Starting phenix.real_space_refine on Tue Aug 26 01:36:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ss6_40745/08_2025/8ss6_40745.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ss6_40745/08_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_40745/08_2025/8ss6_40745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ss6_40745/08_2025/8ss6_40745.map" model { file = "/net/cci-nas-00/data/ceres_data/8ss6_40745/08_2025/8ss6_40745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ss6_40745/08_2025/8ss6_40745.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.59, per 1000 atoms: 0.21 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: 2.35 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.84 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: 6.40 Time building geometry restraints manager: 3.10 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 1110) selection = (chain 'C' and resid 10 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 202 or (resid 203 and (name C13 or name C14 or n \ ame 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 25.840 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.730 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG C 141 TYR 0.028 0.002 TYR B 177 PHE 0.024 0.003 PHE D 101 TRP 0.041 0.003 TRP C 323 HIS 0.013 0.002 HIS C 93 Details of bonding type rmsd covalent geometry : bond 0.01703 (32291) covalent geometry : angle 1.37606 (43498) SS BOND : bond 0.03264 ( 12) SS BOND : angle 1.22886 ( 24) hydrogen bonds : bond 0.28900 ( 1406) hydrogen bonds : angle 10.41459 ( 4206) *********************** 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 : 1.154 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: 0.2105 time to fit residues: 252.8034 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 : 1.140 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.1980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.0060 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- 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 747 ASN C 10 ASN C 46 HIS ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 GLN C 246 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 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN D 435 HIS D 747 ASN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 HIS F 101 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.165898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.126335 restraints weight = 43442.996| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.89 r_work: 0.3352 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32303 Z= 0.145 Angle : 0.900 35.146 43522 Z= 0.396 Chirality : 0.075 1.843 4710 Planarity : 0.005 0.069 5316 Dihedral : 20.393 179.891 5695 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.74 % Favored : 92.94 % Rotamer: Outliers : 2.03 % Allowed : 9.69 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.03 (0.12), residues: 3754 helix: -1.22 (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 ARG 0.006 0.001 ARG E 104 TYR 0.019 0.001 TYR E 117 PHE 0.022 0.002 PHE A 258 TRP 0.022 0.002 TRP D 323 HIS 0.004 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00310 (32291) covalent geometry : angle 0.89970 (43498) SS BOND : bond 0.00389 ( 12) SS BOND : angle 1.51726 ( 24) hydrogen bonds : bond 0.04547 ( 1406) hydrogen bonds : angle 4.61724 ( 4206) *********************** 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 454 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 388 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6882 (pmt100) cc_final: 0.6107 (ttp80) REVERT: A 274 HIS cc_start: 0.8110 (t-90) cc_final: 0.7800 (t70) REVERT: A 292 MET cc_start: 0.7539 (mtm) cc_final: 0.7246 (mtp) REVERT: A 355 ASN cc_start: 0.6931 (t0) cc_final: 0.6691 (t0) REVERT: A 457 THR cc_start: 0.8366 (m) cc_final: 0.8158 (p) REVERT: A 542 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8234 (tp) REVERT: A 861 TRP cc_start: 0.7395 (m100) cc_final: 0.7091 (m100) REVERT: A 965 PHE cc_start: 0.8002 (m-80) cc_final: 0.7621 (m-10) REVERT: B 79 LYS cc_start: 0.8322 (tmmt) cc_final: 0.8053 (ttpp) REVERT: B 104 ASP cc_start: 0.6821 (p0) cc_final: 0.6573 (p0) REVERT: B 132 LYS cc_start: 0.8995 (ttmm) cc_final: 0.8722 (ttmm) REVERT: B 167 ASN cc_start: 0.7568 (m-40) cc_final: 0.7186 (p0) REVERT: B 265 LEU cc_start: 0.7310 (mt) cc_final: 0.7014 (mt) REVERT: B 286 TYR cc_start: 0.6996 (t80) cc_final: 0.6748 (t80) REVERT: B 414 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8145 (ptp) REVERT: B 576 SER cc_start: 0.8873 (m) cc_final: 0.8653 (m) REVERT: B 808 LEU cc_start: 0.7747 (mt) cc_final: 0.7292 (tt) REVERT: C 42 ARG cc_start: 0.6805 (pmt100) cc_final: 0.6155 (ttp80) REVERT: C 121 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8384 (tp) REVERT: C 197 GLU cc_start: 0.6704 (tt0) cc_final: 0.6143 (pm20) REVERT: C 306 ILE cc_start: 0.3317 (OUTLIER) cc_final: 0.2962 (tp) REVERT: C 420 ARG cc_start: 0.8118 (mtm180) cc_final: 0.7816 (ttp-110) REVERT: C 524 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: C 542 LEU cc_start: 0.8684 (tt) cc_final: 0.8311 (tp) REVERT: C 699 LYS cc_start: 0.7874 (mmtm) cc_final: 0.7502 (tppt) REVERT: C 888 ARG cc_start: 0.4919 (mmt90) cc_final: 0.4067 (mpt180) REVERT: C 1029 MET cc_start: 0.7157 (ttt) cc_final: 0.6880 (ttm) REVERT: D 79 LYS cc_start: 0.8401 (tmmt) cc_final: 0.8193 (ttpp) REVERT: D 167 ASN cc_start: 0.7497 (m-40) cc_final: 0.7197 (p0) REVERT: D 265 LEU cc_start: 0.7589 (mt) cc_final: 0.7263 (mt) REVERT: D 431 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8097 (mm-30) REVERT: E 104 ARG cc_start: 0.5727 (mtp180) cc_final: 0.5508 (mtp180) REVERT: E 116 MET cc_start: 0.2901 (mtm) cc_final: 0.2071 (tmm) REVERT: E 117 TYR cc_start: 0.1814 (m-80) cc_final: 0.1039 (m-80) REVERT: F 104 ARG cc_start: 0.5196 (mmm160) cc_final: 0.4405 (mmm160) REVERT: F 116 MET cc_start: 0.2822 (mmt) cc_final: 0.2084 (mpp) REVERT: F 123 MET cc_start: 0.6583 (mmm) cc_final: 0.6313 (mmt) outliers start: 66 outliers final: 26 residues processed: 442 average time/residue: 0.1783 time to fit residues: 128.1654 Evaluate side-chains 338 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 307 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain F residue 159 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 65 optimal weight: 0.0870 chunk 156 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 217 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 360 optimal weight: 10.0000 chunk 326 optimal weight: 0.0980 chunk 342 optimal weight: 1.9990 chunk 317 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- 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 B 147 GLN B 274 HIS B 359 ASN ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 GLN C 274 HIS D 274 HIS ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.166153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.126473 restraints weight = 43529.867| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.78 r_work: 0.3366 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 32303 Z= 0.113 Angle : 0.838 33.324 43522 Z= 0.356 Chirality : 0.074 1.829 4710 Planarity : 0.004 0.068 5316 Dihedral : 19.421 179.960 5695 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.85 % Favored : 93.02 % Rotamer: Outliers : 2.12 % Allowed : 11.08 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.13), residues: 3754 helix: 0.29 (0.12), residues: 1888 sheet: -2.36 (0.23), residues: 446 loop : -2.60 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 308 TYR 0.022 0.001 TYR E 117 PHE 0.015 0.001 PHE C 109 TRP 0.014 0.001 TRP B 262 HIS 0.014 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00248 (32291) covalent geometry : angle 0.83805 (43498) SS BOND : bond 0.00694 ( 12) SS BOND : angle 1.00682 ( 24) hydrogen bonds : bond 0.03626 ( 1406) hydrogen bonds : angle 3.95005 ( 4206) *********************** 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 423 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 354 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6866 (pmt100) cc_final: 0.6162 (ptm-80) REVERT: A 274 HIS cc_start: 0.8148 (t-90) cc_final: 0.7792 (t70) REVERT: A 355 ASN cc_start: 0.7225 (t0) cc_final: 0.6955 (t0) REVERT: A 457 THR cc_start: 0.8440 (m) cc_final: 0.8190 (p) REVERT: A 524 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: A 861 TRP cc_start: 0.7534 (m100) cc_final: 0.7305 (m100) REVERT: B 79 LYS cc_start: 0.8317 (tmmt) cc_final: 0.8027 (ttpp) REVERT: B 132 LYS cc_start: 0.8974 (ttmm) cc_final: 0.8722 (ttmm) REVERT: B 172 LYS cc_start: 0.7858 (mttt) cc_final: 0.7559 (tptt) REVERT: B 265 LEU cc_start: 0.7248 (mt) cc_final: 0.6941 (mt) REVERT: B 408 MET cc_start: 0.8077 (mmt) cc_final: 0.7634 (mmm) REVERT: B 414 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8147 (ptp) REVERT: B 808 LEU cc_start: 0.7757 (mt) cc_final: 0.7382 (tt) REVERT: C 42 ARG cc_start: 0.6756 (pmt100) cc_final: 0.6198 (ptm-80) REVERT: C 121 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8353 (tp) REVERT: C 197 GLU cc_start: 0.6651 (tt0) cc_final: 0.6168 (pm20) REVERT: C 274 HIS cc_start: 0.8272 (t70) cc_final: 0.8054 (t70) REVERT: C 355 ASN cc_start: 0.7418 (t0) cc_final: 0.7056 (t0) REVERT: C 420 ARG cc_start: 0.8108 (mtm180) cc_final: 0.7884 (ttp-110) REVERT: C 503 MET cc_start: 0.8398 (ttm) cc_final: 0.8139 (ttm) REVERT: C 524 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: C 699 LYS cc_start: 0.7911 (mmtm) cc_final: 0.7605 (tppt) REVERT: C 719 ASP cc_start: 0.6991 (t0) cc_final: 0.6754 (t0) REVERT: C 888 ARG cc_start: 0.5097 (mmt90) cc_final: 0.4106 (mpt180) REVERT: C 1029 MET cc_start: 0.6960 (ttt) cc_final: 0.6594 (mtp) REVERT: D 79 LYS cc_start: 0.8337 (tmmt) cc_final: 0.8050 (ttpp) REVERT: D 167 ASN cc_start: 0.7676 (m-40) cc_final: 0.7340 (p0) REVERT: D 172 LYS cc_start: 0.7925 (mttt) cc_final: 0.7627 (tptt) REVERT: D 265 LEU cc_start: 0.7487 (mt) cc_final: 0.7158 (mt) REVERT: D 408 MET cc_start: 0.8052 (mmt) cc_final: 0.7775 (mmm) REVERT: D 431 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7994 (mm-30) REVERT: D 808 LEU cc_start: 0.7679 (mt) cc_final: 0.7240 (tt) REVERT: E 104 ARG cc_start: 0.5610 (mtp180) cc_final: 0.4385 (mtp180) REVERT: E 116 MET cc_start: 0.2312 (mtm) cc_final: 0.2083 (tmm) REVERT: F 123 MET cc_start: 0.6658 (mmm) cc_final: 0.6411 (mmt) REVERT: F 151 TYR cc_start: 0.6741 (t80) cc_final: 0.6514 (t80) outliers start: 69 outliers final: 35 residues processed: 412 average time/residue: 0.1719 time to fit residues: 116.6613 Evaluate side-chains 331 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 292 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 289 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 704 LEU 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 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 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 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 788 SER Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 143 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 252 optimal weight: 4.9990 chunk 122 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 110 optimal weight: 0.0050 chunk 128 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 349 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- 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 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 GLN ** 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 = 0.4101 r_free = 0.4101 target = 0.164999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.124808 restraints weight = 43644.615| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.10 r_work: 0.3305 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32303 Z= 0.133 Angle : 0.837 33.848 43522 Z= 0.355 Chirality : 0.074 1.804 4710 Planarity : 0.004 0.066 5316 Dihedral : 18.870 179.847 5693 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.61 % Favored : 93.31 % Rotamer: Outliers : 2.71 % Allowed : 11.29 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.14), residues: 3754 helix: 1.06 (0.12), residues: 1874 sheet: -2.28 (0.22), residues: 456 loop : -2.40 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 65 TYR 0.030 0.001 TYR F 72 PHE 0.014 0.001 PHE D 258 TRP 0.014 0.001 TRP B 323 HIS 0.012 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00308 (32291) covalent geometry : angle 0.83726 (43498) SS BOND : bond 0.00304 ( 12) SS BOND : angle 0.83295 ( 24) hydrogen bonds : bond 0.03381 ( 1406) hydrogen bonds : angle 3.77207 ( 4206) *********************** 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 432 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 344 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6918 (pmt100) cc_final: 0.6109 (ptm-80) REVERT: A 274 HIS cc_start: 0.8169 (t-90) cc_final: 0.7884 (t-90) REVERT: A 344 ASN cc_start: 0.7348 (t0) cc_final: 0.7101 (t0) REVERT: A 355 ASN cc_start: 0.7229 (t0) cc_final: 0.6925 (t0) REVERT: A 524 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: A 699 LYS cc_start: 0.7988 (mmtm) cc_final: 0.7640 (ttmm) REVERT: B 46 HIS cc_start: 0.7317 (t70) cc_final: 0.7082 (t70) REVERT: B 79 LYS cc_start: 0.8307 (tmmt) cc_final: 0.8057 (ttpp) REVERT: B 265 LEU cc_start: 0.7163 (mt) cc_final: 0.6810 (mt) REVERT: B 408 MET cc_start: 0.8151 (mmt) cc_final: 0.7899 (mmm) REVERT: B 414 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8113 (ptp) REVERT: B 808 LEU cc_start: 0.7695 (mt) cc_final: 0.7361 (tt) REVERT: C 42 ARG cc_start: 0.6827 (pmt100) cc_final: 0.6119 (ptm-80) REVERT: C 197 GLU cc_start: 0.6783 (tt0) cc_final: 0.6193 (pm20) REVERT: C 274 HIS cc_start: 0.8236 (t70) cc_final: 0.7911 (t70) REVERT: C 306 ILE cc_start: 0.3252 (OUTLIER) cc_final: 0.2885 (tp) REVERT: C 344 ASN cc_start: 0.7327 (t0) cc_final: 0.7051 (t0) REVERT: C 524 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: C 699 LYS cc_start: 0.8043 (mmtm) cc_final: 0.7731 (tppt) REVERT: C 719 ASP cc_start: 0.7041 (t0) cc_final: 0.6834 (t0) REVERT: C 880 MET cc_start: 0.6679 (mmm) cc_final: 0.6445 (mmm) REVERT: C 888 ARG cc_start: 0.4981 (mmt90) cc_final: 0.4032 (mtm-85) REVERT: C 925 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7714 (tt) REVERT: C 1029 MET cc_start: 0.6953 (ttt) cc_final: 0.6532 (mtp) REVERT: D 79 LYS cc_start: 0.8285 (tmmt) cc_final: 0.8037 (ttpp) REVERT: D 167 ASN cc_start: 0.7711 (m-40) cc_final: 0.7293 (p0) REVERT: D 172 LYS cc_start: 0.7965 (mttt) cc_final: 0.7559 (tptt) REVERT: D 265 LEU cc_start: 0.7333 (mt) cc_final: 0.7011 (mt) REVERT: D 408 MET cc_start: 0.8130 (mmt) cc_final: 0.7886 (mmm) REVERT: D 431 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7959 (mm-30) REVERT: D 808 LEU cc_start: 0.7596 (mt) cc_final: 0.7219 (tt) REVERT: E 63 LEU cc_start: 0.6244 (mm) cc_final: 0.5878 (tp) REVERT: E 116 MET cc_start: 0.2807 (mtm) cc_final: 0.2367 (mmt) REVERT: F 116 MET cc_start: 0.2558 (mmt) cc_final: 0.1350 (mpp) REVERT: F 123 MET cc_start: 0.6600 (mmm) cc_final: 0.6325 (mmt) REVERT: F 151 TYR cc_start: 0.6698 (t80) cc_final: 0.6449 (t80) outliers start: 88 outliers final: 49 residues processed: 416 average time/residue: 0.1773 time to fit residues: 120.5432 Evaluate side-chains 353 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 299 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 514 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 527 MET 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 973 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 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 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 B residue 720 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 601 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 925 ILE Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain D residue 44 THR 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 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 F residue 159 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 208 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 373 optimal weight: 0.0970 chunk 53 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 236 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 334 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 412 HIS ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS B 219 HIS B 355 ASN C 60 ASN C 246 GLN ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 HIS ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.159167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.118850 restraints weight = 44043.675| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.11 r_work: 0.3213 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 32303 Z= 0.274 Angle : 0.934 35.987 43522 Z= 0.407 Chirality : 0.075 1.766 4710 Planarity : 0.005 0.070 5316 Dihedral : 19.227 179.949 5693 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.91 % Favored : 91.90 % Rotamer: Outliers : 3.02 % Allowed : 12.37 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.14), residues: 3754 helix: 0.83 (0.12), residues: 1868 sheet: -2.31 (0.22), residues: 468 loop : -2.46 (0.15), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 926 TYR 0.024 0.002 TYR D 77 PHE 0.024 0.002 PHE D 258 TRP 0.019 0.002 TRP D 323 HIS 0.010 0.002 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00661 (32291) covalent geometry : angle 0.93356 (43498) SS BOND : bond 0.00440 ( 12) SS BOND : angle 1.09731 ( 24) hydrogen bonds : bond 0.04130 ( 1406) hydrogen bonds : angle 4.14694 ( 4206) *********************** 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 406 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 308 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6963 (pmt100) cc_final: 0.5989 (ptm-80) REVERT: A 344 ASN cc_start: 0.7483 (t0) cc_final: 0.7148 (t0) REVERT: A 355 ASN cc_start: 0.7093 (t0) cc_final: 0.6733 (t0) REVERT: A 524 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8256 (mp0) REVERT: A 699 LYS cc_start: 0.8029 (mmtm) cc_final: 0.7694 (ttmm) REVERT: B 46 HIS cc_start: 0.7257 (t70) cc_final: 0.7014 (t70) REVERT: B 79 LYS cc_start: 0.8636 (tmmt) cc_final: 0.8418 (ttpp) REVERT: B 167 ASN cc_start: 0.7923 (m-40) cc_final: 0.7330 (p0) REVERT: B 265 LEU cc_start: 0.7170 (mt) cc_final: 0.6842 (mt) REVERT: B 414 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7920 (ptp) REVERT: B 808 LEU cc_start: 0.7644 (mt) cc_final: 0.7352 (tt) REVERT: C 42 ARG cc_start: 0.6893 (pmt100) cc_final: 0.6018 (ptm-80) REVERT: C 306 ILE cc_start: 0.3268 (OUTLIER) cc_final: 0.2763 (tp) REVERT: C 344 ASN cc_start: 0.7522 (t0) cc_final: 0.7196 (t0) REVERT: C 524 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: C 719 ASP cc_start: 0.7533 (t0) cc_final: 0.7034 (t0) REVERT: C 880 MET cc_start: 0.6802 (mmm) cc_final: 0.6503 (tpp) REVERT: C 1029 MET cc_start: 0.7119 (ttt) cc_final: 0.6834 (ttm) REVERT: D 79 LYS cc_start: 0.8600 (tmmt) cc_final: 0.8395 (ttpp) REVERT: D 167 ASN cc_start: 0.7843 (m-40) cc_final: 0.7298 (p0) REVERT: D 265 LEU cc_start: 0.7355 (mt) cc_final: 0.7028 (mt) REVERT: D 431 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8286 (mm-30) REVERT: D 808 LEU cc_start: 0.7613 (mt) cc_final: 0.7314 (tt) REVERT: E 63 LEU cc_start: 0.6312 (mm) cc_final: 0.5937 (tp) REVERT: E 64 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.6145 (mm) REVERT: E 116 MET cc_start: 0.2272 (mtm) cc_final: 0.1963 (mmt) REVERT: F 116 MET cc_start: 0.2764 (mmt) cc_final: 0.1485 (mpp) REVERT: F 151 TYR cc_start: 0.6716 (t80) cc_final: 0.6324 (t80) outliers start: 98 outliers final: 71 residues processed: 390 average time/residue: 0.1971 time to fit residues: 126.3122 Evaluate side-chains 356 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 280 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 329 ILE 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 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 B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 140 ASP 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 233 LEU 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 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 720 THR Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 70 VAL 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 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 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 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 741 SER 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 64 LEU 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 102 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 93 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 303 optimal weight: 9.9990 chunk 172 optimal weight: 0.5980 chunk 288 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 78 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 C 246 GLN D 13 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.164290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.124574 restraints weight = 43504.590| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.07 r_work: 0.3296 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32303 Z= 0.109 Angle : 0.818 33.845 43522 Z= 0.343 Chirality : 0.074 1.819 4710 Planarity : 0.004 0.073 5316 Dihedral : 18.697 179.950 5693 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.18 % Favored : 93.74 % Rotamer: Outliers : 2.03 % Allowed : 13.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.14), residues: 3754 helix: 1.52 (0.13), residues: 1862 sheet: -2.16 (0.23), residues: 460 loop : -2.26 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1031 TYR 0.026 0.001 TYR F 72 PHE 0.014 0.001 PHE A 258 TRP 0.020 0.001 TRP D 323 HIS 0.011 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00245 (32291) covalent geometry : angle 0.81800 (43498) SS BOND : bond 0.00261 ( 12) SS BOND : angle 1.13973 ( 24) hydrogen bonds : bond 0.03183 ( 1406) hydrogen bonds : angle 3.65968 ( 4206) *********************** 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 392 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 326 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6861 (pmt100) cc_final: 0.5789 (ptm-80) REVERT: A 344 ASN cc_start: 0.7343 (t0) cc_final: 0.7023 (t0) REVERT: A 355 ASN cc_start: 0.7288 (t0) cc_final: 0.6925 (t0) REVERT: A 524 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8187 (mp0) REVERT: A 699 LYS cc_start: 0.7963 (mmtm) cc_final: 0.7649 (ttmm) REVERT: A 939 MET cc_start: 0.6740 (ttt) cc_final: 0.6497 (ttt) REVERT: B 265 LEU cc_start: 0.7140 (mt) cc_final: 0.6774 (mt) REVERT: B 414 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7933 (ptp) REVERT: B 459 ILE cc_start: 0.8338 (mt) cc_final: 0.8108 (mm) REVERT: B 808 LEU cc_start: 0.7494 (mt) cc_final: 0.7288 (tt) REVERT: C 42 ARG cc_start: 0.6912 (pmt100) cc_final: 0.6013 (ptm-80) REVERT: C 306 ILE cc_start: 0.3285 (OUTLIER) cc_final: 0.2823 (tp) REVERT: C 524 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8278 (mp0) REVERT: C 699 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7667 (ttmm) REVERT: C 719 ASP cc_start: 0.7357 (t0) cc_final: 0.6915 (t0) REVERT: C 880 MET cc_start: 0.6662 (mmm) cc_final: 0.6367 (tpp) REVERT: C 925 ILE cc_start: 0.7936 (mt) cc_final: 0.7712 (tt) REVERT: C 1029 MET cc_start: 0.7034 (ttt) cc_final: 0.6775 (ttm) REVERT: D 167 ASN cc_start: 0.7860 (m-40) cc_final: 0.7397 (p0) REVERT: D 185 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8194 (pt0) REVERT: D 265 LEU cc_start: 0.7298 (mt) cc_final: 0.6951 (mt) REVERT: D 431 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8124 (mm-30) REVERT: D 808 LEU cc_start: 0.7544 (mt) cc_final: 0.7234 (tt) REVERT: E 63 LEU cc_start: 0.6255 (mm) cc_final: 0.5893 (tp) REVERT: E 64 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6344 (mm) REVERT: E 116 MET cc_start: 0.2205 (mtm) cc_final: 0.1808 (mmt) REVERT: E 117 TYR cc_start: 0.4712 (t80) cc_final: 0.4394 (t80) REVERT: F 151 TYR cc_start: 0.6741 (t80) cc_final: 0.6450 (t80) outliers start: 66 outliers final: 43 residues processed: 377 average time/residue: 0.2071 time to fit residues: 127.1475 Evaluate side-chains 338 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 289 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 511 LYS 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 957 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 82 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 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 543 VAL Chi-restraints excluded: chain B residue 704 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 341 LEU Chi-restraints excluded: chain C residue 511 LYS Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 534 ILE 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 973 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 354 ILE 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 720 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 120 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 121 optimal weight: 5.9990 chunk 357 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 285 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 157 optimal weight: 0.0060 chunk 300 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 189 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** 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 = 0.4087 r_free = 0.4087 target = 0.164063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.124445 restraints weight = 43864.076| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.07 r_work: 0.3298 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4164 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= 0.112 Angle : 0.814 33.740 43522 Z= 0.340 Chirality : 0.073 1.804 4710 Planarity : 0.004 0.078 5316 Dihedral : 18.407 179.021 5693 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.58 % Favored : 93.37 % Rotamer: Outliers : 2.31 % Allowed : 13.51 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.14), residues: 3754 helix: 1.68 (0.13), residues: 1892 sheet: -2.08 (0.23), residues: 456 loop : -2.15 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1031 TYR 0.018 0.001 TYR D 280 PHE 0.012 0.001 PHE C 937 TRP 0.020 0.001 TRP D 323 HIS 0.010 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00255 (32291) covalent geometry : angle 0.81401 (43498) SS BOND : bond 0.00312 ( 12) SS BOND : angle 1.05057 ( 24) hydrogen bonds : bond 0.03097 ( 1406) hydrogen bonds : angle 3.55326 ( 4206) *********************** 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 386 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 311 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6842 (pmt100) cc_final: 0.5770 (ptm-80) REVERT: A 344 ASN cc_start: 0.7348 (t0) cc_final: 0.7017 (t0) REVERT: A 355 ASN cc_start: 0.7236 (t0) cc_final: 0.6905 (t0) REVERT: A 524 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8193 (mp0) REVERT: A 699 LYS cc_start: 0.7958 (mmtm) cc_final: 0.7666 (ttmm) REVERT: B 46 HIS cc_start: 0.7364 (t70) cc_final: 0.7039 (t-170) REVERT: B 265 LEU cc_start: 0.7141 (mt) cc_final: 0.6759 (mt) REVERT: B 414 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7940 (ptp) REVERT: B 808 LEU cc_start: 0.7510 (mt) cc_final: 0.7290 (tt) REVERT: C 42 ARG cc_start: 0.6867 (pmt100) cc_final: 0.5991 (ptm-80) REVERT: C 306 ILE cc_start: 0.3171 (OUTLIER) cc_final: 0.2641 (tp) REVERT: C 524 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8175 (mp0) REVERT: C 544 SER cc_start: 0.8542 (t) cc_final: 0.8135 (p) REVERT: C 699 LYS cc_start: 0.8009 (mmtm) cc_final: 0.7736 (tppt) REVERT: C 719 ASP cc_start: 0.7209 (t0) cc_final: 0.6811 (t0) REVERT: C 880 MET cc_start: 0.6729 (mmm) cc_final: 0.6414 (tpp) REVERT: C 925 ILE cc_start: 0.7900 (mt) cc_final: 0.7684 (tt) REVERT: C 1029 MET cc_start: 0.7013 (ttt) cc_final: 0.6787 (ttm) REVERT: D 167 ASN cc_start: 0.7819 (m-40) cc_final: 0.7384 (p0) REVERT: D 185 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8152 (pt0) REVERT: D 265 LEU cc_start: 0.7253 (mt) cc_final: 0.6906 (mt) REVERT: D 431 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8134 (mm-30) REVERT: D 808 LEU cc_start: 0.7541 (mt) cc_final: 0.7221 (tt) REVERT: E 63 LEU cc_start: 0.6157 (mm) cc_final: 0.5776 (tp) REVERT: E 64 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6228 (mm) REVERT: E 116 MET cc_start: 0.2707 (mtm) cc_final: 0.2083 (mmt) REVERT: F 116 MET cc_start: 0.2613 (mmt) cc_final: 0.1473 (mpp) REVERT: F 151 TYR cc_start: 0.6808 (t80) cc_final: 0.6500 (t80) outliers start: 75 outliers final: 49 residues processed: 368 average time/residue: 0.2047 time to fit residues: 123.2602 Evaluate side-chains 343 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 288 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 957 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL 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 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 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 B residue 795 VAL 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 354 ILE Chi-restraints excluded: chain C residue 524 GLU 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 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 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 720 THR Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain F residue 69 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 chunk 283 optimal weight: 3.9990 chunk 254 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 B 46 HIS C 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.161642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.121953 restraints weight = 43928.815| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.22 r_work: 0.3252 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32303 Z= 0.165 Angle : 0.842 34.598 43522 Z= 0.355 Chirality : 0.074 1.791 4710 Planarity : 0.004 0.082 5316 Dihedral : 18.418 179.109 5693 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.09 % Favored : 92.81 % Rotamer: Outliers : 2.40 % Allowed : 13.51 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.14), residues: 3754 helix: 1.63 (0.12), residues: 1876 sheet: -2.07 (0.22), residues: 470 loop : -2.12 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.019 0.001 TYR B 280 PHE 0.016 0.001 PHE B 531 TRP 0.019 0.001 TRP B 323 HIS 0.010 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00395 (32291) covalent geometry : angle 0.84215 (43498) SS BOND : bond 0.00350 ( 12) SS BOND : angle 0.91137 ( 24) hydrogen bonds : bond 0.03391 ( 1406) hydrogen bonds : angle 3.68967 ( 4206) *********************** 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 368 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 290 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6881 (pmt100) cc_final: 0.5753 (ptm-80) REVERT: A 292 MET cc_start: 0.7467 (mtm) cc_final: 0.7246 (mtp) REVERT: A 344 ASN cc_start: 0.7373 (t0) cc_final: 0.7020 (t0) REVERT: A 355 ASN cc_start: 0.7227 (t0) cc_final: 0.6839 (t0) REVERT: A 524 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8243 (mp0) REVERT: A 699 LYS cc_start: 0.8004 (mmtm) cc_final: 0.7710 (ttmm) REVERT: A 891 PHE cc_start: 0.7221 (m-80) cc_final: 0.6996 (m-80) REVERT: B 46 HIS cc_start: 0.7240 (t-90) cc_final: 0.6895 (t-90) REVERT: B 265 LEU cc_start: 0.7173 (mt) cc_final: 0.6798 (mt) REVERT: B 393 LYS cc_start: 0.8193 (tppt) cc_final: 0.7606 (tptm) REVERT: B 808 LEU cc_start: 0.7557 (mt) cc_final: 0.7318 (tt) REVERT: C 42 ARG cc_start: 0.6929 (pmt100) cc_final: 0.5907 (ptm-80) REVERT: C 292 MET cc_start: 0.7466 (mtm) cc_final: 0.7221 (mtp) REVERT: C 297 ARG cc_start: 0.6640 (OUTLIER) cc_final: 0.6402 (ttm170) REVERT: C 524 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8200 (mp0) REVERT: C 699 LYS cc_start: 0.8029 (mmtm) cc_final: 0.7773 (tppt) REVERT: C 719 ASP cc_start: 0.7334 (t0) cc_final: 0.6909 (t0) REVERT: C 880 MET cc_start: 0.6765 (mmm) cc_final: 0.6493 (tpt) REVERT: C 1029 MET cc_start: 0.7126 (ttt) cc_final: 0.6846 (ttm) REVERT: D 167 ASN cc_start: 0.7878 (m-40) cc_final: 0.7387 (p0) REVERT: D 185 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8113 (pt0) REVERT: D 265 LEU cc_start: 0.7294 (mt) cc_final: 0.6940 (mt) REVERT: D 431 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8214 (mm-30) REVERT: D 808 LEU cc_start: 0.7572 (mt) cc_final: 0.7290 (tt) REVERT: E 63 LEU cc_start: 0.6235 (mm) cc_final: 0.5875 (tp) REVERT: E 64 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6335 (mm) REVERT: E 116 MET cc_start: 0.2579 (mtm) cc_final: 0.1964 (tmm) REVERT: F 116 MET cc_start: 0.2858 (mmt) cc_final: 0.1658 (mpp) REVERT: F 151 TYR cc_start: 0.6839 (t80) cc_final: 0.6521 (t80) outliers start: 78 outliers final: 60 residues processed: 348 average time/residue: 0.2030 time to fit residues: 116.7189 Evaluate side-chains 346 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 281 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 511 LYS 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 842 SER Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL 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 720 THR Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 297 ARG 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 354 ILE Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 524 GLU 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 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 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 64 LEU Chi-restraints excluded: chain E residue 120 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 259 optimal weight: 9.9990 chunk 183 optimal weight: 0.6980 chunk 346 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 340 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 296 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 C 246 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.163245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.123976 restraints weight = 43815.353| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.38 r_work: 0.3264 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32303 Z= 0.119 Angle : 0.820 34.019 43522 Z= 0.343 Chirality : 0.073 1.807 4710 Planarity : 0.004 0.077 5316 Dihedral : 18.254 179.510 5693 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.61 % Favored : 93.34 % Rotamer: Outliers : 2.15 % Allowed : 14.09 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.14), residues: 3754 helix: 1.74 (0.12), residues: 1892 sheet: -1.96 (0.23), residues: 454 loop : -2.08 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 926 TYR 0.019 0.001 TYR E 72 PHE 0.018 0.001 PHE A 109 TRP 0.021 0.001 TRP D 323 HIS 0.010 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00276 (32291) covalent geometry : angle 0.82018 (43498) SS BOND : bond 0.00266 ( 12) SS BOND : angle 0.79748 ( 24) hydrogen bonds : bond 0.03132 ( 1406) hydrogen bonds : angle 3.58024 ( 4206) *********************** 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: 70 poor density : 300 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6874 (pmt100) cc_final: 0.5737 (ptm-80) REVERT: A 292 MET cc_start: 0.7483 (mtm) cc_final: 0.7278 (mtp) REVERT: A 344 ASN cc_start: 0.7318 (t0) cc_final: 0.6957 (t0) REVERT: A 355 ASN cc_start: 0.7247 (t0) cc_final: 0.6910 (t0) REVERT: A 524 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8256 (mp0) REVERT: A 699 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7721 (ttmm) REVERT: A 807 MET cc_start: 0.8248 (mtm) cc_final: 0.8006 (mtm) REVERT: B 46 HIS cc_start: 0.7275 (t-90) cc_final: 0.6899 (t-90) REVERT: B 265 LEU cc_start: 0.7198 (mt) cc_final: 0.6816 (mt) REVERT: C 42 ARG cc_start: 0.6893 (pmt100) cc_final: 0.5910 (ptm-80) REVERT: C 524 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8199 (mp0) REVERT: C 699 LYS cc_start: 0.8037 (mmtm) cc_final: 0.7642 (ttmm) REVERT: C 719 ASP cc_start: 0.7286 (t0) cc_final: 0.6876 (t0) REVERT: C 880 MET cc_start: 0.6749 (mmm) cc_final: 0.6459 (tpp) REVERT: C 1029 MET cc_start: 0.7069 (ttt) cc_final: 0.6821 (ttm) REVERT: D 50 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7137 (pp) REVERT: D 167 ASN cc_start: 0.7935 (m-40) cc_final: 0.7440 (p0) REVERT: D 185 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8181 (pt0) REVERT: D 265 LEU cc_start: 0.7275 (mt) cc_final: 0.6912 (mt) REVERT: D 431 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8195 (mm-30) REVERT: D 808 LEU cc_start: 0.7580 (mt) cc_final: 0.7301 (tt) REVERT: E 63 LEU cc_start: 0.6265 (mm) cc_final: 0.5925 (tp) REVERT: E 64 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6406 (mm) REVERT: E 116 MET cc_start: 0.2546 (mtm) cc_final: 0.1871 (tmm) REVERT: F 116 MET cc_start: 0.2911 (mmt) cc_final: 0.1699 (mpp) REVERT: F 151 TYR cc_start: 0.6852 (t80) cc_final: 0.6537 (t80) outliers start: 70 outliers final: 58 residues processed: 354 average time/residue: 0.2030 time to fit residues: 117.7604 Evaluate side-chains 348 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 285 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 511 LYS 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 957 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL 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 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 720 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 82 VAL 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 354 ILE 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 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 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 720 THR Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 120 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 367 optimal weight: 0.6980 chunk 371 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 359 optimal weight: 2.9990 chunk 291 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 338 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 0.0030 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** 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 = 0.4092 r_free = 0.4092 target = 0.164587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.125389 restraints weight = 43925.256| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.21 r_work: 0.3302 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4421 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= 0.105 Angle : 0.812 33.599 43522 Z= 0.337 Chirality : 0.073 1.815 4710 Planarity : 0.004 0.072 5316 Dihedral : 18.047 179.345 5693 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.18 % Favored : 93.77 % Rotamer: Outliers : 1.97 % Allowed : 14.31 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.14), residues: 3754 helix: 1.89 (0.13), residues: 1894 sheet: -1.90 (0.23), residues: 456 loop : -2.04 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 331 TYR 0.019 0.001 TYR B 280 PHE 0.040 0.001 PHE A 258 TRP 0.021 0.001 TRP D 323 HIS 0.009 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00240 (32291) covalent geometry : angle 0.81166 (43498) SS BOND : bond 0.00248 ( 12) SS BOND : angle 1.03939 ( 24) hydrogen bonds : bond 0.03011 ( 1406) hydrogen bonds : angle 3.50832 ( 4206) ********************** 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 368 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 304 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6913 (pmt100) cc_final: 0.5761 (ptm-80) REVERT: A 344 ASN cc_start: 0.7208 (t0) cc_final: 0.6821 (t0) REVERT: A 355 ASN cc_start: 0.7167 (t0) cc_final: 0.6814 (t0) REVERT: A 524 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: A 699 LYS cc_start: 0.8035 (mmtm) cc_final: 0.7701 (ttmm) REVERT: A 807 MET cc_start: 0.8208 (mtm) cc_final: 0.7953 (mtm) REVERT: B 185 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8231 (pt0) REVERT: B 265 LEU cc_start: 0.7101 (mt) cc_final: 0.6705 (mt) REVERT: C 42 ARG cc_start: 0.6904 (pmt100) cc_final: 0.5898 (ptm-80) REVERT: C 109 PHE cc_start: 0.7327 (m-10) cc_final: 0.6126 (m-10) REVERT: C 175 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6157 (tp30) REVERT: C 524 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8210 (mp0) REVERT: C 544 SER cc_start: 0.8563 (t) cc_final: 0.8109 (p) REVERT: C 699 LYS cc_start: 0.8076 (mmtm) cc_final: 0.7667 (ttmm) REVERT: C 719 ASP cc_start: 0.7198 (t0) cc_final: 0.6842 (t0) REVERT: C 880 MET cc_start: 0.6822 (mmm) cc_final: 0.6541 (tpt) REVERT: C 1029 MET cc_start: 0.7071 (ttt) cc_final: 0.6833 (ttm) REVERT: D 50 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6992 (pp) REVERT: D 185 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8154 (pt0) REVERT: D 262 TRP cc_start: 0.6558 (t-100) cc_final: 0.6041 (t-100) REVERT: D 265 LEU cc_start: 0.7221 (mt) cc_final: 0.6959 (mt) REVERT: D 431 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8129 (mm-30) REVERT: D 808 LEU cc_start: 0.7479 (mt) cc_final: 0.7172 (tt) REVERT: E 63 LEU cc_start: 0.6394 (mm) cc_final: 0.6033 (tp) REVERT: E 64 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6266 (mm) REVERT: E 93 LEU cc_start: 0.7343 (tt) cc_final: 0.6832 (mp) REVERT: E 116 MET cc_start: 0.2725 (mtm) cc_final: 0.1955 (tmm) REVERT: F 63 LEU cc_start: 0.7036 (mp) cc_final: 0.6581 (tp) REVERT: F 116 MET cc_start: 0.2742 (mmt) cc_final: 0.1556 (pmm) REVERT: F 151 TYR cc_start: 0.6815 (t80) cc_final: 0.6512 (t80) outliers start: 64 outliers final: 49 residues processed: 354 average time/residue: 0.2088 time to fit residues: 119.4766 Evaluate side-chains 338 residues out of total 3250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 282 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 511 LYS 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 973 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 185 GLU 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 720 THR Chi-restraints excluded: chain B residue 795 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 341 LEU Chi-restraints excluded: chain C residue 354 ILE 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 590 ASP Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 859 ASP 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 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 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 720 THR Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain F residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 348 optimal weight: 0.8980 chunk 264 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 309 optimal weight: 10.0000 chunk 368 optimal weight: 10.0000 chunk 296 optimal weight: 2.9990 chunk 303 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 249 optimal weight: 6.9990 chunk 219 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 435 HIS C 60 ASN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** 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 = 0.4036 r_free = 0.4036 target = 0.159456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.119317 restraints weight = 44461.141| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.16 r_work: 0.3217 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 32303 Z= 0.246 Angle : 0.902 35.598 43522 Z= 0.387 Chirality : 0.074 1.771 4710 Planarity : 0.004 0.079 5316 Dihedral : 18.392 179.738 5693 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.81 % Favored : 92.09 % Rotamer: Outliers : 2.31 % Allowed : 13.97 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.14), residues: 3754 helix: 1.41 (0.12), residues: 1874 sheet: -1.97 (0.23), residues: 470 loop : -2.16 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 926 TYR 0.033 0.002 TYR F 72 PHE 0.032 0.002 PHE A 258 TRP 0.023 0.002 TRP B 323 HIS 0.010 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00594 (32291) covalent geometry : angle 0.90109 (43498) SS BOND : bond 0.00499 ( 12) SS BOND : angle 1.49830 ( 24) hydrogen bonds : bond 0.03785 ( 1406) hydrogen bonds : angle 3.87304 ( 4206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9265.94 seconds wall clock time: 159 minutes 12.59 seconds (9552.59 seconds total)