT: B 1605 ASP cc_start: 0.7122 (m-30) cc_final: 0.6758 (m-30) REVERT: B 1639 GLU cc_start: 0.0380 (tt0) cc_final: 0.0154 (tt0) outliers start: 42 outliers final: 33 residues processed: 149 average time/residue: 0.8547 time to fit residues: 201.6510 Evaluate side-chains 137 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 4.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1439 ASP Chi-restraints excluded: chain A residue 1501 GLU Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1018 GLU Chi-restraints excluded: chain B residue 1196 MET Chi-restraints excluded: chain B residue 1249 CYS Chi-restraints excluded: chain B residue 1278 VAL Chi-restraints excluded: chain B residue 1323 ASP Chi-restraints excluded: chain B residue 1505 HIS Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1577 THR Chi-restraints excluded: chain B residue 1692 HIS Chi-restraints excluded: chain B residue 1705 SER Chi-restraints excluded: chain B residue 1719 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 193 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 220 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 254 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 353 GLN B 595 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25159 Z= 0.254 Angle : 0.555 7.277 34354 Z= 0.284 Chirality : 0.041 0.156 3868 Planarity : 0.005 0.069 4653 Dihedral : 4.824 54.882 3715 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.36 % Favored : 95.61 % Rotamer: Outliers : 1.74 % Allowed : 10.12 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.14), residues: 3370 helix: 0.96 (0.15), residues: 1282 sheet: -0.18 (0.21), residues: 574 loop : -1.12 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 914 HIS 0.005 0.001 HIS A1692 PHE 0.014 0.001 PHE A 95 TYR 0.012 0.001 TYR B 579 ARG 0.007 0.000 ARG A1518 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 112 time to evaluate : 3.765 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: A 330 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8144 (tm-30) REVERT: A 389 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7776 (mp) REVERT: A 704 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7812 (tt) REVERT: A 1251 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7779 (tp30) REVERT: A 1547 GLU cc_start: 0.7254 (mp0) cc_final: 0.6950 (tt0) REVERT: B 424 ARG cc_start: 0.7623 (tpp-160) cc_final: 0.7329 (mtp85) REVERT: B 807 ASP cc_start: 0.7532 (m-30) cc_final: 0.7216 (t0) REVERT: B 1018 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7298 (tm-30) REVERT: B 1323 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7196 (t0) REVERT: B 1605 ASP cc_start: 0.7124 (m-30) cc_final: 0.6753 (m-30) REVERT: B 1639 GLU cc_start: 0.0355 (tt0) cc_final: 0.0132 (tt0) outliers start: 42 outliers final: 32 residues processed: 147 average time/residue: 0.8960 time to fit residues: 209.6074 Evaluate side-chains 142 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 3.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1439 ASP Chi-restraints excluded: chain A residue 1501 GLU Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1018 GLU Chi-restraints excluded: chain B residue 1196 MET Chi-restraints excluded: chain B residue 1249 CYS Chi-restraints excluded: chain B residue 1278 VAL Chi-restraints excluded: chain B residue 1323 ASP Chi-restraints excluded: chain B residue 1505 HIS Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1577 THR Chi-restraints excluded: chain B residue 1692 HIS Chi-restraints excluded: chain B residue 1705 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 1.9990 chunk 310 optimal weight: 8.9990 chunk 283 optimal weight: 5.9990 chunk 301 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 236 optimal weight: 5.9990 chunk 92 optimal weight: 0.0670 chunk 272 optimal weight: 1.9990 chunk 285 optimal weight: 0.8980 chunk 300 optimal weight: 4.9990 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 595 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25159 Z= 0.162 Angle : 0.519 8.088 34354 Z= 0.260 Chirality : 0.040 0.160 3868 Planarity : 0.005 0.061 4653 Dihedral : 4.500 54.664 3715 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.40 % Allowed : 10.66 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.14), residues: 3370 helix: 1.25 (0.15), residues: 1284 sheet: 0.00 (0.21), residues: 568 loop : -1.01 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1099 HIS 0.004 0.001 HIS B 595 PHE 0.010 0.001 PHE A 95 TYR 0.010 0.001 TYR B 579 ARG 0.007 0.000 ARG A1518 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 3.765 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: A 389 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7798 (mp) REVERT: A 704 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7773 (tt) REVERT: A 1251 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7765 (tp30) REVERT: A 1547 GLU cc_start: 0.7263 (mp0) cc_final: 0.6982 (tt0) REVERT: B 807 ASP cc_start: 0.7453 (m-30) cc_final: 0.7142 (t0) REVERT: B 1018 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: B 1605 ASP cc_start: 0.7120 (m-30) cc_final: 0.6844 (m-30) REVERT: B 1639 GLU cc_start: 0.0318 (tt0) cc_final: 0.0065 (tt0) outliers start: 34 outliers final: 26 residues processed: 146 average time/residue: 0.9346 time to fit residues: 214.0113 Evaluate side-chains 133 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 3.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1439 ASP Chi-restraints excluded: chain A residue 1501 GLU Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1018 GLU Chi-restraints excluded: chain B residue 1249 CYS Chi-restraints excluded: chain B residue 1505 HIS Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1692 HIS Chi-restraints excluded: chain B residue 1705 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 5.9990 chunk 319 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 334 optimal weight: 0.5980 chunk 308 optimal weight: 0.0470 chunk 266 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 163 optimal weight: 0.0070 overall best weight: 1.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25159 Z= 0.222 Angle : 0.534 7.073 34354 Z= 0.269 Chirality : 0.041 0.157 3868 Planarity : 0.005 0.056 4653 Dihedral : 4.471 54.492 3714 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.28 % Allowed : 11.03 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.01 (0.14), residues: 3370 helix: 1.25 (0.15), residues: 1284 sheet: -0.09 (0.21), residues: 570 loop : -1.03 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1627 HIS 0.004 0.001 HIS A1692 PHE 0.011 0.001 PHE A 95 TYR 0.009 0.001 TYR B 579 ARG 0.011 0.000 ARG B 900 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 3.617 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 389 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7773 (mp) REVERT: A 704 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7797 (tt) REVERT: A 1251 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7777 (tp30) REVERT: A 1547 GLU cc_start: 0.7238 (mp0) cc_final: 0.6957 (tt0) REVERT: B 807 ASP cc_start: 0.7492 (m-30) cc_final: 0.7169 (t0) REVERT: B 1018 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: B 1605 ASP cc_start: 0.7142 (m-30) cc_final: 0.6769 (m-30) REVERT: B 1639 GLU cc_start: 0.0255 (tt0) cc_final: -0.0010 (tt0) outliers start: 31 outliers final: 26 residues processed: 138 average time/residue: 0.9178 time to fit residues: 197.6659 Evaluate side-chains 137 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 3.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1439 ASP Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1018 GLU Chi-restraints excluded: chain B residue 1249 CYS Chi-restraints excluded: chain B residue 1505 HIS Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1692 HIS Chi-restraints excluded: chain B residue 1705 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 2.9990 chunk 283 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 245 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 74 optimal weight: 0.3980 chunk 266 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 274 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 595 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.096278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.076539 restraints weight = 194278.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079014 restraints weight = 113606.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.080683 restraints weight = 80473.238| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25159 Z= 0.166 Angle : 0.514 6.964 34354 Z= 0.257 Chirality : 0.040 0.159 3868 Planarity : 0.005 0.055 4653 Dihedral : 4.361 54.192 3714 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.28 % Allowed : 10.79 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.16 (0.14), residues: 3370 helix: 1.37 (0.15), residues: 1286 sheet: 0.09 (0.21), residues: 560 loop : -0.97 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 423 HIS 0.005 0.001 HIS B 595 PHE 0.010 0.001 PHE A 95 TYR 0.011 0.001 TYR A1452 ARG 0.006 0.000 ARG B 900 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8193.74 seconds wall clock time: 144 minutes 0.59 seconds (8640.59 seconds total)