Starting phenix.real_space_refine on Mon Sep 14 19:26:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6tsk_10564/09_2026/6tsk_10564.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tsk_10564/09_2026/6tsk_10564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tsk_10564/09_2026/6tsk_10564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tsk_10564/09_2026/6tsk_10564.map" model { file = "/net/cci-nas-00/data/ceres_data/6tsk_10564/09_2026/6tsk_10564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tsk_10564/09_2026/6tsk_10564.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6tsk_10564/09_2026/6tsk_10564.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6tsk_10564/09_2026/6tsk_10564.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.020 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 Mg 4 5.21 5 S 152 5.16 5 C 20656 2.51 5 N 5780 2.21 5 O 7040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33632 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 8156 Classifications: {'peptide': 1015} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 949} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' MG': 1, '0MK': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 241 Classifications: {'water': 241} Link IDs: {None: 240} Chain: "B" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 241 Classifications: {'water': 241} Link IDs: {None: 240} Chain: "C" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 241 Classifications: {'water': 241} Link IDs: {None: 240} Chain: "D" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 241 Classifications: {'water': 241} Link IDs: {None: 240} Restraints were copied for chains: B, C, D Time building chain proxies: 12.25, per 1000 atoms: 0.36 Number of scatterers: 33632 At special positions: 0 Unit cell: (101.32, 150.28, 195.16, 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 152 16.00 Mg 4 11.99 O 7040 8.00 N 5780 7.00 C 20656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7552 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 56 sheets defined 17.3% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 9 through 14 Processing helix chain 'A' and resid 15 through 18 removed outlier: 3.537A pdb=" N ASN A 18 " --> pdb=" O ASP A 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 15 through 18' Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 131 through 136 removed outlier: 4.195A pdb=" N GLU A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'A' and resid 395 through 406 removed outlier: 4.371A pdb=" N TYR A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 448 removed outlier: 3.608A pdb=" N ARG A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.571A pdb=" N ASP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 524 removed outlier: 3.523A pdb=" N LEU A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.856A pdb=" N TYR A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 removed outlier: 4.248A pdb=" N CYS A 602 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 624 removed outlier: 4.022A pdb=" N GLU A 619 " --> pdb=" O PRO A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 805 through 814 Processing helix chain 'A' and resid 923 through 926 removed outlier: 3.612A pdb=" N TYR A 926 " --> pdb=" O SER A 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 923 through 926' Processing helix chain 'A' and resid 963 through 970 Processing helix chain 'A' and resid 972 through 976 Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'B' and resid 10 through 14 Processing helix chain 'B' and resid 15 through 18 removed outlier: 3.537A pdb=" N ASN B 18 " --> pdb=" O ASP B 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 15 through 18' Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 131 through 136 removed outlier: 4.195A pdb=" N GLU B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 368 through 382 Processing helix chain 'B' and resid 395 through 406 removed outlier: 4.371A pdb=" N TYR B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 448 removed outlier: 3.608A pdb=" N ARG B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.571A pdb=" N ASP B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 524 removed outlier: 3.523A pdb=" N LEU B 524 " --> pdb=" O ILE B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.857A pdb=" N TYR B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 603 removed outlier: 4.248A pdb=" N CYS B 602 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 624 removed outlier: 4.022A pdb=" N GLU B 619 " --> pdb=" O PRO B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 805 through 814 Processing helix chain 'B' and resid 923 through 926 removed outlier: 3.613A pdb=" N TYR B 926 " --> pdb=" O SER B 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 923 through 926' Processing helix chain 'B' and resid 963 through 970 Processing helix chain 'B' and resid 972 through 976 Processing helix chain 'B' and resid 1004 through 1008 Processing helix chain 'C' and resid 10 through 14 Processing helix chain 'C' and resid 15 through 18 removed outlier: 3.537A pdb=" N ASN C 18 " --> pdb=" O ASP C 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 131 through 136 removed outlier: 4.195A pdb=" N GLU C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'C' and resid 368 through 382 Processing helix chain 'C' and resid 395 through 406 removed outlier: 4.371A pdb=" N TYR C 399 " --> pdb=" O HIS C 395 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 448 removed outlier: 3.608A pdb=" N ARG C 439 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.571A pdb=" N ASP C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 524 removed outlier: 3.523A pdb=" N LEU C 524 " --> pdb=" O ILE C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.856A pdb=" N TYR C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 603 removed outlier: 4.248A pdb=" N CYS C 602 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 624 removed outlier: 4.022A pdb=" N GLU C 619 " --> pdb=" O PRO C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 805 through 814 Processing helix chain 'C' and resid 923 through 926 removed outlier: 3.613A pdb=" N TYR C 926 " --> pdb=" O SER C 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 923 through 926' Processing helix chain 'C' and resid 963 through 970 Processing helix chain 'C' and resid 972 through 976 Processing helix chain 'C' and resid 1004 through 1008 Processing helix chain 'D' and resid 10 through 14 Processing helix chain 'D' and resid 15 through 18 removed outlier: 3.537A pdb=" N ASN D 18 " --> pdb=" O ASP D 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 15 through 18' Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 131 through 136 removed outlier: 4.195A pdb=" N GLU D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 198 Processing helix chain 'D' and resid 368 through 382 Processing helix chain 'D' and resid 395 through 406 removed outlier: 4.371A pdb=" N TYR D 399 " --> pdb=" O HIS D 395 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 448 removed outlier: 3.608A pdb=" N ARG D 439 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 479 removed outlier: 3.571A pdb=" N ASP D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 524 removed outlier: 3.522A pdb=" N LEU D 524 " --> pdb=" O ILE D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.856A pdb=" N TYR D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 603 removed outlier: 4.249A pdb=" N CYS D 602 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 624 removed outlier: 4.022A pdb=" N GLU D 619 " --> pdb=" O PRO D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 805 through 814 Processing helix chain 'D' and resid 923 through 926 removed outlier: 3.612A pdb=" N TYR D 926 " --> pdb=" O SER D 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 923 through 926' Processing helix chain 'D' and resid 963 through 970 Processing helix chain 'D' and resid 972 through 976 Processing helix chain 'D' and resid 1004 through 1008 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.842A pdb=" N LEU A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR A 161 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE A 150 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 149 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A 180 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR A 126 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N GLU A 57 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 101 removed outlier: 3.554A pdb=" N ILE A 99 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR A 101 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET A 202 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 231 removed outlier: 5.544A pdb=" N ILE A 222 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N CYS A 247 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A 224 " --> pdb=" O GLN A 245 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 272 removed outlier: 6.769A pdb=" N LEU A 260 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER A 269 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 258 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR A 271 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A 256 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR A 317 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU A 322 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 338 Processing sheet with id=AA8, first strand: chain 'A' and resid 484 through 485 removed outlier: 8.180A pdb=" N GLN A 485 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP A 456 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A 409 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER A 457 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP A 411 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU A 412 " --> pdb=" O CYS A 389 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG A 352 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ARG A 388 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 354 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU A 533 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N PHE A 566 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU A 535 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 575 through 578 Processing sheet with id=AB1, first strand: chain 'A' and resid 627 through 632 Processing sheet with id=AB2, first strand: chain 'A' and resid 661 through 669 removed outlier: 5.905A pdb=" N LEU A 658 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY A 692 " --> pdb=" O GLU A 724 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU A 724 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU A 694 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 716 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN A 702 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE A 714 " --> pdb=" O GLN A 702 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 739 through 742 removed outlier: 6.648A pdb=" N ARG A 755 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N MET A 768 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN A 757 " --> pdb=" O SER A 766 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 776 through 783 removed outlier: 6.506A pdb=" N GLN A 887 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN A 885 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG A 781 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN A 783 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ARG A 881 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 11.948A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP A 954 " --> pdb=" O GLN A1017 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLN A1017 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N GLN A 956 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 13.649A pdb=" N HIS A1015 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 20.718A pdb=" N ASN A 958 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 23.760A pdb=" N ARG A1013 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP A 842 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE A 851 " --> pdb=" O HIS A 840 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N HIS A 840 " --> pdb=" O ILE A 851 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG A 853 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR A 838 " --> pdb=" O ARG A 853 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR A 855 " --> pdb=" O ILE A 836 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE A 836 " --> pdb=" O THR A 855 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG A 857 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 834 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA A 833 " --> pdb=" O THR A 829 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR A 829 " --> pdb=" O ALA A 833 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 835 " --> pdb=" O ALA A 827 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA A 827 " --> pdb=" O LEU A 835 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR A 837 " --> pdb=" O CYS A 825 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS A 825 " --> pdb=" O THR A 837 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA A 839 " --> pdb=" O LEU A 823 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 776 through 783 removed outlier: 6.506A pdb=" N GLN A 887 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN A 885 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG A 781 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN A 783 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ARG A 881 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 11.948A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TRP A 951 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASN A 945 " --> pdb=" O TRP A 951 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLY A 953 " --> pdb=" O GLU A 943 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLU A 943 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE A 957 " --> pdb=" O CYS A 939 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N CYS A 939 " --> pdb=" O PHE A 957 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY A 940 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 900 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU A 898 " --> pdb=" O ARG A 942 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU A 944 " --> pdb=" O ASN A 896 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASN A 896 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR A 946 " --> pdb=" O ARG A 894 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ARG A 894 " --> pdb=" O TYR A 946 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 23 through 24 removed outlier: 6.842A pdb=" N LEU B 152 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR B 161 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE B 150 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 149 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY B 180 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR B 126 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N GLU B 57 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB8, first strand: chain 'B' and resid 99 through 101 removed outlier: 3.554A pdb=" N ILE B 99 " --> pdb=" O ARG B 204 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR B 101 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET B 202 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AC1, first strand: chain 'B' and resid 221 through 231 removed outlier: 5.545A pdb=" N ILE B 222 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N CYS B 247 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 224 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 265 through 272 removed outlier: 6.769A pdb=" N LEU B 260 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER B 269 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B 258 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR B 271 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B 256 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR B 317 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU B 322 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 335 through 338 Processing sheet with id=AC4, first strand: chain 'B' and resid 484 through 485 removed outlier: 8.180A pdb=" N GLN B 485 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP B 456 " --> pdb=" O GLN B 485 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B 409 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER B 457 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP B 411 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU B 412 " --> pdb=" O CYS B 389 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG B 352 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ARG B 388 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 354 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU B 533 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N PHE B 566 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU B 535 " --> pdb=" O PHE B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 575 through 578 Processing sheet with id=AC6, first strand: chain 'B' and resid 627 through 632 Processing sheet with id=AC7, first strand: chain 'B' and resid 661 through 669 removed outlier: 5.905A pdb=" N LEU B 658 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY B 692 " --> pdb=" O GLU B 724 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU B 724 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU B 694 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA B 716 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN B 702 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE B 714 " --> pdb=" O GLN B 702 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 739 through 742 removed outlier: 6.648A pdb=" N ARG B 755 " --> pdb=" O MET B 768 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N MET B 768 " --> pdb=" O ARG B 755 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN B 757 " --> pdb=" O SER B 766 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 776 through 783 removed outlier: 6.506A pdb=" N GLN B 887 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN B 885 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG B 781 " --> pdb=" O GLY B 883 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN B 783 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ARG B 881 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 11.948A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASP B 954 " --> pdb=" O GLN B1017 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN B1017 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N GLN B 956 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 13.649A pdb=" N HIS B1015 " --> pdb=" O GLN B 956 " (cutoff:3.500A) removed outlier: 20.718A pdb=" N ASN B 958 " --> pdb=" O ARG B1013 " (cutoff:3.500A) removed outlier: 23.760A pdb=" N ARG B1013 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP B 842 " --> pdb=" O LEU B 849 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE B 851 " --> pdb=" O HIS B 840 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N HIS B 840 " --> pdb=" O ILE B 851 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG B 853 " --> pdb=" O THR B 838 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR B 838 " --> pdb=" O ARG B 853 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR B 855 " --> pdb=" O ILE B 836 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE B 836 " --> pdb=" O THR B 855 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG B 857 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 834 " --> pdb=" O ARG B 857 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA B 833 " --> pdb=" O THR B 829 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N THR B 829 " --> pdb=" O ALA B 833 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU B 835 " --> pdb=" O ALA B 827 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA B 827 " --> pdb=" O LEU B 835 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR B 837 " --> pdb=" O CYS B 825 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS B 825 " --> pdb=" O THR B 837 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA B 839 " --> pdb=" O LEU B 823 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 776 through 783 removed outlier: 6.506A pdb=" N GLN B 887 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN B 885 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG B 781 " --> pdb=" O GLY B 883 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN B 783 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ARG B 881 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 11.948A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TRP B 951 " --> pdb=" O ASN B 945 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASN B 945 " --> pdb=" O TRP B 951 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLY B 953 " --> pdb=" O GLU B 943 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLU B 943 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE B 957 " --> pdb=" O CYS B 939 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N CYS B 939 " --> pdb=" O PHE B 957 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY B 940 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B 900 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 898 " --> pdb=" O ARG B 942 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU B 944 " --> pdb=" O ASN B 896 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN B 896 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N TYR B 946 " --> pdb=" O ARG B 894 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N ARG B 894 " --> pdb=" O TYR B 946 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.842A pdb=" N LEU C 152 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR C 161 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE C 150 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 149 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY C 180 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR C 126 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N GLU C 57 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AD4, first strand: chain 'C' and resid 99 through 101 removed outlier: 3.554A pdb=" N ILE C 99 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR C 101 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET C 202 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=AD6, first strand: chain 'C' and resid 221 through 231 removed outlier: 5.544A pdb=" N ILE C 222 " --> pdb=" O CYS C 247 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N CYS C 247 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP C 224 " --> pdb=" O GLN C 245 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 265 through 272 removed outlier: 6.769A pdb=" N LEU C 260 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER C 269 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL C 258 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR C 271 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL C 256 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR C 317 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU C 322 " --> pdb=" O THR C 317 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 335 through 338 Processing sheet with id=AD9, first strand: chain 'C' and resid 484 through 485 removed outlier: 8.180A pdb=" N GLN C 485 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP C 456 " --> pdb=" O GLN C 485 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL C 409 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N SER C 457 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP C 411 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU C 412 " --> pdb=" O CYS C 389 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG C 352 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ARG C 388 " --> pdb=" O ARG C 352 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL C 354 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU C 533 " --> pdb=" O GLY C 564 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N PHE C 566 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU C 535 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 575 through 578 Processing sheet with id=AE2, first strand: chain 'C' and resid 627 through 632 Processing sheet with id=AE3, first strand: chain 'C' and resid 661 through 669 removed outlier: 5.905A pdb=" N LEU C 658 " --> pdb=" O PRO C 662 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY C 692 " --> pdb=" O GLU C 724 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU C 724 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU C 694 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA C 716 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN C 702 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE C 714 " --> pdb=" O GLN C 702 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 739 through 742 removed outlier: 6.647A pdb=" N ARG C 755 " --> pdb=" O MET C 768 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N MET C 768 " --> pdb=" O ARG C 755 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN C 757 " --> pdb=" O SER C 766 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 776 through 783 removed outlier: 6.506A pdb=" N GLN C 887 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN C 885 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG C 781 " --> pdb=" O GLY C 883 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN C 783 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ARG C 881 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 11.948A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASP C 954 " --> pdb=" O GLN C1017 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN C1017 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N GLN C 956 " --> pdb=" O HIS C1015 " (cutoff:3.500A) removed outlier: 13.649A pdb=" N HIS C1015 " --> pdb=" O GLN C 956 " (cutoff:3.500A) removed outlier: 20.717A pdb=" N ASN C 958 " --> pdb=" O ARG C1013 " (cutoff:3.500A) removed outlier: 23.760A pdb=" N ARG C1013 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP C 842 " --> pdb=" O LEU C 849 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE C 851 " --> pdb=" O HIS C 840 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N HIS C 840 " --> pdb=" O ILE C 851 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG C 853 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR C 838 " --> pdb=" O ARG C 853 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR C 855 " --> pdb=" O ILE C 836 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE C 836 " --> pdb=" O THR C 855 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG C 857 " --> pdb=" O VAL C 834 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL C 834 " --> pdb=" O ARG C 857 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA C 833 " --> pdb=" O THR C 829 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N THR C 829 " --> pdb=" O ALA C 833 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU C 835 " --> pdb=" O ALA C 827 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA C 827 " --> pdb=" O LEU C 835 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR C 837 " --> pdb=" O CYS C 825 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS C 825 " --> pdb=" O THR C 837 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA C 839 " --> pdb=" O LEU C 823 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 776 through 783 removed outlier: 6.506A pdb=" N GLN C 887 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN C 885 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG C 781 " --> pdb=" O GLY C 883 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN C 783 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ARG C 881 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 11.948A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TRP C 951 " --> pdb=" O ASN C 945 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASN C 945 " --> pdb=" O TRP C 951 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLY C 953 " --> pdb=" O GLU C 943 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLU C 943 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE C 957 " --> pdb=" O CYS C 939 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N CYS C 939 " --> pdb=" O PHE C 957 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY C 940 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU C 900 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU C 898 " --> pdb=" O ARG C 942 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU C 944 " --> pdb=" O ASN C 896 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASN C 896 " --> pdb=" O LEU C 944 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR C 946 " --> pdb=" O ARG C 894 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ARG C 894 " --> pdb=" O TYR C 946 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 23 through 24 removed outlier: 6.842A pdb=" N LEU D 152 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR D 161 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE D 150 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 149 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY D 180 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR D 126 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N GLU D 57 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AE9, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.555A pdb=" N ILE D 99 " --> pdb=" O ARG D 204 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR D 101 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET D 202 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 146 through 147 Processing sheet with id=AF2, first strand: chain 'D' and resid 221 through 231 removed outlier: 5.544A pdb=" N ILE D 222 " --> pdb=" O CYS D 247 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N CYS D 247 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP D 224 " --> pdb=" O GLN D 245 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 265 through 272 removed outlier: 6.769A pdb=" N LEU D 260 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER D 269 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL D 258 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR D 271 " --> pdb=" O VAL D 256 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL D 256 " --> pdb=" O THR D 271 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR D 317 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU D 322 " --> pdb=" O THR D 317 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 335 through 338 Processing sheet with id=AF5, first strand: chain 'D' and resid 484 through 485 removed outlier: 8.180A pdb=" N GLN D 485 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP D 456 " --> pdb=" O GLN D 485 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL D 409 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER D 457 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP D 411 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU D 412 " --> pdb=" O CYS D 389 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG D 352 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ARG D 388 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL D 354 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU D 533 " --> pdb=" O GLY D 564 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N PHE D 566 " --> pdb=" O LEU D 533 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU D 535 " --> pdb=" O PHE D 566 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 575 through 578 Processing sheet with id=AF7, first strand: chain 'D' and resid 627 through 632 Processing sheet with id=AF8, first strand: chain 'D' and resid 661 through 669 removed outlier: 5.905A pdb=" N LEU D 658 " --> pdb=" O PRO D 662 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY D 692 " --> pdb=" O GLU D 724 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU D 724 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU D 694 " --> pdb=" O LEU D 722 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA D 716 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN D 702 " --> pdb=" O ILE D 714 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE D 714 " --> pdb=" O GLN D 702 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 739 through 742 removed outlier: 6.648A pdb=" N ARG D 755 " --> pdb=" O MET D 768 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N MET D 768 " --> pdb=" O ARG D 755 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN D 757 " --> pdb=" O SER D 766 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 776 through 783 removed outlier: 6.506A pdb=" N GLN D 887 " --> pdb=" O LEU D 777 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN D 885 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG D 781 " --> pdb=" O GLY D 883 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN D 783 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ARG D 881 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 11.949A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASP D 954 " --> pdb=" O GLN D1017 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN D1017 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N GLN D 956 " --> pdb=" O HIS D1015 " (cutoff:3.500A) removed outlier: 13.649A pdb=" N HIS D1015 " --> pdb=" O GLN D 956 " (cutoff:3.500A) removed outlier: 20.718A pdb=" N ASN D 958 " --> pdb=" O ARG D1013 " (cutoff:3.500A) removed outlier: 23.760A pdb=" N ARG D1013 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP D 842 " --> pdb=" O LEU D 849 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE D 851 " --> pdb=" O HIS D 840 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N HIS D 840 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG D 853 " --> pdb=" O THR D 838 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR D 838 " --> pdb=" O ARG D 853 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR D 855 " --> pdb=" O ILE D 836 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE D 836 " --> pdb=" O THR D 855 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG D 857 " --> pdb=" O VAL D 834 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL D 834 " --> pdb=" O ARG D 857 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA D 833 " --> pdb=" O THR D 829 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR D 829 " --> pdb=" O ALA D 833 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU D 835 " --> pdb=" O ALA D 827 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA D 827 " --> pdb=" O LEU D 835 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR D 837 " --> pdb=" O CYS D 825 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS D 825 " --> pdb=" O THR D 837 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA D 839 " --> pdb=" O LEU D 823 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 776 through 783 removed outlier: 6.506A pdb=" N GLN D 887 " --> pdb=" O LEU D 777 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN D 885 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG D 781 " --> pdb=" O GLY D 883 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN D 783 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ARG D 881 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 11.949A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TRP D 951 " --> pdb=" O ASN D 945 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASN D 945 " --> pdb=" O TRP D 951 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLY D 953 " --> pdb=" O GLU D 943 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLU D 943 " --> pdb=" O GLY D 953 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE D 957 " --> pdb=" O CYS D 939 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N CYS D 939 " --> pdb=" O PHE D 957 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY D 940 " --> pdb=" O LEU D 900 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU D 900 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU D 898 " --> pdb=" O ARG D 942 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU D 944 " --> pdb=" O ASN D 896 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN D 896 " --> pdb=" O LEU D 944 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR D 946 " --> pdb=" O ARG D 894 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ARG D 894 " --> pdb=" O TYR D 946 " (cutoff:3.500A) 1169 hydrogen bonds defined for protein. 3027 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: 9.97 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 7648 1.33 - 1.47: 9341 1.47 - 1.60: 16403 1.60 - 1.74: 0 1.74 - 1.88: 240 Bond restraints: 33632 Sorted by residual: bond pdb=" N ASP C 164 " pdb=" CA ASP C 164 " ideal model delta sigma weight residual 1.457 1.550 -0.093 1.29e-02 6.01e+03 5.17e+01 bond pdb=" N ASP B 164 " pdb=" CA ASP B 164 " ideal model delta sigma weight residual 1.457 1.550 -0.092 1.29e-02 6.01e+03 5.12e+01 bond pdb=" N ASP A 164 " pdb=" CA ASP A 164 " ideal model delta sigma weight residual 1.457 1.550 -0.092 1.29e-02 6.01e+03 5.12e+01 bond pdb=" N ASP D 164 " pdb=" CA ASP D 164 " ideal model delta sigma weight residual 1.457 1.549 -0.092 1.29e-02 6.01e+03 5.07e+01 bond pdb=" N VAL A 421 " pdb=" CA VAL A 421 " ideal model delta sigma weight residual 1.454 1.499 -0.045 7.70e-03 1.69e+04 3.39e+01 ... (remaining 33627 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 43326 3.10 - 6.21: 2422 6.21 - 9.31: 132 9.31 - 12.42: 4 12.42 - 15.52: 4 Bond angle restraints: 45888 Sorted by residual: angle pdb=" C GLN A 625 " pdb=" CA GLN A 625 " pdb=" CB GLN A 625 " ideal model delta sigma weight residual 110.42 94.90 15.52 1.99e+00 2.53e-01 6.08e+01 angle pdb=" C GLN D 625 " pdb=" CA GLN D 625 " pdb=" CB GLN D 625 " ideal model delta sigma weight residual 110.42 94.90 15.52 1.99e+00 2.53e-01 6.08e+01 angle pdb=" C GLN B 625 " pdb=" CA GLN B 625 " pdb=" CB GLN B 625 " ideal model delta sigma weight residual 110.42 94.90 15.52 1.99e+00 2.53e-01 6.08e+01 angle pdb=" C GLN C 625 " pdb=" CA GLN C 625 " pdb=" CB GLN C 625 " ideal model delta sigma weight residual 110.42 94.90 15.52 1.99e+00 2.53e-01 6.08e+01 angle pdb=" C LYS D 661 " pdb=" N PRO D 662 " pdb=" CA PRO D 662 " ideal model delta sigma weight residual 119.76 126.73 -6.97 1.03e+00 9.43e-01 4.58e+01 ... (remaining 45883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 17683 17.77 - 35.55: 1417 35.55 - 53.32: 320 53.32 - 71.10: 132 71.10 - 88.87: 124 Dihedral angle restraints: 19676 sinusoidal: 7944 harmonic: 11732 Sorted by residual: dihedral pdb=" C GLN A 625 " pdb=" N GLN A 625 " pdb=" CA GLN A 625 " pdb=" CB GLN A 625 " ideal model delta harmonic sigma weight residual -122.60 -103.48 -19.12 0 2.50e+00 1.60e-01 5.85e+01 dihedral pdb=" C GLN D 625 " pdb=" N GLN D 625 " pdb=" CA GLN D 625 " pdb=" CB GLN D 625 " ideal model delta harmonic sigma weight residual -122.60 -103.48 -19.12 0 2.50e+00 1.60e-01 5.85e+01 dihedral pdb=" C GLN B 625 " pdb=" N GLN B 625 " pdb=" CA GLN B 625 " pdb=" CB GLN B 625 " ideal model delta harmonic sigma weight residual -122.60 -103.48 -19.12 0 2.50e+00 1.60e-01 5.85e+01 ... (remaining 19673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2776 0.090 - 0.181: 1516 0.181 - 0.271: 412 0.271 - 0.361: 84 0.361 - 0.451: 8 Chirality restraints: 4796 Sorted by residual: chirality pdb=" CA GLN A 625 " pdb=" N GLN A 625 " pdb=" C GLN A 625 " pdb=" CB GLN A 625 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" CA GLN D 625 " pdb=" N GLN D 625 " pdb=" C GLN D 625 " pdb=" CB GLN D 625 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" CA GLN B 625 " pdb=" N GLN B 625 " pdb=" C GLN B 625 " pdb=" CB GLN B 625 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.09e+00 ... (remaining 4793 not shown) Planarity restraints: 6056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 553 " 0.085 2.00e-02 2.50e+03 4.06e-02 4.11e+01 pdb=" CG TRP C 553 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP C 553 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP C 553 " -0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP C 553 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP C 553 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 553 " -0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 553 " 0.040 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 553 " -0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP C 553 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 553 " 0.085 2.00e-02 2.50e+03 4.05e-02 4.11e+01 pdb=" CG TRP A 553 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP A 553 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 553 " -0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP A 553 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 553 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 553 " -0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 553 " 0.040 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 553 " -0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP A 553 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 553 " -0.085 2.00e-02 2.50e+03 4.05e-02 4.10e+01 pdb=" CG TRP D 553 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP D 553 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP D 553 " 0.023 2.00e-02 2.50e+03 pdb=" NE1 TRP D 553 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP D 553 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 553 " 0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 553 " -0.040 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 553 " 0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP D 553 " -0.033 2.00e-02 2.50e+03 ... (remaining 6053 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.21: 30 2.21 - 2.88: 11731 2.88 - 3.55: 44200 3.55 - 4.23: 91673 4.23 - 4.90: 146582 Nonbonded interactions: 294216 Sorted by model distance: nonbonded pdb=" O HOH C3184 " pdb=" O HOH D3184 " model vdw 1.535 3.040 nonbonded pdb=" O HOH A3184 " pdb=" O HOH B3184 " model vdw 1.535 3.040 nonbonded pdb=" O HOH C3107 " pdb=" O HOH C3108 " model vdw 1.614 3.040 nonbonded pdb=" O HOH B3107 " pdb=" O HOH B3108 " model vdw 1.614 3.040 nonbonded pdb=" O HOH A3107 " pdb=" O HOH A3108 " model vdw 1.615 3.040 ... (remaining 294211 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 individual isotropic 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 39.030 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9365 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 0.093 33632 Z= 0.830 Angle : 1.544 15.519 45888 Z= 0.996 Chirality : 0.114 0.451 4796 Planarity : 0.016 0.223 6056 Dihedral : 16.570 88.872 12124 Min Nonbonded Distance : 1.535 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.89 % Favored : 97.01 % Rotamer: Outliers : 2.42 % Allowed : 5.41 % Favored : 92.17 % Cbeta Deviations : 0.64 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.12), residues: 4052 helix: -1.84 (0.19), residues: 480 sheet: 0.13 (0.14), residues: 1268 loop : -0.83 (0.11), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG A 282 TYR 0.056 0.010 TYR D 100 PHE 0.039 0.007 PHE D 171 TRP 0.085 0.009 TRP C 553 HIS 0.014 0.004 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.01173 / 0.83 (33632) covalent geometry : angle 1.54422 / 1.00 (45888) hydrogen bonds : bond 0.19355 / 12.71 ( 1113) hydrogen bonds : angle 7.17487 / 5.09 ( 3027) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 584 time to evaluate : 1.408 Fit side-chains REVERT: A 46 ARG cc_start: 0.8225 (mtt90) cc_final: 0.7603 (mmm160) REVERT: A 80 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7484 (pp20) REVERT: A 219 THR cc_start: 0.9072 (t) cc_final: 0.8844 (m) REVERT: A 227 VAL cc_start: 0.8819 (OUTLIER) cc_final: 0.8516 (m) REVERT: A 233 ASP cc_start: 0.8348 (p0) cc_final: 0.7965 (p0) REVERT: A 237 ARG cc_start: 0.8791 (mtp-110) cc_final: 0.8589 (ttp-110) REVERT: A 245 GLN cc_start: 0.8984 (mt0) cc_final: 0.8590 (tt0) REVERT: A 251 ARG cc_start: 0.8654 (mmt180) cc_final: 0.8313 (mmt180) REVERT: A 262 GLN cc_start: 0.8570 (tt0) cc_final: 0.8369 (tm-30) REVERT: A 667 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8673 (mp0) REVERT: A 681 GLU cc_start: 0.8424 (tp30) cc_final: 0.8032 (mp0) REVERT: A 687 GLN cc_start: 0.5049 (OUTLIER) cc_final: 0.4843 (tp40) REVERT: A 699 ARG cc_start: 0.9022 (ptp-110) cc_final: 0.8495 (ptm-80) REVERT: A 730 LEU cc_start: 0.5666 (OUTLIER) cc_final: 0.5261 (mt) REVERT: A 748 CYS cc_start: 0.8965 (m) cc_final: 0.8613 (t) REVERT: A 750 GLU cc_start: 0.8559 (mp0) cc_final: 0.8164 (tt0) REVERT: A 768 MET cc_start: 0.8630 (mtp) cc_final: 0.7980 (ttm) REVERT: A 773 LYS cc_start: 0.8578 (tptm) cc_final: 0.8185 (mttp) REVERT: A 875 ASP cc_start: 0.8921 (p0) cc_final: 0.8600 (p0) REVERT: A 968 MET cc_start: 0.9035 (ttm) cc_final: 0.8703 (ttt) REVERT: A 969 GLU cc_start: 0.8536 (pt0) cc_final: 0.8240 (mt-10) REVERT: B 46 ARG cc_start: 0.8239 (mtt90) cc_final: 0.7599 (mmm160) REVERT: B 80 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7487 (pp20) REVERT: B 219 THR cc_start: 0.9071 (t) cc_final: 0.8844 (m) REVERT: B 227 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8517 (m) REVERT: B 233 ASP cc_start: 0.8350 (p0) cc_final: 0.7969 (p0) REVERT: B 245 GLN cc_start: 0.8991 (mt0) cc_final: 0.8593 (tt0) REVERT: B 251 ARG cc_start: 0.8659 (mmt180) cc_final: 0.8317 (mmt180) REVERT: B 667 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8672 (mp0) REVERT: B 681 GLU cc_start: 0.8419 (tp30) cc_final: 0.8032 (mp0) REVERT: B 687 GLN cc_start: 0.5032 (OUTLIER) cc_final: 0.4830 (tp40) REVERT: B 699 ARG cc_start: 0.9025 (ptp-110) cc_final: 0.8498 (ptm-80) REVERT: B 730 LEU cc_start: 0.5649 (OUTLIER) cc_final: 0.5244 (mt) REVERT: B 748 CYS cc_start: 0.8961 (m) cc_final: 0.8618 (t) REVERT: B 750 GLU cc_start: 0.8568 (mp0) cc_final: 0.8172 (tt0) REVERT: B 768 MET cc_start: 0.8626 (mtp) cc_final: 0.7976 (ttm) REVERT: B 773 LYS cc_start: 0.8583 (tptm) cc_final: 0.8186 (mttp) REVERT: B 875 ASP cc_start: 0.8929 (p0) cc_final: 0.8591 (p0) REVERT: B 968 MET cc_start: 0.9033 (ttm) cc_final: 0.8701 (ttt) REVERT: B 969 GLU cc_start: 0.8537 (pt0) cc_final: 0.8245 (mt-10) REVERT: C 46 ARG cc_start: 0.8213 (mtt90) cc_final: 0.7591 (mmm160) REVERT: C 80 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7474 (pp20) REVERT: C 219 THR cc_start: 0.9074 (t) cc_final: 0.8846 (m) REVERT: C 227 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8515 (m) REVERT: C 233 ASP cc_start: 0.8348 (p0) cc_final: 0.7967 (p0) REVERT: C 245 GLN cc_start: 0.8990 (mt0) cc_final: 0.8590 (tt0) REVERT: C 251 ARG cc_start: 0.8654 (mmt180) cc_final: 0.8312 (mmt180) REVERT: C 667 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8666 (mp0) REVERT: C 681 GLU cc_start: 0.8420 (tp30) cc_final: 0.8031 (mp0) REVERT: C 687 GLN cc_start: 0.5036 (OUTLIER) cc_final: 0.4831 (tp40) REVERT: C 699 ARG cc_start: 0.9024 (ptp-110) cc_final: 0.8499 (ptm-80) REVERT: C 730 LEU cc_start: 0.5655 (OUTLIER) cc_final: 0.5246 (mt) REVERT: C 748 CYS cc_start: 0.8961 (m) cc_final: 0.8615 (t) REVERT: C 750 GLU cc_start: 0.8566 (mp0) cc_final: 0.8171 (tt0) REVERT: C 768 MET cc_start: 0.8624 (mtp) cc_final: 0.7975 (ttm) REVERT: C 773 LYS cc_start: 0.8582 (tptm) cc_final: 0.8187 (mttp) REVERT: C 875 ASP cc_start: 0.8923 (p0) cc_final: 0.8586 (p0) REVERT: C 968 MET cc_start: 0.9035 (ttm) cc_final: 0.8702 (ttt) REVERT: C 969 GLU cc_start: 0.8539 (pt0) cc_final: 0.8232 (mt-10) REVERT: D 46 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7599 (mmm160) REVERT: D 80 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7482 (pp20) REVERT: D 219 THR cc_start: 0.9071 (t) cc_final: 0.8845 (m) REVERT: D 227 VAL cc_start: 0.8819 (OUTLIER) cc_final: 0.8518 (m) REVERT: D 233 ASP cc_start: 0.8347 (p0) cc_final: 0.7967 (p0) REVERT: D 245 GLN cc_start: 0.8993 (mt0) cc_final: 0.8594 (tt0) REVERT: D 251 ARG cc_start: 0.8663 (mmt180) cc_final: 0.8314 (mmt180) REVERT: D 667 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8670 (mp0) REVERT: D 681 GLU cc_start: 0.8419 (tp30) cc_final: 0.8033 (mp0) REVERT: D 687 GLN cc_start: 0.5035 (OUTLIER) cc_final: 0.4832 (tp40) REVERT: D 699 ARG cc_start: 0.9024 (ptp-110) cc_final: 0.8497 (ptm-80) REVERT: D 730 LEU cc_start: 0.5646 (OUTLIER) cc_final: 0.5240 (mt) REVERT: D 748 CYS cc_start: 0.8959 (m) cc_final: 0.8615 (t) REVERT: D 750 GLU cc_start: 0.8568 (mp0) cc_final: 0.8172 (tt0) REVERT: D 768 MET cc_start: 0.8626 (mtp) cc_final: 0.7979 (ttm) REVERT: D 773 LYS cc_start: 0.8583 (tptm) cc_final: 0.8186 (mttp) REVERT: D 875 ASP cc_start: 0.8923 (p0) cc_final: 0.8586 (p0) REVERT: D 968 MET cc_start: 0.9034 (ttm) cc_final: 0.8703 (ttt) REVERT: D 969 GLU cc_start: 0.8537 (pt0) cc_final: 0.8228 (mt-10) outliers start: 84 outliers final: 24 residues processed: 632 average time/residue: 0.9049 time to fit residues: 662.1134 Evaluate side-chains 485 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 441 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 687 GLN Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 519 SER Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 687 GLN Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 876 THR Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 667 GLU Chi-restraints excluded: chain D residue 687 GLN Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 876 THR Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN A 266 GLN A 294 ASN A 365 GLN A 583 ASN A 604 ASN A 625 GLN A 634 GLN A 693 GLN A 702 GLN A 739 HIS A 890 GLN B 163 GLN B 266 GLN B 294 ASN B 365 GLN B 583 ASN B 604 ASN B 625 GLN B 634 GLN B 693 GLN B 702 GLN B 739 HIS B 890 GLN C 266 GLN C 294 ASN C 365 GLN C 583 ASN C 604 ASN C 625 GLN C 634 GLN C 693 GLN C 702 GLN C 739 HIS C 890 GLN D 266 GLN D 294 ASN D 365 GLN D 583 ASN D 604 ASN D 625 GLN D 634 GLN D 693 GLN D 702 GLN D 739 HIS D 890 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.115101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.095096 restraints weight = 33336.766| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.18 r_work: 0.2873 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33632 Z= 0.151 Angle : 0.635 7.714 45888 Z= 0.345 Chirality : 0.048 0.169 4796 Planarity : 0.005 0.034 6056 Dihedral : 7.402 69.220 4524 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.07 % Allowed : 9.42 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 4052 helix: -0.68 (0.21), residues: 552 sheet: 0.85 (0.13), residues: 1368 loop : -0.43 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 630 TYR 0.018 0.002 TYR D 100 PHE 0.012 0.002 PHE B 747 TRP 0.043 0.002 TRP B 553 HIS 0.006 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (33632) covalent geometry : angle 0.63542 / 0.35 (45888) hydrogen bonds : bond 0.05031 / 3.32 ( 1113) hydrogen bonds : angle 5.45241 / 3.86 ( 3027) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 469 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8359 (m) REVERT: A 245 GLN cc_start: 0.8442 (mt0) cc_final: 0.8123 (tt0) REVERT: A 370 GLN cc_start: 0.8131 (tt0) cc_final: 0.7928 (mm110) REVERT: A 579 ASP cc_start: 0.7643 (p0) cc_final: 0.7405 (p0) REVERT: A 667 GLU cc_start: 0.8105 (pt0) cc_final: 0.7751 (pm20) REVERT: A 710 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8146 (mm-30) REVERT: A 730 LEU cc_start: 0.5687 (OUTLIER) cc_final: 0.5367 (mt) REVERT: A 748 CYS cc_start: 0.8331 (m) cc_final: 0.7906 (t) REVERT: A 768 MET cc_start: 0.8142 (mtp) cc_final: 0.7551 (ttm) REVERT: A 770 ILE cc_start: 0.8746 (mt) cc_final: 0.8495 (mm) REVERT: A 773 LYS cc_start: 0.7910 (tptm) cc_final: 0.7643 (mppt) REVERT: A 875 ASP cc_start: 0.8669 (p0) cc_final: 0.8359 (p0) REVERT: A 968 MET cc_start: 0.8963 (ttm) cc_final: 0.8548 (ttt) REVERT: B 227 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8361 (m) REVERT: B 245 GLN cc_start: 0.8454 (mt0) cc_final: 0.8120 (tt0) REVERT: B 579 ASP cc_start: 0.7641 (p0) cc_final: 0.7400 (p0) REVERT: B 667 GLU cc_start: 0.8093 (pt0) cc_final: 0.7745 (pm20) REVERT: B 710 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8139 (mm-30) REVERT: B 730 LEU cc_start: 0.5682 (OUTLIER) cc_final: 0.5366 (mt) REVERT: B 748 CYS cc_start: 0.8334 (m) cc_final: 0.7919 (t) REVERT: B 768 MET cc_start: 0.8157 (mtp) cc_final: 0.7560 (ttm) REVERT: B 770 ILE cc_start: 0.8745 (mt) cc_final: 0.8495 (mm) REVERT: B 773 LYS cc_start: 0.7926 (tptm) cc_final: 0.7650 (mppt) REVERT: B 875 ASP cc_start: 0.8668 (p0) cc_final: 0.8335 (p0) REVERT: B 968 MET cc_start: 0.8962 (ttm) cc_final: 0.8546 (ttt) REVERT: C 227 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8362 (m) REVERT: C 245 GLN cc_start: 0.8448 (mt0) cc_final: 0.8120 (tt0) REVERT: C 579 ASP cc_start: 0.7650 (p0) cc_final: 0.7410 (p0) REVERT: C 667 GLU cc_start: 0.8111 (pt0) cc_final: 0.7768 (pm20) REVERT: C 710 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8141 (mm-30) REVERT: C 730 LEU cc_start: 0.5697 (OUTLIER) cc_final: 0.5380 (mt) REVERT: C 748 CYS cc_start: 0.8323 (m) cc_final: 0.7908 (t) REVERT: C 768 MET cc_start: 0.8136 (mtp) cc_final: 0.7550 (ttm) REVERT: C 770 ILE cc_start: 0.8752 (mt) cc_final: 0.8502 (mm) REVERT: C 773 LYS cc_start: 0.7920 (tptm) cc_final: 0.7645 (mppt) REVERT: C 875 ASP cc_start: 0.8673 (p0) cc_final: 0.8362 (p0) REVERT: C 968 MET cc_start: 0.8970 (ttm) cc_final: 0.8554 (ttt) REVERT: D 227 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8364 (m) REVERT: D 237 ARG cc_start: 0.8565 (ttp-110) cc_final: 0.8356 (ttp-170) REVERT: D 245 GLN cc_start: 0.8440 (mt0) cc_final: 0.8113 (tt0) REVERT: D 370 GLN cc_start: 0.8136 (tt0) cc_final: 0.7927 (mm110) REVERT: D 579 ASP cc_start: 0.7639 (p0) cc_final: 0.7407 (p0) REVERT: D 667 GLU cc_start: 0.8103 (pt0) cc_final: 0.7762 (pm20) REVERT: D 710 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8143 (mm-30) REVERT: D 730 LEU cc_start: 0.5665 (OUTLIER) cc_final: 0.5359 (mt) REVERT: D 748 CYS cc_start: 0.8345 (m) cc_final: 0.7923 (t) REVERT: D 768 MET cc_start: 0.8150 (mtp) cc_final: 0.7559 (ttm) REVERT: D 770 ILE cc_start: 0.8756 (mt) cc_final: 0.8505 (mm) REVERT: D 773 LYS cc_start: 0.7930 (tptm) cc_final: 0.7662 (mppt) REVERT: D 875 ASP cc_start: 0.8665 (p0) cc_final: 0.8359 (p0) REVERT: D 968 MET cc_start: 0.8968 (ttm) cc_final: 0.8553 (ttt) outliers start: 72 outliers final: 16 residues processed: 501 average time/residue: 0.8596 time to fit residues: 504.0030 Evaluate side-chains 498 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 470 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 710 GLU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 710 GLU Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 276 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 377 optimal weight: 9.9990 chunk 379 optimal weight: 8.9990 chunk 351 optimal weight: 20.0000 chunk 274 optimal weight: 0.0000 chunk 229 optimal weight: 30.0000 chunk 145 optimal weight: 5.9990 chunk 16 optimal weight: 30.0000 chunk 179 optimal weight: 7.9990 chunk 239 optimal weight: 20.0000 overall best weight: 4.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 583 ASN ** A 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 761 GLN B 583 ASN ** B 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 761 GLN C 163 GLN C 583 ASN ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 761 GLN D 163 GLN D 583 ASN ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 761 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.115508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.095648 restraints weight = 33528.158| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.18 r_work: 0.2890 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9109 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 33632 Z= 0.132 Angle : 0.580 7.068 45888 Z= 0.311 Chirality : 0.046 0.141 4796 Planarity : 0.004 0.033 6056 Dihedral : 5.599 55.350 4460 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.67 % Allowed : 10.54 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.13), residues: 4052 helix: -0.21 (0.22), residues: 552 sheet: 1.13 (0.14), residues: 1364 loop : -0.31 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 630 TYR 0.020 0.002 TYR D 100 PHE 0.012 0.001 PHE A 747 TRP 0.036 0.002 TRP D 553 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (33632) covalent geometry : angle 0.58018 / 0.31 (45888) hydrogen bonds : bond 0.04419 / 2.92 ( 1113) hydrogen bonds : angle 5.14501 / 3.64 ( 3027) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 490 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7620 (mtt90) cc_final: 0.7263 (mtm180) REVERT: A 57 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8337 (mt-10) REVERT: A 245 GLN cc_start: 0.8420 (mt0) cc_final: 0.8124 (tt0) REVERT: A 252 ASP cc_start: 0.7576 (m-30) cc_final: 0.7369 (p0) REVERT: A 579 ASP cc_start: 0.7650 (p0) cc_final: 0.7442 (p0) REVERT: A 667 GLU cc_start: 0.8124 (pt0) cc_final: 0.7781 (pm20) REVERT: A 710 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8047 (mm-30) REVERT: A 730 LEU cc_start: 0.5617 (OUTLIER) cc_final: 0.5330 (mt) REVERT: A 748 CYS cc_start: 0.8284 (m) cc_final: 0.7908 (t) REVERT: A 768 MET cc_start: 0.8177 (mtp) cc_final: 0.7666 (ttm) REVERT: A 770 ILE cc_start: 0.8732 (mt) cc_final: 0.8498 (mm) REVERT: A 875 ASP cc_start: 0.8611 (p0) cc_final: 0.8325 (p0) REVERT: A 968 MET cc_start: 0.8959 (ttm) cc_final: 0.8529 (ttt) REVERT: B 46 ARG cc_start: 0.7617 (mtt90) cc_final: 0.7258 (mtm180) REVERT: B 57 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8336 (mt-10) REVERT: B 245 GLN cc_start: 0.8421 (mt0) cc_final: 0.8127 (tt0) REVERT: B 579 ASP cc_start: 0.7649 (p0) cc_final: 0.7439 (p0) REVERT: B 667 GLU cc_start: 0.8119 (pt0) cc_final: 0.7776 (pm20) REVERT: B 710 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8077 (mm-30) REVERT: B 730 LEU cc_start: 0.5625 (OUTLIER) cc_final: 0.5340 (mt) REVERT: B 748 CYS cc_start: 0.8268 (m) cc_final: 0.7902 (t) REVERT: B 768 MET cc_start: 0.8168 (mtp) cc_final: 0.7659 (ttm) REVERT: B 770 ILE cc_start: 0.8731 (mt) cc_final: 0.8497 (mm) REVERT: B 875 ASP cc_start: 0.8607 (p0) cc_final: 0.8324 (p0) REVERT: B 968 MET cc_start: 0.8963 (ttm) cc_final: 0.8532 (ttt) REVERT: C 46 ARG cc_start: 0.7621 (mtt90) cc_final: 0.7256 (mtm180) REVERT: C 57 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8330 (mt-10) REVERT: C 245 GLN cc_start: 0.8421 (mt0) cc_final: 0.8129 (tt0) REVERT: C 252 ASP cc_start: 0.7568 (m-30) cc_final: 0.7366 (p0) REVERT: C 579 ASP cc_start: 0.7635 (p0) cc_final: 0.7432 (p0) REVERT: C 667 GLU cc_start: 0.8124 (pt0) cc_final: 0.7783 (pm20) REVERT: C 710 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8054 (mm-30) REVERT: C 730 LEU cc_start: 0.5631 (OUTLIER) cc_final: 0.5346 (mt) REVERT: C 748 CYS cc_start: 0.8284 (m) cc_final: 0.7909 (t) REVERT: C 768 MET cc_start: 0.8163 (mtp) cc_final: 0.7660 (ttm) REVERT: C 770 ILE cc_start: 0.8730 (mt) cc_final: 0.8496 (mm) REVERT: C 875 ASP cc_start: 0.8610 (p0) cc_final: 0.8328 (p0) REVERT: C 968 MET cc_start: 0.8969 (ttm) cc_final: 0.8536 (ttt) REVERT: D 46 ARG cc_start: 0.7612 (mtt90) cc_final: 0.7257 (mtm180) REVERT: D 57 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8341 (mt-10) REVERT: D 245 GLN cc_start: 0.8415 (mt0) cc_final: 0.8125 (tt0) REVERT: D 579 ASP cc_start: 0.7649 (p0) cc_final: 0.7441 (p0) REVERT: D 667 GLU cc_start: 0.8125 (pt0) cc_final: 0.7784 (pm20) REVERT: D 710 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8061 (mm-30) REVERT: D 730 LEU cc_start: 0.5628 (OUTLIER) cc_final: 0.5337 (mt) REVERT: D 748 CYS cc_start: 0.8282 (m) cc_final: 0.7914 (t) REVERT: D 768 MET cc_start: 0.8171 (mtp) cc_final: 0.7662 (ttm) REVERT: D 770 ILE cc_start: 0.8729 (mt) cc_final: 0.8494 (mm) REVERT: D 875 ASP cc_start: 0.8608 (p0) cc_final: 0.8326 (p0) REVERT: D 968 MET cc_start: 0.8961 (ttm) cc_final: 0.8529 (ttt) outliers start: 58 outliers final: 18 residues processed: 522 average time/residue: 0.8528 time to fit residues: 522.1632 Evaluate side-chains 504 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 474 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 890 GLN Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 710 GLU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 890 GLN Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 710 GLU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 890 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 30 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 227 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 234 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 276 optimal weight: 10.0000 chunk 380 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 340 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 583 ASN ** A 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 761 GLN B 583 ASN ** B 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 761 GLN C 583 ASN ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 761 GLN D 583 ASN ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 761 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.115036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.095210 restraints weight = 33382.185| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.17 r_work: 0.2877 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33632 Z= 0.160 Angle : 0.613 7.656 45888 Z= 0.328 Chirality : 0.047 0.149 4796 Planarity : 0.005 0.038 6056 Dihedral : 5.557 57.849 4456 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.81 % Allowed : 10.02 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.13), residues: 4052 helix: 0.08 (0.22), residues: 528 sheet: 1.14 (0.14), residues: 1368 loop : -0.29 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.022 0.002 TYR A 100 PHE 0.012 0.002 PHE A 747 TRP 0.035 0.002 TRP B 553 HIS 0.005 0.001 HIS D 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (33632) covalent geometry : angle 0.61334 / 0.33 (45888) hydrogen bonds : bond 0.04718 / 3.12 ( 1113) hydrogen bonds : angle 5.22858 / 3.70 ( 3027) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 459 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7608 (mtt90) cc_final: 0.7227 (mtm180) REVERT: A 57 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8327 (mt-10) REVERT: A 117 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: A 245 GLN cc_start: 0.8424 (mt0) cc_final: 0.8148 (tt0) REVERT: A 667 GLU cc_start: 0.8133 (pt0) cc_final: 0.7850 (pm20) REVERT: A 710 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8040 (mm-30) REVERT: A 730 LEU cc_start: 0.5551 (OUTLIER) cc_final: 0.5313 (mt) REVERT: A 748 CYS cc_start: 0.8236 (m) cc_final: 0.7889 (t) REVERT: A 768 MET cc_start: 0.8223 (mtp) cc_final: 0.7788 (ttm) REVERT: A 770 ILE cc_start: 0.8721 (mt) cc_final: 0.8456 (mm) REVERT: A 875 ASP cc_start: 0.8650 (p0) cc_final: 0.8334 (p0) REVERT: A 968 MET cc_start: 0.8941 (ttm) cc_final: 0.8507 (ttt) REVERT: B 46 ARG cc_start: 0.7612 (mtt90) cc_final: 0.7231 (mtm180) REVERT: B 57 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8329 (mt-10) REVERT: B 117 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: B 245 GLN cc_start: 0.8424 (mt0) cc_final: 0.8146 (tt0) REVERT: B 667 GLU cc_start: 0.8134 (pt0) cc_final: 0.7850 (pm20) REVERT: B 710 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8067 (mm-30) REVERT: B 730 LEU cc_start: 0.5588 (OUTLIER) cc_final: 0.5326 (mt) REVERT: B 748 CYS cc_start: 0.8254 (m) cc_final: 0.7898 (t) REVERT: B 768 MET cc_start: 0.8223 (mtp) cc_final: 0.7785 (ttm) REVERT: B 770 ILE cc_start: 0.8717 (mt) cc_final: 0.8452 (mm) REVERT: B 875 ASP cc_start: 0.8650 (p0) cc_final: 0.8334 (p0) REVERT: B 968 MET cc_start: 0.8946 (ttm) cc_final: 0.8511 (ttt) REVERT: C 46 ARG cc_start: 0.7610 (mtt90) cc_final: 0.7227 (mtm180) REVERT: C 57 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8330 (mt-10) REVERT: C 117 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: C 245 GLN cc_start: 0.8427 (mt0) cc_final: 0.8153 (tt0) REVERT: C 667 GLU cc_start: 0.8125 (pt0) cc_final: 0.7847 (pm20) REVERT: C 710 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: C 730 LEU cc_start: 0.5595 (OUTLIER) cc_final: 0.5333 (mt) REVERT: C 748 CYS cc_start: 0.8268 (m) cc_final: 0.7908 (t) REVERT: C 768 MET cc_start: 0.8219 (mtp) cc_final: 0.7789 (ttm) REVERT: C 770 ILE cc_start: 0.8720 (mt) cc_final: 0.8455 (mm) REVERT: C 875 ASP cc_start: 0.8655 (p0) cc_final: 0.8336 (p0) REVERT: C 968 MET cc_start: 0.8947 (ttm) cc_final: 0.8510 (ttt) REVERT: D 46 ARG cc_start: 0.7610 (mtt90) cc_final: 0.7230 (mtm180) REVERT: D 57 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8343 (mt-10) REVERT: D 117 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: D 245 GLN cc_start: 0.8420 (mt0) cc_final: 0.8143 (tt0) REVERT: D 667 GLU cc_start: 0.8133 (pt0) cc_final: 0.7848 (pm20) REVERT: D 710 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8082 (mm-30) REVERT: D 730 LEU cc_start: 0.5590 (OUTLIER) cc_final: 0.5328 (mt) REVERT: D 748 CYS cc_start: 0.8268 (m) cc_final: 0.7911 (t) REVERT: D 768 MET cc_start: 0.8200 (mtp) cc_final: 0.7772 (ttm) REVERT: D 770 ILE cc_start: 0.8718 (mt) cc_final: 0.8451 (mm) REVERT: D 875 ASP cc_start: 0.8653 (p0) cc_final: 0.8333 (p0) REVERT: D 968 MET cc_start: 0.8949 (ttm) cc_final: 0.8515 (ttt) outliers start: 63 outliers final: 21 residues processed: 491 average time/residue: 0.8480 time to fit residues: 486.1552 Evaluate side-chains 484 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 447 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 1017 GLN Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 890 GLN Chi-restraints excluded: chain B residue 1017 GLN Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 710 GLU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 890 GLN Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 710 GLU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 890 GLN Chi-restraints excluded: chain D residue 1017 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 242 optimal weight: 30.0000 chunk 150 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 227 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 117 optimal weight: 30.0000 chunk 281 optimal weight: 0.0070 chunk 310 optimal weight: 30.0000 chunk 393 optimal weight: 20.0000 chunk 269 optimal weight: 8.9990 chunk 228 optimal weight: 8.9990 overall best weight: 5.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 583 ASN ** A 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 761 GLN A 863 GLN B 583 ASN ** B 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 761 GLN B 863 GLN C 583 ASN ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 761 GLN D 583 ASN ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 761 GLN D 863 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.115546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.096324 restraints weight = 33659.432| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.13 r_work: 0.2906 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9109 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 33632 Z= 0.137 Angle : 0.572 7.272 45888 Z= 0.305 Chirality : 0.046 0.140 4796 Planarity : 0.004 0.038 6056 Dihedral : 5.304 49.396 4456 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.39 % Allowed : 9.59 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.13), residues: 4052 helix: 0.05 (0.22), residues: 528 sheet: 1.25 (0.14), residues: 1364 loop : -0.24 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 336 TYR 0.020 0.002 TYR D 100 PHE 0.012 0.001 PHE B 747 TRP 0.034 0.002 TRP D 553 HIS 0.004 0.001 HIS C 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (33632) covalent geometry : angle 0.57227 / 0.31 (45888) hydrogen bonds : bond 0.04290 / 2.83 ( 1113) hydrogen bonds : angle 5.08173 / 3.59 ( 3027) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 469 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7631 (mtt90) cc_final: 0.7249 (mtm180) REVERT: A 57 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8376 (mt-10) REVERT: A 117 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: A 245 GLN cc_start: 0.8394 (mt0) cc_final: 0.8173 (tt0) REVERT: A 667 GLU cc_start: 0.8050 (pt0) cc_final: 0.7743 (mp0) REVERT: A 710 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8049 (mm-30) REVERT: A 730 LEU cc_start: 0.5623 (OUTLIER) cc_final: 0.5386 (mt) REVERT: A 748 CYS cc_start: 0.8245 (m) cc_final: 0.7883 (t) REVERT: A 768 MET cc_start: 0.8189 (mtp) cc_final: 0.7802 (ttm) REVERT: A 875 ASP cc_start: 0.8608 (p0) cc_final: 0.8322 (p0) REVERT: A 968 MET cc_start: 0.8964 (ttm) cc_final: 0.8529 (ttt) REVERT: B 46 ARG cc_start: 0.7637 (mtt90) cc_final: 0.7249 (mtm180) REVERT: B 57 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8384 (mt-10) REVERT: B 117 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: B 245 GLN cc_start: 0.8395 (mt0) cc_final: 0.8175 (tt0) REVERT: B 667 GLU cc_start: 0.8051 (pt0) cc_final: 0.7746 (mp0) REVERT: B 710 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8078 (mm-30) REVERT: B 730 LEU cc_start: 0.5630 (OUTLIER) cc_final: 0.5389 (mt) REVERT: B 748 CYS cc_start: 0.8251 (m) cc_final: 0.7885 (t) REVERT: B 768 MET cc_start: 0.8188 (mtp) cc_final: 0.7801 (ttm) REVERT: B 875 ASP cc_start: 0.8608 (p0) cc_final: 0.8322 (p0) REVERT: B 968 MET cc_start: 0.8966 (ttm) cc_final: 0.8532 (ttt) REVERT: C 46 ARG cc_start: 0.7639 (mtt90) cc_final: 0.7247 (mtm180) REVERT: C 57 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8378 (mt-10) REVERT: C 117 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: C 245 GLN cc_start: 0.8392 (mt0) cc_final: 0.8172 (tt0) REVERT: C 667 GLU cc_start: 0.8040 (pt0) cc_final: 0.7740 (mp0) REVERT: C 710 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8060 (mm-30) REVERT: C 730 LEU cc_start: 0.5630 (OUTLIER) cc_final: 0.5390 (mt) REVERT: C 748 CYS cc_start: 0.8247 (m) cc_final: 0.7884 (t) REVERT: C 768 MET cc_start: 0.8185 (mtp) cc_final: 0.7802 (ttm) REVERT: C 875 ASP cc_start: 0.8608 (p0) cc_final: 0.8320 (p0) REVERT: C 968 MET cc_start: 0.8966 (ttm) cc_final: 0.8532 (ttt) REVERT: D 46 ARG cc_start: 0.7630 (mtt90) cc_final: 0.7244 (mtm180) REVERT: D 57 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8374 (mt-10) REVERT: D 117 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: D 245 GLN cc_start: 0.8398 (mt0) cc_final: 0.8175 (tt0) REVERT: D 667 GLU cc_start: 0.8047 (pt0) cc_final: 0.7741 (mp0) REVERT: D 710 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8092 (mm-30) REVERT: D 730 LEU cc_start: 0.5619 (OUTLIER) cc_final: 0.5380 (mt) REVERT: D 748 CYS cc_start: 0.8235 (m) cc_final: 0.7877 (t) REVERT: D 768 MET cc_start: 0.8175 (mtp) cc_final: 0.7792 (ttm) REVERT: D 875 ASP cc_start: 0.8613 (p0) cc_final: 0.8327 (p0) REVERT: D 968 MET cc_start: 0.8965 (ttm) cc_final: 0.8532 (ttt) outliers start: 83 outliers final: 36 residues processed: 513 average time/residue: 0.8207 time to fit residues: 493.6295 Evaluate side-chains 514 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 462 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 1017 GLN Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain B residue 890 GLN Chi-restraints excluded: chain B residue 1017 GLN Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 710 GLU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 876 THR Chi-restraints excluded: chain C residue 890 GLN Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 710 GLU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 876 THR Chi-restraints excluded: chain D residue 890 GLN Chi-restraints excluded: chain D residue 1017 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 379 optimal weight: 7.9990 chunk 387 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 395 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 275 optimal weight: 20.0000 chunk 64 optimal weight: 30.0000 chunk 115 optimal weight: 20.0000 chunk 307 optimal weight: 30.0000 chunk 63 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 583 ASN A 614 HIS ** A 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 761 GLN A 863 GLN B 583 ASN B 614 HIS ** B 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 761 GLN B 863 GLN C 583 ASN C 614 HIS ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 761 GLN C 863 GLN D 583 ASN D 614 HIS ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 761 GLN D 863 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.114450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.095221 restraints weight = 33329.420| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.12 r_work: 0.2887 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 33632 Z= 0.168 Angle : 0.619 7.684 45888 Z= 0.330 Chirality : 0.048 0.148 4796 Planarity : 0.005 0.038 6056 Dihedral : 5.400 41.281 4456 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.02 % Allowed : 10.11 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.13), residues: 4052 helix: 0.20 (0.23), residues: 504 sheet: 1.05 (0.14), residues: 1408 loop : -0.18 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 336 TYR 0.022 0.002 TYR A 100 PHE 0.012 0.002 PHE D 747 TRP 0.034 0.002 TRP D 553 HIS 0.005 0.001 HIS D 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (33632) covalent geometry : angle 0.61874 / 0.33 (45888) hydrogen bonds : bond 0.04773 / 3.15 ( 1113) hydrogen bonds : angle 5.23417 / 3.70 ( 3027) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 468 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7640 (mtt90) cc_final: 0.7253 (mtm180) REVERT: A 57 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8377 (mt-10) REVERT: A 245 GLN cc_start: 0.8392 (mt0) cc_final: 0.8162 (tt0) REVERT: A 667 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: A 710 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8098 (mm-30) REVERT: A 730 LEU cc_start: 0.5648 (OUTLIER) cc_final: 0.5377 (mt) REVERT: A 748 CYS cc_start: 0.8255 (m) cc_final: 0.7913 (t) REVERT: A 750 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7147 (tp30) REVERT: A 768 MET cc_start: 0.8171 (mtp) cc_final: 0.7794 (ttm) REVERT: A 770 ILE cc_start: 0.8755 (mt) cc_final: 0.8469 (mm) REVERT: A 968 MET cc_start: 0.8979 (ttm) cc_final: 0.8548 (ttt) REVERT: B 46 ARG cc_start: 0.7646 (mtt90) cc_final: 0.7251 (mtm180) REVERT: B 57 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8385 (mt-10) REVERT: B 245 GLN cc_start: 0.8397 (mt0) cc_final: 0.8150 (tt0) REVERT: B 667 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: B 710 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8111 (mm-30) REVERT: B 730 LEU cc_start: 0.5645 (OUTLIER) cc_final: 0.5371 (mt) REVERT: B 748 CYS cc_start: 0.8255 (m) cc_final: 0.7909 (t) REVERT: B 750 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7130 (tp30) REVERT: B 768 MET cc_start: 0.8172 (mtp) cc_final: 0.7794 (ttm) REVERT: B 770 ILE cc_start: 0.8752 (mt) cc_final: 0.8465 (mm) REVERT: B 968 MET cc_start: 0.8981 (ttm) cc_final: 0.8552 (ttt) REVERT: C 46 ARG cc_start: 0.7644 (mtt90) cc_final: 0.7249 (mtm180) REVERT: C 57 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8368 (mt-10) REVERT: C 245 GLN cc_start: 0.8390 (mt0) cc_final: 0.8161 (tt0) REVERT: C 667 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: C 710 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8097 (mm-30) REVERT: C 730 LEU cc_start: 0.5646 (OUTLIER) cc_final: 0.5373 (mt) REVERT: C 748 CYS cc_start: 0.8266 (m) cc_final: 0.7923 (t) REVERT: C 750 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7144 (tp30) REVERT: C 768 MET cc_start: 0.8176 (mtp) cc_final: 0.7795 (ttm) REVERT: C 770 ILE cc_start: 0.8751 (mt) cc_final: 0.8464 (mm) REVERT: C 968 MET cc_start: 0.8981 (ttm) cc_final: 0.8550 (ttt) REVERT: D 46 ARG cc_start: 0.7637 (mtt90) cc_final: 0.7248 (mtm180) REVERT: D 57 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8380 (mt-10) REVERT: D 245 GLN cc_start: 0.8399 (mt0) cc_final: 0.8151 (tt0) REVERT: D 667 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: D 710 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8126 (mm-30) REVERT: D 730 LEU cc_start: 0.5648 (OUTLIER) cc_final: 0.5376 (mt) REVERT: D 748 CYS cc_start: 0.8252 (m) cc_final: 0.7914 (t) REVERT: D 750 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7144 (tp30) REVERT: D 768 MET cc_start: 0.8166 (mtp) cc_final: 0.7787 (ttm) REVERT: D 770 ILE cc_start: 0.8746 (mt) cc_final: 0.8459 (mm) REVERT: D 968 MET cc_start: 0.8982 (ttm) cc_final: 0.8553 (ttt) outliers start: 70 outliers final: 36 residues processed: 500 average time/residue: 0.8344 time to fit residues: 486.8371 Evaluate side-chains 514 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 458 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 1017 GLN Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 750 GLU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain B residue 890 GLN Chi-restraints excluded: chain B residue 1017 GLN Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 710 GLU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 876 THR Chi-restraints excluded: chain C residue 890 GLN Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 667 GLU Chi-restraints excluded: chain D residue 710 GLU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 750 GLU Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 876 THR Chi-restraints excluded: chain D residue 890 GLN Chi-restraints excluded: chain D residue 1017 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 163 optimal weight: 30.0000 chunk 259 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 352 optimal weight: 9.9990 chunk 373 optimal weight: 0.0870 chunk 57 optimal weight: 9.9990 chunk 325 optimal weight: 0.3980 chunk 115 optimal weight: 2.9990 chunk 198 optimal weight: 8.9990 chunk 209 optimal weight: 30.0000 chunk 197 optimal weight: 30.0000 overall best weight: 4.0964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 583 ASN ** A 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 761 GLN A 863 GLN B 583 ASN ** B 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 761 GLN B 863 GLN C 583 ASN ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 761 GLN D 583 ASN ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 761 GLN D 863 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.116269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.097128 restraints weight = 33646.924| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.14 r_work: 0.2919 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 33632 Z= 0.118 Angle : 0.552 7.897 45888 Z= 0.293 Chirality : 0.045 0.136 4796 Planarity : 0.004 0.038 6056 Dihedral : 5.116 37.616 4456 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.76 % Allowed : 10.83 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.13), residues: 4052 helix: 0.19 (0.23), residues: 528 sheet: 1.25 (0.14), residues: 1368 loop : -0.16 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 336 TYR 0.019 0.002 TYR D 100 PHE 0.012 0.001 PHE B 747 TRP 0.035 0.002 TRP C 553 HIS 0.003 0.001 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (33632) covalent geometry : angle 0.55220 / 0.29 (45888) hydrogen bonds : bond 0.04027 / 2.66 ( 1113) hydrogen bonds : angle 5.00711 / 3.54 ( 3027) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 459 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7617 (mtt90) cc_final: 0.7245 (mtm180) REVERT: A 57 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8380 (mt-10) REVERT: A 245 GLN cc_start: 0.8386 (mt0) cc_final: 0.8140 (tt0) REVERT: A 710 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8032 (mm-30) REVERT: A 730 LEU cc_start: 0.5651 (OUTLIER) cc_final: 0.5401 (mt) REVERT: A 748 CYS cc_start: 0.8214 (m) cc_final: 0.7867 (t) REVERT: A 768 MET cc_start: 0.8148 (mtp) cc_final: 0.7820 (ttm) REVERT: A 875 ASP cc_start: 0.8592 (p0) cc_final: 0.8233 (p0) REVERT: A 968 MET cc_start: 0.8942 (ttm) cc_final: 0.8525 (ttt) REVERT: B 46 ARG cc_start: 0.7625 (mtt90) cc_final: 0.7245 (mtm180) REVERT: B 57 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8381 (mt-10) REVERT: B 245 GLN cc_start: 0.8390 (mt0) cc_final: 0.8146 (tt0) REVERT: B 710 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8040 (mm-30) REVERT: B 730 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.5404 (mt) REVERT: B 748 CYS cc_start: 0.8216 (m) cc_final: 0.7865 (t) REVERT: B 768 MET cc_start: 0.8159 (mtp) cc_final: 0.7826 (ttm) REVERT: B 875 ASP cc_start: 0.8594 (p0) cc_final: 0.8233 (p0) REVERT: B 968 MET cc_start: 0.8948 (ttm) cc_final: 0.8532 (ttt) REVERT: C 46 ARG cc_start: 0.7623 (mtt90) cc_final: 0.7242 (mtm180) REVERT: C 57 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8373 (mt-10) REVERT: C 245 GLN cc_start: 0.8388 (mt0) cc_final: 0.8142 (tt0) REVERT: C 667 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: C 710 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8044 (mm-30) REVERT: C 730 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.5400 (mt) REVERT: C 748 CYS cc_start: 0.8229 (m) cc_final: 0.7884 (t) REVERT: C 768 MET cc_start: 0.8159 (mtp) cc_final: 0.7827 (ttm) REVERT: C 875 ASP cc_start: 0.8594 (p0) cc_final: 0.8232 (p0) REVERT: C 968 MET cc_start: 0.8946 (ttm) cc_final: 0.8529 (ttt) REVERT: D 46 ARG cc_start: 0.7616 (mtt90) cc_final: 0.7240 (mtm180) REVERT: D 57 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8384 (mt-10) REVERT: D 245 GLN cc_start: 0.8389 (mt0) cc_final: 0.8142 (tt0) REVERT: D 710 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8062 (mm-30) REVERT: D 730 LEU cc_start: 0.5656 (OUTLIER) cc_final: 0.5403 (mt) REVERT: D 748 CYS cc_start: 0.8205 (m) cc_final: 0.7870 (t) REVERT: D 768 MET cc_start: 0.8151 (mtp) cc_final: 0.7823 (ttm) REVERT: D 875 ASP cc_start: 0.8600 (p0) cc_final: 0.8238 (p0) REVERT: D 968 MET cc_start: 0.8947 (ttm) cc_final: 0.8529 (ttt) outliers start: 61 outliers final: 30 residues processed: 491 average time/residue: 0.8916 time to fit residues: 508.7476 Evaluate side-chains 502 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 459 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 1017 GLN Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain B residue 1017 GLN Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 710 GLU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 876 THR Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 667 GLU Chi-restraints excluded: chain D residue 710 GLU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 876 THR Chi-restraints excluded: chain D residue 1017 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 115 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 275 optimal weight: 4.9990 chunk 374 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 chunk 71 optimal weight: 30.0000 chunk 91 optimal weight: 9.9990 chunk 136 optimal weight: 0.0470 chunk 235 optimal weight: 9.9990 chunk 327 optimal weight: 10.0000 chunk 224 optimal weight: 1.9990 overall best weight: 5.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 583 ASN ** A 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 761 GLN A 863 GLN B 583 ASN ** B 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 761 GLN B 863 GLN C 583 ASN ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 761 GLN D 583 ASN ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 761 GLN D 863 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.115839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.096725 restraints weight = 33632.238| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.13 r_work: 0.2909 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9104 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 33632 Z= 0.131 Angle : 0.566 8.299 45888 Z= 0.300 Chirality : 0.045 0.137 4796 Planarity : 0.004 0.038 6056 Dihedral : 5.132 36.072 4456 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.61 % Allowed : 11.18 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.13), residues: 4052 helix: 0.20 (0.23), residues: 528 sheet: 1.25 (0.14), residues: 1368 loop : -0.13 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 336 TYR 0.020 0.002 TYR D 100 PHE 0.013 0.001 PHE D 747 TRP 0.033 0.002 TRP C 553 HIS 0.004 0.001 HIS D 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (33632) covalent geometry : angle 0.56633 / 0.30 (45888) hydrogen bonds : bond 0.04195 / 2.77 ( 1113) hydrogen bonds : angle 5.03825 / 3.56 ( 3027) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 460 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7623 (mtt90) cc_final: 0.7246 (mtm180) REVERT: A 57 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8391 (mt-10) REVERT: A 245 GLN cc_start: 0.8392 (mt0) cc_final: 0.8168 (tt0) REVERT: A 710 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8036 (mm-30) REVERT: A 730 LEU cc_start: 0.5633 (OUTLIER) cc_final: 0.5387 (mt) REVERT: A 748 CYS cc_start: 0.8212 (m) cc_final: 0.7869 (t) REVERT: A 768 MET cc_start: 0.8152 (mtp) cc_final: 0.7829 (ttm) REVERT: A 875 ASP cc_start: 0.8605 (p0) cc_final: 0.8281 (p0) REVERT: A 968 MET cc_start: 0.8944 (ttm) cc_final: 0.8523 (ttt) REVERT: B 46 ARG cc_start: 0.7630 (mtt90) cc_final: 0.7248 (mtm180) REVERT: B 57 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8396 (mt-10) REVERT: B 245 GLN cc_start: 0.8394 (mt0) cc_final: 0.8171 (tt0) REVERT: B 710 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8059 (mm-30) REVERT: B 730 LEU cc_start: 0.5692 (OUTLIER) cc_final: 0.5386 (mt) REVERT: B 748 CYS cc_start: 0.8208 (m) cc_final: 0.7864 (t) REVERT: B 768 MET cc_start: 0.8139 (mtp) cc_final: 0.7815 (ttm) REVERT: B 875 ASP cc_start: 0.8607 (p0) cc_final: 0.8279 (p0) REVERT: B 968 MET cc_start: 0.8949 (ttm) cc_final: 0.8530 (ttt) REVERT: C 46 ARG cc_start: 0.7633 (mtt90) cc_final: 0.7247 (mtm180) REVERT: C 57 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8383 (mt-10) REVERT: C 245 GLN cc_start: 0.8393 (mt0) cc_final: 0.8168 (tt0) REVERT: C 710 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8040 (mm-30) REVERT: C 730 LEU cc_start: 0.5629 (OUTLIER) cc_final: 0.5382 (mt) REVERT: C 748 CYS cc_start: 0.8230 (m) cc_final: 0.7882 (t) REVERT: C 768 MET cc_start: 0.8153 (mtp) cc_final: 0.7827 (ttm) REVERT: C 875 ASP cc_start: 0.8605 (p0) cc_final: 0.8276 (p0) REVERT: C 968 MET cc_start: 0.8953 (ttm) cc_final: 0.8532 (ttt) REVERT: D 46 ARG cc_start: 0.7625 (mtt90) cc_final: 0.7248 (mtm180) REVERT: D 57 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8392 (mt-10) REVERT: D 245 GLN cc_start: 0.8391 (mt0) cc_final: 0.8167 (tt0) REVERT: D 710 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8070 (mm-30) REVERT: D 730 LEU cc_start: 0.5637 (OUTLIER) cc_final: 0.5386 (mt) REVERT: D 748 CYS cc_start: 0.8213 (m) cc_final: 0.7875 (t) REVERT: D 768 MET cc_start: 0.8139 (mtp) cc_final: 0.7819 (ttm) REVERT: D 875 ASP cc_start: 0.8609 (p0) cc_final: 0.8284 (p0) REVERT: D 968 MET cc_start: 0.8953 (ttm) cc_final: 0.8531 (ttt) outliers start: 56 outliers final: 33 residues processed: 491 average time/residue: 0.8888 time to fit residues: 508.2916 Evaluate side-chains 499 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 454 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 1017 GLN Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain B residue 1017 GLN Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 710 GLU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 876 THR Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 710 GLU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 876 THR Chi-restraints excluded: chain D residue 1017 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 274 optimal weight: 50.0000 chunk 108 optimal weight: 30.0000 chunk 221 optimal weight: 9.9990 chunk 203 optimal weight: 20.0000 chunk 34 optimal weight: 0.7980 chunk 315 optimal weight: 9.9990 chunk 284 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 342 optimal weight: 8.9990 chunk 310 optimal weight: 30.0000 chunk 288 optimal weight: 4.9990 overall best weight: 6.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 583 ASN A 739 HIS A 761 GLN A 845 GLN A 863 GLN B 583 ASN B 739 HIS B 761 GLN B 845 GLN B 863 GLN C 583 ASN ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 761 GLN C 845 GLN C 863 GLN D 583 ASN D 739 HIS D 761 GLN D 845 GLN D 863 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.114817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.095632 restraints weight = 33290.639| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.12 r_work: 0.2899 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9115 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 33632 Z= 0.162 Angle : 0.608 8.064 45888 Z= 0.323 Chirality : 0.047 0.145 4796 Planarity : 0.005 0.039 6056 Dihedral : 5.280 34.682 4456 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.67 % Allowed : 11.12 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.13), residues: 4052 helix: 0.32 (0.23), residues: 504 sheet: 1.10 (0.14), residues: 1404 loop : -0.12 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 336 TYR 0.022 0.002 TYR D 100 PHE 0.012 0.002 PHE D 747 TRP 0.033 0.002 TRP C 553 HIS 0.005 0.001 HIS C 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (33632) covalent geometry : angle 0.60826 / 0.32 (45888) hydrogen bonds : bond 0.04629 / 3.06 ( 1113) hydrogen bonds : angle 5.17130 / 3.66 ( 3027) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 466 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7622 (mtt90) cc_final: 0.7232 (mtm180) REVERT: A 57 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8380 (mt-10) REVERT: A 245 GLN cc_start: 0.8389 (mt0) cc_final: 0.8172 (tt0) REVERT: A 710 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8054 (mm-30) REVERT: A 730 LEU cc_start: 0.5728 (OUTLIER) cc_final: 0.5433 (mt) REVERT: A 748 CYS cc_start: 0.8242 (m) cc_final: 0.7899 (t) REVERT: A 768 MET cc_start: 0.8148 (mtp) cc_final: 0.7818 (ttm) REVERT: A 770 ILE cc_start: 0.8738 (mt) cc_final: 0.8478 (mm) REVERT: A 875 ASP cc_start: 0.8585 (p0) cc_final: 0.8247 (p0) REVERT: A 968 MET cc_start: 0.8944 (ttm) cc_final: 0.8527 (ttt) REVERT: B 46 ARG cc_start: 0.7632 (mtt90) cc_final: 0.7238 (mtm180) REVERT: B 57 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8389 (mt-10) REVERT: B 245 GLN cc_start: 0.8392 (mt0) cc_final: 0.8173 (tt0) REVERT: B 710 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8104 (mm-30) REVERT: B 730 LEU cc_start: 0.5724 (OUTLIER) cc_final: 0.5427 (mt) REVERT: B 748 CYS cc_start: 0.8241 (m) cc_final: 0.7893 (t) REVERT: B 768 MET cc_start: 0.8139 (mtp) cc_final: 0.7811 (ttm) REVERT: B 770 ILE cc_start: 0.8737 (mt) cc_final: 0.8475 (mm) REVERT: B 875 ASP cc_start: 0.8581 (p0) cc_final: 0.8239 (p0) REVERT: B 968 MET cc_start: 0.8950 (ttm) cc_final: 0.8534 (ttt) REVERT: C 46 ARG cc_start: 0.7628 (mtt90) cc_final: 0.7234 (mtm180) REVERT: C 57 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8375 (mt-10) REVERT: C 245 GLN cc_start: 0.8392 (mt0) cc_final: 0.8174 (tt0) REVERT: C 667 GLU cc_start: 0.7975 (pt0) cc_final: 0.7744 (mp0) REVERT: C 710 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8062 (mm-30) REVERT: C 730 LEU cc_start: 0.5721 (OUTLIER) cc_final: 0.5420 (mt) REVERT: C 748 CYS cc_start: 0.8262 (m) cc_final: 0.7914 (t) REVERT: C 768 MET cc_start: 0.8148 (mtp) cc_final: 0.7818 (ttm) REVERT: C 770 ILE cc_start: 0.8734 (mt) cc_final: 0.8474 (mm) REVERT: C 875 ASP cc_start: 0.8584 (p0) cc_final: 0.8243 (p0) REVERT: C 968 MET cc_start: 0.8955 (ttm) cc_final: 0.8539 (ttt) REVERT: D 46 ARG cc_start: 0.7631 (mtt90) cc_final: 0.7241 (mtm180) REVERT: D 57 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8382 (mt-10) REVERT: D 245 GLN cc_start: 0.8391 (mt0) cc_final: 0.8173 (tt0) REVERT: D 710 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8091 (mm-30) REVERT: D 730 LEU cc_start: 0.5725 (OUTLIER) cc_final: 0.5427 (mt) REVERT: D 748 CYS cc_start: 0.8252 (m) cc_final: 0.7908 (t) REVERT: D 768 MET cc_start: 0.8138 (mtp) cc_final: 0.7813 (ttm) REVERT: D 770 ILE cc_start: 0.8731 (mt) cc_final: 0.8470 (mm) REVERT: D 875 ASP cc_start: 0.8588 (p0) cc_final: 0.8249 (p0) REVERT: D 968 MET cc_start: 0.8954 (ttm) cc_final: 0.8538 (ttt) outliers start: 58 outliers final: 32 residues processed: 492 average time/residue: 0.8779 time to fit residues: 504.0323 Evaluate side-chains 508 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 464 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 1017 GLN Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain B residue 1017 GLN Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 710 GLU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 876 THR Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 710 GLU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 876 THR Chi-restraints excluded: chain D residue 1017 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 77 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 325 optimal weight: 6.9990 chunk 268 optimal weight: 0.0010 chunk 46 optimal weight: 5.9990 chunk 194 optimal weight: 20.0000 chunk 376 optimal weight: 20.0000 chunk 352 optimal weight: 9.9990 chunk 206 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 108 optimal weight: 0.9980 overall best weight: 4.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 583 ASN A 739 HIS A 761 GLN A 845 GLN A 863 GLN B 583 ASN B 739 HIS B 761 GLN B 845 GLN B 863 GLN C 583 ASN ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 761 GLN C 845 GLN C 863 GLN D 583 ASN D 739 HIS D 761 GLN D 845 GLN D 863 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.116356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.097217 restraints weight = 33711.463| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.13 r_work: 0.2921 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33632 Z= 0.120 Angle : 0.553 8.452 45888 Z= 0.293 Chirality : 0.045 0.135 4796 Planarity : 0.004 0.038 6056 Dihedral : 5.065 34.333 4456 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.47 % Allowed : 11.29 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.13), residues: 4052 helix: 0.25 (0.23), residues: 528 sheet: 1.27 (0.14), residues: 1368 loop : -0.12 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 336 TYR 0.019 0.002 TYR D 100 PHE 0.012 0.001 PHE B 747 TRP 0.035 0.002 TRP A 553 HIS 0.003 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (33632) covalent geometry : angle 0.55330 / 0.29 (45888) hydrogen bonds : bond 0.04019 / 2.66 ( 1113) hydrogen bonds : angle 4.97526 / 3.52 ( 3027) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 456 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7643 (mtt90) cc_final: 0.7259 (mtm180) REVERT: A 57 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8423 (mt-10) REVERT: A 245 GLN cc_start: 0.8375 (mt0) cc_final: 0.8161 (tt0) REVERT: A 667 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: A 710 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8041 (mm-30) REVERT: A 730 LEU cc_start: 0.5762 (OUTLIER) cc_final: 0.5494 (mt) REVERT: A 748 CYS cc_start: 0.8215 (m) cc_final: 0.7889 (t) REVERT: A 768 MET cc_start: 0.8117 (mtp) cc_final: 0.7837 (ttm) REVERT: A 875 ASP cc_start: 0.8556 (p0) cc_final: 0.8264 (p0) REVERT: A 968 MET cc_start: 0.8942 (ttm) cc_final: 0.8518 (ttt) REVERT: B 46 ARG cc_start: 0.7647 (mtt90) cc_final: 0.7256 (mtm180) REVERT: B 57 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8430 (mt-10) REVERT: B 245 GLN cc_start: 0.8380 (mt0) cc_final: 0.8162 (tt0) REVERT: B 667 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: B 710 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8053 (mm-30) REVERT: B 730 LEU cc_start: 0.5757 (OUTLIER) cc_final: 0.5488 (mt) REVERT: B 748 CYS cc_start: 0.8206 (m) cc_final: 0.7880 (t) REVERT: B 768 MET cc_start: 0.8122 (mtp) cc_final: 0.7836 (ttm) REVERT: B 875 ASP cc_start: 0.8554 (p0) cc_final: 0.8257 (p0) REVERT: B 968 MET cc_start: 0.8943 (ttm) cc_final: 0.8520 (ttt) REVERT: C 46 ARG cc_start: 0.7645 (mtt90) cc_final: 0.7253 (mtm180) REVERT: C 57 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8413 (mt-10) REVERT: C 245 GLN cc_start: 0.8381 (mt0) cc_final: 0.8164 (tt0) REVERT: C 667 GLU cc_start: 0.7999 (pt0) cc_final: 0.7764 (mp0) REVERT: C 710 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: C 730 LEU cc_start: 0.5752 (OUTLIER) cc_final: 0.5480 (mt) REVERT: C 748 CYS cc_start: 0.8233 (m) cc_final: 0.7903 (t) REVERT: C 768 MET cc_start: 0.8129 (mtp) cc_final: 0.7842 (ttm) REVERT: C 875 ASP cc_start: 0.8556 (p0) cc_final: 0.8259 (p0) REVERT: C 968 MET cc_start: 0.8940 (ttm) cc_final: 0.8515 (ttt) REVERT: D 46 ARG cc_start: 0.7643 (mtt90) cc_final: 0.7254 (mtm180) REVERT: D 57 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8424 (mt-10) REVERT: D 245 GLN cc_start: 0.8380 (mt0) cc_final: 0.8161 (tt0) REVERT: D 667 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: D 710 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8071 (mm-30) REVERT: D 730 LEU cc_start: 0.5752 (OUTLIER) cc_final: 0.5487 (mt) REVERT: D 748 CYS cc_start: 0.8216 (m) cc_final: 0.7892 (t) REVERT: D 768 MET cc_start: 0.8114 (mtp) cc_final: 0.7836 (ttm) REVERT: D 875 ASP cc_start: 0.8560 (p0) cc_final: 0.8263 (p0) REVERT: D 968 MET cc_start: 0.8944 (ttm) cc_final: 0.8518 (ttt) outliers start: 51 outliers final: 32 residues processed: 486 average time/residue: 0.8874 time to fit residues: 502.2081 Evaluate side-chains 506 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 459 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 1017 GLN Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain B residue 1017 GLN Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 710 GLU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 876 THR Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 667 GLU Chi-restraints excluded: chain D residue 710 GLU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 876 THR Chi-restraints excluded: chain D residue 1017 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 165 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 247 optimal weight: 30.0000 chunk 50 optimal weight: 9.9990 chunk 108 optimal weight: 30.0000 chunk 265 optimal weight: 1.9990 chunk 288 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 363 optimal weight: 8.9990 chunk 225 optimal weight: 30.0000 chunk 105 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 583 ASN A 739 HIS A 761 GLN A 863 GLN B 583 ASN B 739 HIS B 761 GLN B 863 GLN C 583 ASN ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 761 GLN C 863 GLN D 583 ASN D 739 HIS D 761 GLN D 863 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.115279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.096157 restraints weight = 33385.330| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.12 r_work: 0.2900 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 33632 Z= 0.164 Angle : 0.610 8.596 45888 Z= 0.324 Chirality : 0.047 0.144 4796 Planarity : 0.005 0.039 6056 Dihedral : 5.260 34.012 4456 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.70 % Allowed : 11.29 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.13), residues: 4052 helix: 0.34 (0.23), residues: 504 sheet: 1.10 (0.14), residues: 1416 loop : -0.10 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 336 TYR 0.022 0.002 TYR C 100 PHE 0.012 0.002 PHE C 747 TRP 0.033 0.002 TRP C 553 HIS 0.005 0.001 HIS C 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (33632) covalent geometry : angle 0.60994 / 0.32 (45888) hydrogen bonds : bond 0.04624 / 3.06 ( 1113) hydrogen bonds : angle 5.16142 / 3.65 ( 3027) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14390.74 seconds wall clock time: 245 minutes 10.88 seconds (14710.88 seconds total)