Starting phenix.real_space_refine on Fri Jul 3 07:59:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uob_26645/07_2026/7uob_26645_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uob_26645/07_2026/7uob_26645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uob_26645/07_2026/7uob_26645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uob_26645/07_2026/7uob_26645.map" model { file = "/net/cci-nas-00/data/ceres_data/7uob_26645/07_2026/7uob_26645_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uob_26645/07_2026/7uob_26645_neut.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 76 5.49 5 Mg 3 5.21 5 S 82 5.16 5 C 7592 2.51 5 N 2104 2.21 5 O 2859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s 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: 12718 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 7478 Classifications: {'peptide': 929} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 898} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1420 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 559 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "D" Number of atoms: 1419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1419 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "P" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 697 Classifications: {'RNA': 33} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 32} Chain: "T" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 769 Classifications: {'RNA': 36} Modifications used: {'rna3p_pur': 19, 'rna3p_pyr': 17} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 69 Unusual residues: {' MG': 3, ' ZN': 2, 'GTP': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "P" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'L2B': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 231 Classifications: {'water': 231} Link IDs: {None: 230} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "P" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "T" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2462 SG CYS A 301 57.554 99.369 56.439 1.00 6.51 S ATOM 2503 SG CYS A 306 56.004 102.601 55.673 1.00 6.95 S ATOM 2535 SG CYS A 310 55.728 99.686 52.918 1.00 6.84 S ATOM 3943 SG CYS A 487 57.356 96.727 77.177 1.00 5.28 S ATOM 5196 SG CYS A 645 56.187 100.394 76.846 1.00 7.74 S ATOM 5202 SG CYS A 646 58.444 98.558 74.213 1.00 6.47 S Time building chain proxies: 2.42, per 1000 atoms: 0.19 Number of scatterers: 12718 At special positions: 0 Unit cell: (92.88, 129.6, 173.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 82 16.00 P 76 15.00 Mg 3 11.99 O 2859 8.00 N 2104 7.00 C 7592 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 513.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 6 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2646 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 10 sheets defined 57.7% alpha, 15.9% beta 25 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 removed outlier: 3.539A pdb=" N PHE A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.558A pdb=" N GLN A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.631A pdb=" N LYS A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.740A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.501A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.506A pdb=" N GLN A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 4.084A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.248A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.829A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 321 No H-bonds generated for 'chain 'A' and resid 320 through 321' Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.653A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.279A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 455 removed outlier: 3.582A pdb=" N SER A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 459 Processing helix chain 'A' and resid 465 through 477 removed outlier: 3.593A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 481 removed outlier: 3.570A pdb=" N ASP A 481 " --> pdb=" O LYS A 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 478 through 481' Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.746A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.801A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.584A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 693 " --> pdb=" O TYR A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.547A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 808 removed outlier: 3.744A pdb=" N LYS A 807 " --> pdb=" O ASP A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.528A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 854 removed outlier: 3.708A pdb=" N ASP A 851 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLY A 852 " --> pdb=" O LYS A 849 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR A 853 " --> pdb=" O THR A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 867 removed outlier: 3.648A pdb=" N PHE A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 862 " --> pdb=" O ARG A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 903 removed outlier: 3.507A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 916 removed outlier: 3.689A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TRP A 916 " --> pdb=" O SER A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.544A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 32 through 96 removed outlier: 3.515A pdb=" N MET B 55 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR B 68 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.581A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 2 through 20 removed outlier: 3.713A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.513A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.679A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 66 removed outlier: 3.809A pdb=" N VAL C 66 " --> pdb=" O GLN C 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 63 through 66' Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.884A pdb=" N THR D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 82 removed outlier: 3.852A pdb=" N ALA D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET D 55 " --> pdb=" O ARG D 51 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 3.511A pdb=" N ALA D 86 " --> pdb=" O LYS D 82 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET D 87 " --> pdb=" O VAL D 83 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET D 90 " --> pdb=" O ALA D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 112 removed outlier: 3.569A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 4.334A pdb=" N ASN A 52 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP A 29 " --> pdb=" O ASN A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 7.124A pdb=" N ASN A 52 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG A 74 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LYS A 73 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N SER A 115 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.018A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.560A pdb=" N GLY A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.580A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE A 396 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE A 396 " --> pdb=" O ASP A 390 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ASP A 390 " --> pdb=" O PHE A 396 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 758 removed outlier: 3.888A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 822 removed outlier: 4.084A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.022A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR D 146 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP D 143 " --> pdb=" O THR D 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.022A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL D 159 " --> pdb=" O VAL D 167 " (cutoff:3.500A) 599 hydrogen bonds defined for protein. 1674 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3819 1.34 - 1.48: 3591 1.48 - 1.61: 5279 1.61 - 1.74: 12 1.74 - 1.87: 129 Bond restraints: 12830 Sorted by residual: bond pdb=" O5' L2B P 101 " pdb=" P L2B P 101 " ideal model delta sigma weight residual 1.612 1.874 -0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" OP1 L2B P 101 " pdb=" P L2B P 101 " ideal model delta sigma weight residual 1.662 1.497 0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" C5' L2B P 101 " pdb=" O5' L2B P 101 " ideal model delta sigma weight residual 1.470 1.331 0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C1' L2B P 101 " pdb=" N1 L2B P 101 " ideal model delta sigma weight residual 1.500 1.624 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C4' L2B P 101 " pdb=" C5' L2B P 101 " ideal model delta sigma weight residual 1.529 1.633 -0.104 2.00e-02 2.50e+03 2.71e+01 ... (remaining 12825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 17659 3.31 - 6.62: 66 6.62 - 9.93: 12 9.93 - 13.24: 4 13.24 - 16.55: 1 Bond angle restraints: 17742 Sorted by residual: angle pdb=" O2A GTP A1006 " pdb=" PA GTP A1006 " pdb=" O3A GTP A1006 " ideal model delta sigma weight residual 109.50 92.95 16.55 3.00e+00 1.11e-01 3.04e+01 angle pdb=" PA GTP A1006 " pdb=" O3A GTP A1006 " pdb=" PB GTP A1006 " ideal model delta sigma weight residual 120.50 133.49 -12.99 3.00e+00 1.11e-01 1.88e+01 angle pdb=" O5' L2B P 101 " pdb=" P L2B P 101 " pdb=" OP2 L2B P 101 " ideal model delta sigma weight residual 118.50 107.06 11.44 3.00e+00 1.11e-01 1.45e+01 angle pdb=" C5' L2B P 101 " pdb=" C4' L2B P 101 " pdb=" O4' L2B P 101 " ideal model delta sigma weight residual 106.43 116.96 -10.53 3.00e+00 1.11e-01 1.23e+01 angle pdb=" O1A GTP A1006 " pdb=" PA GTP A1006 " pdb=" O3A GTP A1006 " ideal model delta sigma weight residual 108.20 118.57 -10.37 3.00e+00 1.11e-01 1.19e+01 ... (remaining 17737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.03: 7525 35.03 - 70.05: 231 70.05 - 105.08: 28 105.08 - 140.11: 2 140.11 - 175.13: 5 Dihedral angle restraints: 7791 sinusoidal: 3704 harmonic: 4087 Sorted by residual: dihedral pdb=" O2G GTP A1006 " pdb=" O3B GTP A1006 " pdb=" PG GTP A1006 " pdb=" PB GTP A1006 " ideal model delta sinusoidal sigma weight residual 177.30 2.17 175.13 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C4' GTP A1007 " pdb=" C5' GTP A1007 " pdb=" O5' GTP A1007 " pdb=" PA GTP A1007 " ideal model delta sinusoidal sigma weight residual 260.87 86.66 174.22 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O3B GTP A1006 " pdb=" O3A GTP A1006 " pdb=" PB GTP A1006 " pdb=" PA GTP A1006 " ideal model delta sinusoidal sigma weight residual -68.92 101.54 -170.46 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 7788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1753 0.050 - 0.101: 241 0.101 - 0.151: 60 0.151 - 0.202: 0 0.202 - 0.252: 1 Chirality restraints: 2055 Sorted by residual: chirality pdb=" C2' L2B P 101 " pdb=" C1' L2B P 101 " pdb=" C3' L2B P 101 " pdb=" O2' L2B P 101 " both_signs ideal model delta sigma weight residual False -2.83 -2.58 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE A 696 " pdb=" CA ILE A 696 " pdb=" CG1 ILE A 696 " pdb=" CG2 ILE A 696 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA PRO A 227 " pdb=" N PRO A 227 " pdb=" C PRO A 227 " pdb=" CB PRO A 227 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 2052 not shown) Planarity restraints: 2001 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GTP A1007 " -0.031 2.00e-02 2.50e+03 1.24e-02 4.62e+00 pdb=" C2 GTP A1007 " 0.000 2.00e-02 2.50e+03 pdb=" C4 GTP A1007 " 0.006 2.00e-02 2.50e+03 pdb=" C5 GTP A1007 " -0.003 2.00e-02 2.50e+03 pdb=" C6 GTP A1007 " 0.005 2.00e-02 2.50e+03 pdb=" C8 GTP A1007 " 0.011 2.00e-02 2.50e+03 pdb=" N1 GTP A1007 " -0.009 2.00e-02 2.50e+03 pdb=" N2 GTP A1007 " 0.002 2.00e-02 2.50e+03 pdb=" N3 GTP A1007 " 0.010 2.00e-02 2.50e+03 pdb=" N7 GTP A1007 " -0.000 2.00e-02 2.50e+03 pdb=" N9 GTP A1007 " 0.020 2.00e-02 2.50e+03 pdb=" O6 GTP A1007 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP A1006 " -0.018 2.00e-02 2.50e+03 9.69e-03 2.82e+00 pdb=" C2 GTP A1006 " -0.005 2.00e-02 2.50e+03 pdb=" C4 GTP A1006 " 0.015 2.00e-02 2.50e+03 pdb=" C5 GTP A1006 " 0.001 2.00e-02 2.50e+03 pdb=" C6 GTP A1006 " -0.002 2.00e-02 2.50e+03 pdb=" C8 GTP A1006 " -0.002 2.00e-02 2.50e+03 pdb=" N1 GTP A1006 " -0.009 2.00e-02 2.50e+03 pdb=" N2 GTP A1006 " 0.001 2.00e-02 2.50e+03 pdb=" N3 GTP A1006 " 0.007 2.00e-02 2.50e+03 pdb=" N7 GTP A1006 " -0.009 2.00e-02 2.50e+03 pdb=" N9 GTP A1006 " 0.018 2.00e-02 2.50e+03 pdb=" O6 GTP A1006 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 926 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 927 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 927 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 927 " -0.023 5.00e-02 4.00e+02 ... (remaining 1998 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 172 2.60 - 3.18: 10658 3.18 - 3.75: 19980 3.75 - 4.33: 30604 4.33 - 4.90: 47355 Nonbonded interactions: 108769 Sorted by model distance: nonbonded pdb=" OH TYR A 719 " pdb=" O HOH A1101 " model vdw 2.030 3.040 nonbonded pdb=" O HOH A1108 " pdb=" O HOH A1247 " model vdw 2.068 3.040 nonbonded pdb=" O TYR A 915 " pdb=" OH TYR A 921 " model vdw 2.083 3.040 nonbonded pdb=" N GLU A 665 " pdb=" OE1 GLU A 665 " model vdw 2.150 3.120 nonbonded pdb=" O GLY A 486 " pdb=" O HOH A1102 " model vdw 2.164 3.040 ... (remaining 108764 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 'B' and (resid 6 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 25 or (resid 26 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 34 or (resid 35 through \ 36 and (name N or name CA or name C or name O or name CB )) or resid 37 through \ 191)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.010 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 : 0.006 0.262 12839 Z= 0.292 Angle : 0.631 16.546 17748 Z= 0.323 Chirality : 0.039 0.252 2055 Planarity : 0.004 0.044 2001 Dihedral : 16.267 175.132 5145 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.00 % Favored : 96.78 % Rotamer: Outliers : 1.52 % Allowed : 7.15 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.16 (0.22), residues: 1367 helix: 1.01 (0.20), residues: 680 sheet: 0.20 (0.43), residues: 145 loop : -1.04 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 132 TYR 0.013 0.002 TYR A 515 PHE 0.017 0.002 PHE A 652 TRP 0.013 0.002 TRP A 916 HIS 0.009 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.29 (12830) covalent geometry : angle 0.62102 / 0.32 (17742) hydrogen bonds : bond 0.17322 / 11.35 ( 650) hydrogen bonds : angle 5.64538 / 3.85 ( 1798) metal coordination : bond 0.07729 / 4.11 ( 8) metal coordination : angle 6.25675 / 3.34 ( 6) Misc. bond : bond 0.05125 / 2.70 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.461 Fit side-chains REVERT: A 235 ASP cc_start: 0.6340 (OUTLIER) cc_final: 0.6000 (t70) outliers start: 18 outliers final: 5 residues processed: 132 average time/residue: 0.7153 time to fit residues: 100.4527 Evaluate side-chains 103 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 114 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 386 ASN A 552 ASN C 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.084391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.050713 restraints weight = 25025.520| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.24 r_work: 0.2560 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2418 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12839 Z= 0.166 Angle : 0.561 8.567 17748 Z= 0.300 Chirality : 0.041 0.220 2055 Planarity : 0.005 0.076 2001 Dihedral : 16.895 175.100 2627 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.56 % Favored : 97.22 % Rotamer: Outliers : 1.77 % Allowed : 9.60 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.50 (0.23), residues: 1367 helix: 1.32 (0.20), residues: 699 sheet: 0.35 (0.44), residues: 132 loop : -0.97 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 51 TYR 0.016 0.001 TYR A 149 PHE 0.018 0.001 PHE B 49 TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (12830) covalent geometry : angle 0.55971 / 0.30 (17742) hydrogen bonds : bond 0.05749 / 3.70 ( 650) hydrogen bonds : angle 4.16776 / 2.88 ( 1798) metal coordination : bond 0.00482 / 0.33 ( 8) metal coordination : angle 2.00826 / 1.10 ( 6) Misc. bond : bond 0.00556 / 0.29 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.421 Fit side-chains REVERT: A 110 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8246 (mmm) REVERT: A 499 ASP cc_start: 0.9057 (OUTLIER) cc_final: 0.8810 (m-30) REVERT: A 668 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.8541 (ttm) REVERT: A 794 MET cc_start: 0.9239 (ttm) cc_final: 0.8612 (ttm) REVERT: B 56 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7442 (tm-30) REVERT: B 62 MET cc_start: 0.8988 (mmm) cc_final: 0.8672 (mmm) REVERT: B 75 ARG cc_start: 0.8182 (mtp-110) cc_final: 0.7633 (mtm-85) REVERT: D 60 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7636 (pp20) REVERT: D 69 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8291 (tm-30) REVERT: D 135 TYR cc_start: 0.8610 (t80) cc_final: 0.8401 (t80) REVERT: D 168 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8688 (mm110) REVERT: D 171 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8616 (mp0) REVERT: D 174 MET cc_start: 0.7790 (mmm) cc_final: 0.7530 (mmm) outliers start: 21 outliers final: 11 residues processed: 112 average time/residue: 0.7483 time to fit residues: 89.2240 Evaluate side-chains 112 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 114 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 20 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.083268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.049760 restraints weight = 25109.257| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 2.24 r_work: 0.2541 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2400 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12839 Z= 0.183 Angle : 0.537 8.338 17748 Z= 0.285 Chirality : 0.040 0.225 2055 Planarity : 0.004 0.051 2001 Dihedral : 16.700 172.926 2625 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.71 % Favored : 97.07 % Rotamer: Outliers : 2.44 % Allowed : 9.76 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.61 (0.23), residues: 1367 helix: 1.43 (0.20), residues: 697 sheet: 0.20 (0.42), residues: 144 loop : -0.92 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 51 TYR 0.015 0.001 TYR A 149 PHE 0.018 0.001 PHE B 49 TRP 0.013 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (12830) covalent geometry : angle 0.53573 / 0.29 (17742) hydrogen bonds : bond 0.05211 / 3.36 ( 650) hydrogen bonds : angle 3.97355 / 2.75 ( 1798) metal coordination : bond 0.00601 / 0.41 ( 8) metal coordination : angle 1.80409 / 0.98 ( 6) Misc. bond : bond 0.00441 / 0.23 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.467 Fit side-chains REVERT: A 105 ARG cc_start: 0.7714 (ttm-80) cc_final: 0.7464 (ttm-80) REVERT: A 110 MET cc_start: 0.8753 (mmp) cc_final: 0.8142 (mmm) REVERT: A 499 ASP cc_start: 0.9059 (OUTLIER) cc_final: 0.8800 (m-30) REVERT: A 668 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8551 (ttm) REVERT: B 75 ARG cc_start: 0.8099 (mtp-110) cc_final: 0.7630 (mtm-85) REVERT: B 111 ARG cc_start: 0.8518 (ptt180) cc_final: 0.8291 (ptt180) REVERT: C 50 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8186 (mm-30) REVERT: C 72 CYS cc_start: 0.8723 (m) cc_final: 0.8476 (m) REVERT: D 60 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7812 (pp20) REVERT: D 69 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8252 (tm-30) REVERT: D 135 TYR cc_start: 0.8548 (t80) cc_final: 0.8209 (t80) REVERT: D 155 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8445 (tp30) REVERT: D 168 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8625 (mm-40) REVERT: D 171 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8607 (mp0) REVERT: D 174 MET cc_start: 0.7931 (mmm) cc_final: 0.7721 (mmm) outliers start: 29 outliers final: 16 residues processed: 122 average time/residue: 0.6923 time to fit residues: 90.4496 Evaluate side-chains 117 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 129 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 85 optimal weight: 0.0170 chunk 68 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.083563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.049074 restraints weight = 25329.926| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.32 r_work: 0.2552 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2411 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12839 Z= 0.136 Angle : 0.515 8.214 17748 Z= 0.270 Chirality : 0.039 0.225 2055 Planarity : 0.004 0.049 2001 Dihedral : 16.607 170.976 2625 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.85 % Favored : 96.93 % Rotamer: Outliers : 2.36 % Allowed : 10.35 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.73 (0.23), residues: 1367 helix: 1.53 (0.21), residues: 693 sheet: 0.22 (0.41), residues: 146 loop : -0.84 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 51 TYR 0.015 0.001 TYR A 149 PHE 0.015 0.001 PHE D 92 TRP 0.012 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (12830) covalent geometry : angle 0.51427 / 0.27 (17742) hydrogen bonds : bond 0.04561 / 2.95 ( 650) hydrogen bonds : angle 3.85176 / 2.66 ( 1798) metal coordination : bond 0.00474 / 0.32 ( 8) metal coordination : angle 1.54389 / 0.84 ( 6) Misc. bond : bond 0.00062 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.7662 (ttm-80) cc_final: 0.7397 (ttm-80) REVERT: A 110 MET cc_start: 0.8756 (mmp) cc_final: 0.8065 (mmm) REVERT: A 499 ASP cc_start: 0.9044 (OUTLIER) cc_final: 0.8772 (m-30) REVERT: A 668 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8956 (tpp) REVERT: B 19 GLN cc_start: 0.8231 (pp30) cc_final: 0.8013 (pp30) REVERT: B 67 MET cc_start: 0.7867 (mmp) cc_final: 0.7622 (mtp) REVERT: B 75 ARG cc_start: 0.8059 (mtp-110) cc_final: 0.7594 (mtm-85) REVERT: C 50 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8197 (mm-30) REVERT: C 72 CYS cc_start: 0.8696 (m) cc_final: 0.8443 (m) REVERT: D 60 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7843 (pp20) REVERT: D 69 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8241 (tm-30) REVERT: D 135 TYR cc_start: 0.8506 (t80) cc_final: 0.8289 (t80) REVERT: D 155 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8372 (tp30) REVERT: D 168 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8623 (mm-40) REVERT: D 171 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8664 (mp0) REVERT: D 174 MET cc_start: 0.7958 (mmm) cc_final: 0.7757 (mmm) outliers start: 28 outliers final: 19 residues processed: 120 average time/residue: 0.8844 time to fit residues: 113.1761 Evaluate side-chains 120 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 129 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 104 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 135 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 18 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.083278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.049884 restraints weight = 25236.598| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.24 r_work: 0.2547 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2405 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12839 Z= 0.156 Angle : 0.517 8.086 17748 Z= 0.270 Chirality : 0.039 0.227 2055 Planarity : 0.004 0.064 2001 Dihedral : 16.458 165.614 2625 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.93 % Favored : 96.85 % Rotamer: Outliers : 2.78 % Allowed : 10.35 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.77 (0.23), residues: 1367 helix: 1.61 (0.21), residues: 693 sheet: 0.13 (0.40), residues: 156 loop : -0.85 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 51 TYR 0.015 0.001 TYR A 149 PHE 0.015 0.001 PHE D 92 TRP 0.013 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (12830) covalent geometry : angle 0.51650 / 0.27 (17742) hydrogen bonds : bond 0.04542 / 2.94 ( 650) hydrogen bonds : angle 3.79016 / 2.62 ( 1798) metal coordination : bond 0.00515 / 0.35 ( 8) metal coordination : angle 1.51410 / 0.83 ( 6) Misc. bond : bond 0.00079 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.8779 (mmp) cc_final: 0.8079 (mmm) REVERT: A 402 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8362 (p) REVERT: A 463 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.9058 (ttt) REVERT: A 499 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8759 (m-30) REVERT: A 668 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8957 (tpp) REVERT: A 756 MET cc_start: 0.9373 (ttp) cc_final: 0.9136 (ttp) REVERT: B 19 GLN cc_start: 0.8257 (pp30) cc_final: 0.8018 (pp30) REVERT: B 75 ARG cc_start: 0.8070 (mtp-110) cc_final: 0.7628 (mtm-85) REVERT: C 50 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8233 (mm-30) REVERT: C 72 CYS cc_start: 0.8746 (m) cc_final: 0.8538 (m) REVERT: D 60 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7849 (pp20) REVERT: D 69 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8294 (tm-30) REVERT: D 135 TYR cc_start: 0.8529 (t80) cc_final: 0.8312 (t80) REVERT: D 155 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8327 (tp30) REVERT: D 157 GLN cc_start: 0.8403 (mm110) cc_final: 0.8138 (mm110) REVERT: D 168 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8646 (mm-40) REVERT: D 171 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8671 (mp0) REVERT: D 174 MET cc_start: 0.7946 (mmm) cc_final: 0.7743 (mmm) outliers start: 33 outliers final: 15 residues processed: 122 average time/residue: 0.8016 time to fit residues: 104.6964 Evaluate side-chains 116 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 62 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 41 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 chunk 44 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 33 optimal weight: 0.0570 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.084053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.049615 restraints weight = 25249.227| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.32 r_work: 0.2571 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2430 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12839 Z= 0.110 Angle : 0.503 9.405 17748 Z= 0.260 Chirality : 0.038 0.225 2055 Planarity : 0.004 0.066 2001 Dihedral : 16.256 157.438 2621 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.71 % Favored : 97.07 % Rotamer: Outliers : 2.10 % Allowed : 11.62 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.97 (0.23), residues: 1367 helix: 1.72 (0.21), residues: 693 sheet: 0.35 (0.40), residues: 146 loop : -0.70 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 51 TYR 0.013 0.001 TYR A 149 PHE 0.012 0.001 PHE A 694 TRP 0.011 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (12830) covalent geometry : angle 0.50259 / 0.26 (17742) hydrogen bonds : bond 0.03897 / 2.54 ( 650) hydrogen bonds : angle 3.65639 / 2.53 ( 1798) metal coordination : bond 0.00400 / 0.26 ( 8) metal coordination : angle 1.37283 / 0.75 ( 6) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.7771 (ttm-80) cc_final: 0.7519 (ttm-80) REVERT: A 110 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8067 (mmm) REVERT: A 402 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8341 (p) REVERT: A 499 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8735 (m-30) REVERT: A 668 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8917 (tpp) REVERT: A 756 MET cc_start: 0.9368 (ttp) cc_final: 0.9115 (ttp) REVERT: B 19 GLN cc_start: 0.8273 (pp30) cc_final: 0.8033 (pp30) REVERT: B 67 MET cc_start: 0.7796 (mmp) cc_final: 0.7458 (mtp) REVERT: B 75 ARG cc_start: 0.8042 (mtp-110) cc_final: 0.7625 (mtm-85) REVERT: C 50 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8196 (mm-30) REVERT: D 57 ARG cc_start: 0.7342 (mtm-85) cc_final: 0.6412 (mtm-85) REVERT: D 60 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7805 (pp20) REVERT: D 69 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8278 (tm-30) REVERT: D 155 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8302 (tp30) REVERT: D 168 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8611 (mm-40) REVERT: D 171 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8655 (mp0) outliers start: 25 outliers final: 11 residues processed: 116 average time/residue: 0.8700 time to fit residues: 107.5903 Evaluate side-chains 111 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 137 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 25 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.082794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.048614 restraints weight = 25271.809| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 2.32 r_work: 0.2528 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2386 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12839 Z= 0.208 Angle : 0.551 10.550 17748 Z= 0.285 Chirality : 0.041 0.229 2055 Planarity : 0.004 0.047 2001 Dihedral : 16.112 148.716 2620 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.15 % Favored : 96.63 % Rotamer: Outliers : 2.78 % Allowed : 11.28 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.86 (0.23), residues: 1367 helix: 1.64 (0.21), residues: 699 sheet: 0.24 (0.40), residues: 156 loop : -0.79 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 96 TYR 0.017 0.002 TYR A 788 PHE 0.017 0.002 PHE D 92 TRP 0.013 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (12830) covalent geometry : angle 0.55028 / 0.28 (17742) hydrogen bonds : bond 0.04791 / 3.09 ( 650) hydrogen bonds : angle 3.71676 / 2.58 ( 1798) metal coordination : bond 0.00604 / 0.41 ( 8) metal coordination : angle 1.47544 / 0.81 ( 6) Misc. bond : bond 0.00117 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.513 Fit side-chains REVERT: A 110 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8062 (mmm) REVERT: A 402 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8369 (p) REVERT: A 463 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.9071 (ttt) REVERT: A 499 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8741 (m-30) REVERT: A 668 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.8606 (ttm) REVERT: A 756 MET cc_start: 0.9377 (ttp) cc_final: 0.9176 (ttp) REVERT: A 924 MET cc_start: 0.9503 (OUTLIER) cc_final: 0.8877 (mmm) REVERT: B 19 GLN cc_start: 0.8218 (pp30) cc_final: 0.7988 (pp30) REVERT: C 50 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8235 (mm-30) REVERT: D 57 ARG cc_start: 0.7455 (mtm-85) cc_final: 0.6521 (mtm-85) REVERT: D 60 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7857 (pp20) REVERT: D 69 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8321 (tm-30) REVERT: D 155 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8016 (tp30) REVERT: D 157 GLN cc_start: 0.8376 (mm110) cc_final: 0.8090 (mm110) REVERT: D 174 MET cc_start: 0.8230 (mmm) cc_final: 0.7924 (mmm) outliers start: 33 outliers final: 18 residues processed: 118 average time/residue: 0.8308 time to fit residues: 104.9114 Evaluate side-chains 121 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 137 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 26 optimal weight: 0.3980 chunk 71 optimal weight: 0.0980 chunk 12 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.083628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.049202 restraints weight = 25054.487| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 2.32 r_work: 0.2565 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2424 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12839 Z= 0.120 Angle : 0.533 11.315 17748 Z= 0.273 Chirality : 0.038 0.225 2055 Planarity : 0.004 0.062 2001 Dihedral : 15.952 132.880 2620 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.56 % Favored : 97.22 % Rotamer: Outliers : 2.27 % Allowed : 12.63 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.04 (0.23), residues: 1367 helix: 1.72 (0.21), residues: 694 sheet: 0.48 (0.41), residues: 146 loop : -0.63 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 51 TYR 0.017 0.001 TYR D 135 PHE 0.013 0.001 PHE A 694 TRP 0.011 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (12830) covalent geometry : angle 0.53275 / 0.27 (17742) hydrogen bonds : bond 0.03945 / 2.56 ( 650) hydrogen bonds : angle 3.59985 / 2.50 ( 1798) metal coordination : bond 0.00448 / 0.28 ( 8) metal coordination : angle 1.33845 / 0.74 ( 6) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.475 Fit side-chains REVERT: A 105 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7582 (ttm-80) REVERT: A 110 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8079 (mmm) REVERT: A 402 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8288 (p) REVERT: A 499 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8740 (m-30) REVERT: A 668 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8922 (tpp) REVERT: A 756 MET cc_start: 0.9368 (ttp) cc_final: 0.9128 (ttp) REVERT: B 19 GLN cc_start: 0.8182 (pp30) cc_final: 0.7926 (pp30) REVERT: B 75 ARG cc_start: 0.8069 (mtp85) cc_final: 0.7731 (mtm-85) REVERT: C 50 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8207 (mm-30) REVERT: D 57 ARG cc_start: 0.7400 (mtm-85) cc_final: 0.6516 (mtm-85) REVERT: D 60 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7817 (pp20) REVERT: D 69 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8345 (tm-30) REVERT: D 155 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8019 (tp30) REVERT: D 157 GLN cc_start: 0.8439 (mm110) cc_final: 0.8130 (mm110) REVERT: D 168 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8751 (mm110) REVERT: D 174 MET cc_start: 0.8233 (mmm) cc_final: 0.7995 (mmm) outliers start: 27 outliers final: 16 residues processed: 119 average time/residue: 0.8411 time to fit residues: 106.9403 Evaluate side-chains 117 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 137 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 62 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.0270 chunk 15 optimal weight: 2.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.083654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.049437 restraints weight = 25393.668| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.33 r_work: 0.2571 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2429 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12839 Z= 0.118 Angle : 0.534 11.892 17748 Z= 0.274 Chirality : 0.038 0.224 2055 Planarity : 0.004 0.060 2001 Dihedral : 15.781 128.239 2620 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.85 % Favored : 96.93 % Rotamer: Outliers : 1.85 % Allowed : 13.05 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.04 (0.23), residues: 1367 helix: 1.71 (0.21), residues: 694 sheet: 0.53 (0.41), residues: 146 loop : -0.60 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 51 TYR 0.013 0.001 TYR A 788 PHE 0.016 0.001 PHE D 15 TRP 0.011 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (12830) covalent geometry : angle 0.53333 / 0.27 (17742) hydrogen bonds : bond 0.03844 / 2.50 ( 650) hydrogen bonds : angle 3.57624 / 2.48 ( 1798) metal coordination : bond 0.00446 / 0.29 ( 8) metal coordination : angle 1.33198 / 0.73 ( 6) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.7850 (ttm-80) cc_final: 0.7587 (ttm-80) REVERT: A 110 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8092 (mmm) REVERT: A 402 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8260 (p) REVERT: A 499 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8729 (m-30) REVERT: A 668 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8940 (tpp) REVERT: A 756 MET cc_start: 0.9366 (ttp) cc_final: 0.9160 (ttp) REVERT: B 19 GLN cc_start: 0.8202 (pp30) cc_final: 0.7944 (pp30) REVERT: B 75 ARG cc_start: 0.8067 (mtp85) cc_final: 0.7697 (mtm-85) REVERT: C 50 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8196 (mm-30) REVERT: D 57 ARG cc_start: 0.7410 (mtm-85) cc_final: 0.6524 (mtm-85) REVERT: D 60 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7820 (pp20) REVERT: D 69 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8327 (tm-30) REVERT: D 135 TYR cc_start: 0.8587 (t80) cc_final: 0.8384 (t80) REVERT: D 155 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8121 (tp30) REVERT: D 157 GLN cc_start: 0.8463 (mm110) cc_final: 0.8176 (mm110) REVERT: D 171 GLU cc_start: 0.8405 (pm20) cc_final: 0.7884 (pm20) outliers start: 22 outliers final: 17 residues processed: 115 average time/residue: 0.8563 time to fit residues: 105.0892 Evaluate side-chains 120 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 80 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.083857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.049853 restraints weight = 25277.088| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 2.32 r_work: 0.2562 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2421 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12839 Z= 0.138 Angle : 0.562 12.461 17748 Z= 0.286 Chirality : 0.038 0.225 2055 Planarity : 0.004 0.068 2001 Dihedral : 15.648 128.340 2620 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.71 % Favored : 97.15 % Rotamer: Outliers : 1.94 % Allowed : 12.79 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.04 (0.23), residues: 1367 helix: 1.69 (0.21), residues: 695 sheet: 0.56 (0.41), residues: 146 loop : -0.61 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 51 TYR 0.015 0.001 TYR A 788 PHE 0.016 0.001 PHE D 15 TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (12830) covalent geometry : angle 0.56155 / 0.29 (17742) hydrogen bonds : bond 0.04008 / 2.60 ( 650) hydrogen bonds : angle 3.56878 / 2.48 ( 1798) metal coordination : bond 0.00458 / 0.30 ( 8) metal coordination : angle 1.29526 / 0.71 ( 6) Misc. bond : bond 0.00057 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.482 Fit side-chains REVERT: A 105 ARG cc_start: 0.7848 (ttm-80) cc_final: 0.7580 (ttm-80) REVERT: A 110 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8099 (mmm) REVERT: A 402 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8254 (p) REVERT: A 499 ASP cc_start: 0.9063 (OUTLIER) cc_final: 0.8728 (m-30) REVERT: A 668 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8903 (tpp) REVERT: A 756 MET cc_start: 0.9371 (ttp) cc_final: 0.9136 (ttp) REVERT: A 899 MET cc_start: 0.8561 (tpp) cc_final: 0.8287 (mmt) REVERT: B 19 GLN cc_start: 0.8209 (pp30) cc_final: 0.7951 (pp30) REVERT: B 75 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7738 (mtm-85) REVERT: C 50 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8187 (mm-30) REVERT: D 57 ARG cc_start: 0.7460 (mtm-85) cc_final: 0.6576 (mtm-85) REVERT: D 60 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7831 (pp20) REVERT: D 69 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8338 (tm-30) REVERT: D 155 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8124 (tp30) REVERT: D 157 GLN cc_start: 0.8527 (mm110) cc_final: 0.8251 (mm110) REVERT: D 171 GLU cc_start: 0.8367 (pm20) cc_final: 0.7799 (pm20) outliers start: 23 outliers final: 16 residues processed: 116 average time/residue: 0.8667 time to fit residues: 107.2807 Evaluate side-chains 117 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 91 optimal weight: 0.0470 chunk 8 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.083497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.049301 restraints weight = 25277.106| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.33 r_work: 0.2567 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2425 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12839 Z= 0.130 Angle : 0.549 11.976 17748 Z= 0.280 Chirality : 0.038 0.225 2055 Planarity : 0.004 0.073 2001 Dihedral : 15.501 128.467 2620 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.93 % Favored : 96.93 % Rotamer: Outliers : 1.94 % Allowed : 12.96 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.23), residues: 1367 helix: 1.69 (0.21), residues: 695 sheet: 0.54 (0.41), residues: 146 loop : -0.58 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 57 TYR 0.014 0.001 TYR D 135 PHE 0.017 0.001 PHE D 15 TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (12830) covalent geometry : angle 0.54869 / 0.28 (17742) hydrogen bonds : bond 0.03923 / 2.55 ( 650) hydrogen bonds : angle 3.56128 / 2.47 ( 1798) metal coordination : bond 0.00450 / 0.29 ( 8) metal coordination : angle 1.28135 / 0.70 ( 6) Misc. bond : bond 0.00058 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5329.48 seconds wall clock time: 91 minutes 37.18 seconds (5497.18 seconds total)