Starting phenix.real_space_refine on Sat Jun 28 04:14:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ghf_40044/06_2025/8ghf_40044.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ghf_40044/06_2025/8ghf_40044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ghf_40044/06_2025/8ghf_40044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ghf_40044/06_2025/8ghf_40044.map" model { file = "/net/cci-nas-00/data/ceres_data/8ghf_40044/06_2025/8ghf_40044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ghf_40044/06_2025/8ghf_40044.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 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: 8 Type Number sf(0) Gaussians Ca 8 9.91 5 P 72 5.49 5 Mg 4 5.21 5 S 184 5.16 5 Na 4 4.78 5 C 21072 2.51 5 N 4764 2.21 5 O 5812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31920 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7119 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 892, 7111 Classifications: {'peptide': 892} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 864} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 892, 7111 Classifications: {'peptide': 892} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 864} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 7268 Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 7119 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 892, 7111 Classifications: {'peptide': 892} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 864} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 892, 7111 Classifications: {'peptide': 892} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 864} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 7268 Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 7119 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 892, 7111 Classifications: {'peptide': 892} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 864} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 892, 7111 Classifications: {'peptide': 892} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 864} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 7268 Chain: "C" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 7119 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 892, 7111 Classifications: {'peptide': 892} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 864} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 892, 7111 Classifications: {'peptide': 892} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 864} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 7268 Chain: "D" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 804 Unusual residues: {' CA': 2, ' MG': 1, ' NA': 1, 'CLR': 6, 'POV': 23} Classifications: {'undetermined': 33} Link IDs: {None: 32} Unresolved non-hydrogen bonds: 568 Unresolved non-hydrogen angles: 626 Unresolved non-hydrogen dihedrals: 540 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-2': 6, 'POV:plan-1': 17} Unresolved non-hydrogen planarities: 95 Chain: "B" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 738 Unusual residues: {' CA': 2, ' MG': 1, ' NA': 1, 'CLR': 6, 'POV': 21} Classifications: {'undetermined': 31} Link IDs: {None: 30} Unresolved non-hydrogen bonds: 530 Unresolved non-hydrogen angles: 576 Unresolved non-hydrogen dihedrals: 510 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-2': 6, 'POV:plan-1': 17} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 771 Unusual residues: {' CA': 2, ' MG': 1, ' NA': 1, 'CLR': 6, 'POV': 22} Classifications: {'undetermined': 32} Link IDs: {None: 31} Unresolved non-hydrogen bonds: 549 Unresolved non-hydrogen angles: 601 Unresolved non-hydrogen dihedrals: 525 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-2': 6, 'POV:plan-1': 17} Unresolved non-hydrogen planarities: 95 Chain: "D" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 771 Unusual residues: {' CA': 2, ' MG': 1, ' NA': 1, 'CLR': 6, 'POV': 22} Classifications: {'undetermined': 32} Link IDs: {None: 31} Unresolved non-hydrogen bonds: 549 Unresolved non-hydrogen angles: 601 Unresolved non-hydrogen dihedrals: 525 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-2': 6, 'POV:plan-1': 17} Unresolved non-hydrogen planarities: 95 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AASN A 826 " occ=0.61 ... (14 atoms not shown) pdb=" ND2BASN A 826 " occ=0.39 residue: pdb=" N AASN B 826 " occ=0.66 ... (14 atoms not shown) pdb=" ND2BASN B 826 " occ=0.34 residue: pdb=" N AASN C 826 " occ=0.66 ... (14 atoms not shown) pdb=" ND2BASN C 826 " occ=0.34 residue: pdb=" N AASN D 826 " occ=0.68 ... (14 atoms not shown) pdb=" ND2BASN D 826 " occ=0.32 Time building chain proxies: 31.82, per 1000 atoms: 1.00 Number of scatterers: 31920 At special positions: 0 Unit cell: (150.829, 150.829, 129.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 8 19.99 S 184 16.00 P 72 15.00 Mg 4 11.99 Na 4 11.00 O 5812 8.00 N 4764 7.00 C 21072 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=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.01 Conformation dependent library (CDL) restraints added in 6.5 seconds 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6904 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 24 sheets defined 53.9% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'A' and resid 21 through 47 removed outlier: 3.789A pdb=" N PHE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 106 removed outlier: 3.517A pdb=" N VAL A 97 " --> pdb=" O TRP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 134 removed outlier: 3.797A pdb=" N ILE A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 170 removed outlier: 3.599A pdb=" N ILE A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.615A pdb=" N LEU A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 200 Proline residue: A 191 - end of helix removed outlier: 3.583A pdb=" N PHE A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.652A pdb=" N ARG A 210 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 214 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 215 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 231 through 260 Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 297 through 327 removed outlier: 3.635A pdb=" N PHE A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 352 through 364 removed outlier: 3.588A pdb=" N ASP A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 432 through 451 removed outlier: 3.818A pdb=" N GLU A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 470 removed outlier: 3.796A pdb=" N LYS A 466 " --> pdb=" O GLN A 462 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA A 467 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS A 468 " --> pdb=" O HIS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 498 Processing helix chain 'A' and resid 502 through 509 Processing helix chain 'A' and resid 523 through 533 removed outlier: 3.962A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 562 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.564A pdb=" N ARG A 607 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 740 through 743 removed outlier: 3.883A pdb=" N ALA A 743 " --> pdb=" O PRO A 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 743' Processing helix chain 'A' and resid 747 through 751 removed outlier: 3.592A pdb=" N LEU A 751 " --> pdb=" O TYR A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 765 removed outlier: 4.177A pdb=" N ARG A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 770 Processing helix chain 'A' and resid 785 through 792 removed outlier: 3.607A pdb=" N VAL A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 removed outlier: 3.638A pdb=" N CYS A 797 " --> pdb=" O ILE A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 829 removed outlier: 3.591A pdb=" N SER A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 876 removed outlier: 3.646A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 891 removed outlier: 3.685A pdb=" N VAL A 888 " --> pdb=" O ASP A 885 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 905 Processing helix chain 'A' and resid 906 through 912 Processing helix chain 'A' and resid 918 through 921 removed outlier: 3.638A pdb=" N ASP A 921 " --> pdb=" O SER A 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 918 through 921' Processing helix chain 'A' and resid 922 through 930 removed outlier: 3.682A pdb=" N TYR A 928 " --> pdb=" O MET A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 942 Processing helix chain 'A' and resid 946 through 957 Processing helix chain 'A' and resid 969 through 973 removed outlier: 3.925A pdb=" N ARG A 972 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1008 Processing helix chain 'B' and resid 21 through 47 removed outlier: 3.747A pdb=" N PHE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 106 removed outlier: 3.518A pdb=" N VAL B 97 " --> pdb=" O TRP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 134 removed outlier: 3.783A pdb=" N ILE B 124 " --> pdb=" O PHE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 170 removed outlier: 3.593A pdb=" N ILE B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 removed outlier: 3.616A pdb=" N LEU B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 200 Proline residue: B 191 - end of helix removed outlier: 3.582A pdb=" N PHE B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.657A pdb=" N ARG B 210 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 214 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 215 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 231 through 260 Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 297 through 327 removed outlier: 3.638A pdb=" N PHE B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 312 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 352 through 364 removed outlier: 3.612A pdb=" N ASP B 362 " --> pdb=" O ASN B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 432 through 451 removed outlier: 3.819A pdb=" N GLU B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 470 removed outlier: 3.796A pdb=" N LYS B 466 " --> pdb=" O GLN B 462 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 467 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS B 468 " --> pdb=" O HIS B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 498 Processing helix chain 'B' and resid 502 through 509 Processing helix chain 'B' and resid 523 through 533 removed outlier: 3.958A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 562 Processing helix chain 'B' and resid 603 through 609 removed outlier: 3.558A pdb=" N ARG B 607 " --> pdb=" O GLU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 703 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 740 through 743 removed outlier: 3.883A pdb=" N ALA B 743 " --> pdb=" O PRO B 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 740 through 743' Processing helix chain 'B' and resid 747 through 751 removed outlier: 3.592A pdb=" N LEU B 751 " --> pdb=" O TYR B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 765 removed outlier: 4.178A pdb=" N ARG B 765 " --> pdb=" O GLU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 770 Processing helix chain 'B' and resid 785 through 792 removed outlier: 3.607A pdb=" N VAL B 792 " --> pdb=" O ASP B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 797 removed outlier: 3.638A pdb=" N CYS B 797 " --> pdb=" O ILE B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 829 removed outlier: 3.500A pdb=" N LYS B 828 " --> pdb=" O SER B 824 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 876 removed outlier: 3.649A pdb=" N ASN B 875 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 891 removed outlier: 3.686A pdb=" N VAL B 888 " --> pdb=" O ASP B 885 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 905 Processing helix chain 'B' and resid 906 through 912 Processing helix chain 'B' and resid 918 through 921 removed outlier: 3.636A pdb=" N ASP B 921 " --> pdb=" O SER B 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 918 through 921' Processing helix chain 'B' and resid 922 through 930 removed outlier: 3.656A pdb=" N TYR B 928 " --> pdb=" O MET B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 942 Processing helix chain 'B' and resid 946 through 957 Processing helix chain 'B' and resid 969 through 973 removed outlier: 3.924A pdb=" N ARG B 972 " --> pdb=" O LEU B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1008 Processing helix chain 'C' and resid 21 through 47 removed outlier: 3.719A pdb=" N PHE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 106 removed outlier: 3.500A pdb=" N SER C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 134 removed outlier: 3.797A pdb=" N ILE C 124 " --> pdb=" O PHE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 170 removed outlier: 3.596A pdb=" N ILE C 152 " --> pdb=" O PHE C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 removed outlier: 3.612A pdb=" N LEU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 200 Proline residue: C 191 - end of helix removed outlier: 3.578A pdb=" N PHE C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.657A pdb=" N ARG C 210 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 214 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE C 215 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 231 through 260 Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 297 through 327 removed outlier: 3.643A pdb=" N PHE C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 312 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 352 through 364 removed outlier: 3.615A pdb=" N ASP C 362 " --> pdb=" O ASN C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 432 through 451 removed outlier: 3.816A pdb=" N GLU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 470 removed outlier: 3.791A pdb=" N LYS C 466 " --> pdb=" O GLN C 462 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA C 467 " --> pdb=" O TYR C 463 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS C 468 " --> pdb=" O HIS C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 498 Processing helix chain 'C' and resid 502 through 509 Processing helix chain 'C' and resid 523 through 533 removed outlier: 3.962A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 533 " --> pdb=" O LEU C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 562 Processing helix chain 'C' and resid 603 through 609 removed outlier: 3.559A pdb=" N ARG C 607 " --> pdb=" O GLU C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 703 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 740 through 743 removed outlier: 3.879A pdb=" N ALA C 743 " --> pdb=" O PRO C 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 740 through 743' Processing helix chain 'C' and resid 747 through 751 removed outlier: 3.593A pdb=" N LEU C 751 " --> pdb=" O TYR C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 765 removed outlier: 4.178A pdb=" N ARG C 765 " --> pdb=" O GLU C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 770 Processing helix chain 'C' and resid 785 through 792 removed outlier: 3.606A pdb=" N VAL C 792 " --> pdb=" O ASP C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 797 removed outlier: 3.639A pdb=" N CYS C 797 " --> pdb=" O ILE C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 829 removed outlier: 3.512A pdb=" N LYS C 828 " --> pdb=" O SER C 824 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 829 " --> pdb=" O LEU C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 876 removed outlier: 3.614A pdb=" N ASN C 875 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 891 removed outlier: 3.684A pdb=" N VAL C 888 " --> pdb=" O ASP C 885 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 905 Processing helix chain 'C' and resid 906 through 912 Processing helix chain 'C' and resid 918 through 921 removed outlier: 3.634A pdb=" N ASP C 921 " --> pdb=" O SER C 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 918 through 921' Processing helix chain 'C' and resid 922 through 930 removed outlier: 3.689A pdb=" N TYR C 928 " --> pdb=" O MET C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 932 through 942 Processing helix chain 'C' and resid 946 through 957 Processing helix chain 'C' and resid 969 through 973 removed outlier: 3.937A pdb=" N ARG C 972 " --> pdb=" O LEU C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1008 Processing helix chain 'D' and resid 21 through 47 removed outlier: 3.727A pdb=" N PHE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR D 32 " --> pdb=" O SER D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 106 removed outlier: 3.515A pdb=" N VAL D 97 " --> pdb=" O TRP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 134 removed outlier: 3.798A pdb=" N ILE D 124 " --> pdb=" O PHE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 170 removed outlier: 3.593A pdb=" N ILE D 152 " --> pdb=" O PHE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 removed outlier: 3.616A pdb=" N LEU D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 200 Proline residue: D 191 - end of helix removed outlier: 3.581A pdb=" N PHE D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 removed outlier: 3.658A pdb=" N ARG D 210 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D 214 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE D 215 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 231 through 260 Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'D' and resid 273 through 286 Processing helix chain 'D' and resid 297 through 327 removed outlier: 3.636A pdb=" N PHE D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU D 312 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 352 through 364 removed outlier: 3.617A pdb=" N ASP D 362 " --> pdb=" O ASN D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 407 through 414 Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 432 through 451 removed outlier: 3.817A pdb=" N GLU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 470 removed outlier: 3.794A pdb=" N LYS D 466 " --> pdb=" O GLN D 462 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA D 467 " --> pdb=" O TYR D 463 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS D 468 " --> pdb=" O HIS D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 498 Processing helix chain 'D' and resid 502 through 509 Processing helix chain 'D' and resid 523 through 533 removed outlier: 3.959A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY D 531 " --> pdb=" O TYR D 527 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER D 533 " --> pdb=" O LEU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 562 Processing helix chain 'D' and resid 603 through 609 removed outlier: 3.557A pdb=" N ARG D 607 " --> pdb=" O GLU D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 703 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 734 through 739 Processing helix chain 'D' and resid 740 through 743 removed outlier: 3.885A pdb=" N ALA D 743 " --> pdb=" O PRO D 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 740 through 743' Processing helix chain 'D' and resid 747 through 751 removed outlier: 3.593A pdb=" N LEU D 751 " --> pdb=" O TYR D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 through 765 removed outlier: 4.178A pdb=" N ARG D 765 " --> pdb=" O GLU D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 770 Processing helix chain 'D' and resid 785 through 792 removed outlier: 3.605A pdb=" N VAL D 792 " --> pdb=" O ASP D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 797 removed outlier: 3.636A pdb=" N CYS D 797 " --> pdb=" O ILE D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 829 removed outlier: 3.514A pdb=" N LYS D 828 " --> pdb=" O SER D 824 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER D 829 " --> pdb=" O LEU D 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 872 through 876 removed outlier: 3.617A pdb=" N ASN D 875 " --> pdb=" O THR D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 891 removed outlier: 3.695A pdb=" N VAL D 888 " --> pdb=" O ASP D 885 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 905 Processing helix chain 'D' and resid 906 through 912 Processing helix chain 'D' and resid 918 through 921 removed outlier: 3.635A pdb=" N ASP D 921 " --> pdb=" O SER D 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 918 through 921' Processing helix chain 'D' and resid 922 through 930 removed outlier: 3.683A pdb=" N TYR D 928 " --> pdb=" O MET D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 932 through 942 Processing helix chain 'D' and resid 946 through 957 Processing helix chain 'D' and resid 969 through 973 removed outlier: 3.937A pdb=" N ARG D 972 " --> pdb=" O LEU D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1008 Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 140 removed outlier: 3.880A pdb=" N SER A 140 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 202 " --> pdb=" O SER A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 402 removed outlier: 3.542A pdb=" N HIS A 379 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY A 349 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N HIS A 344 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N CYS A 422 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N GLN A 459 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE A 424 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 535 through 539 removed outlier: 4.017A pdb=" N ALA A 567 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE A 598 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N MET A 565 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 580 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 686 through 687 removed outlier: 4.415A pdb=" N TYR A 686 " --> pdb=" O GLY A 962 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.528A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU A 779 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE A 756 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 719 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL A 757 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 721 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 720 " --> pdb=" O MET A 799 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 976 through 981 removed outlier: 3.967A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU A1052 " --> pdb=" O CYS A1011 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N CYS A1011 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 139 through 140 removed outlier: 3.885A pdb=" N SER B 140 " --> pdb=" O SER B 202 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B 202 " --> pdb=" O SER B 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 398 through 402 removed outlier: 3.541A pdb=" N HIS B 379 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLY B 349 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N HIS B 344 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N LEU B 423 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU B 425 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N CYS B 348 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N CYS B 422 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLN B 459 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE B 424 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 535 through 539 removed outlier: 3.933A pdb=" N ALA B 567 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE B 598 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N MET B 565 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 686 through 687 removed outlier: 4.415A pdb=" N TYR B 686 " --> pdb=" O GLY B 962 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 776 through 780 removed outlier: 6.530A pdb=" N ILE B 754 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU B 779 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE B 756 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 719 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL B 757 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL B 721 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 720 " --> pdb=" O MET B 799 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 976 through 981 removed outlier: 3.973A pdb=" N GLY B1013 " --> pdb=" O PHE B1050 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU B1052 " --> pdb=" O CYS B1011 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N CYS B1011 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 139 through 140 removed outlier: 3.875A pdb=" N SER C 140 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER C 202 " --> pdb=" O SER C 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 398 through 402 removed outlier: 3.545A pdb=" N HIS C 379 " --> pdb=" O TYR C 401 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N HIS C 344 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N LEU C 423 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N CYS C 422 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N GLN C 459 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE C 424 " --> pdb=" O GLN C 459 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 535 through 539 removed outlier: 3.943A pdb=" N ALA C 567 " --> pdb=" O PHE C 596 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE C 598 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N MET C 565 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 686 through 687 removed outlier: 4.412A pdb=" N TYR C 686 " --> pdb=" O GLY C 962 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.529A pdb=" N ILE C 754 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU C 779 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE C 756 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL C 719 " --> pdb=" O VAL C 755 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL C 757 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL C 721 " --> pdb=" O VAL C 757 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 720 " --> pdb=" O MET C 799 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 976 through 981 removed outlier: 3.980A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU C1052 " --> pdb=" O CYS C1011 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N CYS C1011 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 139 through 140 removed outlier: 3.852A pdb=" N SER D 140 " --> pdb=" O SER D 202 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER D 202 " --> pdb=" O SER D 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 398 through 402 removed outlier: 3.543A pdb=" N HIS D 379 " --> pdb=" O TYR D 401 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY D 349 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N HIS D 344 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N LEU D 423 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU D 425 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N CYS D 348 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N CYS D 422 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLN D 459 " --> pdb=" O CYS D 422 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE D 424 " --> pdb=" O GLN D 459 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 535 through 539 removed outlier: 3.949A pdb=" N ALA D 567 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE D 598 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N MET D 565 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 686 through 687 removed outlier: 4.407A pdb=" N TYR D 686 " --> pdb=" O GLY D 962 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 776 through 780 removed outlier: 6.530A pdb=" N ILE D 754 " --> pdb=" O SER D 777 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU D 779 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE D 756 " --> pdb=" O LEU D 779 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL D 719 " --> pdb=" O VAL D 755 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL D 757 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL D 721 " --> pdb=" O VAL D 757 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL D 720 " --> pdb=" O MET D 799 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N CYS D 800 " --> pdb=" O ILE D 879 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N GLU D 881 " --> pdb=" O CYS D 800 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE D 802 " --> pdb=" O GLU D 881 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 976 through 981 removed outlier: 3.978A pdb=" N GLY D1013 " --> pdb=" O PHE D1050 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU D1052 " --> pdb=" O CYS D1011 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N CYS D1011 " --> pdb=" O LEU D1052 " (cutoff:3.500A) 1283 hydrogen bonds defined for protein. 3538 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.25 Time building geometry restraints manager: 9.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5139 1.33 - 1.45: 8343 1.45 - 1.57: 18634 1.57 - 1.69: 144 1.69 - 1.82: 276 Bond restraints: 32536 Sorted by residual: bond pdb=" N PRO D 191 " pdb=" CA PRO D 191 " ideal model delta sigma weight residual 1.465 1.495 -0.031 2.03e-02 2.43e+03 2.27e+00 bond pdb=" N PRO A 191 " pdb=" CA PRO A 191 " ideal model delta sigma weight residual 1.465 1.495 -0.031 2.03e-02 2.43e+03 2.27e+00 bond pdb=" N PRO C 191 " pdb=" CA PRO C 191 " ideal model delta sigma weight residual 1.465 1.495 -0.030 2.03e-02 2.43e+03 2.23e+00 bond pdb=" N PRO B 191 " pdb=" CA PRO B 191 " ideal model delta sigma weight residual 1.465 1.495 -0.030 2.03e-02 2.43e+03 2.16e+00 bond pdb=" C PRO C 191 " pdb=" N PRO C 192 " ideal model delta sigma weight residual 1.335 1.352 -0.018 1.28e-02 6.10e+03 1.91e+00 ... (remaining 32531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 43269 1.92 - 3.84: 578 3.84 - 5.76: 104 5.76 - 7.67: 28 7.67 - 9.59: 13 Bond angle restraints: 43992 Sorted by residual: angle pdb=" N GLY D 205 " pdb=" CA GLY D 205 " pdb=" C GLY D 205 " ideal model delta sigma weight residual 111.36 116.04 -4.68 1.17e+00 7.31e-01 1.60e+01 angle pdb=" N GLY A 205 " pdb=" CA GLY A 205 " pdb=" C GLY A 205 " ideal model delta sigma weight residual 111.36 116.02 -4.66 1.17e+00 7.31e-01 1.59e+01 angle pdb=" N GLY B 205 " pdb=" CA GLY B 205 " pdb=" C GLY B 205 " ideal model delta sigma weight residual 111.36 116.01 -4.65 1.17e+00 7.31e-01 1.58e+01 angle pdb=" N GLY C 205 " pdb=" CA GLY C 205 " pdb=" C GLY C 205 " ideal model delta sigma weight residual 111.36 115.98 -4.62 1.17e+00 7.31e-01 1.56e+01 angle pdb=" N PRO D 191 " pdb=" CA PRO D 191 " pdb=" C PRO D 191 " ideal model delta sigma weight residual 110.70 115.33 -4.63 1.22e+00 6.72e-01 1.44e+01 ... (remaining 43987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.34: 18104 22.34 - 44.69: 1939 44.69 - 67.03: 519 67.03 - 89.37: 64 89.37 - 111.72: 25 Dihedral angle restraints: 20651 sinusoidal: 9991 harmonic: 10660 Sorted by residual: dihedral pdb=" C1 CLR A1517 " pdb=" C2 CLR A1517 " pdb=" C3 CLR A1517 " pdb=" C4 CLR A1517 " ideal model delta sinusoidal sigma weight residual 57.41 -54.31 111.72 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" C1 CLR C1520 " pdb=" C2 CLR C1520 " pdb=" C3 CLR C1520 " pdb=" C4 CLR C1520 " ideal model delta sinusoidal sigma weight residual 57.41 -54.12 111.53 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" C1 CLR D1520 " pdb=" C2 CLR D1520 " pdb=" C3 CLR D1520 " pdb=" C4 CLR D1520 " ideal model delta sinusoidal sigma weight residual 57.41 -53.95 111.36 1 3.00e+01 1.11e-03 1.46e+01 ... (remaining 20648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3103 0.033 - 0.066: 1175 0.066 - 0.100: 380 0.100 - 0.133: 185 0.133 - 0.166: 13 Chirality restraints: 4856 Sorted by residual: chirality pdb=" CA THR B 968 " pdb=" N THR B 968 " pdb=" C THR B 968 " pdb=" CB THR B 968 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CA THR A 968 " pdb=" N THR A 968 " pdb=" C THR A 968 " pdb=" CB THR A 968 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA THR D 968 " pdb=" N THR D 968 " pdb=" C THR D 968 " pdb=" CB THR D 968 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.68e-01 ... (remaining 4853 not shown) Planarity restraints: 5180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 985 " -0.053 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO A 986 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 965 " 0.052 5.00e-02 4.00e+02 7.88e-02 9.93e+00 pdb=" N PRO C 966 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO C 966 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 966 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 965 " 0.052 5.00e-02 4.00e+02 7.87e-02 9.92e+00 pdb=" N PRO A 966 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 966 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 966 " 0.044 5.00e-02 4.00e+02 ... (remaining 5177 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 9573 2.84 - 3.35: 25965 3.35 - 3.87: 49566 3.87 - 4.38: 58280 4.38 - 4.90: 103874 Nonbonded interactions: 247258 Sorted by model distance: nonbonded pdb=" O LYS C1002 " pdb=" OG1 THR C1006 " model vdw 2.321 3.040 nonbonded pdb=" O LYS D1002 " pdb=" OG1 THR D1006 " model vdw 2.322 3.040 nonbonded pdb=" O LYS A1002 " pdb=" OG1 THR A1006 " model vdw 2.327 3.040 nonbonded pdb=" O LYS B1002 " pdb=" OG1 THR B1006 " model vdw 2.331 3.040 nonbonded pdb=" O GLY D 102 " pdb=" OG SER D 106 " model vdw 2.343 3.040 ... (remaining 247253 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 825 or resid 827 through 1056 or resid 1401 thr \ ough 1418 or (resid 1512 and (name C1 or name C2 or name O11 or name O12 or name \ O13 or name O14)) or (resid 1514 and (name N or name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C2 or name C3 or name O11 or name O \ 12 or name O13 or name O14 or name O21 or name O31 or name P )) or (resid 1518 a \ nd (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C1 \ 5 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or \ name O31 or name O32 or name P )) or (resid 1521 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or na \ me C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C3 or name C31 or name C32 or name O11 or name O12 or name O1 \ 3 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or (r \ esid 1522 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C2 or name C21 or name C22 or name C23 or name C3 or name C \ 31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or na \ me C38 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 o \ r name O31 or name O32 or name P )) or (resid 1530 and (name C31 or name C32 or \ name C33 or name C34)) or (resid 1531 and (name C1 or name C2 or name C21 or nam \ e C22 or name C3 or name O21 or name O22 or name O31)))) selection = (chain 'B' and (resid 19 through 825 or resid 827 through 1056 or resid 1401 thr \ ough 1418 or (resid 1512 and (name C1 or name C2 or name O11 or name O12 or name \ O13 or name O14)) or (resid 1514 and (name N or name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C2 or name C3 or name O11 or name O \ 12 or name O13 or name O14 or name O21 or name O31 or name P )) or (resid 1518 a \ nd (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C1 \ 5 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or \ name O31 or name O32 or name P )) or (resid 1521 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or na \ me C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C3 or name C31 or name C32 or name O11 or name O12 or name O1 \ 3 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or (r \ esid 1522 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C2 or name C21 or name C22 or name C23 or name C3 or name C \ 31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or na \ me C38 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 o \ r name O31 or name O32 or name P )) or (resid 1530 and (name C31 or name C32 or \ name C33 or name C34)) or (resid 1531 and (name C1 or name C2 or name C21 or nam \ e C22 or name C3 or name O21 or name O22 or name O31)))) selection = (chain 'C' and (resid 19 through 825 or resid 827 through 1056 or resid 1401 thr \ ough 1418 or (resid 1512 and (name C1 or name C2 or name O11 or name O12 or name \ O13 or name O14)) or resid 1514 or (resid 1518 and (name N or name C1 or name C \ 11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or nam \ e C22 or name C23 or name C24 or name C25 or name C26 or name O11 or name O12 or \ name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P \ )) or (resid 1521 and (name N or name C1 or name C11 or name C12 or name C13 or \ name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 \ or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C \ 31 or name C32 or name O11 or name O12 or name O13 or name O14 or name O21 or na \ me O22 or name O31 or name O32 or name P )) or (resid 1522 and (name N or name C \ 1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name \ C21 or name C22 or name C23 or name C3 or name C31 or name C32 or name C33 or n \ ame C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name O12 \ or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name \ P )) or (resid 1530 and (name C31 or name C32 or name C33 or name C34)) or (resi \ d 1531 and (name C1 or name C2 or name C21 or name C22 or name C3 or name O21 or \ name O22 or name O31)))) selection = (chain 'D' and (resid 19 through 825 or resid 827 through 1056 or resid 1401 thr \ ough 1418 or (resid 1512 and (name C1 or name C2 or name O11 or name O12 or name \ O13 or name O14)) or resid 1514 or (resid 1518 and (name N or name C1 or name C \ 11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or nam \ e C22 or name C23 or name C24 or name C25 or name C26 or name O11 or name O12 or \ name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P \ )) or (resid 1521 and (name N or name C1 or name C11 or name C12 or name C13 or \ name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 \ or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C \ 31 or name C32 or name O11 or name O12 or name O13 or name O14 or name O21 or na \ me O22 or name O31 or name O32 or name P )) or (resid 1522 and (name N or name C \ 1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name \ C21 or name C22 or name C23 or name C3 or name C31 or name C32 or name C33 or n \ ame C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name O12 \ or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name \ P )) or (resid 1530 and (name C31 or name C32 or name C33 or name C34)) or (resi \ d 1531 and (name C1 or name C2 or name C21 or name C22 or name C3 or name O21 or \ name O22 or name O31)))) } 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=0.32 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.430 Check model and map are aligned: 0.280 Set scattering table: 0.330 Process input model: 92.080 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 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 : 0.002 0.040 32556 Z= 0.131 Angle : 0.604 9.594 43992 Z= 0.311 Chirality : 0.042 0.166 4856 Planarity : 0.005 0.080 5180 Dihedral : 18.869 111.716 13747 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.45 % Allowed : 23.63 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.13), residues: 3540 helix: -0.27 (0.11), residues: 1724 sheet: 0.75 (0.28), residues: 380 loop : -1.18 (0.14), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 93 HIS 0.016 0.001 HIS D 586 PHE 0.017 0.001 PHE A 144 TYR 0.032 0.001 TYR B1007 ARG 0.002 0.000 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.15601 ( 1283) hydrogen bonds : angle 5.30427 ( 3538) covalent geometry : bond 0.00249 (32536) covalent geometry : angle 0.60358 (43992) Misc. bond : bond 0.00055 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 299 time to evaluate : 3.410 Fit side-chains REVERT: A 587 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8258 (mm) REVERT: B 43 TRP cc_start: 0.6798 (OUTLIER) cc_final: 0.6066 (t60) REVERT: B 587 LEU cc_start: 0.8707 (tt) cc_final: 0.8210 (mm) REVERT: C 587 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8226 (mm) REVERT: C 983 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7758 (mp) REVERT: D 587 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8209 (mm) outliers start: 104 outliers final: 89 residues processed: 388 average time/residue: 0.9961 time to fit residues: 488.5773 Evaluate side-chains 384 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 290 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 925 SER Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 982 LEU Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 871 THR Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 922 SER Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 974 ARG Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 871 THR Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 974 ARG Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 282 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 210 optimal weight: 0.7980 chunk 326 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 449 ASN A 471 ASN A 496 GLN A 586 HIS A 590 GLN A 771 HIS A 807 GLN A 893 GLN A 907 GLN A 967 GLN A1027 GLN B 449 ASN B 471 ASN B 496 GLN B 586 HIS B 590 GLN B 771 HIS B 893 GLN B 907 GLN B 967 GLN B1027 GLN C 449 ASN C 471 ASN C 496 GLN C 586 HIS C 590 GLN C 771 HIS C 893 GLN C 907 GLN C 967 GLN C1027 GLN D 449 ASN D 471 ASN D 496 GLN D 586 HIS D 590 GLN D 771 HIS D 893 GLN D 907 GLN D 967 GLN D1027 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.149365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.100708 restraints weight = 71294.146| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.04 r_work: 0.3043 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 32556 Z= 0.127 Angle : 0.499 6.320 43992 Z= 0.250 Chirality : 0.040 0.149 4856 Planarity : 0.004 0.065 5180 Dihedral : 15.207 89.983 7325 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.84 % Allowed : 22.96 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3540 helix: 0.53 (0.12), residues: 1708 sheet: 0.65 (0.27), residues: 388 loop : -0.68 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 100 HIS 0.007 0.001 HIS B 586 PHE 0.013 0.001 PHE C 307 TYR 0.012 0.001 TYR A 928 ARG 0.003 0.000 ARG C 972 Details of bonding type rmsd hydrogen bonds : bond 0.04738 ( 1283) hydrogen bonds : angle 4.39782 ( 3538) covalent geometry : bond 0.00298 (32536) covalent geometry : angle 0.49888 (43992) Misc. bond : bond 0.00027 ( 20) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 287 time to evaluate : 3.554 Fit side-chains REVERT: A 983 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7587 (mp) REVERT: A 1005 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6918 (tppt) REVERT: B 983 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7595 (mp) REVERT: B 1005 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6910 (tppt) REVERT: C 1005 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.6950 (tppt) REVERT: D 983 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7617 (mp) REVERT: D 1005 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.6969 (tppt) outliers start: 85 outliers final: 38 residues processed: 337 average time/residue: 1.2594 time to fit residues: 515.6442 Evaluate side-chains 326 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 3.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1005 LYS Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1005 LYS Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 974 ARG Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1005 LYS Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 974 ARG Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 1005 LYS Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 150 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 201 optimal weight: 0.0970 chunk 34 optimal weight: 0.5980 chunk 193 optimal weight: 5.9990 chunk 11 optimal weight: 0.1980 chunk 288 optimal weight: 0.8980 chunk 255 optimal weight: 5.9990 chunk 336 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS A 586 HIS A 693 HIS A 807 GLN B 586 HIS B 693 HIS C 451 HIS C 586 HIS D 586 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.152246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.103540 restraints weight = 69047.098| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.07 r_work: 0.3067 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 32556 Z= 0.080 Angle : 0.428 6.315 43992 Z= 0.217 Chirality : 0.039 0.137 4856 Planarity : 0.004 0.063 5180 Dihedral : 14.350 89.845 7236 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.46 % Allowed : 23.06 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3540 helix: 0.93 (0.13), residues: 1708 sheet: 0.72 (0.28), residues: 364 loop : -0.49 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 93 HIS 0.007 0.001 HIS A 586 PHE 0.011 0.001 PHE C 315 TYR 0.012 0.001 TYR C1007 ARG 0.002 0.000 ARG B 974 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 1283) hydrogen bonds : angle 4.19579 ( 3538) covalent geometry : bond 0.00161 (32536) covalent geometry : angle 0.42847 (43992) Misc. bond : bond 0.00028 ( 20) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 290 time to evaluate : 3.302 Fit side-chains REVERT: A 983 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7576 (mp) REVERT: D 983 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7565 (mp) outliers start: 73 outliers final: 31 residues processed: 338 average time/residue: 1.1643 time to fit residues: 481.6054 Evaluate side-chains 310 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 277 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 165 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 163 optimal weight: 20.0000 chunk 224 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 342 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 320 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS B 586 HIS C 200 ASN C 586 HIS C 693 HIS D 200 ASN ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 HIS D 693 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.147615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099744 restraints weight = 60584.841| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.82 r_work: 0.3026 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32556 Z= 0.139 Angle : 0.497 6.808 43992 Z= 0.250 Chirality : 0.041 0.141 4856 Planarity : 0.004 0.061 5180 Dihedral : 14.363 89.947 7220 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.96 % Allowed : 21.34 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.14), residues: 3540 helix: 0.88 (0.13), residues: 1708 sheet: 0.52 (0.27), residues: 384 loop : -0.50 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 275 HIS 0.006 0.001 HIS B 586 PHE 0.013 0.001 PHE C 315 TYR 0.012 0.001 TYR D 928 ARG 0.002 0.000 ARG A 368 Details of bonding type rmsd hydrogen bonds : bond 0.04855 ( 1283) hydrogen bonds : angle 4.34120 ( 3538) covalent geometry : bond 0.00335 (32536) covalent geometry : angle 0.49693 (43992) Misc. bond : bond 0.00032 ( 20) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 279 time to evaluate : 5.947 Fit side-chains REVERT: A 28 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8259 (p) REVERT: A 983 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7661 (mp) REVERT: B 94 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.6726 (mpp) REVERT: B 831 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8149 (mt0) REVERT: B 983 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7659 (mp) REVERT: C 94 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.6715 (mpp) REVERT: C 565 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8795 (ttt) REVERT: C 831 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8142 (mt0) REVERT: D 28 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.8240 (p) REVERT: D 565 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8808 (ttt) REVERT: D 831 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8164 (mt0) REVERT: D 983 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7671 (mp) outliers start: 120 outliers final: 45 residues processed: 355 average time/residue: 1.2157 time to fit residues: 530.0894 Evaluate side-chains 334 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 277 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 831 GLN Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 831 GLN Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 95 optimal weight: 0.9990 chunk 199 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 339 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS B 586 HIS C 586 HIS D 586 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.148510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.099802 restraints weight = 77275.624| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.11 r_work: 0.3025 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32556 Z= 0.112 Angle : 0.462 6.713 43992 Z= 0.234 Chirality : 0.040 0.140 4856 Planarity : 0.004 0.061 5180 Dihedral : 14.025 89.710 7220 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.68 % Allowed : 22.58 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3540 helix: 0.97 (0.13), residues: 1708 sheet: 0.66 (0.28), residues: 364 loop : -0.51 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 275 HIS 0.007 0.001 HIS A 586 PHE 0.015 0.001 PHE C 315 TYR 0.009 0.001 TYR C 928 ARG 0.005 0.000 ARG A 976 Details of bonding type rmsd hydrogen bonds : bond 0.04249 ( 1283) hydrogen bonds : angle 4.27151 ( 3538) covalent geometry : bond 0.00264 (32536) covalent geometry : angle 0.46236 (43992) Misc. bond : bond 0.00033 ( 20) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 285 time to evaluate : 4.300 Fit side-chains REVERT: A 586 HIS cc_start: 0.7038 (OUTLIER) cc_final: 0.6638 (p90) REVERT: A 587 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7745 (mm) REVERT: A 983 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7654 (mp) REVERT: A 1002 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7379 (tmtm) REVERT: B 586 HIS cc_start: 0.7000 (OUTLIER) cc_final: 0.6606 (p90) REVERT: B 587 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7764 (mm) REVERT: B 983 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7639 (mp) REVERT: C 94 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.6636 (mpp) REVERT: C 586 HIS cc_start: 0.7058 (OUTLIER) cc_final: 0.6684 (p90) REVERT: C 587 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7766 (mm) REVERT: C 982 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8134 (mt) REVERT: D 28 SER cc_start: 0.8505 (OUTLIER) cc_final: 0.8246 (p) REVERT: D 983 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7653 (mp) REVERT: D 1002 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7394 (tmtm) outliers start: 80 outliers final: 37 residues processed: 334 average time/residue: 1.3891 time to fit residues: 569.4087 Evaluate side-chains 338 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 287 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 586 HIS Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 1002 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 339 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 240 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 356 optimal weight: 0.0020 chunk 243 optimal weight: 0.8980 chunk 340 optimal weight: 4.9990 chunk 44 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS B 586 HIS C 586 HIS D 586 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.150300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101400 restraints weight = 78734.234| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.16 r_work: 0.3032 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 32556 Z= 0.083 Angle : 0.436 6.978 43992 Z= 0.220 Chirality : 0.039 0.137 4856 Planarity : 0.003 0.061 5180 Dihedral : 13.666 89.267 7216 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.40 % Allowed : 22.55 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.14), residues: 3540 helix: 1.15 (0.13), residues: 1704 sheet: 0.68 (0.28), residues: 364 loop : -0.42 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 23 HIS 0.021 0.001 HIS A 586 PHE 0.012 0.001 PHE C 315 TYR 0.007 0.001 TYR A 928 ARG 0.003 0.000 ARG A 976 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 1283) hydrogen bonds : angle 4.18358 ( 3538) covalent geometry : bond 0.00174 (32536) covalent geometry : angle 0.43556 (43992) Misc. bond : bond 0.00029 ( 20) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 289 time to evaluate : 7.548 Fit side-chains REVERT: A 983 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7654 (mp) REVERT: B 94 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6653 (mpp) REVERT: B 831 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8145 (mt0) REVERT: B 983 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7649 (mp) REVERT: C 94 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6612 (mpp) REVERT: C 831 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: D 94 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6668 (mpp) REVERT: D 831 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8163 (mt0) REVERT: D 983 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7644 (mp) outliers start: 71 outliers final: 35 residues processed: 323 average time/residue: 1.4381 time to fit residues: 577.9382 Evaluate side-chains 328 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 284 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 831 GLN Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 831 GLN Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 271 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 280 optimal weight: 5.9990 chunk 278 optimal weight: 0.0570 chunk 224 optimal weight: 2.9990 chunk 307 optimal weight: 0.3980 chunk 34 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 64 optimal weight: 0.0670 chunk 104 optimal weight: 2.9990 overall best weight: 1.1040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS B 586 HIS C 586 HIS D 586 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.149222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100117 restraints weight = 81517.351| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.21 r_work: 0.3030 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 32556 Z= 0.100 Angle : 0.447 7.152 43992 Z= 0.226 Chirality : 0.040 0.137 4856 Planarity : 0.004 0.060 5180 Dihedral : 13.473 88.573 7213 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.75 % Allowed : 22.13 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.14), residues: 3540 helix: 1.13 (0.13), residues: 1704 sheet: 0.69 (0.28), residues: 364 loop : -0.41 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 23 HIS 0.009 0.001 HIS A 586 PHE 0.014 0.001 PHE A 315 TYR 0.011 0.001 TYR B1007 ARG 0.003 0.000 ARG A 976 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 1283) hydrogen bonds : angle 4.19614 ( 3538) covalent geometry : bond 0.00226 (32536) covalent geometry : angle 0.44684 (43992) Misc. bond : bond 0.00029 ( 20) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 283 time to evaluate : 3.300 Fit side-chains REVERT: A 957 ASN cc_start: 0.7235 (m110) cc_final: 0.6844 (m110) REVERT: A 983 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7647 (mp) REVERT: B 50 TRP cc_start: 0.4946 (OUTLIER) cc_final: 0.4295 (t60) REVERT: B 831 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8143 (mt0) REVERT: B 983 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7636 (mp) REVERT: C 94 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.6665 (mpp) REVERT: C 831 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8145 (mt0) REVERT: C 957 ASN cc_start: 0.7253 (m110) cc_final: 0.6859 (m110) REVERT: D 831 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8160 (mt0) REVERT: D 983 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7664 (mp) outliers start: 82 outliers final: 46 residues processed: 331 average time/residue: 1.2775 time to fit residues: 523.7403 Evaluate side-chains 337 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 283 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 831 GLN Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 831 GLN Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 1004 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 264 optimal weight: 1.9990 chunk 298 optimal weight: 0.0980 chunk 85 optimal weight: 10.0000 chunk 346 optimal weight: 0.3980 chunk 323 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 341 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS B 586 HIS C 586 HIS D 586 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.149197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100894 restraints weight = 70114.850| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.00 r_work: 0.3027 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 32556 Z= 0.099 Angle : 0.448 7.058 43992 Z= 0.226 Chirality : 0.040 0.137 4856 Planarity : 0.003 0.060 5180 Dihedral : 13.232 88.637 7212 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.36 % Allowed : 22.42 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.14), residues: 3540 helix: 1.15 (0.13), residues: 1704 sheet: 0.73 (0.29), residues: 364 loop : -0.39 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 23 HIS 0.008 0.001 HIS A 586 PHE 0.013 0.001 PHE C 315 TYR 0.010 0.001 TYR A1007 ARG 0.003 0.000 ARG A 976 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 1283) hydrogen bonds : angle 4.18973 ( 3538) covalent geometry : bond 0.00226 (32536) covalent geometry : angle 0.44802 (43992) Misc. bond : bond 0.00029 ( 20) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 288 time to evaluate : 3.291 Fit side-chains REVERT: A 957 ASN cc_start: 0.7238 (m110) cc_final: 0.6839 (m110) REVERT: A 983 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7660 (mp) REVERT: B 50 TRP cc_start: 0.4954 (OUTLIER) cc_final: 0.4288 (t60) REVERT: B 831 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8140 (mt0) REVERT: B 957 ASN cc_start: 0.7234 (m110) cc_final: 0.6845 (m110) REVERT: B 983 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7631 (mp) REVERT: B 990 LEU cc_start: 0.8303 (mt) cc_final: 0.7961 (tt) REVERT: C 831 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8126 (mt0) REVERT: C 957 ASN cc_start: 0.7225 (m110) cc_final: 0.6828 (m110) REVERT: C 982 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8140 (mt) REVERT: D 586 HIS cc_start: 0.6998 (OUTLIER) cc_final: 0.6591 (p90) REVERT: D 587 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7760 (mm) REVERT: D 831 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8156 (mt0) REVERT: D 957 ASN cc_start: 0.7228 (m110) cc_final: 0.6833 (m110) REVERT: D 983 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7668 (mp) outliers start: 70 outliers final: 45 residues processed: 330 average time/residue: 1.1674 time to fit residues: 474.0402 Evaluate side-chains 337 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 282 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 831 GLN Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 586 HIS Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 831 GLN Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 1004 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 112 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 354 optimal weight: 1.9990 chunk 266 optimal weight: 0.0980 chunk 125 optimal weight: 0.9990 chunk 216 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 142 optimal weight: 0.3980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS B 586 HIS C 586 HIS D 586 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.150511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.101715 restraints weight = 77697.258| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.15 r_work: 0.3039 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 32556 Z= 0.084 Angle : 0.431 6.846 43992 Z= 0.218 Chirality : 0.039 0.136 4856 Planarity : 0.003 0.060 5180 Dihedral : 12.969 88.444 7212 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.27 % Allowed : 22.61 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.14), residues: 3540 helix: 1.25 (0.13), residues: 1704 sheet: 0.76 (0.29), residues: 364 loop : -0.34 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 23 HIS 0.013 0.001 HIS D 586 PHE 0.012 0.001 PHE A 315 TYR 0.010 0.001 TYR B1007 ARG 0.003 0.000 ARG A 976 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 1283) hydrogen bonds : angle 4.13344 ( 3538) covalent geometry : bond 0.00179 (32536) covalent geometry : angle 0.43088 (43992) Misc. bond : bond 0.00025 ( 20) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 285 time to evaluate : 3.433 Fit side-chains REVERT: A 50 TRP cc_start: 0.4938 (OUTLIER) cc_final: 0.4295 (t60) REVERT: A 957 ASN cc_start: 0.7209 (m110) cc_final: 0.6811 (m110) REVERT: A 983 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7660 (mp) REVERT: B 50 TRP cc_start: 0.4917 (OUTLIER) cc_final: 0.4253 (t60) REVERT: B 831 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: B 957 ASN cc_start: 0.7194 (m110) cc_final: 0.6804 (m110) REVERT: B 983 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7641 (mp) REVERT: B 990 LEU cc_start: 0.8328 (mt) cc_final: 0.7980 (tt) REVERT: C 50 TRP cc_start: 0.4887 (OUTLIER) cc_final: 0.4244 (t60) REVERT: C 831 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8141 (mt0) REVERT: C 957 ASN cc_start: 0.7205 (m110) cc_final: 0.6812 (m110) REVERT: D 831 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: D 957 ASN cc_start: 0.7207 (m110) cc_final: 0.6814 (m110) REVERT: D 983 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7688 (mp) outliers start: 67 outliers final: 40 residues processed: 328 average time/residue: 1.1891 time to fit residues: 482.7236 Evaluate side-chains 330 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 281 time to evaluate : 3.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 50 TRP Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 831 GLN Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 831 GLN Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 329 optimal weight: 7.9990 chunk 212 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 308 optimal weight: 0.5980 chunk 142 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 281 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS B 200 ASN B 534 ASN B 586 HIS C 534 ASN C 586 HIS ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.146045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.099356 restraints weight = 50513.706| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.59 r_work: 0.3010 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32556 Z= 0.159 Angle : 0.514 7.831 43992 Z= 0.258 Chirality : 0.042 0.149 4856 Planarity : 0.004 0.060 5180 Dihedral : 13.432 89.745 7212 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.33 % Allowed : 22.48 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3540 helix: 0.95 (0.13), residues: 1708 sheet: 0.63 (0.27), residues: 384 loop : -0.43 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 23 HIS 0.013 0.002 HIS D 586 PHE 0.012 0.001 PHE A 307 TYR 0.012 0.001 TYR C 928 ARG 0.003 0.000 ARG A 976 Details of bonding type rmsd hydrogen bonds : bond 0.05085 ( 1283) hydrogen bonds : angle 4.37469 ( 3538) covalent geometry : bond 0.00392 (32536) covalent geometry : angle 0.51384 (43992) Misc. bond : bond 0.00039 ( 20) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 289 time to evaluate : 3.459 Fit side-chains REVERT: A 957 ASN cc_start: 0.7255 (m110) cc_final: 0.6867 (m110) REVERT: A 983 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7730 (mp) REVERT: B 957 ASN cc_start: 0.7246 (m110) cc_final: 0.6861 (m110) REVERT: B 983 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7723 (mp) REVERT: B 990 LEU cc_start: 0.8300 (mt) cc_final: 0.7905 (tt) REVERT: C 957 ASN cc_start: 0.7264 (m110) cc_final: 0.6875 (m110) REVERT: C 982 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8174 (mt) REVERT: D 957 ASN cc_start: 0.7255 (m110) cc_final: 0.6866 (m110) REVERT: D 983 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7737 (mp) outliers start: 69 outliers final: 39 residues processed: 334 average time/residue: 1.1369 time to fit residues: 468.0403 Evaluate side-chains 333 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 290 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 175 optimal weight: 8.9990 chunk 139 optimal weight: 0.6980 chunk 234 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 284 optimal weight: 0.0770 chunk 142 optimal weight: 0.0980 chunk 74 optimal weight: 0.9980 chunk 297 optimal weight: 3.9990 chunk 270 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS B 534 ASN B 586 HIS C 534 ASN C 586 HIS D 586 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.150629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.101855 restraints weight = 79597.407| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.18 r_work: 0.3043 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 32556 Z= 0.082 Angle : 0.434 6.929 43992 Z= 0.219 Chirality : 0.039 0.139 4856 Planarity : 0.003 0.061 5180 Dihedral : 12.857 89.866 7212 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.34 % Allowed : 23.41 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.14), residues: 3540 helix: 1.24 (0.13), residues: 1704 sheet: 0.82 (0.29), residues: 364 loop : -0.34 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 23 HIS 0.009 0.001 HIS D 586 PHE 0.011 0.001 PHE C 315 TYR 0.012 0.001 TYR B1007 ARG 0.003 0.000 ARG A 976 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 1283) hydrogen bonds : angle 4.15092 ( 3538) covalent geometry : bond 0.00170 (32536) covalent geometry : angle 0.43447 (43992) Misc. bond : bond 0.00025 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25069.17 seconds wall clock time: 434 minutes 14.11 seconds (26054.11 seconds total)