Starting phenix.real_space_refine on Mon Jul 6 08:52:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zyy_15028/07_2026/7zyy_15028.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zyy_15028/07_2026/7zyy_15028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zyy_15028/07_2026/7zyy_15028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zyy_15028/07_2026/7zyy_15028.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7zyy_15028/07_2026/7zyy_15028.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zyy_15028/07_2026/7zyy_15028.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zyy_15028/07_2026/7zyy_15028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zyy_15028/07_2026/7zyy_15028.map" } resolution = 2.12 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= 0.004 sd= 0.030 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: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 20 5.49 5 Mg 8 5.21 5 S 128 5.16 5 C 21228 2.51 5 N 5800 2.21 5 O 6736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33924 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8309 Classifications: {'peptide': 1056} Link IDs: {'PCIS': 3, 'PTRANS': 42, 'TRANS': 1010} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 8309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8309 Classifications: {'peptide': 1056} Link IDs: {'PCIS': 3, 'PTRANS': 42, 'TRANS': 1010} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 8309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8309 Classifications: {'peptide': 1056} Link IDs: {'PCIS': 3, 'PTRANS': 42, 'TRANS': 1010} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 8309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8309 Classifications: {'peptide': 1056} Link IDs: {'PCIS': 3, 'PTRANS': 42, 'TRANS': 1010} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 91 Unusual residues: {' MG': 2, ' MN': 1, 'ACO': 1, 'ADP': 1, 'BCT': 1, 'PYR': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 91 Unusual residues: {' MG': 2, ' MN': 1, 'ACO': 1, 'ADP': 1, 'BCT': 1, 'PYR': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 91 Unusual residues: {' MG': 2, ' MN': 1, 'ACO': 1, 'ADP': 1, 'BCT': 1, 'PYR': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 91 Unusual residues: {' MG': 2, ' MN': 1, 'ACO': 1, 'ADP': 1, 'BCT': 1, 'PYR': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "B" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 155 Classifications: {'water': 155} Link IDs: {None: 154} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Time building chain proxies: 6.88, per 1000 atoms: 0.20 Number of scatterers: 33924 At special positions: 0 Unit cell: (181.26, 157.94, 122.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 128 16.00 P 20 15.00 Mg 8 11.99 O 6736 8.00 N 5800 7.00 C 21228 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: 2.94 Conformation dependent library (CDL) restraints added in 1.3 seconds 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7768 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 28 sheets defined 50.1% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 9 through 23 removed outlier: 3.525A pdb=" N ALA A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 36 Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.084A pdb=" N PHE A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 63 through 73 Processing helix chain 'A' and resid 88 through 98 Processing helix chain 'A' and resid 106 through 115 removed outlier: 3.679A pdb=" N ASP A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 172 through 192 Processing helix chain 'A' and resid 247 through 266 Processing helix chain 'A' and resid 294 through 303 removed outlier: 4.110A pdb=" N THR A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 315 Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.962A pdb=" N GLY A 350 " --> pdb=" O PRO A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 414 Processing helix chain 'A' and resid 422 through 432 Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 459 through 475 Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 511 through 521 Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 545 through 551 removed outlier: 3.805A pdb=" N GLY A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 560 Processing helix chain 'A' and resid 572 through 580 removed outlier: 3.737A pdb=" N TYR A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 596 Processing helix chain 'A' and resid 617 through 632 Processing helix chain 'A' and resid 645 through 658 removed outlier: 4.544A pdb=" N LYS A 650 " --> pdb=" O PRO A 646 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER A 651 " --> pdb=" O GLN A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.567A pdb=" N THR A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 725 Processing helix chain 'A' and resid 739 through 751 Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 770 through 778 removed outlier: 3.606A pdb=" N LEU A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 804 removed outlier: 3.657A pdb=" N HIS A 797 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A 798 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS A 804 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 810 Proline residue: A 808 - end of helix No H-bonds generated for 'chain 'A' and resid 805 through 810' Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'A' and resid 826 through 839 Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 845 through 860 Processing helix chain 'A' and resid 868 through 883 removed outlier: 3.658A pdb=" N VAL A 872 " --> pdb=" O PRO A 868 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 873 " --> pdb=" O SER A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 893 Processing helix chain 'A' and resid 894 through 897 Processing helix chain 'A' and resid 900 through 908 Processing helix chain 'A' and resid 921 through 927 Processing helix chain 'A' and resid 945 through 957 Processing helix chain 'A' and resid 962 through 972 Processing helix chain 'A' and resid 972 through 987 Processing helix chain 'A' and resid 988 through 992 Processing helix chain 'A' and resid 993 through 1000 Processing helix chain 'B' and resid 9 through 23 removed outlier: 3.611A pdb=" N ALA B 13 " --> pdb=" O ARG B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 36 Processing helix chain 'B' and resid 38 through 43 removed outlier: 4.150A pdb=" N PHE B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 62 through 73 Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 106 through 115 removed outlier: 3.772A pdb=" N ASP B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 126 Processing helix chain 'B' and resid 139 through 150 Processing helix chain 'B' and resid 172 through 192 Processing helix chain 'B' and resid 247 through 266 Processing helix chain 'B' and resid 294 through 303 removed outlier: 4.004A pdb=" N THR B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 315 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.949A pdb=" N GLY B 350 " --> pdb=" O PRO B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 414 Processing helix chain 'B' and resid 422 through 432 Processing helix chain 'B' and resid 432 through 437 Processing helix chain 'B' and resid 448 through 453 removed outlier: 3.651A pdb=" N ASN B 453 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 475 Processing helix chain 'B' and resid 502 through 510 Processing helix chain 'B' and resid 511 through 521 Processing helix chain 'B' and resid 533 through 540 Processing helix chain 'B' and resid 545 through 560 removed outlier: 3.925A pdb=" N GLY B 551 " --> pdb=" O GLN B 547 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE B 552 " --> pdb=" O ASP B 548 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLN B 554 " --> pdb=" O LYS B 550 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ALA B 555 " --> pdb=" O GLY B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 580 removed outlier: 3.684A pdb=" N TYR B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 596 Processing helix chain 'B' and resid 617 through 632 Processing helix chain 'B' and resid 645 through 658 removed outlier: 4.881A pdb=" N LYS B 650 " --> pdb=" O PRO B 646 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N SER B 651 " --> pdb=" O GLN B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 695 removed outlier: 3.533A pdb=" N THR B 695 " --> pdb=" O GLU B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 725 Processing helix chain 'B' and resid 739 through 751 Processing helix chain 'B' and resid 759 through 763 Processing helix chain 'B' and resid 770 through 778 Processing helix chain 'B' and resid 788 through 804 removed outlier: 3.784A pdb=" N TYR B 798 " --> pdb=" O GLN B 794 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 804 " --> pdb=" O GLU B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 810 Proline residue: B 808 - end of helix No H-bonds generated for 'chain 'B' and resid 805 through 810' Processing helix chain 'B' and resid 819 through 824 Processing helix chain 'B' and resid 826 through 840 removed outlier: 3.757A pdb=" N VAL B 840 " --> pdb=" O GLN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 844 No H-bonds generated for 'chain 'B' and resid 842 through 844' Processing helix chain 'B' and resid 845 through 860 Processing helix chain 'B' and resid 868 through 883 Processing helix chain 'B' and resid 886 through 894 Processing helix chain 'B' and resid 900 through 908 Processing helix chain 'B' and resid 919 through 927 Processing helix chain 'B' and resid 945 through 957 Processing helix chain 'B' and resid 962 through 972 Processing helix chain 'B' and resid 972 through 987 Processing helix chain 'B' and resid 988 through 992 Processing helix chain 'B' and resid 993 through 1000 Processing helix chain 'C' and resid 9 through 23 removed outlier: 3.599A pdb=" N ALA C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 36 Processing helix chain 'C' and resid 38 through 43 removed outlier: 4.067A pdb=" N PHE C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 62 through 73 Processing helix chain 'C' and resid 88 through 98 Processing helix chain 'C' and resid 106 through 115 removed outlier: 3.899A pdb=" N ASP C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 172 through 191 Processing helix chain 'C' and resid 247 through 266 Processing helix chain 'C' and resid 294 through 303 removed outlier: 4.119A pdb=" N THR C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 315 Processing helix chain 'C' and resid 327 through 331 Processing helix chain 'C' and resid 346 through 350 removed outlier: 4.005A pdb=" N GLY C 350 " --> pdb=" O PRO C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 414 Processing helix chain 'C' and resid 422 through 432 Processing helix chain 'C' and resid 432 through 437 Processing helix chain 'C' and resid 448 through 453 removed outlier: 3.624A pdb=" N ASN C 453 " --> pdb=" O SER C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 475 Processing helix chain 'C' and resid 502 through 510 Processing helix chain 'C' and resid 511 through 521 Processing helix chain 'C' and resid 533 through 540 Processing helix chain 'C' and resid 545 through 550 Processing helix chain 'C' and resid 552 through 560 Processing helix chain 'C' and resid 572 through 580 removed outlier: 3.763A pdb=" N TYR C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 596 Processing helix chain 'C' and resid 617 through 632 Processing helix chain 'C' and resid 645 through 658 removed outlier: 4.675A pdb=" N LYS C 650 " --> pdb=" O PRO C 646 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N SER C 651 " --> pdb=" O GLN C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 695 removed outlier: 3.521A pdb=" N THR C 695 " --> pdb=" O GLU C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 723 Processing helix chain 'C' and resid 739 through 751 Processing helix chain 'C' and resid 759 through 763 Processing helix chain 'C' and resid 770 through 778 Processing helix chain 'C' and resid 788 through 804 removed outlier: 3.770A pdb=" N HIS C 797 " --> pdb=" O GLU C 793 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR C 798 " --> pdb=" O GLN C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 810 Proline residue: C 808 - end of helix No H-bonds generated for 'chain 'C' and resid 805 through 810' Processing helix chain 'C' and resid 819 through 824 Processing helix chain 'C' and resid 826 through 840 Processing helix chain 'C' and resid 842 through 844 No H-bonds generated for 'chain 'C' and resid 842 through 844' Processing helix chain 'C' and resid 845 through 860 Processing helix chain 'C' and resid 868 through 883 removed outlier: 3.649A pdb=" N VAL C 872 " --> pdb=" O PRO C 868 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 873 " --> pdb=" O SER C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 893 Processing helix chain 'C' and resid 894 through 896 No H-bonds generated for 'chain 'C' and resid 894 through 896' Processing helix chain 'C' and resid 900 through 908 Processing helix chain 'C' and resid 919 through 928 Processing helix chain 'C' and resid 945 through 958 Processing helix chain 'C' and resid 962 through 972 Processing helix chain 'C' and resid 972 through 987 Processing helix chain 'C' and resid 988 through 992 Processing helix chain 'C' and resid 993 through 1000 Processing helix chain 'D' and resid 9 through 23 removed outlier: 3.596A pdb=" N ALA D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 36 Processing helix chain 'D' and resid 38 through 43 removed outlier: 4.043A pdb=" N PHE D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 62 through 73 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 106 through 114 Processing helix chain 'D' and resid 115 through 126 Processing helix chain 'D' and resid 139 through 150 Processing helix chain 'D' and resid 172 through 191 Processing helix chain 'D' and resid 247 through 265 Processing helix chain 'D' and resid 294 through 303 removed outlier: 4.018A pdb=" N THR D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 315 Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 346 through 350 removed outlier: 3.925A pdb=" N GLY D 350 " --> pdb=" O PRO D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 414 Processing helix chain 'D' and resid 422 through 432 Processing helix chain 'D' and resid 432 through 438 Processing helix chain 'D' and resid 448 through 453 Processing helix chain 'D' and resid 459 through 475 Processing helix chain 'D' and resid 502 through 510 Processing helix chain 'D' and resid 511 through 521 Processing helix chain 'D' and resid 533 through 540 Processing helix chain 'D' and resid 545 through 560 removed outlier: 3.991A pdb=" N ILE D 552 " --> pdb=" O ASP D 548 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN D 554 " --> pdb=" O LYS D 550 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ALA D 555 " --> pdb=" O GLY D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 580 removed outlier: 3.808A pdb=" N TYR D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 596 Processing helix chain 'D' and resid 617 through 632 Processing helix chain 'D' and resid 645 through 658 removed outlier: 4.724A pdb=" N LYS D 650 " --> pdb=" O PRO D 646 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N SER D 651 " --> pdb=" O GLN D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 695 removed outlier: 3.574A pdb=" N THR D 695 " --> pdb=" O GLU D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 723 Processing helix chain 'D' and resid 739 through 751 Processing helix chain 'D' and resid 759 through 763 Processing helix chain 'D' and resid 770 through 778 Processing helix chain 'D' and resid 788 through 804 removed outlier: 3.631A pdb=" N HIS D 797 " --> pdb=" O GLU D 793 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR D 798 " --> pdb=" O GLN D 794 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS D 804 " --> pdb=" O GLU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 805 through 810 Proline residue: D 808 - end of helix No H-bonds generated for 'chain 'D' and resid 805 through 810' Processing helix chain 'D' and resid 819 through 824 Processing helix chain 'D' and resid 826 through 840 Processing helix chain 'D' and resid 842 through 844 No H-bonds generated for 'chain 'D' and resid 842 through 844' Processing helix chain 'D' and resid 845 through 860 Processing helix chain 'D' and resid 868 through 883 removed outlier: 3.697A pdb=" N VAL D 872 " --> pdb=" O PRO D 868 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL D 873 " --> pdb=" O SER D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 893 Processing helix chain 'D' and resid 894 through 896 No H-bonds generated for 'chain 'D' and resid 894 through 896' Processing helix chain 'D' and resid 900 through 908 Processing helix chain 'D' and resid 921 through 927 Processing helix chain 'D' and resid 945 through 957 Processing helix chain 'D' and resid 962 through 972 Processing helix chain 'D' and resid 972 through 987 Processing helix chain 'D' and resid 988 through 992 Processing helix chain 'D' and resid 993 through 1000 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 49 removed outlier: 4.130A pdb=" N VAL A 30 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS A 3 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N HIS A 79 " --> pdb=" O LYS A 3 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A 5 " --> pdb=" O HIS A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 170 removed outlier: 3.721A pdb=" N VAL A 154 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 281 through 288 removed outlier: 5.548A pdb=" N PHE A 282 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LYS A 278 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N PHE A 284 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU A 276 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 286 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N HIS A 207 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N HIS A 224 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU A 213 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N HIS A 222 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER A 229 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE A 238 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN A 231 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS A 236 " --> pdb=" O GLN A 231 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL A 237 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG A 341 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER A 336 " --> pdb=" O PHE A 396 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE A 396 " --> pdb=" O SER A 336 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 338 " --> pdb=" O CYS A 394 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N CYS A 394 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N CYS A 340 " --> pdb=" O LYS A 392 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS A 392 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE A 342 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AA5, first strand: chain 'A' and resid 360 through 362 Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 529 removed outlier: 6.767A pdb=" N LEU A 527 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLU A 567 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASP A 529 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TRP A 569 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA A 566 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N LEU A 604 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N MET A 568 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE A 636 " --> pdb=" O GLU A 663 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR A 665 " --> pdb=" O PHE A 636 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE A 638 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N CYS A 667 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA A 662 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ALA A 701 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA A 664 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N KCX A 703 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE A 666 " --> pdb=" O KCX A 703 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 526 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL A 757 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N THR A 528 " --> pdb=" O VAL A 757 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1006 through 1012 removed outlier: 6.851A pdb=" N LYS A1015 " --> pdb=" O ILE A1011 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU A1021 " --> pdb=" O ASN A1038 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN A1038 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 49 removed outlier: 4.031A pdb=" N VAL B 30 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS B 3 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N HIS B 79 " --> pdb=" O LYS B 3 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU B 5 " --> pdb=" O HIS B 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 167 through 170 Processing sheet with id=AB1, first strand: chain 'B' and resid 282 through 288 removed outlier: 5.654A pdb=" N PHE B 284 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU B 276 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU B 286 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N HIS B 207 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N HIS B 224 " --> pdb=" O GLN B 211 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU B 213 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N HIS B 222 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER B 229 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE B 238 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLN B 231 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS B 236 " --> pdb=" O GLN B 231 " (cutoff:3.500A) removed outlier: 15.395A pdb=" N GLN B 235 " --> pdb=" O THR B 343 " (cutoff:3.500A) removed outlier: 12.066A pdb=" N THR B 343 " --> pdb=" O GLN B 235 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL B 237 " --> pdb=" O ARG B 341 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG B 341 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER B 336 " --> pdb=" O PHE B 396 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE B 396 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE B 338 " --> pdb=" O CYS B 394 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS B 394 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N CYS B 340 " --> pdb=" O LYS B 392 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS B 392 " --> pdb=" O CYS B 340 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE B 342 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 356 through 357 Processing sheet with id=AB3, first strand: chain 'B' and resid 360 through 362 Processing sheet with id=AB4, first strand: chain 'B' and resid 526 through 529 removed outlier: 6.787A pdb=" N LEU B 527 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLU B 567 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP B 529 " --> pdb=" O GLU B 567 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N TRP B 569 " --> pdb=" O ASP B 529 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA B 566 " --> pdb=" O GLN B 602 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N LEU B 604 " --> pdb=" O ALA B 566 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N MET B 568 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE B 636 " --> pdb=" O GLU B 663 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR B 665 " --> pdb=" O PHE B 636 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE B 638 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N CYS B 667 " --> pdb=" O ILE B 638 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N THR B 733 " --> pdb=" O ASP B 756 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 526 " --> pdb=" O ILE B 755 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B 757 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR B 528 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1006 through 1012 removed outlier: 7.067A pdb=" N LYS B1015 " --> pdb=" O ILE B1011 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LEU B1021 " --> pdb=" O ASN B1038 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN B1038 " --> pdb=" O LEU B1021 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 46 through 49 removed outlier: 4.045A pdb=" N VAL C 30 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS C 3 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N HIS C 79 " --> pdb=" O LYS C 3 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU C 5 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 167 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 281 through 288 removed outlier: 5.357A pdb=" N PHE C 282 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LYS C 278 " --> pdb=" O PHE C 282 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N PHE C 284 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LEU C 276 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU C 286 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N HIS C 207 " --> pdb=" O CYS C 228 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N HIS C 224 " --> pdb=" O GLN C 211 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU C 213 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N HIS C 222 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N SER C 229 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE C 238 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN C 231 " --> pdb=" O LYS C 236 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS C 236 " --> pdb=" O GLN C 231 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL C 237 " --> pdb=" O ARG C 341 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG C 341 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N SER C 336 " --> pdb=" O PHE C 396 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE C 396 " --> pdb=" O SER C 336 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE C 338 " --> pdb=" O CYS C 394 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N CYS C 394 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS C 340 " --> pdb=" O LYS C 392 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS C 392 " --> pdb=" O CYS C 340 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE C 342 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 356 through 357 Processing sheet with id=AC1, first strand: chain 'C' and resid 360 through 362 removed outlier: 3.522A pdb=" N THR C 360 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 526 through 529 removed outlier: 6.789A pdb=" N LEU C 527 " --> pdb=" O SER C 565 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N GLU C 567 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP C 529 " --> pdb=" O GLU C 567 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TRP C 569 " --> pdb=" O ASP C 529 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA C 566 " --> pdb=" O GLN C 602 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N LEU C 604 " --> pdb=" O ALA C 566 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N MET C 568 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE C 636 " --> pdb=" O GLU C 663 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR C 665 " --> pdb=" O PHE C 636 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE C 638 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N CYS C 667 " --> pdb=" O ILE C 638 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA C 662 " --> pdb=" O ILE C 699 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ALA C 701 " --> pdb=" O ALA C 662 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA C 664 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N KCX C 703 " --> pdb=" O ALA C 664 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE C 666 " --> pdb=" O KCX C 703 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N THR C 733 " --> pdb=" O ASP C 756 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU C 526 " --> pdb=" O ILE C 755 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL C 757 " --> pdb=" O LEU C 526 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N THR C 528 " --> pdb=" O VAL C 757 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1006 through 1012 removed outlier: 6.754A pdb=" N LYS C1015 " --> pdb=" O ILE C1011 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU C1021 " --> pdb=" O ASN C1038 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN C1038 " --> pdb=" O LEU C1021 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 46 through 49 removed outlier: 4.043A pdb=" N VAL D 30 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS D 3 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N HIS D 79 " --> pdb=" O LYS D 3 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU D 5 " --> pdb=" O HIS D 79 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 167 through 170 removed outlier: 3.664A pdb=" N ALA D 170 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL D 154 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 282 through 288 removed outlier: 5.791A pdb=" N PHE D 284 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU D 276 " --> pdb=" O PHE D 284 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU D 286 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N HIS D 207 " --> pdb=" O CYS D 228 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N HIS D 224 " --> pdb=" O GLN D 211 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU D 213 " --> pdb=" O HIS D 222 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N HIS D 222 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER D 229 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE D 238 " --> pdb=" O SER D 229 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN D 231 " --> pdb=" O LYS D 236 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS D 236 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 15.324A pdb=" N GLN D 235 " --> pdb=" O THR D 343 " (cutoff:3.500A) removed outlier: 11.965A pdb=" N THR D 343 " --> pdb=" O GLN D 235 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL D 237 " --> pdb=" O ARG D 341 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG D 341 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER D 336 " --> pdb=" O PHE D 396 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE D 396 " --> pdb=" O SER D 336 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE D 338 " --> pdb=" O CYS D 394 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS D 394 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N CYS D 340 " --> pdb=" O LYS D 392 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS D 392 " --> pdb=" O CYS D 340 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE D 342 " --> pdb=" O LEU D 390 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 356 through 357 Processing sheet with id=AC8, first strand: chain 'D' and resid 360 through 362 Processing sheet with id=AC9, first strand: chain 'D' and resid 526 through 529 removed outlier: 6.765A pdb=" N LEU D 527 " --> pdb=" O SER D 565 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLU D 567 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASP D 529 " --> pdb=" O GLU D 567 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N TRP D 569 " --> pdb=" O ASP D 529 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA D 566 " --> pdb=" O GLN D 602 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU D 604 " --> pdb=" O ALA D 566 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N MET D 568 " --> pdb=" O LEU D 604 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE D 601 " --> pdb=" O VAL D 635 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ARG D 637 " --> pdb=" O PHE D 601 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N MET D 603 " --> pdb=" O ARG D 637 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE D 636 " --> pdb=" O GLU D 663 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR D 665 " --> pdb=" O PHE D 636 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE D 638 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N CYS D 667 " --> pdb=" O ILE D 638 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA D 662 " --> pdb=" O ILE D 699 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ALA D 701 " --> pdb=" O ALA D 662 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA D 664 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N KCX D 703 " --> pdb=" O ALA D 664 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE D 666 " --> pdb=" O KCX D 703 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU D 526 " --> pdb=" O ILE D 755 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL D 757 " --> pdb=" O LEU D 526 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N THR D 528 " --> pdb=" O VAL D 757 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 1006 through 1012 removed outlier: 6.816A pdb=" N LYS D1015 " --> pdb=" O ILE D1011 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU D1021 " --> pdb=" O ASN D1038 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASN D1038 " --> pdb=" O LEU D1021 " (cutoff:3.500A) 1590 hydrogen bonds defined for protein. 4521 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.12 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5781 1.31 - 1.44: 8736 1.44 - 1.57: 19490 1.57 - 1.70: 33 1.70 - 1.83: 228 Bond restraints: 34268 Sorted by residual: bond pdb=" C5A ACO C1205 " pdb=" N7A ACO C1205 " ideal model delta sigma weight residual 1.387 1.516 -0.129 1.00e-02 1.00e+04 1.66e+02 bond pdb=" C5A ACO A1205 " pdb=" N7A ACO A1205 " ideal model delta sigma weight residual 1.387 1.516 -0.129 1.00e-02 1.00e+04 1.66e+02 bond pdb=" C5A ACO D1205 " pdb=" N7A ACO D1205 " ideal model delta sigma weight residual 1.387 1.515 -0.128 1.00e-02 1.00e+04 1.64e+02 bond pdb=" C5A ACO B1205 " pdb=" N7A ACO B1205 " ideal model delta sigma weight residual 1.387 1.514 -0.127 1.00e-02 1.00e+04 1.61e+02 bond pdb=" C6A ACO C1205 " pdb=" N6A ACO C1205 " ideal model delta sigma weight residual 1.337 1.449 -0.112 1.00e-02 1.00e+04 1.25e+02 ... (remaining 34263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 45981 3.65 - 7.30: 329 7.30 - 10.96: 74 10.96 - 14.61: 20 14.61 - 18.26: 8 Bond angle restraints: 46412 Sorted by residual: angle pdb=" C4A ACO C1205 " pdb=" N9A ACO C1205 " pdb=" C8A ACO C1205 " ideal model delta sigma weight residual 105.72 122.44 -16.72 1.00e+00 1.00e+00 2.80e+02 angle pdb=" C4A ACO B1205 " pdb=" N9A ACO B1205 " pdb=" C8A ACO B1205 " ideal model delta sigma weight residual 105.72 122.35 -16.63 1.00e+00 1.00e+00 2.76e+02 angle pdb=" C4A ACO D1205 " pdb=" N9A ACO D1205 " pdb=" C8A ACO D1205 " ideal model delta sigma weight residual 105.72 122.29 -16.57 1.00e+00 1.00e+00 2.74e+02 angle pdb=" C4A ACO A1205 " pdb=" N9A ACO A1205 " pdb=" C8A ACO A1205 " ideal model delta sigma weight residual 105.72 122.27 -16.55 1.00e+00 1.00e+00 2.74e+02 angle pdb=" P1A ACO A1205 " pdb=" O3A ACO A1205 " pdb=" P2A ACO A1205 " ideal model delta sigma weight residual 136.83 124.34 12.49 1.00e+00 1.00e+00 1.56e+02 ... (remaining 46407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.62: 19729 34.62 - 69.23: 713 69.23 - 103.84: 73 103.84 - 138.46: 3 138.46 - 173.07: 2 Dihedral angle restraints: 20520 sinusoidal: 8368 harmonic: 12152 Sorted by residual: dihedral pdb=" C5' ADP C1203 " pdb=" O5' ADP C1203 " pdb=" PA ADP C1203 " pdb=" O2A ADP C1203 " ideal model delta sinusoidal sigma weight residual 300.00 126.93 173.07 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O1B ADP A1203 " pdb=" O3A ADP A1203 " pdb=" PB ADP A1203 " pdb=" PA ADP A1203 " ideal model delta sinusoidal sigma weight residual -60.00 80.20 -140.20 1 2.00e+01 2.50e-03 4.24e+01 dihedral pdb=" O2A ADP A1203 " pdb=" O3A ADP A1203 " pdb=" PA ADP A1203 " pdb=" PB ADP A1203 " ideal model delta sinusoidal sigma weight residual -60.00 57.16 -117.16 1 2.00e+01 2.50e-03 3.50e+01 ... (remaining 20517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 4156 0.062 - 0.123: 861 0.123 - 0.185: 62 0.185 - 0.246: 14 0.246 - 0.308: 7 Chirality restraints: 5100 Sorted by residual: chirality pdb=" CG LEU D 833 " pdb=" CB LEU D 833 " pdb=" CD1 LEU D 833 " pdb=" CD2 LEU D 833 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C2B ACO D1205 " pdb=" C1B ACO D1205 " pdb=" C3B ACO D1205 " pdb=" O2B ACO D1205 " both_signs ideal model delta sigma weight residual False -2.72 -2.46 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C2B ACO A1205 " pdb=" C1B ACO A1205 " pdb=" C3B ACO A1205 " pdb=" O2B ACO A1205 " both_signs ideal model delta sigma weight residual False -2.72 -2.46 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 5097 not shown) Planarity restraints: 6072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 186 " -0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" CD GLU C 186 " 0.060 2.00e-02 2.50e+03 pdb=" OE1 GLU C 186 " -0.022 2.00e-02 2.50e+03 pdb=" OE2 GLU C 186 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C BCT B1207 " 0.058 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" O1 BCT B1207 " -0.022 2.00e-02 2.50e+03 pdb=" O2 BCT B1207 " -0.022 2.00e-02 2.50e+03 pdb=" O3 BCT B1207 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C BCT D1207 " -0.057 2.00e-02 2.50e+03 3.32e-02 1.11e+01 pdb=" O1 BCT D1207 " 0.022 2.00e-02 2.50e+03 pdb=" O2 BCT D1207 " 0.021 2.00e-02 2.50e+03 pdb=" O3 BCT D1207 " 0.014 2.00e-02 2.50e+03 ... (remaining 6069 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 450 2.59 - 3.16: 27842 3.16 - 3.74: 59911 3.74 - 4.32: 83351 4.32 - 4.90: 133289 Nonbonded interactions: 304843 Sorted by model distance: nonbonded pdb=" O2A ADP D1203 " pdb="MG MG D1204 " model vdw 2.008 2.170 nonbonded pdb=" O2A ADP C1203 " pdb="MG MG C1204 " model vdw 2.012 2.170 nonbonded pdb=" O2B ADP D1203 " pdb="MG MG D1204 " model vdw 2.025 2.170 nonbonded pdb=" OE1 GLU D 274 " pdb="MG MG D1204 " model vdw 2.041 2.170 nonbonded pdb=" OE1 GLU C 274 " pdb="MG MG C1204 " model vdw 2.057 2.170 ... (remaining 304838 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: 0.04 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: 2.180 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: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 30.210 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 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 : 0.007 0.199 34268 Z= 0.436 Angle : 0.887 18.260 46412 Z= 0.513 Chirality : 0.049 0.308 5100 Planarity : 0.005 0.064 6072 Dihedral : 17.240 173.074 12752 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.19 % Allowed : 16.87 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.12), residues: 4204 helix: -0.07 (0.11), residues: 1892 sheet: -0.51 (0.19), residues: 744 loop : -0.61 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 845 TYR 0.019 0.002 TYR C 613 PHE 0.037 0.002 PHE B 191 TRP 0.010 0.002 TRP B 799 HIS 0.007 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.44 (34268) covalent geometry : angle 0.88712 / 0.51 (46412) hydrogen bonds : bond 0.15749 / 10.58 ( 1590) hydrogen bonds : angle 7.47243 / 5.28 ( 4521) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 35 residues processed: 205 average time/residue: 0.6758 time to fit residues: 165.2445 Evaluate side-chains 202 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 569 TRP Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 569 TRP Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 967 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 691 GLU Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 948 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 GLN B 883 ASN B 955 GLN C 505 ASN D 269 ASN D 882 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.074965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.061275 restraints weight = 85516.823| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.34 r_work: 0.3238 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 34268 Z= 0.181 Angle : 0.590 14.301 46412 Z= 0.305 Chirality : 0.044 0.202 5100 Planarity : 0.004 0.055 6072 Dihedral : 8.689 177.302 4787 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.90 % Allowed : 15.46 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.13), residues: 4204 helix: 0.77 (0.12), residues: 1892 sheet: -0.56 (0.18), residues: 716 loop : -0.24 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 845 TYR 0.012 0.001 TYR B 685 PHE 0.013 0.002 PHE C 146 TRP 0.007 0.001 TRP C 799 HIS 0.005 0.001 HIS B 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (34268) covalent geometry : angle 0.58976 / 0.31 (46412) hydrogen bonds : bond 0.04958 / 3.31 ( 1590) hydrogen bonds : angle 5.80332 / 4.12 ( 4521) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 174 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.7076 (p0) REVERT: B 334 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7847 (mt) REVERT: B 650 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7222 (mtmm) REVERT: B 891 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.6992 (t80) outliers start: 67 outliers final: 25 residues processed: 230 average time/residue: 0.6785 time to fit residues: 186.3088 Evaluate side-chains 192 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 569 TRP Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 891 TYR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 569 TRP Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 691 GLU Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 920 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 346 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 371 optimal weight: 7.9990 chunk 318 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 387 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 183 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 784 HIS B 832 ASN C 505 ASN D 269 ASN D 492 GLN D 609 ASN D 882 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.074949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.061263 restraints weight = 85389.912| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.35 r_work: 0.3237 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 34268 Z= 0.167 Angle : 0.573 13.550 46412 Z= 0.293 Chirality : 0.044 0.199 5100 Planarity : 0.004 0.057 6072 Dihedral : 8.332 169.376 4765 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.18 % Allowed : 15.15 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.13), residues: 4204 helix: 1.09 (0.12), residues: 1888 sheet: -0.60 (0.18), residues: 716 loop : -0.22 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 182 TYR 0.012 0.001 TYR B 685 PHE 0.017 0.001 PHE B 191 TRP 0.005 0.001 TRP C 586 HIS 0.005 0.001 HIS B 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (34268) covalent geometry : angle 0.57251 / 0.29 (46412) hydrogen bonds : bond 0.04589 / 3.07 ( 1590) hydrogen bonds : angle 5.55151 / 3.94 ( 4521) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 171 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7089 (p0) REVERT: B 334 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7889 (mt) REVERT: B 650 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7226 (mtmm) REVERT: B 854 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7762 (ttt180) REVERT: B 891 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.6939 (t80) REVERT: C 173 ASP cc_start: 0.7263 (m-30) cc_final: 0.6955 (m-30) REVERT: D 414 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8091 (t80) outliers start: 77 outliers final: 33 residues processed: 232 average time/residue: 0.6736 time to fit residues: 186.1152 Evaluate side-chains 197 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 569 TRP Chi-restraints excluded: chain B residue 600 MET Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 854 ARG Chi-restraints excluded: chain B residue 891 TYR Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 569 TRP Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 691 GLU Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 932 VAL Chi-restraints excluded: chain D residue 1029 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 419 optimal weight: 8.9990 chunk 366 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 373 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 300 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 832 ASN D 269 ASN D 882 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.075484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.061963 restraints weight = 84884.202| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.45 r_work: 0.3243 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 34268 Z= 0.135 Angle : 0.543 13.179 46412 Z= 0.276 Chirality : 0.043 0.197 5100 Planarity : 0.003 0.057 6072 Dihedral : 8.128 159.052 4762 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.18 % Allowed : 15.06 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.13), residues: 4204 helix: 1.24 (0.12), residues: 1900 sheet: -0.56 (0.18), residues: 708 loop : -0.16 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 171 TYR 0.010 0.001 TYR A 853 PHE 0.019 0.001 PHE B 191 TRP 0.005 0.001 TRP B 644 HIS 0.005 0.001 HIS C 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (34268) covalent geometry : angle 0.54277 / 0.28 (46412) hydrogen bonds : bond 0.04116 / 2.76 ( 1590) hydrogen bonds : angle 5.35065 / 3.80 ( 4521) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 166 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.7082 (p0) REVERT: B 334 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7937 (mt) REVERT: B 650 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7239 (mtmm) REVERT: B 854 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7751 (ttt180) REVERT: B 891 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.6893 (t80) REVERT: D 414 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8087 (t80) outliers start: 77 outliers final: 35 residues processed: 228 average time/residue: 0.6436 time to fit residues: 176.6463 Evaluate side-chains 195 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 569 TRP Chi-restraints excluded: chain B residue 600 MET Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 854 ARG Chi-restraints excluded: chain B residue 891 TYR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 569 TRP Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 891 TYR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 691 GLU Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 932 VAL Chi-restraints excluded: chain D residue 1029 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 250 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 324 optimal weight: 4.9990 chunk 330 optimal weight: 20.0000 chunk 314 optimal weight: 10.0000 chunk 417 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 340 optimal weight: 9.9990 chunk 134 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 832 ASN B 882 GLN C 832 ASN D 269 ASN D 882 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.075641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.061560 restraints weight = 85061.015| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.42 r_work: 0.3237 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34268 Z= 0.142 Angle : 0.553 12.969 46412 Z= 0.280 Chirality : 0.043 0.196 5100 Planarity : 0.003 0.057 6072 Dihedral : 8.048 156.449 4758 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.27 % Allowed : 15.01 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.13), residues: 4204 helix: 1.29 (0.12), residues: 1904 sheet: -0.49 (0.18), residues: 692 loop : -0.15 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 845 TYR 0.011 0.001 TYR B 685 PHE 0.020 0.001 PHE B 191 TRP 0.005 0.001 TRP C 799 HIS 0.005 0.001 HIS B 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (34268) covalent geometry : angle 0.55297 / 0.28 (46412) hydrogen bonds : bond 0.04139 / 2.78 ( 1590) hydrogen bonds : angle 5.30540 / 3.77 ( 4521) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 164 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.7048 (p0) REVERT: B 334 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7954 (mt) REVERT: B 433 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7219 (pm20) REVERT: B 650 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7269 (mtmm) REVERT: B 854 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7824 (ttt180) REVERT: B 891 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.6900 (t80) REVERT: D 414 PHE cc_start: 0.9319 (OUTLIER) cc_final: 0.8082 (t80) outliers start: 80 outliers final: 40 residues processed: 232 average time/residue: 0.6654 time to fit residues: 184.7757 Evaluate side-chains 205 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 569 TRP Chi-restraints excluded: chain B residue 600 MET Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 854 ARG Chi-restraints excluded: chain B residue 891 TYR Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 569 TRP Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 849 ILE Chi-restraints excluded: chain C residue 891 TYR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 932 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 234 optimal weight: 10.0000 chunk 341 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 294 optimal weight: 0.5980 chunk 219 optimal weight: 0.9990 chunk 306 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 330 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 369 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 269 ASN D 882 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.076010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.061979 restraints weight = 84580.910| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.42 r_work: 0.3248 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34268 Z= 0.125 Angle : 0.539 12.772 46412 Z= 0.272 Chirality : 0.043 0.195 5100 Planarity : 0.003 0.056 6072 Dihedral : 7.865 152.620 4755 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.01 % Allowed : 15.46 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.13), residues: 4204 helix: 1.36 (0.12), residues: 1908 sheet: -0.46 (0.18), residues: 692 loop : -0.09 (0.17), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 233 TYR 0.010 0.001 TYR B 853 PHE 0.022 0.001 PHE B 191 TRP 0.005 0.001 TRP B 644 HIS 0.005 0.001 HIS C 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (34268) covalent geometry : angle 0.53857 / 0.27 (46412) hydrogen bonds : bond 0.03898 / 2.62 ( 1590) hydrogen bonds : angle 5.21380 / 3.70 ( 4521) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 168 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.7047 (p0) REVERT: B 334 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7975 (mt) REVERT: B 650 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7268 (mtmm) REVERT: B 854 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7827 (ttt180) REVERT: B 891 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.6830 (t80) REVERT: C 414 PHE cc_start: 0.9248 (OUTLIER) cc_final: 0.8207 (t80) REVERT: D 414 PHE cc_start: 0.9311 (OUTLIER) cc_final: 0.8089 (t80) outliers start: 71 outliers final: 37 residues processed: 225 average time/residue: 0.7661 time to fit residues: 205.2956 Evaluate side-chains 202 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 158 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 569 TRP Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 854 ARG Chi-restraints excluded: chain B residue 891 TYR Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 569 TRP Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 849 ILE Chi-restraints excluded: chain C residue 891 TYR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 932 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 334 optimal weight: 3.9990 chunk 276 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 366 optimal weight: 0.9980 chunk 135 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 357 optimal weight: 6.9990 chunk 287 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 832 ASN D 269 ASN D 882 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.075008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.061154 restraints weight = 85593.450| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.40 r_work: 0.3227 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34268 Z= 0.166 Angle : 0.574 12.853 46412 Z= 0.291 Chirality : 0.044 0.193 5100 Planarity : 0.004 0.056 6072 Dihedral : 7.869 154.784 4752 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.87 % Allowed : 15.80 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.13), residues: 4204 helix: 1.32 (0.12), residues: 1904 sheet: -0.50 (0.18), residues: 692 loop : -0.11 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 233 TYR 0.014 0.001 TYR B 685 PHE 0.026 0.002 PHE B 879 TRP 0.006 0.001 TRP C 799 HIS 0.006 0.001 HIS B 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (34268) covalent geometry : angle 0.57446 / 0.29 (46412) hydrogen bonds : bond 0.04299 / 2.89 ( 1590) hydrogen bonds : angle 5.29480 / 3.76 ( 4521) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 164 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.7082 (p0) REVERT: B 334 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7967 (mt) REVERT: B 433 GLU cc_start: 0.7517 (pm20) cc_final: 0.7284 (pm20) REVERT: B 650 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7280 (mtmm) REVERT: B 891 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.6850 (t80) outliers start: 66 outliers final: 38 residues processed: 219 average time/residue: 0.7522 time to fit residues: 196.9902 Evaluate side-chains 201 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 569 TRP Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 891 TYR Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 569 TRP Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 849 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 932 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 39 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 313 optimal weight: 6.9990 chunk 232 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 367 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 251 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 265 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN A 836 GLN C 832 ASN D 269 ASN D 882 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.075215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.061109 restraints weight = 84047.407| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.41 r_work: 0.3225 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 34268 Z= 0.171 Angle : 0.586 13.116 46412 Z= 0.298 Chirality : 0.044 0.248 5100 Planarity : 0.004 0.056 6072 Dihedral : 7.887 153.000 4752 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.84 % Allowed : 15.86 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.13), residues: 4204 helix: 1.32 (0.12), residues: 1904 sheet: -0.51 (0.18), residues: 692 loop : -0.12 (0.17), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 182 TYR 0.018 0.001 TYR A 197 PHE 0.023 0.002 PHE B 191 TRP 0.005 0.001 TRP B 799 HIS 0.006 0.001 HIS B 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (34268) covalent geometry : angle 0.58637 / 0.30 (46412) hydrogen bonds : bond 0.04326 / 2.91 ( 1590) hydrogen bonds : angle 5.31667 / 3.77 ( 4521) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 163 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 ARG cc_start: 0.7311 (mmp80) cc_final: 0.6972 (mmp-170) REVERT: B 280 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.7110 (p0) REVERT: B 334 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7992 (mt) REVERT: B 433 GLU cc_start: 0.7566 (pm20) cc_final: 0.7308 (pm20) REVERT: B 650 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7274 (mtmm) REVERT: B 854 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7802 (ttt180) REVERT: B 891 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.6794 (t80) outliers start: 65 outliers final: 41 residues processed: 217 average time/residue: 0.7237 time to fit residues: 188.1393 Evaluate side-chains 206 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 569 TRP Chi-restraints excluded: chain B residue 600 MET Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 854 ARG Chi-restraints excluded: chain B residue 891 TYR Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 569 TRP Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 849 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 932 VAL Chi-restraints excluded: chain D residue 1029 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 419 optimal weight: 10.0000 chunk 323 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 297 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 0 HIS A 269 ASN A 836 GLN B 832 ASN D 269 ASN D 882 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.074487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.060838 restraints weight = 85131.235| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.47 r_work: 0.3214 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 34268 Z= 0.197 Angle : 0.608 13.348 46412 Z= 0.311 Chirality : 0.045 0.205 5100 Planarity : 0.004 0.056 6072 Dihedral : 7.968 151.944 4752 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.87 % Allowed : 15.91 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.13), residues: 4204 helix: 1.29 (0.12), residues: 1900 sheet: -0.56 (0.18), residues: 692 loop : -0.16 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 233 TYR 0.015 0.001 TYR A 197 PHE 0.021 0.002 PHE B 879 TRP 0.006 0.002 TRP B 799 HIS 0.007 0.001 HIS B 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (34268) covalent geometry : angle 0.60824 / 0.31 (46412) hydrogen bonds : bond 0.04575 / 3.08 ( 1590) hydrogen bonds : angle 5.38603 / 3.83 ( 4521) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 164 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 334 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7933 (mt) REVERT: B 433 GLU cc_start: 0.7565 (pm20) cc_final: 0.7304 (pm20) REVERT: B 650 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7285 (mtmm) REVERT: B 854 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7768 (ttt180) outliers start: 66 outliers final: 39 residues processed: 216 average time/residue: 0.7389 time to fit residues: 190.5848 Evaluate side-chains 203 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 569 TRP Chi-restraints excluded: chain B residue 600 MET Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 854 ARG Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 569 TRP Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 849 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 813 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 349 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 319 optimal weight: 8.9990 chunk 287 optimal weight: 0.9990 chunk 229 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 314 optimal weight: 6.9990 chunk 277 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 389 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 0 HIS A 269 ASN A 836 GLN B 832 ASN D 269 ASN D 882 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.074245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.060537 restraints weight = 85544.599| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.35 r_work: 0.3219 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 34268 Z= 0.217 Angle : 0.632 16.749 46412 Z= 0.320 Chirality : 0.046 0.192 5100 Planarity : 0.004 0.056 6072 Dihedral : 8.031 150.314 4752 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.47 % Allowed : 16.45 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.13), residues: 4204 helix: 1.22 (0.12), residues: 1896 sheet: -0.58 (0.18), residues: 692 loop : -0.19 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 233 TYR 0.015 0.002 TYR A 197 PHE 0.020 0.002 PHE B 879 TRP 0.006 0.002 TRP B 799 HIS 0.007 0.001 HIS B 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.22 (34268) covalent geometry : angle 0.63181 / 0.32 (46412) hydrogen bonds : bond 0.04735 / 3.19 ( 1590) hydrogen bonds : angle 5.44486 / 3.87 ( 4521) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 164 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 TYR cc_start: 0.7290 (p90) cc_final: 0.7062 (p90) REVERT: B 182 ARG cc_start: 0.7356 (mmp80) cc_final: 0.6932 (mmp-170) REVERT: B 334 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7922 (mt) REVERT: B 650 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7277 (mtmm) REVERT: C 155 MET cc_start: 0.7655 (ttp) cc_final: 0.7407 (ttm) outliers start: 52 outliers final: 38 residues processed: 207 average time/residue: 0.7252 time to fit residues: 178.7960 Evaluate side-chains 203 residues out of total 3532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 569 TRP Chi-restraints excluded: chain B residue 600 MET Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 569 TRP Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 849 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 813 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 408 optimal weight: 0.9980 chunk 359 optimal weight: 0.5980 chunk 332 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 261 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 338 optimal weight: 0.7980 chunk 387 optimal weight: 3.9990 chunk 331 optimal weight: 9.9990 chunk 390 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 0 HIS A 269 ASN A 836 GLN B 832 ASN D 269 ASN D 882 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.075877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.062426 restraints weight = 85303.637| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.48 r_work: 0.3258 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34268 Z= 0.115 Angle : 0.559 12.938 46412 Z= 0.280 Chirality : 0.043 0.193 5100 Planarity : 0.003 0.055 6072 Dihedral : 7.749 146.833 4752 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.36 % Allowed : 16.62 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.13), residues: 4204 helix: 1.46 (0.12), residues: 1908 sheet: -0.59 (0.18), residues: 708 loop : -0.04 (0.17), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 233 TYR 0.011 0.001 TYR A 197 PHE 0.018 0.001 PHE D 879 TRP 0.009 0.001 TRP B 644 HIS 0.006 0.001 HIS B 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (34268) covalent geometry : angle 0.55893 / 0.28 (46412) hydrogen bonds : bond 0.03742 / 2.52 ( 1590) hydrogen bonds : angle 5.14906 / 3.65 ( 4521) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15030.93 seconds wall clock time: 256 minutes 2.44 seconds (15362.44 seconds total)