Starting phenix.real_space_refine on Sat Jul 4 21:48:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kgh_22870/07_2026/7kgh_22870.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kgh_22870/07_2026/7kgh_22870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kgh_22870/07_2026/7kgh_22870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kgh_22870/07_2026/7kgh_22870.map" model { file = "/net/cci-nas-00/data/ceres_data/7kgh_22870/07_2026/7kgh_22870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kgh_22870/07_2026/7kgh_22870.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7kgh_22870/07_2026/7kgh_22870.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kgh_22870/07_2026/7kgh_22870.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= -0.000 sd= 0.138 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 135 5.16 5 C 15234 2.51 5 N 3801 2.21 5 O 4332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23505 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "B" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "C" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' ET': 2, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Time building chain proxies: 4.78, per 1000 atoms: 0.20 Number of scatterers: 23505 At special positions: 0 Unit cell: (122.04, 113.4, 141.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 P 3 15.00 O 4332 8.00 N 3801 7.00 C 15234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 731.1 milliseconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5706 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 24 sheets defined 61.4% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.205A pdb=" N PHE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.504A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE A 15 " --> pdb=" O PHE A 11 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) Proline residue: A 28 - end of helix Processing helix chain 'A' and resid 53 through 61 removed outlier: 3.750A pdb=" N ASP A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.697A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.512A pdb=" N VAL A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.920A pdb=" N ARG A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 removed outlier: 3.768A pdb=" N LEU A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.964A pdb=" N VAL A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 315 removed outlier: 3.670A pdb=" N THR A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 360 Processing helix chain 'A' and resid 361 through 387 removed outlier: 4.435A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix removed outlier: 3.624A pdb=" N VAL A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 424 removed outlier: 3.783A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 454 removed outlier: 5.391A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 3.905A pdb=" N PHE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.658A pdb=" N ALA A 459 " --> pdb=" O MET A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 497 removed outlier: 3.698A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 3.857A pdb=" N THR A 495 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 533 Processing helix chain 'A' and resid 535 through 556 Processing helix chain 'A' and resid 580 through 598 Processing helix chain 'A' and resid 635 through 647 Processing helix chain 'A' and resid 683 through 701 removed outlier: 4.160A pdb=" N LEU A 687 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 688 " --> pdb=" O MET A 684 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 692 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A 697 " --> pdb=" O GLU A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 733 through 745 Processing helix chain 'A' and resid 773 through 780 removed outlier: 4.212A pdb=" N ILE A 777 " --> pdb=" O GLN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 796 removed outlier: 4.385A pdb=" N VAL A 795 " --> pdb=" O SER A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 842 Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'A' and resid 860 through 884 removed outlier: 4.267A pdb=" N MET A 864 " --> pdb=" O SER A 860 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA A 865 " --> pdb=" O GLU A 861 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N PHE A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 893 Processing helix chain 'A' and resid 895 through 911 Processing helix chain 'A' and resid 915 through 946 removed outlier: 3.630A pdb=" N LYS A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 946 " --> pdb=" O MET A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 981 removed outlier: 5.053A pdb=" N ARG A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Proline residue: A 964 - end of helix Proline residue: A 978 - end of helix removed outlier: 3.788A pdb=" N ILE A 981 " --> pdb=" O ILE A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1027 removed outlier: 4.340A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A1009 " --> pdb=" O THR A1005 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N PHE A1010 " --> pdb=" O ILE A1006 " (cutoff:3.500A) Proline residue: A1013 - end of helix Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.629A pdb=" N PHE B 5 " --> pdb=" O SER B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 30 removed outlier: 3.610A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Proline residue: B 28 - end of helix Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.860A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 99 through 112 removed outlier: 3.559A pdb=" N ALA B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.575A pdb=" N VAL B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 197 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 298 through 317 removed outlier: 4.070A pdb=" N LEU B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 360 removed outlier: 4.072A pdb=" N VAL B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 370 Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.616A pdb=" N ILE B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 removed outlier: 4.188A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 423 Processing helix chain 'B' and resid 426 through 438 Processing helix chain 'B' and resid 438 through 458 removed outlier: 3.719A pdb=" N ILE B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Proline residue: B 455 - end of helix removed outlier: 3.897A pdb=" N PHE B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 496 removed outlier: 3.619A pdb=" N GLN B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 509 through 533 Processing helix chain 'B' and resid 534 through 556 removed outlier: 3.528A pdb=" N ALA B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP B 556 " --> pdb=" O GLY B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 597 removed outlier: 3.562A pdb=" N THR B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP B 597 " --> pdb=" O ASN B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 650 removed outlier: 3.622A pdb=" N SER B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 700 removed outlier: 3.565A pdb=" N LEU B 688 " --> pdb=" O MET B 684 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS B 700 " --> pdb=" O ALA B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 733 through 743 removed outlier: 3.585A pdb=" N ILE B 740 " --> pdb=" O ASP B 736 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 741 " --> pdb=" O VAL B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 772 removed outlier: 4.244A pdb=" N MET B 772 " --> pdb=" O LYS B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 779 removed outlier: 4.173A pdb=" N ILE B 777 " --> pdb=" O GLN B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 795 No H-bonds generated for 'chain 'B' and resid 792 through 795' Processing helix chain 'B' and resid 827 through 841 removed outlier: 3.740A pdb=" N LYS B 841 " --> pdb=" O GLN B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 884 removed outlier: 3.658A pdb=" N GLN B 856 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA B 865 " --> pdb=" O GLU B 861 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N PHE B 866 " --> pdb=" O SER B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 894 removed outlier: 3.746A pdb=" N SER B 891 " --> pdb=" O ALA B 887 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 892 " --> pdb=" O ILE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 911 removed outlier: 3.614A pdb=" N GLY B 899 " --> pdb=" O VAL B 895 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY B 902 " --> pdb=" O LEU B 898 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE B 905 " --> pdb=" O PHE B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 946 removed outlier: 4.222A pdb=" N PHE B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B 946 " --> pdb=" O MET B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 961 Processing helix chain 'B' and resid 961 through 982 removed outlier: 3.502A pdb=" N ILE B 965 " --> pdb=" O ARG B 961 " (cutoff:3.500A) Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 986 through 1007 removed outlier: 3.780A pdb=" N GLN B 990 " --> pdb=" O SER B 986 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1027 Proline residue: B1013 - end of helix removed outlier: 3.598A pdb=" N VAL B1023 " --> pdb=" O ILE B1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.957A pdb=" N ILE C 6 " --> pdb=" O SER C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 30 removed outlier: 3.563A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Proline residue: C 28 - end of helix Processing helix chain 'C' and resid 53 through 61 removed outlier: 3.583A pdb=" N VAL C 61 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.971A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 113 through 117 removed outlier: 4.368A pdb=" N ALA C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 162 through 168 removed outlier: 3.518A pdb=" N LYS C 167 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 197 Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 261 through 264 Processing helix chain 'C' and resid 298 through 316 removed outlier: 3.802A pdb=" N LEU C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 360 removed outlier: 3.526A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 387 removed outlier: 4.306A pdb=" N THR C 365 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 366 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix Proline residue: C 373 - end of helix removed outlier: 3.550A pdb=" N PHE C 380 " --> pdb=" O LEU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 424 removed outlier: 4.409A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA C 409 " --> pdb=" O ILE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 453 removed outlier: 5.453A pdb=" N SER C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Proline residue: C 441 - end of helix Processing helix chain 'C' and resid 453 through 458 Processing helix chain 'C' and resid 461 through 497 removed outlier: 3.799A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix removed outlier: 3.538A pdb=" N LEU C 497 " --> pdb=" O CYS C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 534 removed outlier: 3.663A pdb=" N HIS C 534 " --> pdb=" O LYS C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 556 removed outlier: 3.934A pdb=" N MET C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET C 539 " --> pdb=" O THR C 535 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL C 540 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 541 " --> pdb=" O PRO C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 596 removed outlier: 3.582A pdb=" N LEU C 595 " --> pdb=" O PHE C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 647 removed outlier: 3.531A pdb=" N MET C 647 " --> pdb=" O VAL C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 701 removed outlier: 3.663A pdb=" N LYS C 700 " --> pdb=" O ALA C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 733 through 746 removed outlier: 3.937A pdb=" N VAL C 737 " --> pdb=" O LYS C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 780 Processing helix chain 'C' and resid 792 through 795 No H-bonds generated for 'chain 'C' and resid 792 through 795' Processing helix chain 'C' and resid 827 through 840 Processing helix chain 'C' and resid 852 through 860 Processing helix chain 'C' and resid 862 through 884 Processing helix chain 'C' and resid 887 through 894 removed outlier: 4.204A pdb=" N SER C 891 " --> pdb=" O ALA C 887 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 892 " --> pdb=" O ILE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 911 removed outlier: 4.288A pdb=" N GLY C 899 " --> pdb=" O VAL C 895 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE C 900 " --> pdb=" O VAL C 896 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY C 902 " --> pdb=" O LEU C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 946 Processing helix chain 'C' and resid 949 through 981 removed outlier: 4.765A pdb=" N ARG C 963 " --> pdb=" O LYS C 959 " (cutoff:3.500A) Proline residue: C 964 - end of helix Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 986 through 1027 removed outlier: 3.746A pdb=" N GLN C 990 " --> pdb=" O SER C 986 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL C 997 " --> pdb=" O LEU C 993 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C1002 " --> pdb=" O PHE C 998 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE C1010 " --> pdb=" O ILE C1006 " (cutoff:3.500A) Proline residue: C1013 - end of helix removed outlier: 3.770A pdb=" N GLU C1024 " --> pdb=" O LEU C1020 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.346A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 83 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER A 817 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.346A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 83 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.788A pdb=" N GLN A 292 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL A 175 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ALA A 290 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N SER A 177 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ALA A 288 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.788A pdb=" N GLN A 292 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL A 175 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ALA A 290 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N SER A 177 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ALA A 288 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.569A pdb=" N GLU A 269 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LYS A 182 " --> pdb=" O MET A 759 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLN A 761 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN A 751 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL A 764 " --> pdb=" O TYR A 749 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR A 749 " --> pdb=" O VAL A 764 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 235 removed outlier: 6.881A pdb=" N SER A 235 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE C 722 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 252 Processing sheet with id=AA8, first strand: chain 'A' and resid 799 through 803 removed outlier: 3.704A pdb=" N ILE B 232 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 removed outlier: 7.638A pdb=" N THR B 87 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR B 82 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU B 89 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ALA B 80 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR B 91 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR B 78 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR B 93 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N MET B 706 " --> pdb=" O ILE B 821 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 130 removed outlier: 7.638A pdb=" N THR B 87 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR B 82 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU B 89 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ALA B 80 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR B 91 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR B 78 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR B 93 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.983A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU B 293 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE B 136 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU B 137 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP B 328 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU B 139 " --> pdb=" O PRO B 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.885A pdb=" N ILE B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B 603 " --> pdb=" O THR B 625 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 621 " --> pdb=" O ILE B 607 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.644A pdb=" N LYS B 182 " --> pdb=" O GLN B 761 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE B 763 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N MET B 184 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN B 751 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL B 764 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N TYR B 749 " --> pdb=" O VAL B 764 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 250 through 252 Processing sheet with id=AB6, first strand: chain 'B' and resid 796 through 797 Processing sheet with id=AB7, first strand: chain 'B' and resid 796 through 797 Processing sheet with id=AB8, first strand: chain 'B' and resid 781 through 782 Processing sheet with id=AB9, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.861A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP C 83 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.712A pdb=" N PHE C 136 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU C 293 " --> pdb=" O PHE C 136 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.457A pdb=" N LYS C 182 " --> pdb=" O MET C 759 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLN C 761 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN C 751 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL C 764 " --> pdb=" O TYR C 749 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N TYR C 749 " --> pdb=" O VAL C 764 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 251 through 252 Processing sheet with id=AC4, first strand: chain 'C' and resid 284 through 285 removed outlier: 4.270A pdb=" N SER C 603 " --> pdb=" O THR C 625 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR C 605 " --> pdb=" O PHE C 623 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 704 through 710 removed outlier: 4.116A pdb=" N SER C 817 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 781 through 782 1553 hydrogen bonds defined for protein. 4521 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.42 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.26: 3843 1.26 - 1.40: 5291 1.40 - 1.54: 14153 1.54 - 1.68: 383 1.68 - 1.82: 264 Bond restraints: 23934 Sorted by residual: bond pdb=" C ASN B 205 " pdb=" O ASN B 205 " ideal model delta sigma weight residual 1.237 1.131 0.106 1.17e-02 7.31e+03 8.21e+01 bond pdb=" C HIS C 342 " pdb=" O HIS C 342 " ideal model delta sigma weight residual 1.237 1.132 0.105 1.17e-02 7.31e+03 8.02e+01 bond pdb=" C GLN C 863 " pdb=" O GLN C 863 " ideal model delta sigma weight residual 1.236 1.126 0.110 1.26e-02 6.30e+03 7.68e+01 bond pdb=" C8 PTY B1101 " pdb=" O7 PTY B1101 " ideal model delta sigma weight residual 1.331 1.458 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C ASN C 298 " pdb=" O ASN C 298 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.21e-02 6.83e+03 3.55e+01 ... (remaining 23929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 32105 3.40 - 6.80: 312 6.80 - 10.21: 19 10.21 - 13.61: 4 13.61 - 17.01: 2 Bond angle restraints: 32442 Sorted by residual: angle pdb=" C ASN C 298 " pdb=" N ALA C 299 " pdb=" CA ALA C 299 " ideal model delta sigma weight residual 120.44 130.93 -10.49 1.30e+00 5.92e-01 6.51e+01 angle pdb=" CA ASN C 298 " pdb=" C ASN C 298 " pdb=" O ASN C 298 " ideal model delta sigma weight residual 120.49 112.27 8.22 1.16e+00 7.43e-01 5.02e+01 angle pdb=" CA HIS C 342 " pdb=" C HIS C 342 " pdb=" O HIS C 342 " ideal model delta sigma weight residual 120.55 113.11 7.44 1.06e+00 8.90e-01 4.92e+01 angle pdb=" CA ASN B 205 " pdb=" C ASN B 205 " pdb=" O ASN B 205 " ideal model delta sigma weight residual 120.55 113.41 7.14 1.06e+00 8.90e-01 4.54e+01 angle pdb=" CA PHE C 550 " pdb=" C PHE C 550 " pdb=" O PHE C 550 " ideal model delta sigma weight residual 119.97 112.47 7.50 1.15e+00 7.56e-01 4.25e+01 ... (remaining 32437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.59: 14100 32.59 - 65.19: 345 65.19 - 97.78: 34 97.78 - 130.38: 1 130.38 - 162.97: 1 Dihedral angle restraints: 14481 sinusoidal: 5664 harmonic: 8817 Sorted by residual: dihedral pdb=" C TYR A 77 " pdb=" N TYR A 77 " pdb=" CA TYR A 77 " pdb=" CB TYR A 77 " ideal model delta harmonic sigma weight residual -122.60 -137.51 14.91 0 2.50e+00 1.60e-01 3.56e+01 dihedral pdb=" N TYR A 77 " pdb=" C TYR A 77 " pdb=" CA TYR A 77 " pdb=" CB TYR A 77 " ideal model delta harmonic sigma weight residual 122.80 136.64 -13.84 0 2.50e+00 1.60e-01 3.06e+01 dihedral pdb=" C ASN A 74 " pdb=" N ASN A 74 " pdb=" CA ASN A 74 " pdb=" CB ASN A 74 " ideal model delta harmonic sigma weight residual -122.60 -136.35 13.75 0 2.50e+00 1.60e-01 3.02e+01 ... (remaining 14478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 3733 0.111 - 0.221: 125 0.221 - 0.332: 13 0.332 - 0.443: 0 0.443 - 0.553: 2 Chirality restraints: 3873 Sorted by residual: chirality pdb=" CA TYR A 77 " pdb=" N TYR A 77 " pdb=" C TYR A 77 " pdb=" CB TYR A 77 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.66e+00 chirality pdb=" CA ASN A 74 " pdb=" N ASN A 74 " pdb=" C ASN A 74 " pdb=" CB ASN A 74 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" CA ILE A 291 " pdb=" N ILE A 291 " pdb=" C ILE A 291 " pdb=" CB ILE A 291 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 3870 not shown) Planarity restraints: 4066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 330 " 0.077 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO B 331 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO B 331 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 331 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 765 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C GLN B 765 " -0.070 2.00e-02 2.50e+03 pdb=" O GLN B 765 " 0.026 2.00e-02 2.50e+03 pdb=" N VAL B 766 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 44 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C ASN A 44 " 0.070 2.00e-02 2.50e+03 pdb=" O ASN A 44 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE A 45 " -0.025 2.00e-02 2.50e+03 ... (remaining 4063 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 100 2.51 - 3.11: 18582 3.11 - 3.70: 35769 3.70 - 4.30: 50957 4.30 - 4.90: 85576 Nonbonded interactions: 190984 Sorted by model distance: nonbonded pdb=" O ASN B 248 " pdb=" ND2 ASN B 248 " model vdw 1.910 3.120 nonbonded pdb=" OH TYR A 749 " pdb=" OD1 ASP A 752 " model vdw 2.062 3.040 nonbonded pdb=" O LEU B 898 " pdb=" OG SER B1003 " model vdw 2.074 3.040 nonbonded pdb=" OE1 GLN B 120 " pdb=" NH2 ARG B 123 " model vdw 2.093 3.120 nonbonded pdb=" NZ LYS C 602 " pdb=" O LYS C 627 " model vdw 2.095 3.120 ... (remaining 190979 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 1027 or (resid 1101 and (name C1 or 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 C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C \ 34 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or name O \ 12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 )))) selection = (chain 'B' and (resid 1 through 1027 or (resid 1101 and (name C1 or 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 C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C \ 34 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or name O \ 12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 )))) selection = (chain 'C' and (resid 1 through 1027 or (resid 1101 and (name C1 or 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 C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C \ 34 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or name O \ 12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 )))) } 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 group one per residue 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: 0.130 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.150 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 0.127 23934 Z= 0.298 Angle : 0.803 17.008 32442 Z= 0.504 Chirality : 0.047 0.553 3873 Planarity : 0.006 0.114 4066 Dihedral : 14.355 162.970 8775 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.97 % Allowed : 1.33 % Favored : 97.70 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.15), residues: 3048 helix: 1.80 (0.13), residues: 1644 sheet: -0.01 (0.24), residues: 402 loop : -0.08 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 961 TYR 0.028 0.002 TYR C 78 PHE 0.038 0.001 PHE B 136 TRP 0.010 0.001 TRP A 800 HIS 0.003 0.001 HIS C 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.30 (23934) covalent geometry : angle 0.80312 / 0.50 (32442) hydrogen bonds : bond 0.14830 / 9.67 ( 1505) hydrogen bonds : angle 6.08394 / 4.30 ( 4521) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 569 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6741 (mm-30) REVERT: A 156 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6621 (t70) REVERT: A 280 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6270 (mm) REVERT: A 304 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6586 (tt0) REVERT: A 376 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6291 (mp) REVERT: A 693 GLU cc_start: 0.7370 (tp30) cc_final: 0.6907 (tm-30) REVERT: A 807 TYR cc_start: 0.7869 (m-80) cc_final: 0.7449 (m-80) REVERT: A 1001 MET cc_start: 0.5261 (ttm) cc_final: 0.4998 (ttm) REVERT: B 165 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6766 (mm-30) REVERT: B 184 MET cc_start: 0.6705 (mmm) cc_final: 0.6097 (mmm) REVERT: B 309 LYS cc_start: 0.7709 (tptp) cc_final: 0.7283 (tptp) REVERT: B 527 MET cc_start: 0.6965 (ttt) cc_final: 0.6667 (ttm) REVERT: B 654 GLU cc_start: 0.6316 (mt-10) cc_final: 0.5681 (pt0) REVERT: B 695 MET cc_start: 0.7395 (mmm) cc_final: 0.6715 (mmt) REVERT: B 813 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6966 (mtt-85) REVERT: B 844 LYS cc_start: 0.7329 (tppt) cc_final: 0.7085 (tppt) REVERT: B 931 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7341 (tttm) REVERT: C 8 ARG cc_start: 0.7374 (mtt180) cc_final: 0.7032 (mmm-85) REVERT: C 68 GLU cc_start: 0.6175 (mp0) cc_final: 0.5501 (mp0) REVERT: C 363 ARG cc_start: 0.7138 (mmt180) cc_final: 0.6759 (mmt-90) REVERT: C 423 GLU cc_start: 0.7086 (mp0) cc_final: 0.6673 (mp0) REVERT: C 467 TYR cc_start: 0.7398 (m-10) cc_final: 0.7116 (m-80) REVERT: C 471 THR cc_start: 0.7946 (m) cc_final: 0.7712 (p) REVERT: C 533 LYS cc_start: 0.7601 (tmtt) cc_final: 0.7371 (tptp) REVERT: C 589 ASN cc_start: 0.6050 (m110) cc_final: 0.5624 (m-40) REVERT: C 826 THR cc_start: 0.8084 (m) cc_final: 0.7878 (m) outliers start: 25 outliers final: 5 residues processed: 589 average time/residue: 0.1313 time to fit residues: 124.6963 Evaluate side-chains 520 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 508 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 813 ARG Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 709 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0670 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 9.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 GLN A 342 HIS A 590 GLN A 701 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 GLN B 360 HIS B 566 GLN B 617 GLN B 801 ASN B 859 GLN B 863 GLN C 273 GLN C 282 ASN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN C 991 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.179748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.148915 restraints weight = 27394.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.146974 restraints weight = 21004.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.147271 restraints weight = 21779.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.147743 restraints weight = 18792.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.147959 restraints weight = 17900.849| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23934 Z= 0.182 Angle : 0.667 13.032 32442 Z= 0.345 Chirality : 0.045 0.278 3873 Planarity : 0.005 0.059 4066 Dihedral : 7.614 171.330 3300 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.72 % Allowed : 9.55 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.15), residues: 3048 helix: 1.67 (0.12), residues: 1676 sheet: -0.07 (0.22), residues: 440 loop : -0.13 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 418 TYR 0.020 0.002 TYR C 848 PHE 0.033 0.002 PHE A 517 TRP 0.012 0.001 TRP A 800 HIS 0.005 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (23934) covalent geometry : angle 0.66685 / 0.34 (32442) hydrogen bonds : bond 0.05293 / 3.54 ( 1505) hydrogen bonds : angle 4.92771 / 3.52 ( 4521) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 539 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.6768 (mt) REVERT: A 304 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6385 (tt0) REVERT: A 311 GLU cc_start: 0.7306 (mm-30) cc_final: 0.7101 (mm-30) REVERT: A 374 ILE cc_start: 0.6899 (mt) cc_final: 0.6311 (mt) REVERT: A 376 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7109 (mt) REVERT: A 693 GLU cc_start: 0.7722 (tp30) cc_final: 0.7235 (tp30) REVERT: A 769 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6447 (ttpt) REVERT: B 165 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6855 (mm-30) REVERT: B 182 LYS cc_start: 0.7104 (mtmm) cc_final: 0.6558 (ptpp) REVERT: B 235 SER cc_start: 0.8222 (t) cc_final: 0.7983 (p) REVERT: B 518 ASP cc_start: 0.6521 (t0) cc_final: 0.6287 (t0) REVERT: B 522 LYS cc_start: 0.7700 (mtmm) cc_final: 0.7372 (mtmm) REVERT: B 527 MET cc_start: 0.6946 (ttt) cc_final: 0.6687 (ttm) REVERT: B 554 LYS cc_start: 0.7447 (mptt) cc_final: 0.7165 (tppt) REVERT: B 654 GLU cc_start: 0.6300 (mt-10) cc_final: 0.5913 (pt0) REVERT: B 656 MET cc_start: 0.7548 (tpp) cc_final: 0.7101 (tpt) REVERT: B 783 MET cc_start: 0.3958 (mmm) cc_final: 0.3489 (mmm) REVERT: C 68 GLU cc_start: 0.6451 (mp0) cc_final: 0.5580 (mp0) REVERT: C 213 GLU cc_start: 0.7302 (tt0) cc_final: 0.6881 (tt0) REVERT: C 321 MET cc_start: 0.6692 (mtm) cc_final: 0.6372 (mtm) REVERT: C 356 TYR cc_start: 0.6460 (t80) cc_final: 0.6067 (t80) REVERT: C 423 GLU cc_start: 0.7014 (mp0) cc_final: 0.6676 (mp0) REVERT: C 467 TYR cc_start: 0.7450 (m-10) cc_final: 0.7000 (m-80) REVERT: C 519 LYS cc_start: 0.7459 (mmmt) cc_final: 0.7187 (pttt) REVERT: C 528 LEU cc_start: 0.5813 (tp) cc_final: 0.5590 (tp) REVERT: C 589 ASN cc_start: 0.6184 (m110) cc_final: 0.5777 (m-40) REVERT: C 602 LYS cc_start: 0.7838 (mttp) cc_final: 0.7614 (mmtt) REVERT: C 826 THR cc_start: 0.8185 (m) cc_final: 0.7675 (p) REVERT: C 849 GLU cc_start: 0.7017 (mp0) cc_final: 0.5962 (tt0) outliers start: 44 outliers final: 22 residues processed: 563 average time/residue: 0.1429 time to fit residues: 128.5892 Evaluate side-chains 538 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 511 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 821 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 147 optimal weight: 0.0370 chunk 88 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 236 optimal weight: 7.9990 chunk 259 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 250 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 204 ASN A 360 HIS A 590 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 360 HIS ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 566 GLN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.177581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.147785 restraints weight = 27392.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.147027 restraints weight = 32041.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.148501 restraints weight = 29299.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.148447 restraints weight = 22696.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.148575 restraints weight = 20907.315| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23934 Z= 0.169 Angle : 0.621 11.326 32442 Z= 0.321 Chirality : 0.044 0.210 3873 Planarity : 0.005 0.055 4066 Dihedral : 7.114 175.081 3286 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.42 % Allowed : 11.70 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.15), residues: 3048 helix: 1.63 (0.12), residues: 1677 sheet: -0.19 (0.22), residues: 460 loop : -0.14 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 418 TYR 0.025 0.002 TYR C 848 PHE 0.031 0.002 PHE A 517 TRP 0.015 0.001 TRP A 800 HIS 0.003 0.001 HIS A 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (23934) covalent geometry : angle 0.62088 / 0.32 (32442) hydrogen bonds : bond 0.04978 / 3.33 ( 1505) hydrogen bonds : angle 4.72311 / 3.37 ( 4521) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 528 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4918 (tpp) cc_final: 0.4659 (mmt) REVERT: A 99 ASP cc_start: 0.5364 (m-30) cc_final: 0.5094 (p0) REVERT: A 104 GLN cc_start: 0.7816 (tt0) cc_final: 0.7587 (tt0) REVERT: A 213 GLU cc_start: 0.6575 (mt-10) cc_final: 0.6152 (mt-10) REVERT: A 304 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6548 (tt0) REVERT: A 376 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7212 (mt) REVERT: A 474 MET cc_start: 0.6548 (ttt) cc_final: 0.6245 (ttt) REVERT: A 570 MET cc_start: 0.7902 (ttp) cc_final: 0.7598 (ttm) REVERT: A 572 SER cc_start: 0.8413 (t) cc_final: 0.7931 (m) REVERT: A 693 GLU cc_start: 0.7188 (tp30) cc_final: 0.6958 (tp30) REVERT: A 769 LYS cc_start: 0.7020 (pttm) cc_final: 0.6350 (ttpt) REVERT: A 939 PHE cc_start: 0.6616 (m-80) cc_final: 0.6216 (t80) REVERT: B 182 LYS cc_start: 0.6948 (mtmm) cc_final: 0.6737 (mtmm) REVERT: B 184 MET cc_start: 0.6160 (mmp) cc_final: 0.5924 (mmm) REVERT: B 518 ASP cc_start: 0.6498 (t0) cc_final: 0.6191 (t0) REVERT: B 522 LYS cc_start: 0.7720 (mtmm) cc_final: 0.7337 (mtmm) REVERT: B 527 MET cc_start: 0.7005 (ttt) cc_final: 0.6730 (ttm) REVERT: B 554 LYS cc_start: 0.7439 (mptt) cc_final: 0.7211 (tppt) REVERT: B 654 GLU cc_start: 0.6361 (mt-10) cc_final: 0.5893 (pt0) REVERT: B 771 ARG cc_start: 0.8027 (ptt90) cc_final: 0.7733 (ptt90) REVERT: B 783 MET cc_start: 0.3762 (mmm) cc_final: 0.3274 (mmm) REVERT: B 807 TYR cc_start: 0.7782 (m-80) cc_final: 0.7439 (m-80) REVERT: B 844 LYS cc_start: 0.7660 (tppt) cc_final: 0.7112 (mmtm) REVERT: C 68 GLU cc_start: 0.6405 (mp0) cc_final: 0.5547 (mp0) REVERT: C 213 GLU cc_start: 0.7267 (tt0) cc_final: 0.6806 (tt0) REVERT: C 356 TYR cc_start: 0.6429 (t80) cc_final: 0.6082 (t80) REVERT: C 363 ARG cc_start: 0.7291 (mmt180) cc_final: 0.6900 (mmt-90) REVERT: C 423 GLU cc_start: 0.7049 (mp0) cc_final: 0.6663 (mp0) REVERT: C 589 ASN cc_start: 0.6216 (m110) cc_final: 0.5812 (m-40) REVERT: C 602 LYS cc_start: 0.7778 (mttp) cc_final: 0.7531 (mmtm) REVERT: C 769 LYS cc_start: 0.7925 (tmmt) cc_final: 0.7531 (tmtt) REVERT: C 826 THR cc_start: 0.8155 (m) cc_final: 0.7678 (p) REVERT: C 849 GLU cc_start: 0.7069 (mp0) cc_final: 0.6539 (mp0) outliers start: 62 outliers final: 38 residues processed: 560 average time/residue: 0.1406 time to fit residues: 126.2856 Evaluate side-chains 548 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 508 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 791 SER Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 277 optimal weight: 7.9990 chunk 301 optimal weight: 8.9990 chunk 221 optimal weight: 9.9990 chunk 234 optimal weight: 6.9990 chunk 42 optimal weight: 40.0000 chunk 88 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 269 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 GLN A 108 GLN A 148 GLN A 237 GLN A 360 HIS A 574 GLN A 590 GLN A 714 GLN B 360 HIS ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN B 773 GLN C 589 ASN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.173603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.141807 restraints weight = 27408.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.141141 restraints weight = 34923.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.141255 restraints weight = 34581.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.141747 restraints weight = 28727.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.142214 restraints weight = 25799.240| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 23934 Z= 0.231 Angle : 0.684 12.077 32442 Z= 0.353 Chirality : 0.046 0.311 3873 Planarity : 0.005 0.067 4066 Dihedral : 7.036 167.264 3281 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.24 % Allowed : 14.07 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.15), residues: 3048 helix: 1.45 (0.12), residues: 1677 sheet: -0.27 (0.23), residues: 462 loop : -0.33 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 418 TYR 0.025 0.002 TYR C 848 PHE 0.029 0.002 PHE A 517 TRP 0.015 0.002 TRP A 800 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.23 (23934) covalent geometry : angle 0.68379 / 0.35 (32442) hydrogen bonds : bond 0.05414 / 3.63 ( 1505) hydrogen bonds : angle 4.83610 / 3.45 ( 4521) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 525 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6443 (mt-10) REVERT: A 213 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6591 (mt-10) REVERT: A 357 LEU cc_start: 0.8014 (mm) cc_final: 0.7784 (mm) REVERT: A 570 MET cc_start: 0.7973 (ttp) cc_final: 0.7761 (ttm) REVERT: A 684 MET cc_start: 0.7327 (mpp) cc_final: 0.5539 (mmm) REVERT: A 693 GLU cc_start: 0.7132 (tp30) cc_final: 0.6911 (tp30) REVERT: A 748 MET cc_start: 0.6339 (pmm) cc_final: 0.6073 (pmm) REVERT: A 769 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6331 (ttpt) REVERT: A 884 GLU cc_start: 0.5909 (mp0) cc_final: 0.5620 (mp0) REVERT: A 939 PHE cc_start: 0.6480 (m-80) cc_final: 0.5980 (t80) REVERT: B 5 PHE cc_start: 0.8520 (m-80) cc_final: 0.8306 (m-80) REVERT: B 182 LYS cc_start: 0.7034 (mtmm) cc_final: 0.6811 (mtmm) REVERT: B 184 MET cc_start: 0.6299 (mmp) cc_final: 0.6072 (mmm) REVERT: B 522 LYS cc_start: 0.7702 (mtmm) cc_final: 0.7295 (mtmm) REVERT: B 527 MET cc_start: 0.6938 (ttt) cc_final: 0.6643 (ttm) REVERT: B 553 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.5947 (ttp) REVERT: B 638 LYS cc_start: 0.7395 (tmtt) cc_final: 0.6939 (tptp) REVERT: B 654 GLU cc_start: 0.6230 (mt-10) cc_final: 0.5884 (pt0) REVERT: B 656 MET cc_start: 0.8131 (tpt) cc_final: 0.7498 (tpt) REVERT: B 771 ARG cc_start: 0.8024 (ptt90) cc_final: 0.7714 (ptt90) REVERT: B 783 MET cc_start: 0.3665 (mmm) cc_final: 0.3220 (mmm) REVERT: B 807 TYR cc_start: 0.7778 (m-80) cc_final: 0.7461 (m-80) REVERT: C 356 TYR cc_start: 0.6541 (t80) cc_final: 0.6282 (t80) REVERT: C 363 ARG cc_start: 0.7424 (mmt180) cc_final: 0.7190 (mmt-90) REVERT: C 423 GLU cc_start: 0.7029 (mp0) cc_final: 0.6620 (mp0) REVERT: C 589 ASN cc_start: 0.6275 (m-40) cc_final: 0.5866 (m-40) REVERT: C 704 PHE cc_start: 0.8032 (m-10) cc_final: 0.7761 (m-10) REVERT: C 769 LYS cc_start: 0.7930 (tmmt) cc_final: 0.7526 (tmtt) REVERT: C 826 THR cc_start: 0.8214 (m) cc_final: 0.7689 (p) REVERT: C 849 GLU cc_start: 0.7273 (mp0) cc_final: 0.5977 (mt-10) outliers start: 83 outliers final: 58 residues processed: 565 average time/residue: 0.1416 time to fit residues: 128.3951 Evaluate side-chains 560 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 499 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 753 PHE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 791 SER Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 281 optimal weight: 0.0370 chunk 129 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 78 optimal weight: 50.0000 chunk 70 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 GLN A 108 GLN A 148 GLN A 590 GLN B 360 HIS ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.174950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.144251 restraints weight = 27279.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.143603 restraints weight = 31551.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.145169 restraints weight = 28553.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.144956 restraints weight = 23384.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.145496 restraints weight = 20700.074| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23934 Z= 0.181 Angle : 0.640 11.530 32442 Z= 0.329 Chirality : 0.044 0.360 3873 Planarity : 0.005 0.070 4066 Dihedral : 6.724 161.048 3276 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.08 % Allowed : 16.10 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.15), residues: 3048 helix: 1.46 (0.12), residues: 1677 sheet: -0.26 (0.23), residues: 462 loop : -0.30 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 771 TYR 0.025 0.002 TYR C 848 PHE 0.028 0.002 PHE A 517 TRP 0.016 0.001 TRP A 800 HIS 0.010 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (23934) covalent geometry : angle 0.63984 / 0.33 (32442) hydrogen bonds : bond 0.04981 / 3.34 ( 1505) hydrogen bonds : angle 4.69697 / 3.35 ( 4521) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 519 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6409 (mt-10) REVERT: A 213 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6579 (mt-10) REVERT: A 304 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6612 (tt0) REVERT: A 357 LEU cc_start: 0.7906 (mm) cc_final: 0.7688 (mm) REVERT: A 570 MET cc_start: 0.7877 (ttp) cc_final: 0.7663 (ttm) REVERT: A 572 SER cc_start: 0.8462 (t) cc_final: 0.7970 (m) REVERT: A 693 GLU cc_start: 0.7074 (tp30) cc_final: 0.6866 (tp30) REVERT: A 769 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6326 (ttpt) REVERT: A 939 PHE cc_start: 0.6323 (m-80) cc_final: 0.5875 (t80) REVERT: B 5 PHE cc_start: 0.8488 (m-80) cc_final: 0.8281 (m-80) REVERT: B 164 GLU cc_start: 0.6665 (tp30) cc_final: 0.6439 (tp30) REVERT: B 182 LYS cc_start: 0.6954 (mtmm) cc_final: 0.6750 (mtmm) REVERT: B 518 ASP cc_start: 0.6596 (t0) cc_final: 0.6235 (t0) REVERT: B 522 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7482 (mtmm) REVERT: B 527 MET cc_start: 0.6918 (ttt) cc_final: 0.6648 (ttm) REVERT: B 553 MET cc_start: 0.6496 (OUTLIER) cc_final: 0.5817 (ttp) REVERT: B 564 GLU cc_start: 0.7806 (tp30) cc_final: 0.7078 (tp30) REVERT: B 638 LYS cc_start: 0.7412 (tmtt) cc_final: 0.6961 (tptp) REVERT: B 654 GLU cc_start: 0.6191 (mt-10) cc_final: 0.5899 (pt0) REVERT: B 656 MET cc_start: 0.8076 (tpt) cc_final: 0.7235 (tpt) REVERT: B 771 ARG cc_start: 0.8041 (ptt90) cc_final: 0.7672 (ptt90) REVERT: B 783 MET cc_start: 0.3543 (mmm) cc_final: 0.3107 (mmm) REVERT: B 807 TYR cc_start: 0.7784 (m-80) cc_final: 0.7445 (m-80) REVERT: B 844 LYS cc_start: 0.7665 (tppt) cc_final: 0.7221 (mmtm) REVERT: B 890 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7955 (tt) REVERT: C 8 ARG cc_start: 0.7617 (mtt180) cc_final: 0.7372 (mtt180) REVERT: C 356 TYR cc_start: 0.6529 (t80) cc_final: 0.6270 (t80) REVERT: C 363 ARG cc_start: 0.7442 (mmt180) cc_final: 0.7203 (mmt-90) REVERT: C 423 GLU cc_start: 0.7050 (mp0) cc_final: 0.6638 (mp0) REVERT: C 589 ASN cc_start: 0.6208 (m-40) cc_final: 0.5840 (m-40) REVERT: C 769 LYS cc_start: 0.7876 (tmmt) cc_final: 0.7527 (tmtt) REVERT: C 826 THR cc_start: 0.8169 (m) cc_final: 0.7666 (p) REVERT: C 849 GLU cc_start: 0.7285 (mp0) cc_final: 0.5896 (mm-30) outliers start: 79 outliers final: 56 residues processed: 554 average time/residue: 0.1321 time to fit residues: 117.7029 Evaluate side-chains 560 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 498 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 753 PHE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 791 SER Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 82 optimal weight: 50.0000 chunk 39 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 199 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 73 optimal weight: 40.0000 chunk 70 optimal weight: 1.9990 chunk 229 optimal weight: 20.0000 chunk 147 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 415 ASN A 574 GLN A 590 GLN B 360 HIS ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.175301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.144783 restraints weight = 27252.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.144106 restraints weight = 32882.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.144657 restraints weight = 27521.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.144013 restraints weight = 27478.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.145452 restraints weight = 21637.660| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23934 Z= 0.173 Angle : 0.635 11.464 32442 Z= 0.326 Chirality : 0.044 0.393 3873 Planarity : 0.005 0.071 4066 Dihedral : 6.599 153.469 3276 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.51 % Allowed : 16.96 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.15), residues: 3048 helix: 1.46 (0.12), residues: 1679 sheet: -0.29 (0.23), residues: 464 loop : -0.32 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 418 TYR 0.029 0.002 TYR C 467 PHE 0.027 0.002 PHE A 517 TRP 0.016 0.001 TRP A 800 HIS 0.007 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (23934) covalent geometry : angle 0.63494 / 0.33 (32442) hydrogen bonds : bond 0.04826 / 3.23 ( 1505) hydrogen bonds : angle 4.63657 / 3.31 ( 4521) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 513 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6433 (mt-10) REVERT: A 213 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6743 (mt-10) REVERT: A 357 LEU cc_start: 0.7936 (mm) cc_final: 0.7707 (mm) REVERT: A 395 MET cc_start: 0.7510 (mmp) cc_final: 0.7247 (mmp) REVERT: A 435 MET cc_start: 0.5050 (mmm) cc_final: 0.4612 (mmm) REVERT: A 570 MET cc_start: 0.7873 (ttp) cc_final: 0.7657 (ttm) REVERT: A 572 SER cc_start: 0.8468 (t) cc_final: 0.8004 (m) REVERT: A 676 LEU cc_start: 0.5735 (OUTLIER) cc_final: 0.5390 (mm) REVERT: A 684 MET cc_start: 0.7382 (mpp) cc_final: 0.5553 (mmm) REVERT: A 693 GLU cc_start: 0.7224 (tp30) cc_final: 0.6933 (tp30) REVERT: A 706 MET cc_start: 0.6241 (mtp) cc_final: 0.5892 (mtt) REVERT: A 769 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6397 (ttpt) REVERT: A 872 MET cc_start: 0.7223 (mpp) cc_final: 0.6992 (mpp) REVERT: A 939 PHE cc_start: 0.6281 (m-80) cc_final: 0.5852 (t80) REVERT: A 951 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.7117 (mm) REVERT: B 309 LYS cc_start: 0.8189 (tptp) cc_final: 0.7739 (tptp) REVERT: B 522 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7451 (mtmm) REVERT: B 527 MET cc_start: 0.6928 (ttt) cc_final: 0.6690 (ttm) REVERT: B 564 GLU cc_start: 0.7811 (tp30) cc_final: 0.7015 (tp30) REVERT: B 638 LYS cc_start: 0.7426 (tmtt) cc_final: 0.6947 (tptp) REVERT: B 654 GLU cc_start: 0.6177 (mt-10) cc_final: 0.5950 (pt0) REVERT: B 656 MET cc_start: 0.8014 (tpt) cc_final: 0.6948 (tpt) REVERT: B 771 ARG cc_start: 0.8062 (ptt90) cc_final: 0.7707 (ptt90) REVERT: B 783 MET cc_start: 0.3409 (mmm) cc_final: 0.3019 (mmm) REVERT: B 807 TYR cc_start: 0.7786 (m-80) cc_final: 0.7501 (m-80) REVERT: B 844 LYS cc_start: 0.7647 (tppt) cc_final: 0.7162 (mmtm) REVERT: B 890 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7948 (tt) REVERT: C 8 ARG cc_start: 0.7494 (mtt180) cc_final: 0.7263 (mtt180) REVERT: C 356 TYR cc_start: 0.6535 (t80) cc_final: 0.6261 (t80) REVERT: C 363 ARG cc_start: 0.7510 (mmt180) cc_final: 0.7042 (mmt-90) REVERT: C 423 GLU cc_start: 0.7100 (mp0) cc_final: 0.6634 (mp0) REVERT: C 589 ASN cc_start: 0.6210 (m-40) cc_final: 0.5819 (m-40) REVERT: C 704 PHE cc_start: 0.8083 (m-10) cc_final: 0.7827 (m-10) REVERT: C 769 LYS cc_start: 0.7876 (tmmt) cc_final: 0.7486 (tmtt) REVERT: C 826 THR cc_start: 0.8254 (m) cc_final: 0.7729 (p) REVERT: C 849 GLU cc_start: 0.7294 (mp0) cc_final: 0.5819 (mm-30) REVERT: C 948 MET cc_start: 0.3855 (ptp) cc_final: 0.3526 (ptt) REVERT: C 970 LEU cc_start: 0.8387 (mp) cc_final: 0.8139 (mt) outliers start: 90 outliers final: 57 residues processed: 558 average time/residue: 0.1375 time to fit residues: 123.2063 Evaluate side-chains 568 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 505 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 753 PHE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 791 SER Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 250 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 82 optimal weight: 50.0000 chunk 247 optimal weight: 8.9990 chunk 268 optimal weight: 7.9990 chunk 279 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 202 optimal weight: 3.9990 chunk 122 optimal weight: 30.0000 chunk 293 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN A 415 ASN A 590 GLN A 709 ASN B 108 GLN B 176 GLN B 360 HIS ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 ASN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.177518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.147951 restraints weight = 27242.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.147067 restraints weight = 33422.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.148461 restraints weight = 29008.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.147900 restraints weight = 23704.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.148298 restraints weight = 20722.145| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23934 Z= 0.140 Angle : 0.616 12.128 32442 Z= 0.314 Chirality : 0.043 0.376 3873 Planarity : 0.005 0.069 4066 Dihedral : 6.362 147.133 3276 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.53 % Allowed : 18.32 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.15), residues: 3048 helix: 1.56 (0.12), residues: 1674 sheet: -0.28 (0.23), residues: 468 loop : -0.25 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 418 TYR 0.031 0.001 TYR C 467 PHE 0.027 0.001 PHE A 901 TRP 0.017 0.001 TRP A 800 HIS 0.006 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (23934) covalent geometry : angle 0.61591 / 0.31 (32442) hydrogen bonds : bond 0.04452 / 2.98 ( 1505) hydrogen bonds : angle 4.50800 / 3.22 ( 4521) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 506 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.7582 (p0) cc_final: 0.7253 (p0) REVERT: A 75 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7856 (tt) REVERT: A 213 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6689 (mt-10) REVERT: A 357 LEU cc_start: 0.7810 (mm) cc_final: 0.7592 (mm) REVERT: A 435 MET cc_start: 0.5094 (mmm) cc_final: 0.4695 (mmm) REVERT: A 473 THR cc_start: 0.7788 (t) cc_final: 0.6437 (p) REVERT: A 474 MET cc_start: 0.6324 (ttt) cc_final: 0.5912 (mtp) REVERT: A 570 MET cc_start: 0.7892 (ttp) cc_final: 0.7627 (ttm) REVERT: A 572 SER cc_start: 0.8345 (t) cc_final: 0.7897 (m) REVERT: A 684 MET cc_start: 0.7393 (mpp) cc_final: 0.5547 (mmm) REVERT: A 693 GLU cc_start: 0.7217 (tp30) cc_final: 0.6959 (tm-30) REVERT: A 697 MET cc_start: 0.7580 (mpp) cc_final: 0.7000 (mmp) REVERT: A 706 MET cc_start: 0.6174 (mtp) cc_final: 0.5957 (mtt) REVERT: A 745 MET cc_start: 0.5670 (tpp) cc_final: 0.5389 (tmm) REVERT: A 769 LYS cc_start: 0.6918 (pttm) cc_final: 0.6279 (ttpt) REVERT: A 939 PHE cc_start: 0.6243 (m-80) cc_final: 0.5845 (t80) REVERT: B 1 MET cc_start: 0.5552 (OUTLIER) cc_final: 0.5168 (ptt) REVERT: B 309 LYS cc_start: 0.8215 (tptp) cc_final: 0.7939 (tptp) REVERT: B 522 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7445 (mtmm) REVERT: B 527 MET cc_start: 0.6977 (ttt) cc_final: 0.6693 (ttm) REVERT: B 564 GLU cc_start: 0.7766 (tp30) cc_final: 0.7073 (tp30) REVERT: B 638 LYS cc_start: 0.7387 (tmtt) cc_final: 0.6921 (tptp) REVERT: B 654 GLU cc_start: 0.6159 (mt-10) cc_final: 0.5926 (pt0) REVERT: B 656 MET cc_start: 0.7926 (tpt) cc_final: 0.6806 (tpt) REVERT: B 719 SER cc_start: 0.8800 (t) cc_final: 0.8320 (m) REVERT: B 771 ARG cc_start: 0.8026 (ptt90) cc_final: 0.7664 (ptt90) REVERT: B 783 MET cc_start: 0.3416 (mmm) cc_final: 0.3028 (mmm) REVERT: B 890 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7837 (tt) REVERT: C 68 GLU cc_start: 0.6524 (mp0) cc_final: 0.5651 (mp0) REVERT: C 356 TYR cc_start: 0.6474 (t80) cc_final: 0.6207 (t80) REVERT: C 363 ARG cc_start: 0.7507 (mmt180) cc_final: 0.7036 (mmt-90) REVERT: C 423 GLU cc_start: 0.7142 (mp0) cc_final: 0.6672 (mp0) REVERT: C 589 ASN cc_start: 0.6175 (m-40) cc_final: 0.5782 (m-40) REVERT: C 704 PHE cc_start: 0.7999 (m-10) cc_final: 0.7712 (m-10) REVERT: C 745 MET cc_start: 0.7978 (mmm) cc_final: 0.7546 (tpp) REVERT: C 769 LYS cc_start: 0.7862 (tmmt) cc_final: 0.7471 (tmtt) REVERT: C 826 THR cc_start: 0.8232 (m) cc_final: 0.7716 (p) REVERT: C 849 GLU cc_start: 0.7269 (mp0) cc_final: 0.5805 (mm-30) outliers start: 65 outliers final: 45 residues processed: 542 average time/residue: 0.1409 time to fit residues: 122.5227 Evaluate side-chains 545 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 496 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 791 SER Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 50 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 chunk 76 optimal weight: 50.0000 chunk 204 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 293 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 228 GLN A 415 ASN A 574 GLN A 590 GLN B 108 GLN B 298 ASN B 360 HIS ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.174603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.144159 restraints weight = 27268.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.143703 restraints weight = 31229.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.145099 restraints weight = 28761.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.145098 restraints weight = 22220.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.145178 restraints weight = 20622.183| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 23934 Z= 0.200 Angle : 0.675 14.863 32442 Z= 0.345 Chirality : 0.045 0.365 3873 Planarity : 0.005 0.072 4066 Dihedral : 6.424 137.220 3276 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.81 % Allowed : 18.52 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.15), residues: 3048 helix: 1.45 (0.12), residues: 1673 sheet: -0.30 (0.23), residues: 470 loop : -0.37 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 418 TYR 0.025 0.002 TYR C 467 PHE 0.024 0.002 PHE A 517 TRP 0.018 0.002 TRP A 800 HIS 0.005 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (23934) covalent geometry : angle 0.67457 / 0.34 (32442) hydrogen bonds : bond 0.04925 / 3.30 ( 1505) hydrogen bonds : angle 4.63922 / 3.31 ( 4521) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 509 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.7576 (p0) cc_final: 0.7257 (p0) REVERT: A 68 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6970 (tm-30) REVERT: A 110 LYS cc_start: 0.7382 (mmmt) cc_final: 0.6531 (mmtt) REVERT: A 164 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6443 (mt-10) REVERT: A 357 LEU cc_start: 0.7807 (mm) cc_final: 0.7596 (mm) REVERT: A 473 THR cc_start: 0.7809 (t) cc_final: 0.6482 (p) REVERT: A 570 MET cc_start: 0.7859 (ttp) cc_final: 0.7641 (ttm) REVERT: A 684 MET cc_start: 0.7287 (mpp) cc_final: 0.5657 (mmm) REVERT: A 745 MET cc_start: 0.5714 (tpp) cc_final: 0.5411 (tmm) REVERT: A 769 LYS cc_start: 0.6958 (pttm) cc_final: 0.6270 (ttpt) REVERT: A 939 PHE cc_start: 0.6275 (m-80) cc_final: 0.5864 (t80) REVERT: A 951 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.7199 (mm) REVERT: B 1 MET cc_start: 0.5911 (ptt) cc_final: 0.5215 (ptt) REVERT: B 182 LYS cc_start: 0.6835 (mtmm) cc_final: 0.6148 (ptpp) REVERT: B 184 MET cc_start: 0.6012 (mmm) cc_final: 0.5654 (mmm) REVERT: B 284 LYS cc_start: 0.7064 (mmtm) cc_final: 0.6842 (mmmt) REVERT: B 522 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7460 (mtmm) REVERT: B 527 MET cc_start: 0.6973 (ttt) cc_final: 0.6673 (ttm) REVERT: B 564 GLU cc_start: 0.7899 (tp30) cc_final: 0.7379 (tp30) REVERT: B 638 LYS cc_start: 0.7548 (tmtt) cc_final: 0.7094 (tptp) REVERT: B 656 MET cc_start: 0.8026 (tpt) cc_final: 0.7044 (tpt) REVERT: B 719 SER cc_start: 0.8859 (t) cc_final: 0.8394 (m) REVERT: B 771 ARG cc_start: 0.8001 (ptt90) cc_final: 0.7631 (ptt90) REVERT: B 783 MET cc_start: 0.3428 (mmm) cc_final: 0.3055 (mmm) REVERT: B 844 LYS cc_start: 0.7661 (tppt) cc_final: 0.7144 (mmtm) REVERT: B 890 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7947 (tt) REVERT: C 68 GLU cc_start: 0.6518 (mp0) cc_final: 0.5592 (mp0) REVERT: C 356 TYR cc_start: 0.6442 (t80) cc_final: 0.6201 (t80) REVERT: C 363 ARG cc_start: 0.7585 (mmt180) cc_final: 0.7131 (mmt-90) REVERT: C 423 GLU cc_start: 0.7163 (mp0) cc_final: 0.6610 (mp0) REVERT: C 589 ASN cc_start: 0.6166 (m-40) cc_final: 0.5789 (m-40) REVERT: C 602 LYS cc_start: 0.7937 (mttp) cc_final: 0.7539 (mmtm) REVERT: C 745 MET cc_start: 0.8079 (mmm) cc_final: 0.7667 (tpp) REVERT: C 769 LYS cc_start: 0.7867 (tmmt) cc_final: 0.7482 (tmtt) REVERT: C 826 THR cc_start: 0.8273 (m) cc_final: 0.7777 (p) REVERT: C 849 GLU cc_start: 0.7394 (mp0) cc_final: 0.5899 (mt-10) outliers start: 72 outliers final: 58 residues processed: 543 average time/residue: 0.1378 time to fit residues: 120.2481 Evaluate side-chains 564 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 502 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 753 PHE Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 791 SER Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 948 MET Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 6.9990 chunk 247 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 292 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 301 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 228 GLN A 415 ASN A 574 GLN A 590 GLN B 176 GLN B 360 HIS ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.179874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.148410 restraints weight = 27251.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.148022 restraints weight = 30677.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.149479 restraints weight = 28432.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.149964 restraints weight = 22470.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.149950 restraints weight = 19744.682| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23934 Z= 0.146 Angle : 0.644 14.428 32442 Z= 0.326 Chirality : 0.043 0.355 3873 Planarity : 0.005 0.069 4066 Dihedral : 6.260 132.516 3276 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.26 % Allowed : 19.30 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.15), residues: 3048 helix: 1.53 (0.12), residues: 1668 sheet: -0.26 (0.23), residues: 470 loop : -0.34 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 418 TYR 0.023 0.001 TYR C 467 PHE 0.030 0.001 PHE A 901 TRP 0.019 0.001 TRP A 800 HIS 0.005 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (23934) covalent geometry : angle 0.64412 / 0.33 (32442) hydrogen bonds : bond 0.04495 / 3.02 ( 1505) hydrogen bonds : angle 4.52508 / 3.23 ( 4521) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 513 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.7539 (p0) cc_final: 0.7199 (p0) REVERT: A 75 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7881 (tt) REVERT: A 110 LYS cc_start: 0.7587 (mmmt) cc_final: 0.6621 (mmtt) REVERT: A 164 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6355 (mt-10) REVERT: A 357 LEU cc_start: 0.7802 (mm) cc_final: 0.7584 (mm) REVERT: A 473 THR cc_start: 0.7782 (t) cc_final: 0.6339 (p) REVERT: A 570 MET cc_start: 0.7894 (ttp) cc_final: 0.7655 (ttm) REVERT: A 572 SER cc_start: 0.8372 (t) cc_final: 0.7962 (m) REVERT: A 684 MET cc_start: 0.7348 (mpp) cc_final: 0.5687 (mmm) REVERT: A 697 MET cc_start: 0.7479 (mpp) cc_final: 0.6981 (mmp) REVERT: A 745 MET cc_start: 0.5908 (tpp) cc_final: 0.5475 (tmm) REVERT: A 769 LYS cc_start: 0.6958 (pttm) cc_final: 0.6265 (ttpt) REVERT: A 939 PHE cc_start: 0.6215 (m-80) cc_final: 0.5785 (t80) REVERT: A 951 ILE cc_start: 0.7310 (OUTLIER) cc_final: 0.7069 (mm) REVERT: B 1 MET cc_start: 0.5709 (OUTLIER) cc_final: 0.5240 (ppp) REVERT: B 182 LYS cc_start: 0.6775 (mtmm) cc_final: 0.6100 (ptpp) REVERT: B 184 MET cc_start: 0.6176 (mmm) cc_final: 0.5872 (mmm) REVERT: B 522 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7534 (mtmm) REVERT: B 527 MET cc_start: 0.6936 (ttt) cc_final: 0.6655 (ttm) REVERT: B 564 GLU cc_start: 0.7782 (tp30) cc_final: 0.7453 (tp30) REVERT: B 638 LYS cc_start: 0.7475 (tmtt) cc_final: 0.7002 (tptp) REVERT: B 656 MET cc_start: 0.7957 (tpt) cc_final: 0.6678 (tpt) REVERT: B 719 SER cc_start: 0.8802 (t) cc_final: 0.8267 (m) REVERT: B 771 ARG cc_start: 0.7983 (ptt90) cc_final: 0.7622 (ptt90) REVERT: B 783 MET cc_start: 0.3424 (mmm) cc_final: 0.2735 (mmm) REVERT: B 844 LYS cc_start: 0.7672 (tppt) cc_final: 0.7175 (mmtm) REVERT: B 890 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7806 (tt) REVERT: C 356 TYR cc_start: 0.6408 (t80) cc_final: 0.6165 (t80) REVERT: C 363 ARG cc_start: 0.7570 (mmt180) cc_final: 0.7079 (mmt-90) REVERT: C 423 GLU cc_start: 0.7154 (mp0) cc_final: 0.6585 (mp0) REVERT: C 589 ASN cc_start: 0.6266 (m-40) cc_final: 0.6020 (m-40) REVERT: C 702 LYS cc_start: 0.7334 (pttp) cc_final: 0.7092 (mppt) REVERT: C 769 LYS cc_start: 0.7885 (tmmt) cc_final: 0.7484 (tmtt) REVERT: C 826 THR cc_start: 0.8240 (m) cc_final: 0.7696 (p) REVERT: C 849 GLU cc_start: 0.7311 (mp0) cc_final: 0.5774 (mm-30) REVERT: C 948 MET cc_start: 0.3609 (ptp) cc_final: 0.2802 (ptt) outliers start: 58 outliers final: 46 residues processed: 537 average time/residue: 0.1335 time to fit residues: 115.3954 Evaluate side-chains 550 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 498 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 791 SER Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 948 MET Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 732 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 241 optimal weight: 0.0050 chunk 36 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 262 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 162 optimal weight: 8.9990 chunk 293 optimal weight: 0.8980 overall best weight: 2.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN A 415 ASN A 574 GLN A 590 GLN B 360 HIS ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.177901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.147345 restraints weight = 27219.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.147120 restraints weight = 30762.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.149203 restraints weight = 29061.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.148846 restraints weight = 19531.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.148911 restraints weight = 18298.598| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23934 Z= 0.140 Angle : 0.648 14.052 32442 Z= 0.328 Chirality : 0.043 0.362 3873 Planarity : 0.005 0.069 4066 Dihedral : 6.125 128.374 3276 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.26 % Allowed : 19.45 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.15), residues: 3048 helix: 1.55 (0.12), residues: 1670 sheet: -0.19 (0.23), residues: 456 loop : -0.35 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 418 TYR 0.024 0.001 TYR C 848 PHE 0.030 0.001 PHE A 901 TRP 0.019 0.001 TRP A 800 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (23934) covalent geometry : angle 0.64765 / 0.33 (32442) hydrogen bonds : bond 0.04364 / 2.93 ( 1505) hydrogen bonds : angle 4.48725 / 3.21 ( 4521) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 509 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.7544 (p0) cc_final: 0.7181 (p0) REVERT: A 110 LYS cc_start: 0.7226 (mmmt) cc_final: 0.6500 (mmtt) REVERT: A 164 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6380 (mt-10) REVERT: A 248 ASN cc_start: 0.6225 (m-40) cc_final: 0.5959 (m110) REVERT: A 357 LEU cc_start: 0.7750 (mm) cc_final: 0.7514 (mm) REVERT: A 359 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6557 (mm) REVERT: A 395 MET cc_start: 0.7441 (mmp) cc_final: 0.7224 (mmp) REVERT: A 473 THR cc_start: 0.7776 (t) cc_final: 0.6336 (p) REVERT: A 570 MET cc_start: 0.7832 (ttp) cc_final: 0.7564 (ttm) REVERT: A 572 SER cc_start: 0.8287 (t) cc_final: 0.7897 (m) REVERT: A 684 MET cc_start: 0.7316 (mpp) cc_final: 0.5597 (mmm) REVERT: A 745 MET cc_start: 0.6261 (tpp) cc_final: 0.5543 (tmm) REVERT: A 769 LYS cc_start: 0.6992 (pttm) cc_final: 0.6298 (ttpt) REVERT: A 939 PHE cc_start: 0.6181 (m-80) cc_final: 0.5787 (t80) REVERT: A 951 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.7013 (mm) REVERT: B 1 MET cc_start: 0.5751 (OUTLIER) cc_final: 0.5275 (ppp) REVERT: B 182 LYS cc_start: 0.6753 (mtmm) cc_final: 0.6052 (ptpp) REVERT: B 184 MET cc_start: 0.6232 (mmm) cc_final: 0.5858 (mmm) REVERT: B 522 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7525 (mtmm) REVERT: B 527 MET cc_start: 0.6950 (ttt) cc_final: 0.6647 (ttm) REVERT: B 564 GLU cc_start: 0.7765 (tp30) cc_final: 0.7450 (tp30) REVERT: B 638 LYS cc_start: 0.7514 (tmtt) cc_final: 0.7013 (tptp) REVERT: B 656 MET cc_start: 0.7915 (tpt) cc_final: 0.6643 (tpt) REVERT: B 719 SER cc_start: 0.8742 (t) cc_final: 0.8130 (m) REVERT: B 771 ARG cc_start: 0.7980 (ptt90) cc_final: 0.7605 (ptt90) REVERT: B 783 MET cc_start: 0.3392 (mmm) cc_final: 0.2695 (mmm) REVERT: B 844 LYS cc_start: 0.7669 (tppt) cc_final: 0.7171 (mmtm) REVERT: B 890 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7791 (tt) REVERT: C 68 GLU cc_start: 0.6460 (mp0) cc_final: 0.5515 (mp0) REVERT: C 356 TYR cc_start: 0.6345 (t80) cc_final: 0.6091 (t80) REVERT: C 363 ARG cc_start: 0.7626 (mmt180) cc_final: 0.7112 (mmt-90) REVERT: C 456 MET cc_start: 0.7165 (tpt) cc_final: 0.6751 (tpt) REVERT: C 589 ASN cc_start: 0.6261 (m-40) cc_final: 0.6001 (m-40) REVERT: C 602 LYS cc_start: 0.7740 (mttp) cc_final: 0.7339 (mmtt) REVERT: C 702 LYS cc_start: 0.7289 (pttp) cc_final: 0.7063 (mppt) REVERT: C 745 MET cc_start: 0.8042 (mmm) cc_final: 0.7603 (tpp) REVERT: C 769 LYS cc_start: 0.7894 (tmmt) cc_final: 0.7465 (tmtt) REVERT: C 826 THR cc_start: 0.8216 (m) cc_final: 0.7682 (p) REVERT: C 948 MET cc_start: 0.3588 (ptp) cc_final: 0.2999 (ptt) outliers start: 58 outliers final: 45 residues processed: 536 average time/residue: 0.1343 time to fit residues: 116.3253 Evaluate side-chains 551 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 500 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 791 SER Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 948 MET Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 777 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 157 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 124 optimal weight: 30.0000 chunk 90 optimal weight: 3.9990 chunk 256 optimal weight: 0.0370 chunk 273 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 overall best weight: 2.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 228 GLN A 415 ASN A 574 GLN A 590 GLN B 176 GLN B 360 HIS ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.177358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.146469 restraints weight = 27198.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.145263 restraints weight = 34346.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.147414 restraints weight = 30722.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.147436 restraints weight = 22421.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.147705 restraints weight = 20038.338| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23934 Z= 0.152 Angle : 0.653 14.265 32442 Z= 0.331 Chirality : 0.043 0.360 3873 Planarity : 0.005 0.071 4066 Dihedral : 6.058 123.466 3276 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.38 % Allowed : 19.38 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.15), residues: 3048 helix: 1.52 (0.12), residues: 1670 sheet: -0.24 (0.23), residues: 472 loop : -0.36 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 418 TYR 0.024 0.001 TYR C 848 PHE 0.029 0.001 PHE A 901 TRP 0.019 0.001 TRP A 800 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (23934) covalent geometry : angle 0.65260 / 0.33 (32442) hydrogen bonds : bond 0.04447 / 3.00 ( 1505) hydrogen bonds : angle 4.49246 / 3.21 ( 4521) =============================================================================== Job complete usr+sys time: 3554.91 seconds wall clock time: 62 minutes 19.48 seconds (3739.48 seconds total)