Starting phenix.real_space_refine on Mon Nov 18 13:23:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otx_17186/11_2024/8otx_17186_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otx_17186/11_2024/8otx_17186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otx_17186/11_2024/8otx_17186.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otx_17186/11_2024/8otx_17186.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otx_17186/11_2024/8otx_17186_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otx_17186/11_2024/8otx_17186_trim.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 74 5.16 5 C 10344 2.51 5 N 2668 2.21 5 O 2876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 15966 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 7889 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1054, 7882 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 1023} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 381 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 195 Conformer: "B" Number of residues, atoms: 1054, 7882 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 1023} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 381 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 195 bond proxies already assigned to first conformer: 8013 Chain: "A" Number of atoms: 7889 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1054, 7882 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 1023} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 381 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 195 Conformer: "B" Number of residues, atoms: 1054, 7882 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 1023} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 381 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 195 bond proxies already assigned to first conformer: 8013 Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 18.05, per 1000 atoms: 1.13 Number of scatterers: 15966 At special positions: 0 Unit cell: (150.76, 106.903, 123.349, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 4 15.00 O 2876 8.00 N 2668 7.00 C 10344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.33 Conformation dependent library (CDL) restraints added in 4.0 seconds 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3980 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 8 sheets defined 72.4% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'B' and resid 76 through 95 removed outlier: 3.670A pdb=" N PHE B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 120 removed outlier: 3.980A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.597A pdb=" N GLU B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 120 through 126' Processing helix chain 'B' and resid 134 through 154 Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.626A pdb=" N SER B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 189 Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 210 through 220 removed outlier: 3.777A pdb=" N VAL B 214 " --> pdb=" O PRO B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 254 Processing helix chain 'B' and resid 260 through 291 removed outlier: 4.549A pdb=" N GLY B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 296 through 317 removed outlier: 3.686A pdb=" N GLU B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 342 through 376 removed outlier: 3.704A pdb=" N ARG B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY B 369 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 370 " --> pdb=" O MET B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 379 No H-bonds generated for 'chain 'B' and resid 377 through 379' Processing helix chain 'B' and resid 381 through 413 removed outlier: 4.375A pdb=" N TRP B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 432 through 446 removed outlier: 3.998A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 481 removed outlier: 5.407A pdb=" N LYS B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE B 455 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 456 " --> pdb=" O GLY B 452 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR B 472 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 515 Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 574 through 600 Processing helix chain 'B' and resid 605 through 621 Processing helix chain 'B' and resid 634 through 639 Processing helix chain 'B' and resid 641 through 654 removed outlier: 3.818A pdb=" N LYS B 645 " --> pdb=" O TYR B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 677 Processing helix chain 'B' and resid 677 through 704 removed outlier: 3.919A pdb=" N GLU B 681 " --> pdb=" O HIS B 677 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 724 through 750 Processing helix chain 'B' and resid 756 through 761 removed outlier: 3.810A pdb=" N SER B 761 " --> pdb=" O HIS B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 783 removed outlier: 3.806A pdb=" N LYS B 765 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE B 766 " --> pdb=" O HIS B 762 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 767 " --> pdb=" O TRP B 763 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR B 783 " --> pdb=" O ILE B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 806 removed outlier: 4.503A pdb=" N LEU B 804 " --> pdb=" O LEU B 801 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LEU B 805 " --> pdb=" O PHE B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 812 removed outlier: 3.915A pdb=" N LEU B 811 " --> pdb=" O GLY B 807 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 812 " --> pdb=" O LEU B 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 807 through 812' Processing helix chain 'B' and resid 813 through 857 Proline residue: B 819 - end of helix Processing helix chain 'B' and resid 863 through 889 removed outlier: 4.003A pdb=" N ILE B 870 " --> pdb=" O GLU B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 removed outlier: 3.982A pdb=" N ALA B 893 " --> pdb=" O HIS B 889 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL B 894 " --> pdb=" O PRO B 890 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 895 " --> pdb=" O GLY B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.610A pdb=" N ASN B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 959 Processing helix chain 'B' and resid 966 through 976 removed outlier: 3.647A pdb=" N ILE B 970 " --> pdb=" O ASP B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1050 Processing helix chain 'B' and resid 1069 through 1080 Processing helix chain 'B' and resid 1085 through 1107 removed outlier: 3.696A pdb=" N THR B1100 " --> pdb=" O ILE B1096 " (cutoff:3.500A) Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1115 through 1123 removed outlier: 3.621A pdb=" N ARG B1123 " --> pdb=" O LEU B1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 95 removed outlier: 3.665A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.985A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.601A pdb=" N GLU A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 120 through 126' Processing helix chain 'A' and resid 134 through 154 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 removed outlier: 3.628A pdb=" N SER A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 210 through 220 removed outlier: 3.736A pdb=" N VAL A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 Processing helix chain 'A' and resid 260 through 291 removed outlier: 4.550A pdb=" N GLY A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 296 through 317 removed outlier: 3.687A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 342 through 376 removed outlier: 3.706A pdb=" N ARG A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 369 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 370 " --> pdb=" O MET A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 381 through 413 removed outlier: 4.394A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 446 removed outlier: 4.052A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 481 removed outlier: 5.406A pdb=" N LYS A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 455 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 515 Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 574 through 600 Processing helix chain 'A' and resid 605 through 621 Processing helix chain 'A' and resid 634 through 639 Processing helix chain 'A' and resid 641 through 654 removed outlier: 3.822A pdb=" N LYS A 645 " --> pdb=" O TYR A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 677 Processing helix chain 'A' and resid 677 through 704 removed outlier: 3.855A pdb=" N GLU A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 724 through 750 Processing helix chain 'A' and resid 755 through 761 removed outlier: 4.105A pdb=" N ILE A 759 " --> pdb=" O GLY A 755 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 761 " --> pdb=" O HIS A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 783 removed outlier: 3.737A pdb=" N LYS A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 766 " --> pdb=" O HIS A 762 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP A 767 " --> pdb=" O TRP A 763 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 783 " --> pdb=" O ILE A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 806 removed outlier: 4.546A pdb=" N LEU A 804 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU A 805 " --> pdb=" O PHE A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 812 removed outlier: 4.061A pdb=" N LEU A 811 " --> pdb=" O GLY A 807 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 807 through 812' Processing helix chain 'A' and resid 813 through 857 removed outlier: 3.536A pdb=" N LEU A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) Proline residue: A 819 - end of helix removed outlier: 3.512A pdb=" N ARG A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 889 removed outlier: 4.047A pdb=" N ILE A 870 " --> pdb=" O GLU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 3.958A pdb=" N ALA A 893 " --> pdb=" O HIS A 889 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 894 " --> pdb=" O PRO A 890 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 895 " --> pdb=" O GLY A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.677A pdb=" N ASN A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 959 Processing helix chain 'A' and resid 966 through 976 removed outlier: 3.645A pdb=" N ILE A 970 " --> pdb=" O ASP A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1069 through 1080 Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.698A pdb=" N THR A1100 " --> pdb=" O ILE A1096 " (cutoff:3.500A) Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1115 through 1123 removed outlier: 3.636A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 979 through 982 removed outlier: 3.659A pdb=" N SER B1003 " --> pdb=" O GLN B1064 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N TYR B1066 " --> pdb=" O ILE B1001 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE B1001 " --> pdb=" O TYR B1066 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 987 through 989 removed outlier: 6.877A pdb=" N VAL B 987 " --> pdb=" O CYS B1059 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N CYS B1059 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 989 " --> pdb=" O VAL B1057 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B1057 " --> pdb=" O VAL B 989 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 1125 through 1126 removed outlier: 6.819A pdb=" N ARG B1185 " --> pdb=" O ILE B1148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1153 through 1154 removed outlier: 3.937A pdb=" N TYR B1153 " --> pdb=" O THR B1175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 979 through 982 removed outlier: 3.652A pdb=" N SER A1003 " --> pdb=" O GLN A1064 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR A1066 " --> pdb=" O ILE A1001 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A1001 " --> pdb=" O TYR A1066 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.880A pdb=" N VAL A 987 " --> pdb=" O CYS A1059 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N CYS A1059 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 989 " --> pdb=" O VAL A1057 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A1057 " --> pdb=" O VAL A 989 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 6.747A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1153 through 1154 removed outlier: 3.914A pdb=" N TYR A1153 " --> pdb=" O THR A1175 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 3309 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.65 Time building geometry restraints manager: 4.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2812 1.33 - 1.45: 3843 1.45 - 1.57: 9448 1.57 - 1.69: 1 1.69 - 1.81: 140 Bond restraints: 16244 Sorted by residual: bond pdb=" N PRO A1184 " pdb=" CD PRO A1184 " ideal model delta sigma weight residual 1.473 1.537 -0.064 1.40e-02 5.10e+03 2.11e+01 bond pdb=" N PRO A1184 " pdb=" CA PRO A1184 " ideal model delta sigma weight residual 1.470 1.421 0.050 1.23e-02 6.61e+03 1.62e+01 bond pdb=" CB PRO A1184 " pdb=" CG PRO A1184 " ideal model delta sigma weight residual 1.492 1.688 -0.196 5.00e-02 4.00e+02 1.54e+01 bond pdb=" CG PRO A1184 " pdb=" CD PRO A1184 " ideal model delta sigma weight residual 1.503 1.371 0.132 3.40e-02 8.65e+02 1.50e+01 bond pdb=" N GLY A 836 " pdb=" CA GLY A 836 " ideal model delta sigma weight residual 1.454 1.444 0.010 1.22e-02 6.72e+03 6.79e-01 ... (remaining 16239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 22045 4.14 - 8.28: 6 8.28 - 12.43: 2 12.43 - 16.57: 0 16.57 - 20.71: 1 Bond angle restraints: 22054 Sorted by residual: angle pdb=" CA PRO A1184 " pdb=" N PRO A1184 " pdb=" CD PRO A1184 " ideal model delta sigma weight residual 112.00 91.29 20.71 1.40e+00 5.10e-01 2.19e+02 angle pdb=" N PRO A1184 " pdb=" CD PRO A1184 " pdb=" CG PRO A1184 " ideal model delta sigma weight residual 103.20 93.22 9.98 1.50e+00 4.44e-01 4.42e+01 angle pdb=" CA PRO A1184 " pdb=" CB PRO A1184 " pdb=" CG PRO A1184 " ideal model delta sigma weight residual 104.50 95.15 9.35 1.90e+00 2.77e-01 2.42e+01 angle pdb=" N PRO A1184 " pdb=" CA PRO A1184 " pdb=" CB PRO A1184 " ideal model delta sigma weight residual 103.36 100.30 3.06 8.30e-01 1.45e+00 1.36e+01 angle pdb=" N PRO A1184 " pdb=" CA PRO A1184 " pdb=" C PRO A1184 " ideal model delta sigma weight residual 110.55 116.16 -5.61 1.63e+00 3.76e-01 1.19e+01 ... (remaining 22049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.08: 9278 33.08 - 66.17: 438 66.17 - 99.25: 28 99.25 - 132.34: 0 132.34 - 165.42: 2 Dihedral angle restraints: 9746 sinusoidal: 3612 harmonic: 6134 Sorted by residual: dihedral pdb=" C21 3PH A1402 " pdb=" C2 3PH A1402 " pdb=" O21 3PH A1402 " pdb=" C3 3PH A1402 " ideal model delta sinusoidal sigma weight residual 147.58 -17.84 165.42 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C21 3PH B1402 " pdb=" C2 3PH B1402 " pdb=" O21 3PH B1402 " pdb=" C3 3PH B1402 " ideal model delta sinusoidal sigma weight residual 147.58 -17.67 165.25 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA VAL B1171 " pdb=" C VAL B1171 " pdb=" N HIS B1172 " pdb=" CA HIS B1172 " ideal model delta harmonic sigma weight residual 180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 9743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2235 0.052 - 0.104: 400 0.104 - 0.156: 22 0.156 - 0.208: 0 0.208 - 0.259: 1 Chirality restraints: 2658 Sorted by residual: chirality pdb=" CA PRO A1184 " pdb=" N PRO A1184 " pdb=" C PRO A1184 " pdb=" CB PRO A1184 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA VAL B 321 " pdb=" N VAL B 321 " pdb=" C VAL B 321 " pdb=" CB VAL B 321 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA VAL A 321 " pdb=" N VAL A 321 " pdb=" C VAL A 321 " pdb=" CB VAL A 321 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 2655 not shown) Planarity restraints: 2754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A1183 " -0.115 5.00e-02 4.00e+02 1.54e-01 3.77e+01 pdb=" N PRO A1184 " 0.264 5.00e-02 4.00e+02 pdb=" CA PRO A1184 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO A1184 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 641 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO A 642 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 642 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 642 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 641 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO B 642 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 642 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 642 " 0.023 5.00e-02 4.00e+02 ... (remaining 2751 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 202 2.63 - 3.19: 16452 3.19 - 3.76: 24747 3.76 - 4.33: 30964 4.33 - 4.90: 52442 Nonbonded interactions: 124807 Sorted by model distance: nonbonded pdb=" OD1 ASP B1139 " pdb=" OG1 THR B1141 " model vdw 2.057 3.040 nonbonded pdb=" N GLU B 924 " pdb=" OE1 GLU B 924 " model vdw 2.083 3.120 nonbonded pdb=" OE1 GLU A 590 " pdb=" OH TYR A 594 " model vdw 2.104 3.040 nonbonded pdb=" OE1 GLU B 590 " pdb=" OH TYR B 594 " model vdw 2.106 3.040 nonbonded pdb=" O PRO A 952 " pdb=" ND2 ASN A 955 " model vdw 2.134 3.120 ... (remaining 124802 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 68 through 131 or resid 133 through 1190 or resid 1401 thr \ ough 1402)) selection = (chain 'B' and (resid 68 through 131 or resid 133 through 1190 or resid 1401 thr \ ough 1402)) } 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=0.36 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: 5.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 48.730 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.100 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:3.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 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 : 0.003 0.196 16244 Z= 0.192 Angle : 0.444 20.712 22054 Z= 0.258 Chirality : 0.035 0.259 2658 Planarity : 0.004 0.154 2754 Dihedral : 17.926 165.422 5766 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 35.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 34.19 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.20), residues: 2094 helix: 2.80 (0.14), residues: 1426 sheet: -0.01 (0.56), residues: 76 loop : -1.50 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 278 HIS 0.007 0.001 HIS B1172 PHE 0.011 0.001 PHE A1134 TYR 0.008 0.001 TYR B 309 ARG 0.006 0.000 ARG A1185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.768 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2485 time to fit residues: 53.1510 Evaluate side-chains 129 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 164 optimal weight: 50.0000 chunk 63 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 190 optimal weight: 7.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1149 ASN A1154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 16244 Z= 0.468 Angle : 0.701 12.497 22054 Z= 0.362 Chirality : 0.044 0.186 2658 Planarity : 0.004 0.071 2754 Dihedral : 9.886 157.927 2404 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.21 % Favored : 94.74 % Rotamer: Outliers : 3.39 % Allowed : 31.69 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.19), residues: 2094 helix: 2.28 (0.14), residues: 1430 sheet: 0.56 (0.66), residues: 58 loop : -1.82 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 278 HIS 0.010 0.001 HIS A1172 PHE 0.016 0.002 PHE B1134 TYR 0.013 0.002 TYR B 191 ARG 0.006 0.001 ARG B 856 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 140 time to evaluate : 1.930 Fit side-chains REVERT: B 512 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9028 (mm) REVERT: B 837 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.8027 (m-80) REVERT: B 967 MET cc_start: 0.8229 (mmm) cc_final: 0.7908 (tmm) REVERT: B 1107 MET cc_start: 0.7566 (tmm) cc_final: 0.7285 (tmm) REVERT: A 849 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8680 (mp0) REVERT: A 1107 MET cc_start: 0.7452 (tmm) cc_final: 0.7171 (tmm) outliers start: 53 outliers final: 20 residues processed: 184 average time/residue: 0.2664 time to fit residues: 75.5442 Evaluate side-chains 156 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 895 SER Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1181 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 4.9990 chunk 59 optimal weight: 50.0000 chunk 158 optimal weight: 0.0070 chunk 129 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 170 optimal weight: 50.0000 chunk 189 optimal weight: 0.5980 chunk 65 optimal weight: 50.0000 chunk 153 optimal weight: 7.9990 overall best weight: 1.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 16244 Z= 0.301 Angle : 0.618 12.690 22054 Z= 0.317 Chirality : 0.041 0.172 2658 Planarity : 0.004 0.078 2754 Dihedral : 9.462 145.168 2404 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.14 % Allowed : 31.18 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.19), residues: 2094 helix: 2.39 (0.13), residues: 1430 sheet: -1.03 (0.60), residues: 82 loop : -1.90 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 278 HIS 0.009 0.001 HIS A1172 PHE 0.020 0.001 PHE B1134 TYR 0.018 0.001 TYR B 641 ARG 0.003 0.001 ARG B1185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 148 time to evaluate : 1.851 Fit side-chains revert: symmetry clash REVERT: B 512 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9019 (mm) REVERT: B 609 ARG cc_start: 0.9295 (tpt90) cc_final: 0.9028 (tmm-80) REVERT: B 837 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.8100 (m-80) REVERT: B 849 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8698 (mp0) REVERT: B 967 MET cc_start: 0.8232 (mmm) cc_final: 0.7918 (tmm) REVERT: B 1107 MET cc_start: 0.7469 (tmm) cc_final: 0.7140 (tmm) REVERT: A 512 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8885 (mm) REVERT: A 602 MET cc_start: 0.6513 (mmp) cc_final: 0.6186 (mmp) REVERT: A 849 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8616 (mp0) REVERT: A 967 MET cc_start: 0.7938 (mmm) cc_final: 0.7666 (tmm) REVERT: A 976 ARG cc_start: 0.6696 (OUTLIER) cc_final: 0.6442 (ttm110) REVERT: A 1107 MET cc_start: 0.7610 (tmm) cc_final: 0.7275 (tmm) outliers start: 49 outliers final: 23 residues processed: 188 average time/residue: 0.2663 time to fit residues: 77.2539 Evaluate side-chains 167 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 895 SER Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1181 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 128 optimal weight: 0.6980 chunk 191 optimal weight: 3.9990 chunk 202 optimal weight: 0.7980 chunk 100 optimal weight: 0.0980 chunk 181 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1156 HIS ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16244 Z= 0.172 Angle : 0.579 12.286 22054 Z= 0.292 Chirality : 0.039 0.161 2658 Planarity : 0.004 0.082 2754 Dihedral : 8.862 130.466 2404 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.35 % Favored : 95.60 % Rotamer: Outliers : 2.94 % Allowed : 31.24 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.19), residues: 2094 helix: 2.60 (0.13), residues: 1420 sheet: -0.95 (0.60), residues: 82 loop : -1.70 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 635 HIS 0.006 0.001 HIS A1172 PHE 0.029 0.001 PHE B 598 TYR 0.016 0.001 TYR B 641 ARG 0.004 0.001 ARG B 609 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 1.727 Fit side-chains REVERT: B 249 MET cc_start: 0.9002 (tmm) cc_final: 0.8756 (tmm) REVERT: B 483 MET cc_start: 0.9232 (mtp) cc_final: 0.8989 (mtp) REVERT: B 837 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: B 849 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8595 (mp0) REVERT: B 967 MET cc_start: 0.8279 (mmm) cc_final: 0.7919 (tmm) REVERT: B 976 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.6335 (ttm110) REVERT: B 1066 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: B 1107 MET cc_start: 0.7519 (tmm) cc_final: 0.7127 (tmm) REVERT: A 129 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7827 (t0) REVERT: A 249 MET cc_start: 0.8890 (tmm) cc_final: 0.8636 (tmm) REVERT: A 849 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8468 (mp0) REVERT: A 1107 MET cc_start: 0.7490 (tmm) cc_final: 0.7197 (tmm) outliers start: 46 outliers final: 28 residues processed: 185 average time/residue: 0.2802 time to fit residues: 78.7622 Evaluate side-chains 171 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1181 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 50.0000 chunk 115 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 140 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 182 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 16244 Z= 0.299 Angle : 0.598 10.470 22054 Z= 0.305 Chirality : 0.040 0.181 2658 Planarity : 0.004 0.078 2754 Dihedral : 9.023 127.923 2404 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.23 % Allowed : 29.83 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.19), residues: 2094 helix: 2.57 (0.14), residues: 1422 sheet: 0.07 (0.62), residues: 68 loop : -1.70 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 635 HIS 0.009 0.001 HIS A1172 PHE 0.028 0.001 PHE B 598 TYR 0.016 0.001 TYR B 641 ARG 0.008 0.000 ARG A 609 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 143 time to evaluate : 1.815 Fit side-chains REVERT: B 220 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7900 (mp) REVERT: B 483 MET cc_start: 0.9259 (mtp) cc_final: 0.8955 (mtp) REVERT: B 512 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9014 (mm) REVERT: B 837 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.7879 (m-80) REVERT: B 849 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8636 (mp0) REVERT: B 935 GLU cc_start: 0.8717 (tp30) cc_final: 0.8516 (tp30) REVERT: B 967 MET cc_start: 0.8309 (mmm) cc_final: 0.7903 (tmm) REVERT: B 1107 MET cc_start: 0.7534 (tmm) cc_final: 0.7302 (tmm) REVERT: B 1139 ASP cc_start: 0.6188 (OUTLIER) cc_final: 0.5942 (p0) REVERT: A 220 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7791 (mp) REVERT: A 512 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8860 (mm) REVERT: A 609 ARG cc_start: 0.9504 (tpt90) cc_final: 0.9061 (ptm160) REVERT: A 849 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8495 (mp0) REVERT: A 967 MET cc_start: 0.8268 (tpp) cc_final: 0.8040 (tmm) REVERT: A 1107 MET cc_start: 0.7502 (tmm) cc_final: 0.7267 (tmm) outliers start: 66 outliers final: 39 residues processed: 198 average time/residue: 0.2640 time to fit residues: 81.5663 Evaluate side-chains 182 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 900 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1181 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 10.0000 chunk 182 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 168 optimal weight: 50.0000 chunk 94 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 67 optimal weight: 40.0000 chunk 106 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16244 Z= 0.206 Angle : 0.569 9.603 22054 Z= 0.290 Chirality : 0.039 0.184 2658 Planarity : 0.004 0.077 2754 Dihedral : 8.972 122.486 2404 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.88 % Allowed : 31.11 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.19), residues: 2094 helix: 2.59 (0.14), residues: 1422 sheet: 0.77 (0.68), residues: 58 loop : -1.70 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 643 HIS 0.008 0.001 HIS A1172 PHE 0.022 0.001 PHE B 598 TYR 0.011 0.001 TYR B 641 ARG 0.010 0.000 ARG B 609 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 1.756 Fit side-chains REVERT: B 220 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7859 (mp) REVERT: B 483 MET cc_start: 0.9257 (mtp) cc_final: 0.8981 (mtp) REVERT: B 609 ARG cc_start: 0.9391 (tpt90) cc_final: 0.9066 (ptt180) REVERT: B 837 TYR cc_start: 0.8907 (OUTLIER) cc_final: 0.7875 (m-80) REVERT: B 849 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8585 (mp0) REVERT: B 935 GLU cc_start: 0.8718 (tp30) cc_final: 0.8508 (tp30) REVERT: B 967 MET cc_start: 0.8305 (mmm) cc_final: 0.7878 (tmm) REVERT: B 1107 MET cc_start: 0.7518 (tmm) cc_final: 0.7290 (tmm) REVERT: B 1139 ASP cc_start: 0.6229 (OUTLIER) cc_final: 0.5965 (p0) REVERT: A 220 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7763 (mp) REVERT: A 512 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8851 (mm) REVERT: A 609 ARG cc_start: 0.9481 (tpt90) cc_final: 0.9039 (ptm160) REVERT: A 849 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8455 (mp0) REVERT: A 967 MET cc_start: 0.8265 (tpp) cc_final: 0.7983 (tmm) REVERT: A 1107 MET cc_start: 0.7504 (tmm) cc_final: 0.7264 (tmm) outliers start: 45 outliers final: 30 residues processed: 181 average time/residue: 0.2531 time to fit residues: 71.2944 Evaluate side-chains 177 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 900 GLN Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1127 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 0.0070 chunk 22 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 171 optimal weight: 50.0000 chunk 113 optimal weight: 0.5980 chunk 202 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16244 Z= 0.171 Angle : 0.556 9.278 22054 Z= 0.282 Chirality : 0.038 0.200 2658 Planarity : 0.004 0.075 2754 Dihedral : 8.911 117.743 2404 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.71 % Allowed : 29.77 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.19), residues: 2094 helix: 2.65 (0.14), residues: 1422 sheet: 0.87 (0.66), residues: 58 loop : -1.66 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 643 HIS 0.007 0.001 HIS A1172 PHE 0.018 0.001 PHE B 598 TYR 0.007 0.001 TYR B 309 ARG 0.009 0.000 ARG B 609 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 142 time to evaluate : 1.811 Fit side-chains REVERT: B 220 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7845 (mp) REVERT: B 483 MET cc_start: 0.9251 (mtp) cc_final: 0.9001 (mtp) REVERT: B 512 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.8998 (mm) REVERT: B 609 ARG cc_start: 0.9362 (tpt90) cc_final: 0.9048 (ptt180) REVERT: B 837 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.7721 (m-80) REVERT: B 849 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8547 (mp0) REVERT: B 924 GLU cc_start: 0.7726 (mp0) cc_final: 0.7250 (mp0) REVERT: B 935 GLU cc_start: 0.8711 (tp30) cc_final: 0.8500 (tp30) REVERT: B 967 MET cc_start: 0.8286 (mmm) cc_final: 0.7841 (tmm) REVERT: B 1066 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: B 1107 MET cc_start: 0.7484 (tmm) cc_final: 0.7261 (tmm) REVERT: B 1139 ASP cc_start: 0.6210 (OUTLIER) cc_final: 0.5683 (p0) REVERT: A 129 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7918 (t0) REVERT: A 220 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7730 (mp) REVERT: A 512 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8849 (mm) REVERT: A 595 TRP cc_start: 0.8696 (OUTLIER) cc_final: 0.7810 (m100) REVERT: A 602 MET cc_start: 0.6474 (mmp) cc_final: 0.6038 (mmp) REVERT: A 609 ARG cc_start: 0.9440 (tpt90) cc_final: 0.9032 (ptm160) REVERT: A 849 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8407 (mp0) REVERT: A 967 MET cc_start: 0.8285 (tpp) cc_final: 0.7975 (tmm) REVERT: A 1107 MET cc_start: 0.7487 (tmm) cc_final: 0.7250 (tmm) outliers start: 58 outliers final: 36 residues processed: 194 average time/residue: 0.2745 time to fit residues: 81.2558 Evaluate side-chains 188 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 575 PHE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 900 GLN Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1127 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 60 optimal weight: 30.0000 chunk 39 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 137 optimal weight: 0.5980 chunk 100 optimal weight: 7.9990 chunk 18 optimal weight: 0.4980 chunk 159 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16244 Z= 0.178 Angle : 0.573 15.642 22054 Z= 0.285 Chirality : 0.038 0.236 2658 Planarity : 0.004 0.081 2754 Dihedral : 8.712 112.335 2404 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.35 % Favored : 95.55 % Rotamer: Outliers : 3.39 % Allowed : 29.58 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.19), residues: 2094 helix: 2.70 (0.14), residues: 1422 sheet: 1.08 (0.66), residues: 58 loop : -1.65 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 635 HIS 0.007 0.001 HIS A1172 PHE 0.036 0.001 PHE B 598 TYR 0.010 0.001 TYR B 641 ARG 0.008 0.000 ARG B 609 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 138 time to evaluate : 1.828 Fit side-chains REVERT: B 483 MET cc_start: 0.9273 (mtp) cc_final: 0.8947 (mtp) REVERT: B 512 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.8980 (mm) REVERT: B 609 ARG cc_start: 0.9337 (tpt90) cc_final: 0.9051 (ptt180) REVERT: B 837 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.7458 (m-80) REVERT: B 849 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8565 (mp0) REVERT: B 924 GLU cc_start: 0.7711 (mp0) cc_final: 0.7261 (mp0) REVERT: B 935 GLU cc_start: 0.8702 (tp30) cc_final: 0.8483 (tp30) REVERT: B 967 MET cc_start: 0.8289 (mmm) cc_final: 0.7834 (tmm) REVERT: B 1066 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.7768 (m-80) REVERT: B 1107 MET cc_start: 0.7476 (tmm) cc_final: 0.7256 (tmm) REVERT: B 1139 ASP cc_start: 0.6210 (OUTLIER) cc_final: 0.5682 (p0) REVERT: A 220 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7761 (mp) REVERT: A 512 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8856 (mm) REVERT: A 595 TRP cc_start: 0.8708 (OUTLIER) cc_final: 0.7805 (m100) REVERT: A 602 MET cc_start: 0.6415 (mmp) cc_final: 0.6042 (mmp) REVERT: A 609 ARG cc_start: 0.9437 (tpt90) cc_final: 0.9042 (ptm160) REVERT: A 849 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: A 967 MET cc_start: 0.8348 (tpp) cc_final: 0.8031 (tmm) REVERT: A 1107 MET cc_start: 0.7382 (tmm) cc_final: 0.7144 (tmm) outliers start: 53 outliers final: 37 residues processed: 183 average time/residue: 0.2579 time to fit residues: 73.4961 Evaluate side-chains 182 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 900 GLN Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1127 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 188 optimal weight: 0.4980 chunk 113 optimal weight: 0.6980 chunk 82 optimal weight: 0.0970 chunk 148 optimal weight: 0.9990 chunk 57 optimal weight: 20.0000 chunk 170 optimal weight: 50.0000 chunk 178 optimal weight: 8.9990 chunk 187 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 ASN ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 16244 Z= 0.163 Angle : 0.578 15.760 22054 Z= 0.286 Chirality : 0.038 0.226 2658 Planarity : 0.004 0.081 2754 Dihedral : 8.535 109.685 2404 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.45 % Favored : 95.46 % Rotamer: Outliers : 3.01 % Allowed : 29.90 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.19), residues: 2094 helix: 2.71 (0.14), residues: 1422 sheet: 1.17 (0.64), residues: 58 loop : -1.60 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 635 HIS 0.007 0.001 HIS A1172 PHE 0.030 0.001 PHE B 598 TYR 0.018 0.001 TYR A 641 ARG 0.007 0.000 ARG B 609 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 1.775 Fit side-chains REVERT: B 483 MET cc_start: 0.9279 (mtp) cc_final: 0.8961 (mtp) REVERT: B 512 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.8973 (mm) REVERT: B 609 ARG cc_start: 0.9340 (tpt90) cc_final: 0.9074 (ptt180) REVERT: B 837 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.7323 (m-80) REVERT: B 849 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8474 (mp0) REVERT: B 924 GLU cc_start: 0.7715 (mp0) cc_final: 0.7285 (mp0) REVERT: B 935 GLU cc_start: 0.8685 (tp30) cc_final: 0.8463 (tp30) REVERT: B 967 MET cc_start: 0.8296 (mmm) cc_final: 0.7836 (tmm) REVERT: B 1107 MET cc_start: 0.7444 (tmm) cc_final: 0.7233 (tmm) REVERT: B 1139 ASP cc_start: 0.6194 (OUTLIER) cc_final: 0.5653 (p0) REVERT: A 129 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7943 (t0) REVERT: A 220 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7743 (mp) REVERT: A 512 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8814 (mm) REVERT: A 595 TRP cc_start: 0.8706 (OUTLIER) cc_final: 0.7832 (m100) REVERT: A 602 MET cc_start: 0.6412 (mmp) cc_final: 0.6008 (mmp) REVERT: A 609 ARG cc_start: 0.9395 (tpt90) cc_final: 0.9020 (ptm160) REVERT: A 849 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8345 (mp0) REVERT: A 928 HIS cc_start: 0.8088 (m-70) cc_final: 0.7822 (m-70) REVERT: A 967 MET cc_start: 0.8375 (tpp) cc_final: 0.8052 (tmm) REVERT: A 1107 MET cc_start: 0.7354 (tmm) cc_final: 0.7118 (tmm) outliers start: 47 outliers final: 35 residues processed: 183 average time/residue: 0.2615 time to fit residues: 74.3709 Evaluate side-chains 179 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 900 GLN Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1118 LYS Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 209 optimal weight: 9.9990 chunk 192 optimal weight: 3.9990 chunk 166 optimal weight: 50.0000 chunk 17 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 ASN ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16244 Z= 0.202 Angle : 0.598 15.787 22054 Z= 0.296 Chirality : 0.039 0.356 2658 Planarity : 0.004 0.081 2754 Dihedral : 8.479 108.637 2404 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.49 % Favored : 95.36 % Rotamer: Outliers : 2.94 % Allowed : 30.35 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.19), residues: 2094 helix: 2.72 (0.14), residues: 1422 sheet: 1.27 (0.65), residues: 58 loop : -1.59 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 635 HIS 0.007 0.001 HIS A1172 PHE 0.029 0.001 PHE B 598 TYR 0.013 0.001 TYR A 641 ARG 0.007 0.000 ARG B 609 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 137 time to evaluate : 1.634 Fit side-chains REVERT: B 483 MET cc_start: 0.9281 (mtp) cc_final: 0.8952 (mtp) REVERT: B 512 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.8964 (mm) REVERT: B 609 ARG cc_start: 0.9350 (tpt90) cc_final: 0.9077 (ptt180) REVERT: B 837 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.7308 (m-80) REVERT: B 849 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8487 (mp0) REVERT: B 924 GLU cc_start: 0.7784 (mp0) cc_final: 0.7406 (mp0) REVERT: B 935 GLU cc_start: 0.8688 (tp30) cc_final: 0.8466 (tp30) REVERT: B 967 MET cc_start: 0.8303 (mmm) cc_final: 0.7839 (tmm) REVERT: B 1107 MET cc_start: 0.7406 (tmm) cc_final: 0.7191 (tmm) REVERT: B 1139 ASP cc_start: 0.6198 (OUTLIER) cc_final: 0.5632 (p0) REVERT: A 129 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7911 (t0) REVERT: A 154 MET cc_start: 0.8979 (tpp) cc_final: 0.8350 (tpt) REVERT: A 220 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7732 (mp) REVERT: A 512 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8826 (mm) REVERT: A 595 TRP cc_start: 0.8719 (OUTLIER) cc_final: 0.7841 (m100) REVERT: A 602 MET cc_start: 0.6393 (mmp) cc_final: 0.6005 (mmp) REVERT: A 609 ARG cc_start: 0.9402 (tpt90) cc_final: 0.9026 (ptm160) REVERT: A 849 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8373 (mp0) REVERT: A 967 MET cc_start: 0.8368 (tpp) cc_final: 0.8032 (tmm) REVERT: A 1107 MET cc_start: 0.7307 (tmm) cc_final: 0.7059 (tmm) outliers start: 46 outliers final: 36 residues processed: 180 average time/residue: 0.2749 time to fit residues: 77.0874 Evaluate side-chains 181 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 136 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 900 GLN Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1118 LYS Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.0270 chunk 51 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 166 optimal weight: 50.0000 chunk 69 optimal weight: 6.9990 chunk 171 optimal weight: 30.0000 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 ASN ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.115170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.073654 restraints weight = 60699.188| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.66 r_work: 0.2994 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 16244 Z= 0.348 Angle : 0.956 59.199 22054 Z= 0.554 Chirality : 0.041 0.461 2658 Planarity : 0.004 0.081 2754 Dihedral : 8.490 108.629 2404 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.59 % Favored : 95.27 % Rotamer: Outliers : 2.94 % Allowed : 30.47 % Favored : 66.58 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.19), residues: 2094 helix: 2.71 (0.14), residues: 1422 sheet: 1.27 (0.65), residues: 58 loop : -1.59 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 635 HIS 0.007 0.001 HIS A1172 PHE 0.026 0.001 PHE B 598 TYR 0.011 0.001 TYR A 641 ARG 0.006 0.000 ARG B 609 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3498.41 seconds wall clock time: 64 minutes 42.54 seconds (3882.54 seconds total)