Starting phenix.real_space_refine on Thu May 29 17:30:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ss6_40745/05_2025/8ss6_40745.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ss6_40745/05_2025/8ss6_40745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ss6_40745/05_2025/8ss6_40745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ss6_40745/05_2025/8ss6_40745.map" model { file = "/net/cci-nas-00/data/ceres_data/8ss6_40745/05_2025/8ss6_40745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ss6_40745/05_2025/8ss6_40745.cif" } resolution = 3.01 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= 0.006 sd= 0.161 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 24 5.49 5 S 166 5.16 5 Na 1 4.78 5 C 20717 2.51 5 N 4971 2.21 5 O 5718 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31609 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7682 Classifications: {'peptide': 974} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 946} Chain breaks: 4 Chain: "B" Number of atoms: 6177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6177 Classifications: {'peptide': 783} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 759} Chain breaks: 2 Chain: "C" Number of atoms: 7682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7682 Classifications: {'peptide': 974} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 946} Chain breaks: 4 Chain: "D" Number of atoms: 6177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6177 Classifications: {'peptide': 783} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 759} Chain breaks: 2 Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "F" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "A" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 377 Unusual residues: {' NA': 1, '6ZP': 1, 'CLR': 2, 'PCW': 6, 'ZK1': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 325 Unusual residues: {'6ZP': 1, 'CLR': 2, 'PCW': 5, 'ZK1': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 386 Unusual residues: {'6ZP': 1, 'CLR': 2, 'PCW': 6, 'SPD': 1, 'ZK1': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 325 Unusual residues: {'6ZP': 1, 'CLR': 2, 'PCW': 5, 'ZK1': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 73 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 73 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 16.79, per 1000 atoms: 0.53 Number of scatterers: 31609 At special positions: 0 Unit cell: (117.475, 163.725, 197.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 166 16.00 P 24 15.00 Na 1 11.00 F 12 9.00 O 5718 8.00 N 4971 7.00 C 20717 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.02 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS D 589 " distance=2.10 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 589 " - pdb=" SG CYS C 589 " distance=1.94 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.02 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.99 Conformation dependent library (CDL) restraints added in 3.6 seconds 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7004 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 46 sheets defined 50.9% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 54 through 68 removed outlier: 3.504A pdb=" N ARG A 68 " --> pdb=" O SER A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 92 Processing helix chain 'A' and resid 117 through 128 removed outlier: 3.504A pdb=" N LEU A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 removed outlier: 3.504A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 185 Processing helix chain 'A' and resid 197 through 212 removed outlier: 3.549A pdb=" N GLN A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 4.213A pdb=" N GLY A 230 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 4.077A pdb=" N LYS A 234 " --> pdb=" O ASP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 265 removed outlier: 3.702A pdb=" N GLU A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 302 removed outlier: 3.637A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 334 Processing helix chain 'A' and resid 416 through 419 removed outlier: 4.321A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.549A pdb=" N LYS A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.560A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 546 removed outlier: 3.738A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.736A pdb=" N TRP A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 630 removed outlier: 4.092A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 630 " --> pdb=" O VAL A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 642 Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.675A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 removed outlier: 3.691A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.607A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 792 through 820 removed outlier: 3.860A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR A 816 " --> pdb=" O ILE A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 857 removed outlier: 3.572A pdb=" N LEU A 839 " --> pdb=" O LYS A 835 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 925 Processing helix chain 'A' and resid 930 through 952 removed outlier: 3.659A pdb=" N ILE A 948 " --> pdb=" O ILE A 944 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 988 removed outlier: 4.173A pdb=" N PHE A 960 " --> pdb=" O THR A 956 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1033 removed outlier: 3.646A pdb=" N PHE A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A1017 " --> pdb=" O SER A1013 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 81 through 92 Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.511A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 removed outlier: 3.748A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 187 removed outlier: 3.696A pdb=" N LYS B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 removed outlier: 3.563A pdb=" N GLN B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.947A pdb=" N GLY B 230 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 Processing helix chain 'B' and resid 279 through 302 removed outlier: 3.586A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 296 " --> pdb=" O MET B 292 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 removed outlier: 4.226A pdb=" N GLU B 328 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.512A pdb=" N LYS B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.641A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 546 removed outlier: 3.641A pdb=" N VAL B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.734A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.701A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 641 removed outlier: 3.572A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.538A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 675 removed outlier: 3.526A pdb=" N MET B 674 " --> pdb=" O MET B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 707 through 713 removed outlier: 3.507A pdb=" N GLU B 713 " --> pdb=" O ASN B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.564A pdb=" N ASN B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 755 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 817 removed outlier: 3.933A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 54 through 68 removed outlier: 3.504A pdb=" N ARG C 68 " --> pdb=" O SER C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 92 Processing helix chain 'C' and resid 117 through 128 removed outlier: 3.504A pdb=" N LEU C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 157 removed outlier: 3.504A pdb=" N ALA C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 185 Processing helix chain 'C' and resid 197 through 212 removed outlier: 3.548A pdb=" N GLN C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 removed outlier: 4.213A pdb=" N GLY C 230 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 4.077A pdb=" N LYS C 234 " --> pdb=" O ASP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 265 removed outlier: 3.701A pdb=" N GLU C 260 " --> pdb=" O SER C 256 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 302 removed outlier: 3.638A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 334 Processing helix chain 'C' and resid 416 through 419 removed outlier: 4.321A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.549A pdb=" N LYS C 434 " --> pdb=" O ALA C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 469 Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.560A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 removed outlier: 3.738A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE C 546 " --> pdb=" O LEU C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.736A pdb=" N TRP C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 630 removed outlier: 4.093A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 630 " --> pdb=" O VAL C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 642 Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.675A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 removed outlier: 3.689A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.607A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 792 through 820 removed outlier: 3.860A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR C 816 " --> pdb=" O ILE C 812 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 857 removed outlier: 3.572A pdb=" N LEU C 839 " --> pdb=" O LYS C 835 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 843 " --> pdb=" O LEU C 839 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA C 845 " --> pdb=" O SER C 841 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER C 857 " --> pdb=" O GLY C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 925 Processing helix chain 'C' and resid 930 through 952 removed outlier: 3.658A pdb=" N ILE C 948 " --> pdb=" O ILE C 944 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 988 removed outlier: 4.173A pdb=" N PHE C 960 " --> pdb=" O THR C 956 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 970 " --> pdb=" O PHE C 966 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU C 987 " --> pdb=" O SER C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1033 removed outlier: 3.646A pdb=" N PHE C1014 " --> pdb=" O ALA C1010 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C1017 " --> pdb=" O SER C1013 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 54 through 68 Processing helix chain 'D' and resid 81 through 92 Processing helix chain 'D' and resid 117 through 129 removed outlier: 3.512A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 156 removed outlier: 3.749A pdb=" N ALA D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.696A pdb=" N LYS D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.564A pdb=" N GLN D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 230 removed outlier: 3.947A pdb=" N GLY D 230 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 Processing helix chain 'D' and resid 279 through 302 removed outlier: 3.586A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 removed outlier: 4.226A pdb=" N GLU D 328 " --> pdb=" O GLY D 324 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN D 335 " --> pdb=" O ARG D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.511A pdb=" N LYS D 434 " --> pdb=" O ALA D 430 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.642A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 546 removed outlier: 3.639A pdb=" N VAL D 539 " --> pdb=" O GLY D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.733A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.700A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 removed outlier: 3.572A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.539A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG D 660 " --> pdb=" O LYS D 656 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG D 661 " --> pdb=" O GLU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 675 removed outlier: 3.527A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 707 through 713 removed outlier: 3.506A pdb=" N GLU D 713 " --> pdb=" O ASN D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.563A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 755 " --> pdb=" O LEU D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 817 removed outlier: 3.932A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 37 removed outlier: 3.836A pdb=" N THR E 13 " --> pdb=" O CYS E 9 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL E 15 " --> pdb=" O MET E 11 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA E 30 " --> pdb=" O TRP E 26 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE E 31 " --> pdb=" O HIS E 27 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP E 37 " --> pdb=" O GLU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 66 removed outlier: 3.722A pdb=" N CYS E 62 " --> pdb=" O GLU E 58 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU E 64 " --> pdb=" O ILE E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 85 removed outlier: 3.594A pdb=" N GLU E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU E 80 " --> pdb=" O GLY E 76 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS E 84 " --> pdb=" O LEU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 94 Processing helix chain 'E' and resid 94 through 107 removed outlier: 3.608A pdb=" N TYR E 100 " --> pdb=" O PRO E 96 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP E 103 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR E 105 " --> pdb=" O HIS E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 159 removed outlier: 3.554A pdb=" N TRP E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 37 removed outlier: 3.836A pdb=" N THR F 13 " --> pdb=" O CYS F 9 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL F 15 " --> pdb=" O MET F 11 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL F 24 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA F 30 " --> pdb=" O TRP F 26 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE F 31 " --> pdb=" O HIS F 27 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP F 37 " --> pdb=" O GLU F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 66 removed outlier: 3.722A pdb=" N CYS F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 85 removed outlier: 3.593A pdb=" N GLU F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU F 80 " --> pdb=" O GLY F 76 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N CYS F 84 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 94 Processing helix chain 'F' and resid 94 through 107 removed outlier: 3.609A pdb=" N TYR F 100 " --> pdb=" O PRO F 96 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR F 105 " --> pdb=" O HIS F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 159 removed outlier: 3.555A pdb=" N TRP F 136 " --> pdb=" O GLN F 132 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU F 144 " --> pdb=" O ALA F 140 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE F 147 " --> pdb=" O LEU F 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 50 removed outlier: 6.546A pdb=" N ILE A 12 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N HIS A 46 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE A 14 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ASP A 48 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLY A 16 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A 50 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE A 18 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 194 removed outlier: 3.507A pdb=" N ILE A 222 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 194 removed outlier: 3.507A pdb=" N ILE A 222 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 339 through 340 removed outlier: 3.503A pdb=" N GLY A 340 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 343 " --> pdb=" O GLY A 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 399 removed outlier: 6.537A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.710A pdb=" N ALA A 452 " --> pdb=" O ASN A 461 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 461 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 459 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 475 through 480 removed outlier: 7.568A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 475 through 480 removed outlier: 7.568A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.503A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 882 through 884 Processing sheet with id=AB4, first strand: chain 'A' and resid 868 through 869 Processing sheet with id=AB5, first strand: chain 'B' and resid 15 through 17 removed outlier: 6.130A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 159 through 161 removed outlier: 3.878A pdb=" N TYR B 135 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LYS B 132 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ILE B 193 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA B 134 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASP B 195 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU B 136 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE B 245 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY B 244 " --> pdb=" O MET B 361 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 159 through 161 removed outlier: 3.878A pdb=" N TYR B 135 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LYS B 132 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ILE B 193 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA B 134 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASP B 195 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU B 136 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE B 245 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY B 244 " --> pdb=" O MET B 361 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AB9, first strand: chain 'B' and resid 346 through 347 removed outlier: 3.934A pdb=" N LYS B 346 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 394 through 399 Processing sheet with id=AC2, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AC3, first strand: chain 'B' and resid 475 through 480 removed outlier: 4.753A pdb=" N ALA B 477 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLY B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 475 through 480 removed outlier: 4.753A pdb=" N ALA B 477 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLY B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 646 through 648 removed outlier: 8.349A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 42 through 50 removed outlier: 6.546A pdb=" N ILE C 12 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N HIS C 46 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE C 14 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ASP C 48 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY C 16 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU C 50 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE C 18 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AC8, first strand: chain 'C' and resid 191 through 194 removed outlier: 3.506A pdb=" N ILE C 222 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE C 245 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 191 through 194 removed outlier: 3.506A pdb=" N ILE C 222 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE C 245 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 339 through 340 removed outlier: 3.504A pdb=" N GLY C 340 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY C 343 " --> pdb=" O GLY C 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 395 through 399 removed outlier: 6.537A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AD4, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.709A pdb=" N ALA C 452 " --> pdb=" O ASN C 461 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN C 461 " --> pdb=" O ALA C 452 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE C 459 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 475 through 480 removed outlier: 7.568A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 475 through 480 removed outlier: 7.568A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.503A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 882 through 884 Processing sheet with id=AD9, first strand: chain 'C' and resid 868 through 869 Processing sheet with id=AE1, first strand: chain 'D' and resid 15 through 17 removed outlier: 6.130A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 159 through 161 removed outlier: 3.878A pdb=" N TYR D 135 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LYS D 132 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ILE D 193 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA D 134 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ASP D 195 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU D 136 " --> pdb=" O ASP D 195 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE D 245 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY D 244 " --> pdb=" O MET D 361 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 159 through 161 removed outlier: 3.878A pdb=" N TYR D 135 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LYS D 132 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ILE D 193 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA D 134 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ASP D 195 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU D 136 " --> pdb=" O ASP D 195 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE D 245 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY D 244 " --> pdb=" O MET D 361 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AE5, first strand: chain 'D' and resid 346 through 347 removed outlier: 3.934A pdb=" N LYS D 346 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 394 through 399 Processing sheet with id=AE7, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AE8, first strand: chain 'D' and resid 475 through 480 removed outlier: 4.753A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 475 through 480 removed outlier: 4.753A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 646 through 648 removed outlier: 8.349A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 1452 hydrogen bonds defined for protein. 4206 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: 12.95 Time building geometry restraints manager: 9.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.18: 28 1.18 - 1.35: 9545 1.35 - 1.52: 14958 1.52 - 1.69: 7474 1.69 - 1.87: 286 Bond restraints: 32291 Sorted by residual: bond pdb=" C4 CLR A1107 " pdb=" C5 CLR A1107 " ideal model delta sigma weight residual 1.506 1.007 0.499 2.00e-02 2.50e+03 6.23e+02 bond pdb=" C4 CLR B1107 " pdb=" C5 CLR B1107 " ideal model delta sigma weight residual 1.506 1.007 0.499 2.00e-02 2.50e+03 6.22e+02 bond pdb=" C4 CLR A1108 " pdb=" C5 CLR A1108 " ideal model delta sigma weight residual 1.506 1.008 0.498 2.00e-02 2.50e+03 6.21e+02 bond pdb=" C4 CLR C1108 " pdb=" C5 CLR C1108 " ideal model delta sigma weight residual 1.506 1.008 0.498 2.00e-02 2.50e+03 6.20e+02 bond pdb=" C4 CLR D1109 " pdb=" C5 CLR D1109 " ideal model delta sigma weight residual 1.506 1.008 0.498 2.00e-02 2.50e+03 6.19e+02 ... (remaining 32286 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.33: 42914 5.33 - 10.67: 493 10.67 - 16.00: 85 16.00 - 21.34: 4 21.34 - 26.67: 2 Bond angle restraints: 43498 Sorted by residual: angle pdb=" C12 CLR B1107 " pdb=" C13 CLR B1107 " pdb=" C18 CLR B1107 " ideal model delta sigma weight residual 111.01 84.34 26.67 3.00e+00 1.11e-01 7.90e+01 angle pdb=" C12 CLR D1108 " pdb=" C13 CLR D1108 " pdb=" C18 CLR D1108 " ideal model delta sigma weight residual 111.01 84.40 26.61 3.00e+00 1.11e-01 7.87e+01 angle pdb=" C ASP C 378 " pdb=" N LYS C 379 " pdb=" CA LYS C 379 " ideal model delta sigma weight residual 121.54 134.51 -12.97 1.91e+00 2.74e-01 4.61e+01 angle pdb=" C ASP A 378 " pdb=" N LYS A 379 " pdb=" CA LYS A 379 " ideal model delta sigma weight residual 121.54 134.47 -12.93 1.91e+00 2.74e-01 4.58e+01 angle pdb=" C17 CLR B1107 " pdb=" C13 CLR B1107 " pdb=" C18 CLR B1107 " ideal model delta sigma weight residual 110.18 91.40 18.78 3.00e+00 1.11e-01 3.92e+01 ... (remaining 43493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 18897 34.88 - 69.75: 656 69.75 - 104.63: 82 104.63 - 139.51: 53 139.51 - 174.38: 23 Dihedral angle restraints: 19711 sinusoidal: 8755 harmonic: 10956 Sorted by residual: dihedral pdb=" CA ILE B 354 " pdb=" C ILE B 354 " pdb=" N ASN B 355 " pdb=" CA ASN B 355 " ideal model delta harmonic sigma weight residual -180.00 -132.64 -47.36 0 5.00e+00 4.00e-02 8.97e+01 dihedral pdb=" CA ILE D 354 " pdb=" C ILE D 354 " pdb=" N ASN D 355 " pdb=" CA ASN D 355 " ideal model delta harmonic sigma weight residual -180.00 -132.73 -47.27 0 5.00e+00 4.00e-02 8.94e+01 dihedral pdb=" CA GLU D 384 " pdb=" C GLU D 384 " pdb=" N ASP D 385 " pdb=" CA ASP D 385 " ideal model delta harmonic sigma weight residual -180.00 -140.74 -39.26 0 5.00e+00 4.00e-02 6.17e+01 ... (remaining 19708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.128: 4694 1.128 - 2.255: 0 2.255 - 3.383: 2 3.383 - 4.510: 8 4.510 - 5.638: 6 Chirality restraints: 4710 Sorted by residual: chirality pdb=" C13 CLR A1107 " pdb=" C12 CLR A1107 " pdb=" C14 CLR A1107 " pdb=" C17 CLR A1107 " both_signs ideal model delta sigma weight residual False -2.93 2.71 -5.64 2.00e-01 2.50e+01 7.95e+02 chirality pdb=" C13 CLR C1107 " pdb=" C12 CLR C1107 " pdb=" C14 CLR C1107 " pdb=" C17 CLR C1107 " both_signs ideal model delta sigma weight residual False -2.93 2.70 -5.64 2.00e-01 2.50e+01 7.94e+02 chirality pdb=" C13 CLR B1108 " pdb=" C12 CLR B1108 " pdb=" C14 CLR B1108 " pdb=" C17 CLR B1108 " both_signs ideal model delta sigma weight residual False -2.93 2.70 -5.63 2.00e-01 2.50e+01 7.92e+02 ... (remaining 4707 not shown) Planarity restraints: 5316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 6ZP A1101 " -0.028 2.00e-02 2.50e+03 2.15e-02 1.04e+01 pdb=" C03 6ZP A1101 " -0.022 2.00e-02 2.50e+03 pdb=" C04 6ZP A1101 " -0.017 2.00e-02 2.50e+03 pdb=" C05 6ZP A1101 " 0.001 2.00e-02 2.50e+03 pdb=" C06 6ZP A1101 " 0.015 2.00e-02 2.50e+03 pdb=" C07 6ZP A1101 " 0.012 2.00e-02 2.50e+03 pdb=" C08 6ZP A1101 " 0.014 2.00e-02 2.50e+03 pdb=" C09 6ZP A1101 " -0.018 2.00e-02 2.50e+03 pdb=" N01 6ZP A1101 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 135 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.57e+00 pdb=" C TYR B 135 " -0.053 2.00e-02 2.50e+03 pdb=" O TYR B 135 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU B 136 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 135 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.53e+00 pdb=" C TYR D 135 " 0.053 2.00e-02 2.50e+03 pdb=" O TYR D 135 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU D 136 " -0.018 2.00e-02 2.50e+03 ... (remaining 5313 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 9391 2.82 - 3.34: 26949 3.34 - 3.86: 51224 3.86 - 4.38: 62015 4.38 - 4.90: 104903 Nonbonded interactions: 254482 Sorted by model distance: nonbonded pdb=" OH TYR A1026 " pdb=" O2P PCW A1105 " model vdw 2.303 3.040 nonbonded pdb=" OH TYR C 135 " pdb=" OD2 ASP C 195 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR A 135 " pdb=" OD2 ASP A 195 " model vdw 2.306 3.040 nonbonded pdb=" O MET C 33 " pdb=" OG SER C 37 " model vdw 2.315 3.040 nonbonded pdb=" O MET A 33 " pdb=" OG SER A 37 " model vdw 2.315 3.040 ... (remaining 254477 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 10 through 1034 or resid 1101 through 1110)) selection = (chain 'C' and (resid 10 through 1034 or resid 1101 through 1110)) } ncs_group { reference = (chain 'B' and (resid 10 through 817 or resid 1104 through 1106 or resid 1108)) selection = (chain 'D' and (resid 10 through 817 or resid 1104 through 1105 or (resid 1106 a \ nd (name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C20 or name C21 or name C22 or name C23)) or resid 1108)) } ncs_group { reference = (chain 'E' and (resid 2 through 159 or (resid 201 through 203 and (name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23)))) selection = (chain 'F' and (resid 2 through 159 or (resid 201 through 203 and (name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.880 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: 0.030 Extract box with map and model: 1.130 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 67.990 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 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 : 0.017 0.499 32303 Z= 0.846 Angle : 1.376 26.670 43522 Z= 0.653 Chirality : 0.283 5.638 4710 Planarity : 0.007 0.068 5316 Dihedral : 19.010 174.382 12671 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.91 % Favored : 91.66 % Rotamer: Outliers : 1.05 % Allowed : 5.05 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -5.47 (0.10), residues: 3754 helix: -3.89 (0.06), residues: 1840 sheet: -3.07 (0.21), residues: 440 loop : -3.17 (0.13), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP C 323 HIS 0.013 0.002 HIS C 93 PHE 0.024 0.003 PHE D 101 TYR 0.028 0.002 TYR B 177 ARG 0.006 0.001 ARG C 141 Details of bonding type rmsd hydrogen bonds : bond 0.28900 ( 1406) hydrogen bonds : angle 10.41459 ( 4206) SS BOND : bond 0.03264 ( 12) SS BOND : angle 1.22886 ( 24) covalent geometry : bond 0.01703 (32291) covalent geometry : angle 1.37606 (43498) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 760 time to evaluate : 3.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6781 (pmt100) cc_final: 0.6119 (ttp80) REVERT: A 274 HIS cc_start: 0.8035 (t-90) cc_final: 0.7728 (t70) REVERT: A 457 THR cc_start: 0.8420 (m) cc_final: 0.8210 (m) REVERT: A 847 CYS cc_start: 0.7171 (m) cc_final: 0.6794 (t) REVERT: A 907 MET cc_start: 0.1750 (mmt) cc_final: 0.1479 (mmt) REVERT: A 924 MET cc_start: 0.5718 (mmp) cc_final: 0.5438 (mmm) REVERT: B 79 LYS cc_start: 0.8204 (tmmt) cc_final: 0.7974 (ttpp) REVERT: B 265 LEU cc_start: 0.7835 (mt) cc_final: 0.7394 (mt) REVERT: B 286 TYR cc_start: 0.6910 (t80) cc_final: 0.6659 (t80) REVERT: B 393 LYS cc_start: 0.8413 (tppt) cc_final: 0.8085 (tptm) REVERT: C 42 ARG cc_start: 0.6574 (pmt100) cc_final: 0.6242 (ttp80) REVERT: C 274 HIS cc_start: 0.7885 (t-90) cc_final: 0.7580 (t70) REVERT: C 420 ARG cc_start: 0.7961 (mtm180) cc_final: 0.7644 (mtm-85) REVERT: C 601 VAL cc_start: 0.8956 (p) cc_final: 0.8665 (t) REVERT: D 79 LYS cc_start: 0.8267 (tmmt) cc_final: 0.8047 (ttpp) REVERT: D 265 LEU cc_start: 0.7999 (mt) cc_final: 0.7649 (mt) REVERT: D 431 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7960 (mm-30) REVERT: E 25 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7218 (mp) REVERT: E 116 MET cc_start: 0.3617 (mtm) cc_final: 0.3220 (mmt) REVERT: E 117 TYR cc_start: 0.2483 (m-80) cc_final: 0.2168 (m-80) REVERT: F 123 MET cc_start: 0.6812 (mmm) cc_final: 0.6567 (mmt) outliers start: 34 outliers final: 5 residues processed: 783 average time/residue: 0.4744 time to fit residues: 566.5205 Evaluate side-chains 335 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 329 time to evaluate : 3.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain E residue 25 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 0.9980 chunk 286 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 193 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 296 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 220 optimal weight: 0.8980 chunk 343 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 ASN A 318 ASN A 344 ASN A 355 ASN A 726 ASN A 747 ASN A 950 HIS ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN B 10 ASN B 49 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 214 HIS B 224 ASN B 298 ASN B 344 ASN B 359 ASN B 747 ASN C 10 ASN C 46 HIS ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 GLN C 318 ASN C 344 ASN C 355 ASN C 726 ASN C 747 ASN C 950 HIS C 990 ASN D 10 ASN D 35 GLN D 49 ASN D 147 GLN D 164 ASN D 214 HIS D 224 ASN D 298 ASN D 344 ASN D 359 ASN D 435 HIS D 747 ASN E 27 HIS E 101 HIS F 101 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.165301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.125629 restraints weight = 43340.980| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.89 r_work: 0.3344 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32303 Z= 0.144 Angle : 0.900 35.213 43522 Z= 0.396 Chirality : 0.075 1.836 4710 Planarity : 0.005 0.068 5316 Dihedral : 20.416 179.942 5695 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.87 % Favored : 92.81 % Rotamer: Outliers : 2.03 % Allowed : 9.82 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.02 (0.12), residues: 3754 helix: -1.21 (0.11), residues: 1856 sheet: -2.58 (0.22), residues: 444 loop : -2.75 (0.14), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 323 HIS 0.004 0.001 HIS D 93 PHE 0.023 0.002 PHE D 109 TYR 0.019 0.002 TYR E 117 ARG 0.006 0.001 ARG E 104 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 1406) hydrogen bonds : angle 4.60254 ( 4206) SS BOND : bond 0.00313 ( 12) SS BOND : angle 1.39020 ( 24) covalent geometry : bond 0.00318 (32291) covalent geometry : angle 0.89925 (43498) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 380 time to evaluate : 3.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6891 (pmt100) cc_final: 0.6100 (ttp80) REVERT: A 292 MET cc_start: 0.7549 (mtm) cc_final: 0.7256 (mtp) REVERT: A 355 ASN cc_start: 0.6930 (t0) cc_final: 0.6688 (t0) REVERT: A 457 THR cc_start: 0.8374 (m) cc_final: 0.8162 (p) REVERT: A 542 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8247 (tp) REVERT: A 861 TRP cc_start: 0.7417 (m100) cc_final: 0.7124 (m100) REVERT: A 907 MET cc_start: 0.1590 (mmt) cc_final: 0.1382 (mmt) REVERT: B 79 LYS cc_start: 0.8334 (tmmt) cc_final: 0.8055 (ttpp) REVERT: B 104 ASP cc_start: 0.6843 (p0) cc_final: 0.6599 (p0) REVERT: B 132 LYS cc_start: 0.9025 (ttmm) cc_final: 0.8755 (ttmm) REVERT: B 167 ASN cc_start: 0.7616 (m-40) cc_final: 0.7227 (p0) REVERT: B 265 LEU cc_start: 0.7320 (mt) cc_final: 0.7022 (mt) REVERT: B 286 TYR cc_start: 0.7005 (t80) cc_final: 0.6754 (t80) REVERT: B 414 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8146 (ptp) REVERT: B 576 SER cc_start: 0.8877 (m) cc_final: 0.8657 (m) REVERT: B 808 LEU cc_start: 0.7756 (mt) cc_final: 0.7299 (tt) REVERT: C 42 ARG cc_start: 0.6798 (pmt100) cc_final: 0.6136 (ttp80) REVERT: C 121 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8375 (tp) REVERT: C 197 GLU cc_start: 0.6695 (tt0) cc_final: 0.6126 (pm20) REVERT: C 306 ILE cc_start: 0.3323 (OUTLIER) cc_final: 0.2971 (tp) REVERT: C 420 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7856 (mtm-85) REVERT: C 524 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8187 (mp0) REVERT: C 542 LEU cc_start: 0.8689 (tt) cc_final: 0.8310 (tp) REVERT: C 699 LYS cc_start: 0.7887 (mmtm) cc_final: 0.7514 (tppt) REVERT: C 888 ARG cc_start: 0.4932 (mmt90) cc_final: 0.4074 (mpt180) REVERT: C 1029 MET cc_start: 0.7143 (ttt) cc_final: 0.6850 (ttm) REVERT: D 79 LYS cc_start: 0.8407 (tmmt) cc_final: 0.8193 (ttpp) REVERT: D 167 ASN cc_start: 0.7503 (m-40) cc_final: 0.7197 (p0) REVERT: D 265 LEU cc_start: 0.7595 (mt) cc_final: 0.7268 (mt) REVERT: D 431 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8112 (mm-30) REVERT: D 808 LEU cc_start: 0.7799 (mt) cc_final: 0.7286 (tt) REVERT: E 104 ARG cc_start: 0.5735 (mtp180) cc_final: 0.5530 (mtp180) REVERT: E 116 MET cc_start: 0.2904 (mtm) cc_final: 0.2071 (tmm) REVERT: E 117 TYR cc_start: 0.1815 (m-80) cc_final: 0.1005 (m-80) REVERT: F 104 ARG cc_start: 0.5206 (mmm160) cc_final: 0.4410 (mmm160) REVERT: F 116 MET cc_start: 0.2826 (mmt) cc_final: 0.2084 (mpp) REVERT: F 123 MET cc_start: 0.6603 (mmm) cc_final: 0.6332 (mmt) outliers start: 66 outliers final: 27 residues processed: 433 average time/residue: 0.4203 time to fit residues: 293.1132 Evaluate side-chains 341 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 309 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 159 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 106 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 348 optimal weight: 0.8980 chunk 262 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 211 optimal weight: 6.9990 chunk 251 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 GLN C 246 GLN C 274 HIS D 274 HIS ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.163990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.124227 restraints weight = 43457.160| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.88 r_work: 0.3322 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32303 Z= 0.140 Angle : 0.855 33.625 43522 Z= 0.366 Chirality : 0.074 1.813 4710 Planarity : 0.004 0.066 5316 Dihedral : 19.341 179.938 5695 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.93 % Favored : 92.91 % Rotamer: Outliers : 2.68 % Allowed : 10.65 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.13), residues: 3754 helix: 0.31 (0.12), residues: 1870 sheet: -2.36 (0.22), residues: 456 loop : -2.60 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 323 HIS 0.015 0.001 HIS A 883 PHE 0.016 0.002 PHE D 258 TYR 0.022 0.001 TYR E 117 ARG 0.006 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 1406) hydrogen bonds : angle 3.98598 ( 4206) SS BOND : bond 0.00440 ( 12) SS BOND : angle 0.95709 ( 24) covalent geometry : bond 0.00324 (32291) covalent geometry : angle 0.85473 (43498) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 348 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6889 (pmt100) cc_final: 0.6117 (ptm-80) REVERT: A 344 ASN cc_start: 0.7471 (t0) cc_final: 0.7005 (t0) REVERT: A 355 ASN cc_start: 0.7211 (t0) cc_final: 0.6995 (t0) REVERT: A 524 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: A 699 LYS cc_start: 0.7966 (mmtm) cc_final: 0.7559 (ttmm) REVERT: A 907 MET cc_start: 0.1381 (mmt) cc_final: 0.1038 (mmt) REVERT: A 938 PHE cc_start: 0.7501 (m-80) cc_final: 0.7289 (m-80) REVERT: B 79 LYS cc_start: 0.8431 (tmmt) cc_final: 0.8129 (ttpp) REVERT: B 172 LYS cc_start: 0.7936 (mttt) cc_final: 0.7636 (tptt) REVERT: B 265 LEU cc_start: 0.7272 (mt) cc_final: 0.6949 (mt) REVERT: B 408 MET cc_start: 0.8147 (mmt) cc_final: 0.7656 (mmm) REVERT: B 414 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.8008 (ptp) REVERT: B 576 SER cc_start: 0.8814 (m) cc_final: 0.8610 (m) REVERT: B 808 LEU cc_start: 0.7718 (mt) cc_final: 0.7370 (tt) REVERT: C 42 ARG cc_start: 0.6829 (pmt100) cc_final: 0.6166 (ptm-80) REVERT: C 121 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8403 (tp) REVERT: C 197 GLU cc_start: 0.6896 (tt0) cc_final: 0.6311 (pm20) REVERT: C 274 HIS cc_start: 0.8171 (t70) cc_final: 0.7915 (t70) REVERT: C 306 ILE cc_start: 0.3272 (OUTLIER) cc_final: 0.2954 (tp) REVERT: C 355 ASN cc_start: 0.7437 (t0) cc_final: 0.7228 (t0) REVERT: C 524 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: C 699 LYS cc_start: 0.7948 (mmtm) cc_final: 0.7646 (tppt) REVERT: C 719 ASP cc_start: 0.7191 (t0) cc_final: 0.6954 (t0) REVERT: C 888 ARG cc_start: 0.5120 (mmt90) cc_final: 0.4140 (mpt180) REVERT: C 1029 MET cc_start: 0.7050 (ttt) cc_final: 0.6626 (mtp) REVERT: D 79 LYS cc_start: 0.8409 (tmmt) cc_final: 0.8116 (ttpp) REVERT: D 167 ASN cc_start: 0.7736 (m-40) cc_final: 0.7355 (p0) REVERT: D 172 LYS cc_start: 0.7958 (mttt) cc_final: 0.7627 (tptt) REVERT: D 265 LEU cc_start: 0.7467 (mt) cc_final: 0.7136 (mt) REVERT: D 408 MET cc_start: 0.8115 (mmt) cc_final: 0.7763 (mmm) REVERT: D 808 LEU cc_start: 0.7767 (mt) cc_final: 0.7350 (tt) REVERT: E 63 LEU cc_start: 0.6669 (mp) cc_final: 0.6230 (tp) REVERT: E 116 MET cc_start: 0.2177 (mtm) cc_final: 0.1673 (tmm) REVERT: E 117 TYR cc_start: 0.1839 (m-80) cc_final: 0.0981 (m-80) REVERT: F 123 MET cc_start: 0.6628 (mmm) cc_final: 0.6368 (mmt) REVERT: F 151 TYR cc_start: 0.6761 (t80) cc_final: 0.6461 (t80) outliers start: 87 outliers final: 49 residues processed: 420 average time/residue: 0.4267 time to fit residues: 294.4780 Evaluate side-chains 334 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 280 time to evaluate : 3.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 159 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 372 optimal weight: 8.9990 chunk 173 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 327 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.163475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.123672 restraints weight = 43755.394| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.11 r_work: 0.3280 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32303 Z= 0.149 Angle : 0.849 34.210 43522 Z= 0.360 Chirality : 0.073 1.795 4710 Planarity : 0.004 0.067 5316 Dihedral : 18.975 179.817 5693 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.90 % Favored : 92.99 % Rotamer: Outliers : 2.98 % Allowed : 11.32 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3754 helix: 0.97 (0.12), residues: 1874 sheet: -2.34 (0.22), residues: 466 loop : -2.46 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 323 HIS 0.010 0.001 HIS A 883 PHE 0.015 0.001 PHE D 258 TYR 0.030 0.001 TYR F 72 ARG 0.005 0.000 ARG C 926 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 1406) hydrogen bonds : angle 3.82140 ( 4206) SS BOND : bond 0.00335 ( 12) SS BOND : angle 0.88108 ( 24) covalent geometry : bond 0.00352 (32291) covalent geometry : angle 0.84866 (43498) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 319 time to evaluate : 3.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6906 (pmt100) cc_final: 0.6072 (ptm-80) REVERT: A 274 HIS cc_start: 0.8187 (t70) cc_final: 0.7750 (t70) REVERT: A 355 ASN cc_start: 0.7156 (t0) cc_final: 0.6871 (t0) REVERT: A 524 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8181 (mp0) REVERT: A 699 LYS cc_start: 0.7991 (mmtm) cc_final: 0.7662 (ttmm) REVERT: A 907 MET cc_start: 0.1280 (mmt) cc_final: 0.0914 (mmt) REVERT: B 46 HIS cc_start: 0.7306 (t70) cc_final: 0.7045 (t70) REVERT: B 79 LYS cc_start: 0.8371 (tmmt) cc_final: 0.8135 (ttpp) REVERT: B 265 LEU cc_start: 0.7189 (mt) cc_final: 0.6853 (mt) REVERT: B 408 MET cc_start: 0.8180 (mmt) cc_final: 0.7869 (mmm) REVERT: B 414 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.8007 (ptp) REVERT: B 576 SER cc_start: 0.8762 (m) cc_final: 0.8552 (m) REVERT: B 808 LEU cc_start: 0.7629 (mt) cc_final: 0.7337 (tt) REVERT: C 42 ARG cc_start: 0.6849 (pmt100) cc_final: 0.6067 (ptm-80) REVERT: C 306 ILE cc_start: 0.3421 (OUTLIER) cc_final: 0.3054 (tp) REVERT: C 355 ASN cc_start: 0.7554 (t0) cc_final: 0.7267 (t0) REVERT: C 524 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: C 699 LYS cc_start: 0.8009 (mmtm) cc_final: 0.7736 (tppt) REVERT: C 719 ASP cc_start: 0.7246 (t0) cc_final: 0.7028 (t0) REVERT: C 880 MET cc_start: 0.6770 (mmm) cc_final: 0.6562 (mmm) REVERT: C 925 ILE cc_start: 0.8031 (mt) cc_final: 0.7818 (tt) REVERT: C 1029 MET cc_start: 0.6974 (ttt) cc_final: 0.6748 (ttm) REVERT: D 79 LYS cc_start: 0.8382 (tmmt) cc_final: 0.8148 (ttpp) REVERT: D 167 ASN cc_start: 0.7793 (m-40) cc_final: 0.7353 (p0) REVERT: D 265 LEU cc_start: 0.7339 (mt) cc_final: 0.7019 (mt) REVERT: D 808 LEU cc_start: 0.7609 (mt) cc_final: 0.7245 (tt) REVERT: E 63 LEU cc_start: 0.6791 (mp) cc_final: 0.6305 (tp) REVERT: E 143 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7304 (mm) REVERT: F 123 MET cc_start: 0.6644 (mmm) cc_final: 0.6395 (mmt) REVERT: F 151 TYR cc_start: 0.6763 (t80) cc_final: 0.6464 (t80) outliers start: 97 outliers final: 60 residues processed: 400 average time/residue: 0.4062 time to fit residues: 267.4591 Evaluate side-chains 349 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 284 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 159 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 252 optimal weight: 5.9990 chunk 247 optimal weight: 0.5980 chunk 224 optimal weight: 3.9990 chunk 376 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 371 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 338 optimal weight: 1.9990 chunk 236 optimal weight: 6.9990 chunk 291 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.165038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.125345 restraints weight = 43629.839| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.09 r_work: 0.3304 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32303 Z= 0.117 Angle : 0.820 33.757 43522 Z= 0.343 Chirality : 0.074 1.811 4710 Planarity : 0.004 0.071 5316 Dihedral : 18.623 179.940 5693 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.47 % Favored : 93.45 % Rotamer: Outliers : 2.25 % Allowed : 12.74 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.56 (0.14), residues: 3754 helix: 1.47 (0.13), residues: 1872 sheet: -2.23 (0.22), residues: 456 loop : -2.31 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP D 323 HIS 0.010 0.001 HIS A 883 PHE 0.015 0.001 PHE A 258 TYR 0.017 0.001 TYR B 280 ARG 0.018 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 1406) hydrogen bonds : angle 3.62431 ( 4206) SS BOND : bond 0.00542 ( 12) SS BOND : angle 0.93608 ( 24) covalent geometry : bond 0.00270 (32291) covalent geometry : angle 0.81982 (43498) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 326 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6897 (pmt100) cc_final: 0.6021 (ptm-80) REVERT: A 524 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: A 699 LYS cc_start: 0.7968 (mmtm) cc_final: 0.7647 (ttmm) REVERT: A 880 MET cc_start: 0.6363 (tpt) cc_final: 0.5848 (tpt) REVERT: A 907 MET cc_start: 0.1223 (mmt) cc_final: 0.0904 (mmt) REVERT: B 79 LYS cc_start: 0.8404 (tmmt) cc_final: 0.8157 (ttpp) REVERT: B 265 LEU cc_start: 0.7058 (mt) cc_final: 0.6685 (mt) REVERT: B 414 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.8012 (ptp) REVERT: B 454 ASP cc_start: 0.6644 (t0) cc_final: 0.6366 (t0) REVERT: B 808 LEU cc_start: 0.7565 (mt) cc_final: 0.7316 (tt) REVERT: C 42 ARG cc_start: 0.6884 (pmt100) cc_final: 0.6052 (ptm-80) REVERT: C 306 ILE cc_start: 0.3382 (OUTLIER) cc_final: 0.2992 (tp) REVERT: C 355 ASN cc_start: 0.7503 (t0) cc_final: 0.7229 (t0) REVERT: C 524 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8217 (mp0) REVERT: C 699 LYS cc_start: 0.8047 (mmtm) cc_final: 0.7752 (tppt) REVERT: C 719 ASP cc_start: 0.7101 (t0) cc_final: 0.6756 (t0) REVERT: C 925 ILE cc_start: 0.8006 (mt) cc_final: 0.7776 (tt) REVERT: C 1029 MET cc_start: 0.6932 (ttt) cc_final: 0.6705 (ttm) REVERT: D 79 LYS cc_start: 0.8375 (tmmt) cc_final: 0.8129 (ttpp) REVERT: D 265 LEU cc_start: 0.7298 (mt) cc_final: 0.6974 (mt) REVERT: D 808 LEU cc_start: 0.7599 (mt) cc_final: 0.7277 (tt) REVERT: E 116 MET cc_start: 0.1664 (mtm) cc_final: 0.1425 (mmt) REVERT: F 116 MET cc_start: 0.2836 (mmt) cc_final: 0.1474 (mpp) REVERT: F 151 TYR cc_start: 0.6724 (t80) cc_final: 0.6466 (t80) outliers start: 73 outliers final: 48 residues processed: 386 average time/residue: 0.4029 time to fit residues: 254.6530 Evaluate side-chains 343 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 291 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 159 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 37 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 265 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 368 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 189 optimal weight: 0.9980 chunk 307 optimal weight: 1.9990 chunk 346 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN A 435 HIS ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.164636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.124837 restraints weight = 43758.234| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.14 r_work: 0.3297 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32303 Z= 0.118 Angle : 0.815 33.757 43522 Z= 0.340 Chirality : 0.073 1.803 4710 Planarity : 0.004 0.076 5316 Dihedral : 18.472 179.048 5693 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.47 % Favored : 93.47 % Rotamer: Outliers : 2.43 % Allowed : 13.14 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.36 (0.14), residues: 3754 helix: 1.65 (0.13), residues: 1884 sheet: -2.12 (0.22), residues: 456 loop : -2.26 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP D 323 HIS 0.009 0.001 HIS A 883 PHE 0.012 0.001 PHE B 56 TYR 0.018 0.001 TYR B 280 ARG 0.021 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 1406) hydrogen bonds : angle 3.56932 ( 4206) SS BOND : bond 0.00307 ( 12) SS BOND : angle 0.84967 ( 24) covalent geometry : bond 0.00273 (32291) covalent geometry : angle 0.81537 (43498) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 318 time to evaluate : 3.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6933 (pmt100) cc_final: 0.6025 (ptm-80) REVERT: A 524 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: A 699 LYS cc_start: 0.7976 (mmtm) cc_final: 0.7676 (ttmm) REVERT: A 907 MET cc_start: 0.1432 (mmt) cc_final: 0.1091 (mmt) REVERT: B 79 LYS cc_start: 0.8431 (tmmt) cc_final: 0.8118 (ttpp) REVERT: B 265 LEU cc_start: 0.7132 (mt) cc_final: 0.6756 (mt) REVERT: B 414 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7997 (ptp) REVERT: B 454 ASP cc_start: 0.6756 (t0) cc_final: 0.6439 (t0) REVERT: B 808 LEU cc_start: 0.7503 (mt) cc_final: 0.7256 (tt) REVERT: C 42 ARG cc_start: 0.6820 (pmt100) cc_final: 0.5960 (ptm-80) REVERT: C 175 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6258 (tp30) REVERT: C 292 MET cc_start: 0.7469 (mtm) cc_final: 0.7235 (mtp) REVERT: C 306 ILE cc_start: 0.3385 (OUTLIER) cc_final: 0.2977 (tp) REVERT: C 355 ASN cc_start: 0.7582 (t0) cc_final: 0.7318 (t0) REVERT: C 524 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8250 (mp0) REVERT: C 699 LYS cc_start: 0.8027 (mmtm) cc_final: 0.7746 (tppt) REVERT: C 719 ASP cc_start: 0.7079 (t0) cc_final: 0.6670 (t0) REVERT: C 925 ILE cc_start: 0.7955 (mt) cc_final: 0.7737 (tt) REVERT: C 1029 MET cc_start: 0.6950 (ttt) cc_final: 0.6736 (ttm) REVERT: D 185 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8147 (pt0) REVERT: D 265 LEU cc_start: 0.7341 (mt) cc_final: 0.6993 (mt) REVERT: D 808 LEU cc_start: 0.7518 (mt) cc_final: 0.7199 (tt) REVERT: E 104 ARG cc_start: 0.5653 (mtp180) cc_final: 0.5421 (mtp180) REVERT: F 116 MET cc_start: 0.2513 (mmt) cc_final: 0.1218 (mpp) REVERT: F 151 TYR cc_start: 0.6770 (t80) cc_final: 0.6493 (t80) outliers start: 79 outliers final: 59 residues processed: 378 average time/residue: 0.4359 time to fit residues: 268.7660 Evaluate side-chains 348 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 283 time to evaluate : 3.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain F residue 159 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 191 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 364 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 296 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 310 optimal weight: 8.9990 chunk 158 optimal weight: 0.0370 chunk 147 optimal weight: 1.9990 chunk 208 optimal weight: 8.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 355 ASN B 46 HIS ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.161956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.122271 restraints weight = 43873.907| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.22 r_work: 0.3251 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32303 Z= 0.170 Angle : 0.851 34.720 43522 Z= 0.360 Chirality : 0.073 1.788 4710 Planarity : 0.004 0.080 5316 Dihedral : 18.492 178.897 5693 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.95 % Favored : 92.94 % Rotamer: Outliers : 2.62 % Allowed : 13.08 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.42 (0.14), residues: 3754 helix: 1.54 (0.12), residues: 1880 sheet: -2.10 (0.22), residues: 466 loop : -2.21 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP D 323 HIS 0.009 0.001 HIS A 883 PHE 0.016 0.002 PHE B 531 TYR 0.018 0.002 TYR D 280 ARG 0.017 0.001 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 1406) hydrogen bonds : angle 3.70269 ( 4206) SS BOND : bond 0.00337 ( 12) SS BOND : angle 1.03334 ( 24) covalent geometry : bond 0.00408 (32291) covalent geometry : angle 0.85110 (43498) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 291 time to evaluate : 3.847 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6871 (pmt100) cc_final: 0.5872 (ptm-80) REVERT: A 109 PHE cc_start: 0.7561 (m-10) cc_final: 0.7103 (m-10) REVERT: A 292 MET cc_start: 0.7439 (mtm) cc_final: 0.7223 (mtp) REVERT: A 524 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: A 699 LYS cc_start: 0.8006 (mmtm) cc_final: 0.7703 (ttmm) REVERT: A 880 MET cc_start: 0.6780 (mmm) cc_final: 0.6438 (tpp) REVERT: A 907 MET cc_start: 0.1097 (mmt) cc_final: 0.0744 (mmt) REVERT: B 265 LEU cc_start: 0.7185 (mt) cc_final: 0.6822 (mt) REVERT: B 393 LYS cc_start: 0.8067 (tppt) cc_final: 0.7515 (tptm) REVERT: B 808 LEU cc_start: 0.7515 (mt) cc_final: 0.7260 (tt) REVERT: C 42 ARG cc_start: 0.6906 (pmt100) cc_final: 0.5971 (ptm-80) REVERT: C 292 MET cc_start: 0.7417 (mtm) cc_final: 0.7182 (mtp) REVERT: C 306 ILE cc_start: 0.3378 (OUTLIER) cc_final: 0.2898 (tp) REVERT: C 355 ASN cc_start: 0.7452 (t0) cc_final: 0.7174 (t0) REVERT: C 524 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8172 (mp0) REVERT: C 699 LYS cc_start: 0.8040 (mmtm) cc_final: 0.7655 (ttmm) REVERT: C 719 ASP cc_start: 0.7249 (t0) cc_final: 0.6816 (t0) REVERT: C 1029 MET cc_start: 0.7020 (ttt) cc_final: 0.6789 (ttm) REVERT: D 185 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8093 (pt0) REVERT: D 265 LEU cc_start: 0.7356 (mt) cc_final: 0.7014 (mt) REVERT: D 808 LEU cc_start: 0.7524 (mt) cc_final: 0.7215 (tt) REVERT: E 104 ARG cc_start: 0.5630 (mtp180) cc_final: 0.5382 (mtp180) REVERT: F 116 MET cc_start: 0.3002 (mmt) cc_final: 0.1654 (mpp) REVERT: F 151 TYR cc_start: 0.6781 (t80) cc_final: 0.6476 (t80) outliers start: 85 outliers final: 64 residues processed: 357 average time/residue: 0.4170 time to fit residues: 245.3529 Evaluate side-chains 344 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 276 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 511 LYS Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain D residue 33 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 159 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 371 optimal weight: 7.9990 chunk 346 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 322 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 190 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 355 ASN A 435 HIS ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.163253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.123433 restraints weight = 43985.251| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 3.11 r_work: 0.3279 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32303 Z= 0.129 Angle : 0.826 34.137 43522 Z= 0.345 Chirality : 0.073 1.802 4710 Planarity : 0.004 0.072 5316 Dihedral : 18.349 179.352 5693 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.26 % Favored : 93.66 % Rotamer: Outliers : 2.52 % Allowed : 13.32 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.23 (0.14), residues: 3754 helix: 1.74 (0.13), residues: 1870 sheet: -2.01 (0.22), residues: 464 loop : -2.15 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP D 323 HIS 0.008 0.001 HIS A 883 PHE 0.012 0.001 PHE B 56 TYR 0.017 0.001 TYR B 280 ARG 0.025 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 1406) hydrogen bonds : angle 3.59490 ( 4206) SS BOND : bond 0.00327 ( 12) SS BOND : angle 1.05785 ( 24) covalent geometry : bond 0.00304 (32291) covalent geometry : angle 0.82538 (43498) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 290 time to evaluate : 3.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6929 (pmt100) cc_final: 0.5926 (ptm-80) REVERT: A 524 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: A 699 LYS cc_start: 0.8050 (mmtm) cc_final: 0.7702 (ttmm) REVERT: A 880 MET cc_start: 0.6978 (mmm) cc_final: 0.6571 (tpt) REVERT: A 907 MET cc_start: 0.1158 (mmt) cc_final: 0.0796 (mmt) REVERT: B 265 LEU cc_start: 0.7157 (mt) cc_final: 0.6807 (mt) REVERT: B 808 LEU cc_start: 0.7511 (mt) cc_final: 0.7302 (tt) REVERT: C 42 ARG cc_start: 0.6900 (pmt100) cc_final: 0.5937 (ptm-80) REVERT: C 292 MET cc_start: 0.7423 (mtm) cc_final: 0.7205 (mtp) REVERT: C 306 ILE cc_start: 0.3296 (OUTLIER) cc_final: 0.2752 (tp) REVERT: C 524 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8178 (mp0) REVERT: C 699 LYS cc_start: 0.8030 (mmtm) cc_final: 0.7771 (tppt) REVERT: C 719 ASP cc_start: 0.7183 (t0) cc_final: 0.6787 (t0) REVERT: C 880 MET cc_start: 0.6553 (mmm) cc_final: 0.6294 (tpt) REVERT: C 1029 MET cc_start: 0.7014 (ttt) cc_final: 0.6784 (ttm) REVERT: D 50 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7246 (pp) REVERT: D 185 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8094 (pt0) REVERT: D 265 LEU cc_start: 0.7369 (mt) cc_final: 0.7035 (mt) REVERT: D 808 LEU cc_start: 0.7532 (mt) cc_final: 0.7221 (tt) REVERT: E 116 MET cc_start: 0.1603 (mmp) cc_final: 0.0068 (mpp) REVERT: F 116 MET cc_start: 0.2843 (mmt) cc_final: 0.1470 (mpp) REVERT: F 151 TYR cc_start: 0.6810 (t80) cc_final: 0.6502 (t80) outliers start: 82 outliers final: 64 residues processed: 354 average time/residue: 0.4059 time to fit residues: 235.3953 Evaluate side-chains 344 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 275 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain D residue 33 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 104 ARG Chi-restraints excluded: chain F residue 159 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 376 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 288 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 169 optimal weight: 0.0770 chunk 26 optimal weight: 0.0050 chunk 194 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 328 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 overall best weight: 0.5952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.165048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.125528 restraints weight = 43770.881| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.12 r_work: 0.3308 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 32303 Z= 0.104 Angle : 0.809 33.576 43522 Z= 0.336 Chirality : 0.073 1.811 4710 Planarity : 0.004 0.067 5316 Dihedral : 18.092 179.437 5693 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.37 % Favored : 93.58 % Rotamer: Outliers : 2.22 % Allowed : 13.54 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.06 (0.14), residues: 3754 helix: 1.87 (0.13), residues: 1886 sheet: -1.94 (0.23), residues: 456 loop : -2.10 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP D 323 HIS 0.008 0.001 HIS A 883 PHE 0.012 0.001 PHE B 56 TYR 0.018 0.001 TYR D 280 ARG 0.022 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.02988 ( 1406) hydrogen bonds : angle 3.48527 ( 4206) SS BOND : bond 0.00249 ( 12) SS BOND : angle 0.95111 ( 24) covalent geometry : bond 0.00236 (32291) covalent geometry : angle 0.80881 (43498) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 298 time to evaluate : 3.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6919 (pmt100) cc_final: 0.5982 (ptm-80) REVERT: A 524 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: A 699 LYS cc_start: 0.8031 (mmtm) cc_final: 0.7689 (ttmm) REVERT: A 880 MET cc_start: 0.6840 (mmm) cc_final: 0.6445 (tpp) REVERT: A 907 MET cc_start: 0.1245 (mmt) cc_final: 0.0919 (mmt) REVERT: B 265 LEU cc_start: 0.7186 (mt) cc_final: 0.6828 (mt) REVERT: B 808 LEU cc_start: 0.7568 (mt) cc_final: 0.7346 (tt) REVERT: C 42 ARG cc_start: 0.6882 (pmt100) cc_final: 0.5916 (ptm-80) REVERT: C 175 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6150 (tp30) REVERT: C 306 ILE cc_start: 0.3264 (OUTLIER) cc_final: 0.2755 (tp) REVERT: C 524 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8250 (mp0) REVERT: C 699 LYS cc_start: 0.8042 (mmtm) cc_final: 0.7665 (ttmm) REVERT: C 719 ASP cc_start: 0.7110 (t0) cc_final: 0.6734 (t0) REVERT: C 807 MET cc_start: 0.8245 (mtm) cc_final: 0.7954 (mtm) REVERT: C 880 MET cc_start: 0.6801 (mmm) cc_final: 0.6504 (tpt) REVERT: C 1029 MET cc_start: 0.7003 (ttt) cc_final: 0.6777 (ttm) REVERT: D 50 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7203 (pp) REVERT: D 185 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8146 (pt0) REVERT: D 265 LEU cc_start: 0.7386 (mt) cc_final: 0.7019 (mt) REVERT: D 808 LEU cc_start: 0.7534 (mt) cc_final: 0.7228 (tt) REVERT: E 116 MET cc_start: 0.1277 (mmp) cc_final: 0.0172 (ptp) REVERT: F 116 MET cc_start: 0.2874 (mmt) cc_final: 0.1497 (mpp) REVERT: F 151 TYR cc_start: 0.6797 (t80) cc_final: 0.6492 (t80) outliers start: 72 outliers final: 51 residues processed: 353 average time/residue: 0.4173 time to fit residues: 239.9107 Evaluate side-chains 342 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 285 time to evaluate : 3.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 805 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 104 ARG Chi-restraints excluded: chain F residue 159 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 180 optimal weight: 7.9990 chunk 260 optimal weight: 8.9990 chunk 253 optimal weight: 9.9990 chunk 76 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 346 optimal weight: 0.2980 chunk 235 optimal weight: 0.8980 chunk 306 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 276 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 246 GLN A 435 HIS ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.162520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.123133 restraints weight = 43837.323| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.26 r_work: 0.3264 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32303 Z= 0.151 Angle : 0.837 34.354 43522 Z= 0.351 Chirality : 0.073 1.793 4710 Planarity : 0.004 0.067 5316 Dihedral : 18.095 179.213 5693 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.93 % Favored : 92.99 % Rotamer: Outliers : 2.00 % Allowed : 13.72 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3754 helix: 1.74 (0.12), residues: 1880 sheet: -1.86 (0.23), residues: 476 loop : -2.11 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP D 323 HIS 0.014 0.001 HIS A 435 PHE 0.040 0.001 PHE A 258 TYR 0.022 0.001 TYR C 816 ARG 0.021 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 1406) hydrogen bonds : angle 3.60971 ( 4206) SS BOND : bond 0.00338 ( 12) SS BOND : angle 0.99887 ( 24) covalent geometry : bond 0.00360 (32291) covalent geometry : angle 0.83660 (43498) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 289 time to evaluate : 3.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6986 (pmt100) cc_final: 0.6001 (ptm-80) REVERT: A 524 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8227 (mp0) REVERT: A 699 LYS cc_start: 0.8041 (mmtm) cc_final: 0.7715 (ttmm) REVERT: A 807 MET cc_start: 0.8254 (mtm) cc_final: 0.7955 (mtm) REVERT: A 880 MET cc_start: 0.6911 (mmm) cc_final: 0.6547 (tpp) REVERT: A 907 MET cc_start: 0.1027 (mmt) cc_final: 0.0663 (mmt) REVERT: B 71 TYR cc_start: 0.7822 (m-80) cc_final: 0.7509 (m-80) REVERT: B 185 GLU cc_start: 0.8465 (pt0) cc_final: 0.8087 (pt0) REVERT: B 265 LEU cc_start: 0.7155 (mt) cc_final: 0.6794 (mt) REVERT: B 808 LEU cc_start: 0.7478 (mt) cc_final: 0.7259 (tt) REVERT: C 42 ARG cc_start: 0.6950 (pmt100) cc_final: 0.5939 (ptm-80) REVERT: C 524 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8181 (mp0) REVERT: C 699 LYS cc_start: 0.8066 (mmtm) cc_final: 0.7671 (ttmm) REVERT: C 719 ASP cc_start: 0.7223 (t0) cc_final: 0.6794 (t0) REVERT: C 807 MET cc_start: 0.8270 (mtm) cc_final: 0.7990 (mtm) REVERT: C 813 GLU cc_start: 0.7688 (tt0) cc_final: 0.7464 (tt0) REVERT: C 880 MET cc_start: 0.6669 (mmm) cc_final: 0.6393 (tpt) REVERT: C 1029 MET cc_start: 0.7058 (ttt) cc_final: 0.6832 (ttm) REVERT: D 50 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7117 (pp) REVERT: D 185 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8178 (pt0) REVERT: D 265 LEU cc_start: 0.7362 (mt) cc_final: 0.7017 (mt) REVERT: D 808 LEU cc_start: 0.7487 (mt) cc_final: 0.7212 (tt) REVERT: E 116 MET cc_start: 0.1296 (mmp) cc_final: 0.0160 (ptp) REVERT: F 116 MET cc_start: 0.2766 (mmt) cc_final: 0.1364 (mpp) REVERT: F 151 TYR cc_start: 0.6837 (t80) cc_final: 0.6527 (t80) outliers start: 65 outliers final: 56 residues processed: 342 average time/residue: 0.4242 time to fit residues: 236.2717 Evaluate side-chains 339 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 279 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 741 SER Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 104 ARG Chi-restraints excluded: chain F residue 159 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 200 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 257 optimal weight: 0.0770 chunk 47 optimal weight: 0.8980 chunk 234 optimal weight: 0.5980 chunk 177 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 332 optimal weight: 1.9990 chunk 245 optimal weight: 0.9980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 435 HIS ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.164432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.124783 restraints weight = 43772.303| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.12 r_work: 0.3301 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32303 Z= 0.110 Angle : 0.816 33.683 43522 Z= 0.340 Chirality : 0.073 1.811 4710 Planarity : 0.004 0.064 5316 Dihedral : 17.948 179.553 5693 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.31 % Favored : 93.63 % Rotamer: Outliers : 1.94 % Allowed : 14.15 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % 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: 3754 helix: 1.87 (0.13), residues: 1888 sheet: -1.85 (0.23), residues: 454 loop : -2.06 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 323 HIS 0.008 0.001 HIS A 883 PHE 0.037 0.001 PHE A 258 TYR 0.022 0.001 TYR C 816 ARG 0.020 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.03039 ( 1406) hydrogen bonds : angle 3.49854 ( 4206) SS BOND : bond 0.00256 ( 12) SS BOND : angle 0.86901 ( 24) covalent geometry : bond 0.00252 (32291) covalent geometry : angle 0.81627 (43498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17770.31 seconds wall clock time: 307 minutes 50.18 seconds (18470.18 seconds total)