Starting phenix.real_space_refine on Fri Dec 27 18:33:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dew_27401/12_2024/8dew_27401.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dew_27401/12_2024/8dew_27401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dew_27401/12_2024/8dew_27401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dew_27401/12_2024/8dew_27401.map" model { file = "/net/cci-nas-00/data/ceres_data/8dew_27401/12_2024/8dew_27401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dew_27401/12_2024/8dew_27401.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 S 137 5.16 5 C 15834 2.51 5 N 3982 2.21 5 O 4534 1.98 5 H 24295 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 48792 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 16017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 16017 Classifications: {'peptide': 1058} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 40, 'TRANS': 1017} Chain: "B" Number of atoms: 15746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 15746 Classifications: {'peptide': 1040} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 40, 'TRANS': 999} Chain: "C" Number of atoms: 16017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 16017 Classifications: {'peptide': 1058} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 40, 'TRANS': 1017} Chain: "D" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 299 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 252 Unusual residues: {'PTY': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PTY:plan-1': 4, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 285 Unusual residues: {'PTY': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 176 Unusual residues: {'PTY': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PTY:plan-1': 4, 'PTY:plan-2': 5} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 17.22, per 1000 atoms: 0.35 Number of scatterers: 48792 At special positions: 0 Unit cell: (155.52, 133.92, 135, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 137 16.00 P 10 15.00 O 4534 8.00 N 3982 7.00 C 15834 6.00 H 24295 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.25 Conformation dependent library (CDL) restraints added in 3.1 seconds 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5782 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 23 sheets defined 61.2% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.718A pdb=" N PHE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 29 removed outlier: 3.561A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.547A pdb=" N VAL A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 148 through 166 removed outlier: 4.687A pdb=" N VAL A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 197 through 209 Processing helix chain 'A' and resid 240 through 246 Processing helix chain 'A' and resid 296 through 312 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 327 through 358 removed outlier: 3.872A pdb=" N VAL A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 384 removed outlier: 4.476A pdb=" N ILE A 365 " --> pdb=" O ARG A 361 " (cutoff:3.500A) Proline residue: A 366 - end of helix Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 389 through 422 removed outlier: 4.436A pdb=" N GLY A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 452 removed outlier: 5.752A pdb=" N GLY A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ALA A 439 " --> pdb=" O GLN A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 456 Processing helix chain 'A' and resid 461 through 495 removed outlier: 4.520A pdb=" N THR A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) Proline residue: A 488 - end of helix Processing helix chain 'A' and resid 508 through 533 Processing helix chain 'A' and resid 535 through 555 Processing helix chain 'A' and resid 580 through 597 Processing helix chain 'A' and resid 638 through 654 Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.619A pdb=" N ASN A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 706 removed outlier: 4.236A pdb=" N GLY A 706 " --> pdb=" O MET A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 713 removed outlier: 3.590A pdb=" N VAL A 713 " --> pdb=" O PRO A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 734 Processing helix chain 'A' and resid 739 through 752 removed outlier: 4.069A pdb=" N LEU A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 777 Processing helix chain 'A' and resid 780 through 785 removed outlier: 3.634A pdb=" N ASN A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 848 Processing helix chain 'A' and resid 858 through 866 removed outlier: 4.196A pdb=" N GLU A 862 " --> pdb=" O GLY A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 890 Processing helix chain 'A' and resid 893 through 900 removed outlier: 4.216A pdb=" N ALA A 897 " --> pdb=" O SER A 893 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 898 " --> pdb=" O ILE A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 924 removed outlier: 4.156A pdb=" N GLY A 905 " --> pdb=" O VAL A 901 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 906 " --> pdb=" O MET A 902 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 923 " --> pdb=" O PHE A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 963 Processing helix chain 'A' and resid 966 through 993 removed outlier: 5.034A pdb=" N ARG A 980 " --> pdb=" O ARG A 976 " (cutoff:3.500A) Proline residue: A 981 - end of helix Processing helix chain 'A' and resid 993 through 998 Processing helix chain 'A' and resid 1003 through 1040 removed outlier: 3.524A pdb=" N GLN A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A1013 " --> pdb=" O ALA A1009 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE A1027 " --> pdb=" O LEU A1023 " (cutoff:3.500A) Proline residue: A1030 - end of helix Processing helix chain 'A' and resid 1043 through 1058 removed outlier: 3.714A pdb=" N GLU A1048 " --> pdb=" O ALA A1044 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET A1049 " --> pdb=" O HIS A1045 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.598A pdb=" N ASP B 7 " --> pdb=" O LYS B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 29 Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.933A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 115 removed outlier: 3.688A pdb=" N GLU B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 148 through 165 removed outlier: 4.879A pdb=" N VAL B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 197 through 209 Processing helix chain 'B' and resid 240 through 246 removed outlier: 3.506A pdb=" N ASN B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 327 through 358 removed outlier: 3.915A pdb=" N VAL B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 363 through 384 removed outlier: 3.999A pdb=" N THR B 367 " --> pdb=" O THR B 363 " (cutoff:3.500A) Proline residue: B 371 - end of helix Processing helix chain 'B' and resid 389 through 422 removed outlier: 4.431A pdb=" N GLY B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 452 removed outlier: 5.671A pdb=" N GLY B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ALA B 439 " --> pdb=" O GLN B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 456 Processing helix chain 'B' and resid 459 through 495 removed outlier: 3.784A pdb=" N GLN B 467 " --> pdb=" O ASN B 463 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) Proline residue: B 488 - end of helix removed outlier: 3.717A pdb=" N LEU B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 534 removed outlier: 3.878A pdb=" N LYS B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 555 removed outlier: 4.027A pdb=" N MET B 538 " --> pdb=" O LYS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 597 Processing helix chain 'B' and resid 638 through 654 removed outlier: 3.546A pdb=" N GLY B 652 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 705 Processing helix chain 'B' and resid 709 through 713 Processing helix chain 'B' and resid 729 through 736 Processing helix chain 'B' and resid 741 through 751 Processing helix chain 'B' and resid 773 through 777 Processing helix chain 'B' and resid 779 through 785 removed outlier: 3.886A pdb=" N LEU B 784 " --> pdb=" O ALA B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 801 No H-bonds generated for 'chain 'B' and resid 798 through 801' Processing helix chain 'B' and resid 833 through 848 Processing helix chain 'B' and resid 858 through 865 removed outlier: 4.146A pdb=" N GLU B 862 " --> pdb=" O GLY B 858 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS B 865 " --> pdb=" O ARG B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 890 removed outlier: 3.543A pdb=" N ILE B 871 " --> pdb=" O GLY B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 900 removed outlier: 4.123A pdb=" N ALA B 897 " --> pdb=" O SER B 893 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL B 898 " --> pdb=" O ILE B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 924 Processing helix chain 'B' and resid 932 through 964 removed outlier: 3.513A pdb=" N GLY B 964 " --> pdb=" O LEU B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 998 removed outlier: 4.880A pdb=" N ARG B 980 " --> pdb=" O ARG B 976 " (cutoff:3.500A) Proline residue: B 981 - end of helix Proline residue: B 995 - end of helix Processing helix chain 'B' and resid 1003 through 1040 removed outlier: 4.039A pdb=" N PHE B1027 " --> pdb=" O LEU B1023 " (cutoff:3.500A) Proline residue: B1030 - end of helix Processing helix chain 'C' and resid 2 through 8 removed outlier: 3.836A pdb=" N ASP C 7 " --> pdb=" O LYS C 3 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG C 8 " --> pdb=" O PHE C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 29 removed outlier: 3.848A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 148 through 166 removed outlier: 4.598A pdb=" N VAL C 161 " --> pdb=" O GLN C 157 " (cutoff:3.500A) Proline residue: C 162 - end of helix Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 197 through 209 Processing helix chain 'C' and resid 240 through 246 Processing helix chain 'C' and resid 296 through 312 Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 327 through 358 removed outlier: 4.161A pdb=" N VAL C 331 " --> pdb=" O THR C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 384 removed outlier: 3.671A pdb=" N ILE C 365 " --> pdb=" O ARG C 361 " (cutoff:3.500A) Proline residue: C 366 - end of helix removed outlier: 3.675A pdb=" N VAL C 369 " --> pdb=" O ILE C 365 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 370 " --> pdb=" O PRO C 366 " (cutoff:3.500A) Proline residue: C 371 - end of helix Processing helix chain 'C' and resid 389 through 422 removed outlier: 4.500A pdb=" N GLY C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE C 402 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL C 404 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASP C 405 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASP C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA C 407 " --> pdb=" O VAL C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 452 removed outlier: 5.539A pdb=" N GLY C 438 " --> pdb=" O GLY C 434 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ALA C 439 " --> pdb=" O GLN C 435 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE C 451 " --> pdb=" O LEU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 456 Processing helix chain 'C' and resid 458 through 495 removed outlier: 3.561A pdb=" N GLY C 462 " --> pdb=" O SER C 458 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR C 487 " --> pdb=" O ALA C 483 " (cutoff:3.500A) Proline residue: C 488 - end of helix removed outlier: 3.867A pdb=" N LEU C 495 " --> pdb=" O CYS C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 534 removed outlier: 3.550A pdb=" N TRP C 512 " --> pdb=" O GLY C 508 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS C 534 " --> pdb=" O LYS C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 555 Processing helix chain 'C' and resid 580 through 598 Processing helix chain 'C' and resid 628 through 632 Processing helix chain 'C' and resid 638 through 654 Processing helix chain 'C' and resid 667 through 671 Processing helix chain 'C' and resid 687 through 703 Processing helix chain 'C' and resid 729 through 736 Processing helix chain 'C' and resid 739 through 752 removed outlier: 4.131A pdb=" N LEU C 751 " --> pdb=" O LEU C 747 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 752 " --> pdb=" O ALA C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 777 Processing helix chain 'C' and resid 779 through 785 removed outlier: 4.065A pdb=" N ILE C 783 " --> pdb=" O GLN C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 801 No H-bonds generated for 'chain 'C' and resid 798 through 801' Processing helix chain 'C' and resid 833 through 849 removed outlier: 3.778A pdb=" N GLY C 849 " --> pdb=" O VAL C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 890 removed outlier: 3.992A pdb=" N GLU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY C 866 " --> pdb=" O GLU C 862 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY C 867 " --> pdb=" O GLU C 863 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER C 868 " --> pdb=" O ALA C 864 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN C 869 " --> pdb=" O LYS C 865 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR C 870 " --> pdb=" O GLY C 866 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE C 871 " --> pdb=" O GLY C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 900 removed outlier: 3.629A pdb=" N LEU C 900 " --> pdb=" O LEU C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 924 Processing helix chain 'C' and resid 932 through 962 removed outlier: 3.751A pdb=" N ILE C 953 " --> pdb=" O ASN C 949 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 966 through 993 removed outlier: 5.169A pdb=" N ARG C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Proline residue: C 981 - end of helix Processing helix chain 'C' and resid 993 through 998 Processing helix chain 'C' and resid 1003 through 1040 removed outlier: 3.705A pdb=" N GLN C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR C1013 " --> pdb=" O ALA C1009 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE C1027 " --> pdb=" O LEU C1023 " (cutoff:3.500A) Proline residue: C1030 - end of helix Processing helix chain 'C' and resid 1043 through 1058 removed outlier: 4.463A pdb=" N HIS C1053 " --> pdb=" O MET C1049 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYS C1056 " --> pdb=" O ARG C1052 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 130 removed outlier: 7.970A pdb=" N SER A 87 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ALA A 82 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N SER A 89 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR A 80 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER A 91 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET A 78 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR A 93 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 12.137A pdb=" N GLN A 812 " --> pdb=" O GLU A 823 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N GLU A 823 " --> pdb=" O GLN A 812 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL A 814 " --> pdb=" O ALA A 821 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 removed outlier: 7.970A pdb=" N SER A 87 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ALA A 82 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N SER A 89 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR A 80 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER A 91 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET A 78 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR A 93 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 12.137A pdb=" N GLN A 812 " --> pdb=" O GLU A 823 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N GLU A 823 " --> pdb=" O GLN A 812 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL A 814 " --> pdb=" O ALA A 821 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 175 removed outlier: 6.747A pdb=" N VAL A 170 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N SER A 292 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N MET A 287 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE A 139 " --> pdb=" O MET A 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A 289 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU A 291 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASN A 135 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N LEU A 137 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASP A 326 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE A 139 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 270 removed outlier: 8.719A pdb=" N ARG A 180 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG A 767 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 757 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 770 " --> pdb=" O TYR A 755 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TYR A 755 " --> pdb=" O VAL A 770 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 217 removed outlier: 3.998A pdb=" N GLY A 215 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR A 231 " --> pdb=" O LEU B 724 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE B 726 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR A 233 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE B 728 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 248 through 251 removed outlier: 6.770A pdb=" N ILE A 258 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 282 through 284 removed outlier: 4.326A pdb=" N THR A 277 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 805 through 809 removed outlier: 4.374A pdb=" N THR C 231 " --> pdb=" O PRO A 722 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 48 removed outlier: 5.110A pdb=" N SER B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP B 83 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 77 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 12.075A pdb=" N GLN B 812 " --> pdb=" O GLU B 823 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N GLU B 823 " --> pdb=" O GLN B 812 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL B 814 " --> pdb=" O ALA B 821 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 819 " --> pdb=" O PHE B 816 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B 714 " --> pdb=" O SER B 825 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 130 through 131 removed outlier: 5.110A pdb=" N SER B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP B 83 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 77 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 12.075A pdb=" N GLN B 812 " --> pdb=" O GLU B 823 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N GLU B 823 " --> pdb=" O GLN B 812 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL B 814 " --> pdb=" O ALA B 821 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 819 " --> pdb=" O PHE B 816 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 170 through 175 removed outlier: 6.692A pdb=" N MET B 290 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL B 173 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA B 288 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU B 175 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY B 286 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ASN B 283 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER B 143 " --> pdb=" O ASN B 283 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR B 285 " --> pdb=" O MET B 141 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET B 141 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N MET B 287 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE B 139 " --> pdb=" O MET B 287 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 289 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 170 through 175 removed outlier: 6.692A pdb=" N MET B 290 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL B 173 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA B 288 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU B 175 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY B 286 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 284 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR B 277 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N MET B 619 " --> pdb=" O GLY B 609 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 264 through 270 removed outlier: 7.555A pdb=" N ARG B 180 " --> pdb=" O ARG B 767 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N MET B 769 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N MET B 182 " --> pdb=" O MET B 769 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ARG B 764 " --> pdb=" O PRO B 760 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLN B 766 " --> pdb=" O ASP B 758 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASP B 758 " --> pdb=" O GLN B 766 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL B 768 " --> pdb=" O VAL B 756 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 215 through 217 removed outlier: 3.730A pdb=" N GLY B 215 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR B 231 " --> pdb=" O LEU C 724 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE C 726 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR B 233 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE C 728 " --> pdb=" O THR B 233 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 248 through 250 removed outlier: 6.859A pdb=" N ILE B 258 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AB8, first strand: chain 'C' and resid 127 through 130 removed outlier: 4.257A pdb=" N SER C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N GLN C 812 " --> pdb=" O GLU C 823 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N GLU C 823 " --> pdb=" O GLN C 812 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL C 814 " --> pdb=" O ALA C 821 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 127 through 130 removed outlier: 4.257A pdb=" N SER C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N GLN C 812 " --> pdb=" O GLU C 823 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N GLU C 823 " --> pdb=" O GLN C 812 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL C 814 " --> pdb=" O ALA C 821 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER C 677 " --> pdb=" O GLY C 857 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 170 through 175 removed outlier: 6.745A pdb=" N MET C 290 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL C 173 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA C 288 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LEU C 175 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLY C 286 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ASN C 283 " --> pdb=" O SER C 144 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N SER C 144 " --> pdb=" O ASN C 283 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET C 138 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE C 139 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 170 through 175 removed outlier: 6.745A pdb=" N MET C 290 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL C 173 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA C 288 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LEU C 175 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLY C 286 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 284 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR C 277 " --> pdb=" O THR C 284 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N MET C 619 " --> pdb=" O GLY C 609 " (cutoff:3.500A) removed outlier: 9.505A pdb=" N SER C 611 " --> pdb=" O GLN C 617 " (cutoff:3.500A) removed outlier: 10.406A pdb=" N GLN C 617 " --> pdb=" O SER C 611 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 264 through 270 removed outlier: 8.374A pdb=" N ARG C 180 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ARG C 767 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL C 770 " --> pdb=" O TYR C 755 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TYR C 755 " --> pdb=" O VAL C 770 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 248 through 251 removed outlier: 3.525A pdb=" N ARG C 250 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 787 through 788 removed outlier: 3.612A pdb=" N VAL C 796 " --> pdb=" O VAL C 788 " (cutoff:3.500A) 1646 hydrogen bonds defined for protein. 4791 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: 20.47 Time building geometry restraints manager: 11.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 24292 1.01 - 1.21: 34 1.21 - 1.41: 9589 1.41 - 1.61: 14991 1.61 - 1.81: 289 Bond restraints: 49195 Sorted by residual: bond pdb=" C8 PTY C1107 " pdb=" O10 PTY C1107 " ideal model delta sigma weight residual 1.205 1.410 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C30 PTY B1106 " pdb=" O4 PTY B1106 " ideal model delta sigma weight residual 1.331 1.184 0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" C8 PTY C1105 " pdb=" O7 PTY C1105 " ideal model delta sigma weight residual 1.331 1.184 0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C8 PTY C1107 " pdb=" O7 PTY C1107 " ideal model delta sigma weight residual 1.331 1.185 0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" C8 PTY A1106 " pdb=" O7 PTY A1106 " ideal model delta sigma weight residual 1.331 1.185 0.146 2.00e-02 2.50e+03 5.31e+01 ... (remaining 49190 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 88100 3.36 - 6.73: 455 6.73 - 10.09: 47 10.09 - 13.46: 7 13.46 - 16.82: 8 Bond angle restraints: 88617 Sorted by residual: angle pdb=" N PHE A 451 " pdb=" CA PHE A 451 " pdb=" C PHE A 451 " ideal model delta sigma weight residual 111.36 118.38 -7.02 1.09e+00 8.42e-01 4.15e+01 angle pdb=" N ASN C 293 " pdb=" CA ASN C 293 " pdb=" C ASN C 293 " ideal model delta sigma weight residual 110.23 100.92 9.31 1.45e+00 4.76e-01 4.13e+01 angle pdb=" O11 PTY B1101 " pdb=" P1 PTY B1101 " pdb=" O14 PTY B1101 " ideal model delta sigma weight residual 92.90 109.72 -16.82 3.00e+00 1.11e-01 3.14e+01 angle pdb=" O11 PTY B1108 " pdb=" P1 PTY B1108 " pdb=" O14 PTY B1108 " ideal model delta sigma weight residual 92.90 109.67 -16.77 3.00e+00 1.11e-01 3.13e+01 angle pdb=" O11 PTY A1102 " pdb=" P1 PTY A1102 " pdb=" O14 PTY A1102 " ideal model delta sigma weight residual 92.90 109.56 -16.66 3.00e+00 1.11e-01 3.08e+01 ... (remaining 88612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.94: 22518 31.94 - 63.89: 790 63.89 - 95.83: 46 95.83 - 127.78: 6 127.78 - 159.72: 3 Dihedral angle restraints: 23363 sinusoidal: 12996 harmonic: 10367 Sorted by residual: dihedral pdb=" CA LEU A 751 " pdb=" C LEU A 751 " pdb=" N SER A 752 " pdb=" CA SER A 752 " ideal model delta harmonic sigma weight residual -180.00 -153.18 -26.82 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA GLN C 963 " pdb=" C GLN C 963 " pdb=" N GLY C 964 " pdb=" CA GLY C 964 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" C VAL A 452 " pdb=" N VAL A 452 " pdb=" CA VAL A 452 " pdb=" CB VAL A 452 " ideal model delta harmonic sigma weight residual -122.00 -133.46 11.46 0 2.50e+00 1.60e-01 2.10e+01 ... (remaining 23360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3589 0.078 - 0.156: 286 0.156 - 0.234: 12 0.234 - 0.311: 2 0.311 - 0.389: 3 Chirality restraints: 3892 Sorted by residual: chirality pdb=" CA LEU C 220 " pdb=" N LEU C 220 " pdb=" C LEU C 220 " pdb=" CB LEU C 220 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CA PHE A 451 " pdb=" N PHE A 451 " pdb=" C PHE A 451 " pdb=" CB PHE A 451 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CA VAL A 452 " pdb=" N VAL A 452 " pdb=" C VAL A 452 " pdb=" CB VAL A 452 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 3889 not shown) Planarity restraints: 7256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 961 " -0.235 2.00e-02 2.50e+03 3.05e-01 1.39e+03 pdb=" CD GLN A 961 " 0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN A 961 " 0.231 2.00e-02 2.50e+03 pdb=" NE2 GLN A 961 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 961 " 0.470 2.00e-02 2.50e+03 pdb="HE22 GLN A 961 " -0.477 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 30 " 0.252 2.00e-02 2.50e+03 2.65e-01 1.05e+03 pdb=" CG ASN D 30 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN D 30 " -0.243 2.00e-02 2.50e+03 pdb=" ND2 ASN D 30 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN D 30 " -0.380 2.00e-02 2.50e+03 pdb="HD22 ASN D 30 " 0.391 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 22 " -0.157 2.00e-02 2.50e+03 1.79e-01 4.82e+02 pdb=" CD GLN D 22 " 0.005 2.00e-02 2.50e+03 pdb=" OE1 GLN D 22 " 0.156 2.00e-02 2.50e+03 pdb=" NE2 GLN D 22 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN D 22 " 0.268 2.00e-02 2.50e+03 pdb="HE22 GLN D 22 " -0.268 2.00e-02 2.50e+03 ... (remaining 7253 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 2703 2.20 - 2.80: 98400 2.80 - 3.40: 133328 3.40 - 4.00: 176615 4.00 - 4.60: 276462 Nonbonded interactions: 687508 Sorted by model distance: nonbonded pdb=" OD1 ASP B 272 " pdb=" H TYR B 273 " model vdw 1.600 2.450 nonbonded pdb=" HG1 THR A 712 " pdb=" OG SER A 827 " model vdw 1.602 2.450 nonbonded pdb=" OE2 GLU A 412 " pdb=" HE ARG A 980 " model vdw 1.617 2.450 nonbonded pdb=" OD1 ASN A 729 " pdb=" H ALA A 732 " model vdw 1.621 2.450 nonbonded pdb=" O ALA A 999 " pdb=" HE ARG A1008 " model vdw 1.637 2.450 ... (remaining 687503 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 1 through 694 or (resid 695 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) \ or resid 696 through 890 or (resid 891 and (name N or name CA or name C or name \ O or name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resi \ d 892 through 1040 or (resid 1101 and (name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or n \ ame C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C30 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name C39 or name C8 )) or (resid 1102 \ and (name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or na \ me C17 or name C18 or name C19 or name C20 or name C30 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C \ 39 or name C8 or name O10 or name O30 or name O4 or name O7 )) or (resid 1103 an \ d (name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19)) or (resid 1104 and (name C30 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39)) or \ (resid 1105 and (name C11 or name C12 or name C13 or name C14 or name C15 or nam \ e C16 or name C17 or name C18 or name C19 or name C8 )) or (resid 1106 and (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 (resid 1107 and (name C11 or name C12 or 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 C8 or name O10 or name O7 )))) selection = (chain 'B' and (resid 1 through 1040 or (resid 1101 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C1 \ 9 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or nam \ e C26 or name C27 or name C28 or name C30 or name C31 or name C32 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C8 \ )) or (resid 1102 and (name C11 or name C12 or 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 C30 or name \ C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38 or name C39 or name C8 or name O10 or name O30 or name O4 or name O7 )) \ or (resid 1103 and (name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19)) or (resid 1104 and (name C30 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39)) or (resid 1105 and (name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C8 )) or (re \ sid 1106 and (name C13 or name C14 or name C15 or name C16 or name C17 or name C \ 18 or name C19 or name C20 or name C21)) or (resid 1107 and (name C11 or name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C8 or name O10 or name O7 )))) selection = (chain 'C' and (resid 1 through 694 or (resid 695 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) \ or resid 696 through 890 or (resid 891 and (name N or name CA or name C or name \ O or name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resi \ d 892 through 1040 or resid 1101 or (resid 1102 and (name C11 or name C12 or nam \ e C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or \ name C20 or name C30 or name C31 or name C32 or name C33 or name C34 or name C3 \ 5 or name C36 or name C37 or name C38 or name C39 or name C8 or name O10 or name \ O30 or name O4 or name O7 )) or (resid 1103 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19)) or (resid 1104 \ and (name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name C38 or name C39)) or (resid 1105 and (name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or \ name C19 or name C8 )) or (resid 1106 and (name C13 or name C14 or name C15 or n \ ame C16 or name C17 or name C18 or name C19 or name C20 or name C21)) or (resid \ 1107 and (name C11 or name C12 or name C13 or name C14 or name C15 or name C16 o \ r name C17 or name C18 or name C19 or name C20 or name C8 or name O10 or name O7 \ )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 0.640 Extract box with map and model: 1.360 Check model and map are aligned: 0.260 Set scattering table: 0.330 Process input model: 80.230 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.005 0.205 24900 Z= 0.336 Angle : 0.853 16.820 33567 Z= 0.385 Chirality : 0.044 0.389 3892 Planarity : 0.004 0.062 4210 Dihedral : 14.958 159.723 9244 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.16 % Allowed : 0.51 % Favored : 99.33 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.15), residues: 3164 helix: 2.05 (0.12), residues: 1787 sheet: 0.28 (0.23), residues: 499 loop : -0.54 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1016 HIS 0.003 0.001 HIS C 688 PHE 0.020 0.001 PHE B 759 TYR 0.033 0.001 TYR B 49 ARG 0.006 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 499 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8750 (mtm) cc_final: 0.8510 (mtm) REVERT: A 307 ARG cc_start: 0.8316 (tpp-160) cc_final: 0.8099 (tpm170) REVERT: A 353 MET cc_start: 0.8087 (mmt) cc_final: 0.7799 (mmt) REVERT: B 265 LYS cc_start: 0.8188 (mtmm) cc_final: 0.7975 (mttp) REVERT: B 649 MET cc_start: 0.8304 (mtp) cc_final: 0.7863 (mtm) REVERT: C 99 ASP cc_start: 0.7838 (p0) cc_final: 0.7625 (p0) outliers start: 4 outliers final: 0 residues processed: 501 average time/residue: 2.3826 time to fit residues: 1380.4770 Evaluate side-chains 344 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 1.9990 chunk 238 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 chunk 246 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN A 211 GLN A 226 GLN A1053 HIS B 157 GLN C 55 GLN C 68 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24900 Z= 0.267 Angle : 0.550 8.162 33567 Z= 0.299 Chirality : 0.042 0.160 3892 Planarity : 0.004 0.062 4210 Dihedral : 11.892 172.854 3917 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.91 % Allowed : 9.54 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.15), residues: 3164 helix: 2.05 (0.12), residues: 1799 sheet: 0.43 (0.23), residues: 489 loop : -0.63 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1016 HIS 0.003 0.001 HIS C1053 PHE 0.014 0.001 PHE C 551 TYR 0.020 0.001 TYR B 49 ARG 0.005 0.001 ARG C 976 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 355 time to evaluate : 3.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.7941 (p0) cc_final: 0.7701 (t70) REVERT: B 44 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8314 (m) REVERT: B 265 LYS cc_start: 0.8046 (mtmm) cc_final: 0.7784 (mttp) REVERT: B 290 MET cc_start: 0.8915 (mmt) cc_final: 0.7874 (mmt) REVERT: B 307 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8423 (tpt170) REVERT: B 555 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6980 (mtp-110) REVERT: B 649 MET cc_start: 0.8332 (mtp) cc_final: 0.7958 (mtm) REVERT: C 48 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8521 (mp) REVERT: C 141 MET cc_start: 0.8554 (mmt) cc_final: 0.7877 (mmt) REVERT: C 271 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7264 (mt-10) REVERT: C 346 MET cc_start: 0.7875 (mtp) cc_final: 0.7552 (mtp) REVERT: C 421 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: C 736 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7296 (mp10) REVERT: C 751 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.7867 (pp) REVERT: C 876 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8744 (mt) outliers start: 23 outliers final: 5 residues processed: 370 average time/residue: 2.4776 time to fit residues: 1057.3426 Evaluate side-chains 348 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 335 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 876 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 158 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 309 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN B 179 GLN B 936 GLN C 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24900 Z= 0.339 Angle : 0.559 5.556 33567 Z= 0.302 Chirality : 0.042 0.157 3892 Planarity : 0.005 0.083 4210 Dihedral : 11.621 178.895 3917 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.69 % Allowed : 10.95 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.15), residues: 3164 helix: 1.90 (0.12), residues: 1804 sheet: 0.27 (0.23), residues: 522 loop : -0.75 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C1016 HIS 0.004 0.001 HIS C1045 PHE 0.015 0.001 PHE A 457 TYR 0.025 0.002 TYR B 49 ARG 0.006 0.001 ARG A 361 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 347 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 MET cc_start: 0.7993 (mmt) cc_final: 0.7551 (mmp) REVERT: A 494 MET cc_start: 0.8407 (mtp) cc_final: 0.8062 (mtp) REVERT: A 973 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6755 (tp30) REVERT: B 44 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8380 (m) REVERT: B 168 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: B 265 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7796 (mttp) REVERT: B 290 MET cc_start: 0.8951 (mmt) cc_final: 0.7929 (mmt) REVERT: B 307 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8477 (tpt170) REVERT: B 555 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7023 (mtp-110) REVERT: B 649 MET cc_start: 0.8320 (mtp) cc_final: 0.7922 (mtm) REVERT: C 48 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8559 (mp) REVERT: C 68 ASN cc_start: 0.8349 (m-40) cc_final: 0.8121 (m110) REVERT: C 104 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: C 141 MET cc_start: 0.8665 (mmt) cc_final: 0.7944 (mmt) REVERT: C 265 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7694 (mtmm) REVERT: C 271 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7308 (mt-10) REVERT: C 346 MET cc_start: 0.7824 (mtp) cc_final: 0.7537 (mtp) REVERT: C 421 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.6788 (mt-10) REVERT: C 533 ARG cc_start: 0.7953 (mtm110) cc_final: 0.7745 (mtm110) REVERT: C 736 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7285 (mp10) REVERT: C 751 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.7925 (pp) REVERT: C 876 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8774 (mt) outliers start: 43 outliers final: 11 residues processed: 372 average time/residue: 2.4199 time to fit residues: 1045.9437 Evaluate side-chains 348 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 327 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 593 GLN Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 876 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 283 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 chunk 150 optimal weight: 0.0020 chunk 272 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN C 55 GLN C 779 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24900 Z= 0.242 Angle : 0.514 6.141 33567 Z= 0.278 Chirality : 0.040 0.157 3892 Planarity : 0.004 0.074 4210 Dihedral : 10.978 179.591 3917 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.42 % Allowed : 13.00 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.15), residues: 3164 helix: 2.06 (0.12), residues: 1804 sheet: 0.42 (0.23), residues: 492 loop : -0.75 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1016 HIS 0.003 0.001 HIS C1045 PHE 0.015 0.001 PHE A 457 TYR 0.020 0.001 TYR B 49 ARG 0.004 0.000 ARG C 976 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 339 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: A 353 MET cc_start: 0.7880 (mmt) cc_final: 0.7471 (mmp) REVERT: A 494 MET cc_start: 0.8411 (mtp) cc_final: 0.8054 (mtp) REVERT: A 973 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6883 (tp30) REVERT: B 44 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8262 (m) REVERT: B 265 LYS cc_start: 0.8048 (mtmm) cc_final: 0.7738 (mttp) REVERT: B 307 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8440 (tpt170) REVERT: B 555 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6922 (mtp-110) REVERT: B 649 MET cc_start: 0.8308 (mtp) cc_final: 0.7864 (mtm) REVERT: C 48 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8546 (mp) REVERT: C 68 ASN cc_start: 0.8291 (m-40) cc_final: 0.7966 (m110) REVERT: C 104 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: C 265 LYS cc_start: 0.8120 (mtpt) cc_final: 0.7677 (mtmm) REVERT: C 271 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7309 (mt-10) REVERT: C 346 MET cc_start: 0.7778 (mtp) cc_final: 0.7469 (mtp) REVERT: C 421 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: C 628 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7500 (t70) REVERT: C 751 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.7819 (pp) outliers start: 36 outliers final: 10 residues processed: 361 average time/residue: 2.4255 time to fit residues: 1018.0438 Evaluate side-chains 346 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 327 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 784 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 253 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 4 optimal weight: 0.1980 chunk 226 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 259 optimal weight: 0.9980 chunk 210 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 273 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN C 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24900 Z= 0.233 Angle : 0.504 5.674 33567 Z= 0.272 Chirality : 0.040 0.151 3892 Planarity : 0.004 0.084 4210 Dihedral : 10.413 179.991 3917 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.58 % Allowed : 13.51 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.15), residues: 3164 helix: 2.11 (0.12), residues: 1809 sheet: 0.38 (0.23), residues: 502 loop : -0.68 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1016 HIS 0.003 0.001 HIS A 46 PHE 0.013 0.001 PHE A1015 TYR 0.018 0.001 TYR B 49 ARG 0.006 0.000 ARG A 714 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 336 time to evaluate : 3.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8007 (mmt) REVERT: A 353 MET cc_start: 0.7695 (mmt) cc_final: 0.7397 (mmp) REVERT: A 408 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8656 (mt) REVERT: A 494 MET cc_start: 0.8431 (mtp) cc_final: 0.8135 (mtp) REVERT: A 973 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6862 (tp30) REVERT: A 1049 MET cc_start: 0.8398 (mmm) cc_final: 0.8115 (mmm) REVERT: B 44 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8251 (m) REVERT: B 555 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6720 (mtp-110) REVERT: B 649 MET cc_start: 0.8302 (mtp) cc_final: 0.7953 (mtm) REVERT: B 707 LEU cc_start: 0.5836 (OUTLIER) cc_final: 0.5561 (pt) REVERT: C 68 ASN cc_start: 0.8296 (m-40) cc_final: 0.7959 (m110) REVERT: C 265 LYS cc_start: 0.8110 (mtpt) cc_final: 0.7658 (mtmm) REVERT: C 271 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7368 (mt-10) REVERT: C 346 MET cc_start: 0.7766 (mtp) cc_final: 0.7501 (mtp) REVERT: C 421 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: C 628 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7511 (t70) REVERT: C 736 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7412 (mp10) REVERT: C 751 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.7858 (pp) REVERT: C 807 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7954 (pp30) outliers start: 40 outliers final: 14 residues processed: 361 average time/residue: 2.4339 time to fit residues: 1025.9476 Evaluate side-chains 345 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 321 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 807 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 102 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 178 optimal weight: 0.0040 chunk 75 optimal weight: 0.0470 chunk 304 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 160 optimal weight: 0.0970 overall best weight: 0.5890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24900 Z= 0.153 Angle : 0.469 5.464 33567 Z= 0.252 Chirality : 0.039 0.151 3892 Planarity : 0.004 0.087 4210 Dihedral : 9.617 178.240 3917 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.30 % Allowed : 14.14 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.15), residues: 3164 helix: 2.33 (0.12), residues: 1811 sheet: 0.46 (0.23), residues: 494 loop : -0.52 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1016 HIS 0.002 0.000 HIS A 46 PHE 0.012 0.001 PHE A1015 TYR 0.014 0.001 TYR B 49 ARG 0.010 0.000 ARG C 976 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 337 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8159 (mmt) REVERT: A 353 MET cc_start: 0.7599 (mmt) cc_final: 0.7308 (mmp) REVERT: A 494 MET cc_start: 0.8430 (mtp) cc_final: 0.8173 (mtp) REVERT: A 533 ARG cc_start: 0.7242 (ptp-170) cc_final: 0.6925 (ttp-170) REVERT: A 959 ASP cc_start: 0.7416 (m-30) cc_final: 0.6742 (m-30) REVERT: A 973 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6777 (tp30) REVERT: B 44 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8270 (m) REVERT: B 537 ARG cc_start: 0.7479 (mpt180) cc_final: 0.7216 (ttm110) REVERT: B 649 MET cc_start: 0.8277 (mtp) cc_final: 0.7969 (mtm) REVERT: B 707 LEU cc_start: 0.5417 (OUTLIER) cc_final: 0.5115 (pt) REVERT: C 48 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8566 (mp) REVERT: C 68 ASN cc_start: 0.8250 (m-40) cc_final: 0.7900 (m110) REVERT: C 265 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7605 (mtmm) REVERT: C 271 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7350 (mt-10) REVERT: C 346 MET cc_start: 0.7745 (mtp) cc_final: 0.7377 (mtp) REVERT: C 421 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: C 628 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7495 (t70) REVERT: C 736 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7354 (mp10) REVERT: C 751 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.7702 (pp) REVERT: C 807 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7960 (pp30) outliers start: 33 outliers final: 14 residues processed: 355 average time/residue: 2.3543 time to fit residues: 971.3726 Evaluate side-chains 343 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 320 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 807 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 293 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 303 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN B 179 GLN B 859 GLN C 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24900 Z= 0.277 Angle : 0.508 5.911 33567 Z= 0.273 Chirality : 0.041 0.145 3892 Planarity : 0.004 0.088 4210 Dihedral : 9.784 177.236 3917 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.30 % Allowed : 14.50 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.15), residues: 3164 helix: 2.21 (0.12), residues: 1808 sheet: 0.42 (0.24), residues: 495 loop : -0.60 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1016 HIS 0.004 0.001 HIS C1045 PHE 0.013 0.001 PHE A1015 TYR 0.018 0.001 TYR B 49 ARG 0.009 0.000 ARG C 976 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 323 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8282 (mmt) REVERT: A 494 MET cc_start: 0.8420 (mtp) cc_final: 0.8160 (mtp) REVERT: A 959 ASP cc_start: 0.7498 (m-30) cc_final: 0.6782 (m-30) REVERT: A 973 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6847 (tp30) REVERT: A 1049 MET cc_start: 0.8501 (mmm) cc_final: 0.8130 (mmm) REVERT: B 44 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.8258 (m) REVERT: B 649 MET cc_start: 0.8333 (mtp) cc_final: 0.8019 (mtm) REVERT: B 707 LEU cc_start: 0.5940 (OUTLIER) cc_final: 0.5635 (pt) REVERT: C 68 ASN cc_start: 0.8276 (m-40) cc_final: 0.7926 (m110) REVERT: C 265 LYS cc_start: 0.8076 (mtpt) cc_final: 0.7623 (mtmm) REVERT: C 271 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7366 (mt-10) REVERT: C 346 MET cc_start: 0.7749 (mtp) cc_final: 0.7473 (mtp) REVERT: C 421 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: C 628 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7507 (t70) REVERT: C 736 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7463 (mp10) REVERT: C 751 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.7831 (pp) REVERT: C 807 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7956 (pp30) outliers start: 33 outliers final: 16 residues processed: 343 average time/residue: 2.4349 time to fit residues: 972.4374 Evaluate side-chains 340 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 316 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 807 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 187 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 chunk 181 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN C 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24900 Z= 0.225 Angle : 0.496 5.533 33567 Z= 0.267 Chirality : 0.040 0.148 3892 Planarity : 0.004 0.094 4210 Dihedral : 9.617 176.447 3917 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.22 % Allowed : 14.81 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.15), residues: 3164 helix: 2.23 (0.12), residues: 1808 sheet: 0.41 (0.23), residues: 494 loop : -0.61 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C1016 HIS 0.003 0.001 HIS C1045 PHE 0.013 0.001 PHE A1015 TYR 0.016 0.001 TYR B 49 ARG 0.011 0.000 ARG C 976 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 325 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8013 (p0) cc_final: 0.7784 (t70) REVERT: A 141 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8177 (mmt) REVERT: A 353 MET cc_start: 0.7422 (mpm) cc_final: 0.7137 (mmp) REVERT: A 494 MET cc_start: 0.8416 (mtp) cc_final: 0.8165 (mtp) REVERT: A 533 ARG cc_start: 0.7285 (ptp-170) cc_final: 0.6923 (ttp-170) REVERT: A 959 ASP cc_start: 0.7513 (m-30) cc_final: 0.6801 (m-30) REVERT: A 973 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6830 (tp30) REVERT: A 1049 MET cc_start: 0.8522 (mmm) cc_final: 0.8098 (mmm) REVERT: B 44 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8280 (m) REVERT: B 229 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8728 (p) REVERT: B 537 ARG cc_start: 0.7508 (mpt180) cc_final: 0.7249 (ttm110) REVERT: B 649 MET cc_start: 0.8328 (mtp) cc_final: 0.8022 (mtm) REVERT: B 707 LEU cc_start: 0.5487 (OUTLIER) cc_final: 0.5218 (pt) REVERT: C 48 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8554 (mp) REVERT: C 68 ASN cc_start: 0.8292 (m-40) cc_final: 0.7973 (m110) REVERT: C 265 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7613 (mtmm) REVERT: C 271 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7383 (mt-10) REVERT: C 346 MET cc_start: 0.7747 (mtp) cc_final: 0.7468 (mtp) REVERT: C 421 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: C 628 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7491 (t70) REVERT: C 736 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7429 (mp10) REVERT: C 751 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.7792 (pp) REVERT: C 807 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7972 (pp30) outliers start: 31 outliers final: 17 residues processed: 345 average time/residue: 2.3997 time to fit residues: 966.8589 Evaluate side-chains 348 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 321 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 807 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 276 optimal weight: 0.0010 chunk 290 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 281 optimal weight: 0.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN C 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24900 Z= 0.254 Angle : 0.507 6.026 33567 Z= 0.273 Chirality : 0.040 0.147 3892 Planarity : 0.004 0.079 4210 Dihedral : 9.568 176.404 3917 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.26 % Allowed : 14.89 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.15), residues: 3164 helix: 2.19 (0.12), residues: 1808 sheet: 0.39 (0.23), residues: 494 loop : -0.65 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1016 HIS 0.004 0.001 HIS C1045 PHE 0.013 0.001 PHE A1015 TYR 0.017 0.001 TYR B 49 ARG 0.011 0.000 ARG C 976 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 325 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8201 (mmt) REVERT: A 494 MET cc_start: 0.8426 (mtp) cc_final: 0.8174 (mtp) REVERT: A 533 ARG cc_start: 0.7253 (ptp-170) cc_final: 0.6888 (ttp-170) REVERT: A 959 ASP cc_start: 0.7543 (m-30) cc_final: 0.6832 (m-30) REVERT: A 973 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6823 (tp30) REVERT: B 44 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8249 (m) REVERT: B 229 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8736 (p) REVERT: B 649 MET cc_start: 0.8331 (mtp) cc_final: 0.8018 (mtm) REVERT: B 707 LEU cc_start: 0.5905 (OUTLIER) cc_final: 0.5598 (pt) REVERT: C 68 ASN cc_start: 0.8278 (m-40) cc_final: 0.7925 (m110) REVERT: C 265 LYS cc_start: 0.8069 (mtpt) cc_final: 0.7617 (mtmm) REVERT: C 271 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7395 (mt-10) REVERT: C 346 MET cc_start: 0.7748 (mtp) cc_final: 0.7468 (mtp) REVERT: C 421 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: C 628 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7498 (t70) REVERT: C 736 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7415 (mp10) REVERT: C 751 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.7863 (pp) REVERT: C 807 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7975 (pp30) outliers start: 32 outliers final: 20 residues processed: 346 average time/residue: 2.4532 time to fit residues: 993.8958 Evaluate side-chains 349 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 320 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 807 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 185 optimal weight: 3.9990 chunk 299 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 313 optimal weight: 2.9990 chunk 288 optimal weight: 0.0970 chunk 249 optimal weight: 1.9990 chunk 25 optimal weight: 0.0570 chunk 193 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN C 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24900 Z= 0.157 Angle : 0.477 10.227 33567 Z= 0.255 Chirality : 0.039 0.151 3892 Planarity : 0.004 0.097 4210 Dihedral : 9.123 175.920 3917 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.06 % Allowed : 15.13 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.15), residues: 3164 helix: 2.37 (0.12), residues: 1810 sheet: 0.43 (0.23), residues: 492 loop : -0.52 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1016 HIS 0.002 0.000 HIS C1045 PHE 0.012 0.001 PHE A1015 TYR 0.012 0.001 TYR B 49 ARG 0.016 0.000 ARG C 976 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 324 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 MET cc_start: 0.8395 (mtp) cc_final: 0.8156 (mtp) REVERT: A 533 ARG cc_start: 0.7191 (ptp-170) cc_final: 0.6844 (ttp-170) REVERT: A 959 ASP cc_start: 0.7439 (m-30) cc_final: 0.6580 (m-30) REVERT: A 1049 MET cc_start: 0.8512 (mmm) cc_final: 0.8020 (mmm) REVERT: B 44 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8274 (m) REVERT: B 229 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8689 (p) REVERT: B 537 ARG cc_start: 0.7464 (mpt180) cc_final: 0.7205 (ttm110) REVERT: B 649 MET cc_start: 0.8296 (mtp) cc_final: 0.8034 (mtm) REVERT: B 707 LEU cc_start: 0.5420 (OUTLIER) cc_final: 0.5119 (pt) REVERT: C 68 ASN cc_start: 0.8260 (m-40) cc_final: 0.7909 (m110) REVERT: C 265 LYS cc_start: 0.8028 (mtpt) cc_final: 0.7579 (mtmm) REVERT: C 271 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7399 (mt-10) REVERT: C 346 MET cc_start: 0.7728 (mtp) cc_final: 0.7527 (mtp) REVERT: C 421 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: C 628 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7489 (t70) REVERT: C 736 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7446 (mp10) REVERT: C 751 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.7707 (pp) REVERT: C 807 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7945 (pp30) outliers start: 27 outliers final: 15 residues processed: 340 average time/residue: 2.4342 time to fit residues: 962.6332 Evaluate side-chains 343 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 320 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 807 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 198 optimal weight: 0.8980 chunk 266 optimal weight: 0.5980 chunk 76 optimal weight: 0.4980 chunk 230 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 250 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 257 optimal weight: 0.9980 chunk 31 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN B 179 GLN C 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.107855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.088572 restraints weight = 89107.492| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.43 r_work: 0.3079 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24900 Z= 0.152 Angle : 0.471 11.254 33567 Z= 0.251 Chirality : 0.039 0.151 3892 Planarity : 0.004 0.086 4210 Dihedral : 8.789 174.926 3917 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.95 % Allowed : 15.25 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.15), residues: 3164 helix: 2.46 (0.12), residues: 1812 sheet: 0.47 (0.23), residues: 494 loop : -0.47 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1016 HIS 0.002 0.000 HIS C1045 PHE 0.012 0.001 PHE A1015 TYR 0.012 0.001 TYR B 49 ARG 0.014 0.000 ARG C 976 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14821.81 seconds wall clock time: 253 minutes 41.87 seconds (15221.87 seconds total)