Starting phenix.real_space_refine on Fri Mar 22 16:15:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bve_30217/03_2024/7bve_30217_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bve_30217/03_2024/7bve_30217.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bve_30217/03_2024/7bve_30217_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bve_30217/03_2024/7bve_30217_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bve_30217/03_2024/7bve_30217_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bve_30217/03_2024/7bve_30217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bve_30217/03_2024/7bve_30217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bve_30217/03_2024/7bve_30217_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bve_30217/03_2024/7bve_30217_updated.pdb" } resolution = 2.81 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= 0.000 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16931 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 4 5.49 5 S 56 5.16 5 C 11038 2.51 5 N 2936 2.21 5 O 3110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 16": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A ARG 401": "NH1" <-> "NH2" Residue "A ARG 520": "NH1" <-> "NH2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A ARG 605": "NH1" <-> "NH2" Residue "A ARG 670": "NH1" <-> "NH2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 683": "NH1" <-> "NH2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A ARG 847": "NH1" <-> "NH2" Residue "A ARG 852": "NH1" <-> "NH2" Residue "A ARG 907": "NH1" <-> "NH2" Residue "A ARG 944": "NH1" <-> "NH2" Residue "A ARG 975": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1035": "NH1" <-> "NH2" Residue "B ARG 16": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ARG 401": "NH1" <-> "NH2" Residue "B ARG 520": "NH1" <-> "NH2" Residue "B ARG 603": "NH1" <-> "NH2" Residue "B ARG 605": "NH1" <-> "NH2" Residue "B ARG 670": "NH1" <-> "NH2" Residue "B ARG 676": "NH1" <-> "NH2" Residue "B ARG 683": "NH1" <-> "NH2" Residue "B ARG 820": "NH1" <-> "NH2" Residue "B ARG 847": "NH1" <-> "NH2" Residue "B ARG 852": "NH1" <-> "NH2" Residue "B ARG 944": "NH1" <-> "NH2" Residue "B ARG 975": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1035": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17146 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 7888 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 74, 'TRANS': 958} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 7888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 7888 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 74, 'TRANS': 958} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 644 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "D" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 644 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {' CA': 1, '95E': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {' CA': 1, '95E': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PN7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PN7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Time building chain proxies: 9.56, per 1000 atoms: 0.56 Number of scatterers: 17146 At special positions: 0 Unit cell: (127.1, 117.26, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 56 16.00 P 4 15.00 O 3110 8.00 N 2936 7.00 C 11038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 730 " - pdb=" SG CYS A 973 " distance=2.75 Simple disulfide: pdb=" SG CYS B 730 " - pdb=" SG CYS B 973 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.87 Conformation dependent library (CDL) restraints added in 3.3 seconds 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4100 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 15 sheets defined 40.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.61 Creating SS restraints... Processing helix chain 'A' and resid 14 through 35 removed outlier: 3.790A pdb=" N ALA A 19 " --> pdb=" O ALA A 15 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 33 " --> pdb=" O MET A 29 " (cutoff:3.500A) Proline residue: A 34 - end of helix Processing helix chain 'A' and resid 75 through 80 removed outlier: 4.080A pdb=" N GLY A 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 80 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 133 No H-bonds generated for 'chain 'A' and resid 130 through 133' Processing helix chain 'A' and resid 214 through 240 removed outlier: 4.131A pdb=" N ALA A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 272 Processing helix chain 'A' and resid 281 through 293 removed outlier: 4.701A pdb=" N GLU A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N HIS A 292 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 314 through 322 removed outlier: 4.288A pdb=" N HIS A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 330 No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'A' and resid 332 through 348 Processing helix chain 'A' and resid 362 through 378 Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 385 through 405 removed outlier: 3.507A pdb=" N ALA A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 422 Processing helix chain 'A' and resid 426 through 436 removed outlier: 3.914A pdb=" N ILE A 429 " --> pdb=" O PRO A 426 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 430 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 449 removed outlier: 3.642A pdb=" N ALA A 448 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 449 " --> pdb=" O ILE A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 473 Proline residue: A 461 - end of helix removed outlier: 5.119A pdb=" N THR A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ILE A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 492 Processing helix chain 'A' and resid 498 through 508 removed outlier: 3.726A pdb=" N GLU A 501 " --> pdb=" O TRP A 498 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N HIS A 502 " --> pdb=" O PHE A 499 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 508 " --> pdb=" O TYR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 539 Processing helix chain 'A' and resid 548 through 567 removed outlier: 4.302A pdb=" N MET A 566 " --> pdb=" O PHE A 562 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N PHE A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 removed outlier: 3.716A pdb=" N GLY A 577 " --> pdb=" O HIS A 574 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 578 " --> pdb=" O HIS A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 592 Processing helix chain 'A' and resid 602 through 619 Processing helix chain 'A' and resid 647 through 668 Processing helix chain 'A' and resid 681 through 685 Processing helix chain 'A' and resid 688 through 710 Processing helix chain 'A' and resid 717 through 726 removed outlier: 4.197A pdb=" N LEU A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 734 removed outlier: 3.897A pdb=" N ASN A 734 " --> pdb=" O GLY A 731 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 731 through 734' Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 951 through 954 No H-bonds generated for 'chain 'A' and resid 951 through 954' Processing helix chain 'A' and resid 995 through 1004 removed outlier: 3.637A pdb=" N ALA A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) Proline residue: A1003 - end of helix Processing helix chain 'A' and resid 1007 through 1009 No H-bonds generated for 'chain 'A' and resid 1007 through 1009' Processing helix chain 'A' and resid 1012 through 1014 No H-bonds generated for 'chain 'A' and resid 1012 through 1014' Processing helix chain 'A' and resid 1016 through 1019 No H-bonds generated for 'chain 'A' and resid 1016 through 1019' Processing helix chain 'B' and resid 13 through 35 removed outlier: 3.562A pdb=" N LEU B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Proline residue: B 34 - end of helix Processing helix chain 'B' and resid 75 through 80 removed outlier: 4.098A pdb=" N GLY B 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 80 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 130 through 133 No H-bonds generated for 'chain 'B' and resid 130 through 133' Processing helix chain 'B' and resid 214 through 238 Processing helix chain 'B' and resid 258 through 272 Processing helix chain 'B' and resid 281 through 293 removed outlier: 4.702A pdb=" N GLU B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N HIS B 292 " --> pdb=" O ARG B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 314 through 322 removed outlier: 4.289A pdb=" N HIS B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 348 Proline residue: B 333 - end of helix Processing helix chain 'B' and resid 362 through 375 Processing helix chain 'B' and resid 385 through 405 Processing helix chain 'B' and resid 409 through 422 Processing helix chain 'B' and resid 426 through 436 removed outlier: 3.927A pdb=" N ILE B 429 " --> pdb=" O PRO B 426 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 430 " --> pdb=" O THR B 427 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 433 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 449 removed outlier: 3.626A pdb=" N ALA B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS B 449 " --> pdb=" O ILE B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 473 Proline residue: B 461 - end of helix removed outlier: 5.126A pdb=" N THR B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ILE B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE B 471 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU B 472 " --> pdb=" O VAL B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 492 Processing helix chain 'B' and resid 498 through 508 removed outlier: 3.746A pdb=" N GLU B 501 " --> pdb=" O TRP B 498 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N HIS B 502 " --> pdb=" O PHE B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 539 Processing helix chain 'B' and resid 548 through 567 removed outlier: 4.302A pdb=" N MET B 566 " --> pdb=" O PHE B 562 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 579 removed outlier: 3.730A pdb=" N GLY B 577 " --> pdb=" O HIS B 574 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL B 578 " --> pdb=" O HIS B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 592 Processing helix chain 'B' and resid 602 through 619 Processing helix chain 'B' and resid 647 through 668 Processing helix chain 'B' and resid 681 through 685 Processing helix chain 'B' and resid 688 through 710 Processing helix chain 'B' and resid 717 through 726 removed outlier: 4.244A pdb=" N LEU B 725 " --> pdb=" O ASN B 721 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N THR B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 734 removed outlier: 3.896A pdb=" N ASN B 734 " --> pdb=" O GLY B 731 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 731 through 734' Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 951 through 954 No H-bonds generated for 'chain 'B' and resid 951 through 954' Processing helix chain 'B' and resid 995 through 1004 Proline residue: B1003 - end of helix Processing helix chain 'B' and resid 1007 through 1009 No H-bonds generated for 'chain 'B' and resid 1007 through 1009' Processing helix chain 'B' and resid 1012 through 1014 No H-bonds generated for 'chain 'B' and resid 1012 through 1014' Processing helix chain 'B' and resid 1016 through 1019 No H-bonds generated for 'chain 'B' and resid 1016 through 1019' Processing helix chain 'C' and resid 5 through 19 removed outlier: 4.568A pdb=" N ALA C 10 " --> pdb=" O GLU C 6 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY C 11 " --> pdb=" O GLU C 7 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 54 Processing helix chain 'C' and resid 70 through 80 Processing helix chain 'D' and resid 5 through 19 removed outlier: 4.568A pdb=" N ALA D 10 " --> pdb=" O GLU D 6 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY D 11 " --> pdb=" O GLU D 7 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 54 Processing helix chain 'D' and resid 70 through 80 Processing sheet with id= A, first strand: chain 'A' and resid 38 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 44 through 46 removed outlier: 4.144A pdb=" N ASP A 67 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 140 " --> pdb=" O VAL A 155 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 115 through 117 Processing sheet with id= D, first strand: chain 'A' and resid 736 through 738 Processing sheet with id= E, first strand: chain 'A' and resid 762 through 764 removed outlier: 3.639A pdb=" N LEU A 764 " --> pdb=" O VAL A 845 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A 845 " --> pdb=" O LEU A 764 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA A 844 " --> pdb=" O ASP A 929 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 862 through 867 Processing sheet with id= G, first strand: chain 'A' and resid 961 through 963 removed outlier: 6.624A pdb=" N TRP A 989 " --> pdb=" O MET A 962 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A1039 " --> pdb=" O LEU A 992 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU A1040 " --> pdb=" O VAL A1025 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 38 through 40 Processing sheet with id= I, first strand: chain 'B' and resid 44 through 46 Processing sheet with id= J, first strand: chain 'B' and resid 68 through 71 removed outlier: 3.609A pdb=" N TYR B 140 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 115 through 117 Processing sheet with id= L, first strand: chain 'B' and resid 736 through 738 Processing sheet with id= M, first strand: chain 'B' and resid 762 through 764 removed outlier: 3.649A pdb=" N LEU B 764 " --> pdb=" O VAL B 845 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 845 " --> pdb=" O LEU B 764 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 862 through 867 Processing sheet with id= O, first strand: chain 'B' and resid 961 through 963 removed outlier: 6.621A pdb=" N TRP B 989 " --> pdb=" O MET B 962 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER B1039 " --> pdb=" O LEU B 992 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU B1040 " --> pdb=" O VAL B1025 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1767 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: 5.87 Time building geometry restraints manager: 7.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 2756 1.27 - 1.41: 4406 1.41 - 1.54: 10296 1.54 - 1.68: 46 1.68 - 1.82: 94 Bond restraints: 17598 Sorted by residual: bond pdb=" C2 95E B1103 " pdb=" O1 95E B1103 " ideal model delta sigma weight residual 1.412 1.182 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C2 95E A1103 " pdb=" O1 95E A1103 " ideal model delta sigma weight residual 1.412 1.182 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C11 95E A1103 " pdb=" O12 95E A1103 " ideal model delta sigma weight residual 1.412 1.185 0.227 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C11 95E B1103 " pdb=" O12 95E B1103 " ideal model delta sigma weight residual 1.412 1.186 0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C VAL B 118 " pdb=" O VAL B 118 " ideal model delta sigma weight residual 1.236 1.144 0.092 1.03e-02 9.43e+03 7.91e+01 ... (remaining 17593 not shown) Histogram of bond angle deviations from ideal: 97.08 - 104.56: 445 104.56 - 112.04: 8518 112.04 - 119.51: 6401 119.51 - 126.99: 8366 126.99 - 134.47: 374 Bond angle restraints: 24104 Sorted by residual: angle pdb=" N ASP B 931 " pdb=" CA ASP B 931 " pdb=" C ASP B 931 " ideal model delta sigma weight residual 108.31 124.50 -16.19 1.52e+00 4.33e-01 1.13e+02 angle pdb=" CA ASP B 931 " pdb=" C ASP B 931 " pdb=" N LEU B 932 " ideal model delta sigma weight residual 119.52 113.08 6.44 7.90e-01 1.60e+00 6.64e+01 angle pdb=" C PRO A 943 " pdb=" CA PRO A 943 " pdb=" CB PRO A 943 " ideal model delta sigma weight residual 111.12 101.22 9.90 1.29e+00 6.01e-01 5.89e+01 angle pdb=" N GLN B 935 " pdb=" CA GLN B 935 " pdb=" C GLN B 935 " ideal model delta sigma weight residual 111.28 102.96 8.32 1.09e+00 8.42e-01 5.83e+01 angle pdb=" N ALA A 905 " pdb=" CA ALA A 905 " pdb=" C ALA A 905 " ideal model delta sigma weight residual 110.53 120.11 -9.58 1.32e+00 5.74e-01 5.27e+01 ... (remaining 24099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.72: 9819 15.72 - 31.45: 389 31.45 - 47.17: 91 47.17 - 62.90: 15 62.90 - 78.62: 10 Dihedral angle restraints: 10324 sinusoidal: 3948 harmonic: 6376 Sorted by residual: dihedral pdb=" CA ALA A 903 " pdb=" C ALA A 903 " pdb=" N PRO A 904 " pdb=" CA PRO A 904 " ideal model delta harmonic sigma weight residual 0.00 38.25 -38.25 0 5.00e+00 4.00e-02 5.85e+01 dihedral pdb=" N ASP B 931 " pdb=" C ASP B 931 " pdb=" CA ASP B 931 " pdb=" CB ASP B 931 " ideal model delta harmonic sigma weight residual 122.80 140.33 -17.53 0 2.50e+00 1.60e-01 4.92e+01 dihedral pdb=" C ASP B 931 " pdb=" N ASP B 931 " pdb=" CA ASP B 931 " pdb=" CB ASP B 931 " ideal model delta harmonic sigma weight residual -122.60 -139.49 16.89 0 2.50e+00 1.60e-01 4.56e+01 ... (remaining 10321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 2686 0.157 - 0.314: 75 0.314 - 0.471: 7 0.471 - 0.628: 1 0.628 - 0.785: 1 Chirality restraints: 2770 Sorted by residual: chirality pdb=" CA ASP B 931 " pdb=" N ASP B 931 " pdb=" C ASP B 931 " pdb=" CB ASP B 931 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" CA LYS A1030 " pdb=" N LYS A1030 " pdb=" C LYS A1030 " pdb=" CB LYS A1030 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.78e+00 chirality pdb=" CA ILE A 938 " pdb=" N ILE A 938 " pdb=" C ILE A 938 " pdb=" CB ILE A 938 " both_signs ideal model delta sigma weight residual False 2.43 2.89 -0.46 2.00e-01 2.50e+01 5.31e+00 ... (remaining 2767 not shown) Planarity restraints: 3074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 929 " -0.027 2.00e-02 2.50e+03 5.50e-02 3.03e+01 pdb=" C ASP B 929 " 0.095 2.00e-02 2.50e+03 pdb=" O ASP B 929 " -0.036 2.00e-02 2.50e+03 pdb=" N ASP B 930 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 943 " -0.020 2.00e-02 2.50e+03 4.25e-02 1.80e+01 pdb=" C PRO A 943 " 0.073 2.00e-02 2.50e+03 pdb=" O PRO A 943 " -0.029 2.00e-02 2.50e+03 pdb=" N ARG A 944 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B1030 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C LYS B1030 " 0.070 2.00e-02 2.50e+03 pdb=" O LYS B1030 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP B1031 " -0.025 2.00e-02 2.50e+03 ... (remaining 3071 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2208 2.75 - 3.29: 15437 3.29 - 3.82: 26959 3.82 - 4.36: 32236 4.36 - 4.90: 57251 Nonbonded interactions: 134091 Sorted by model distance: nonbonded pdb=" O THR B 123 " pdb=" OG1 THR B 123 " model vdw 2.212 2.440 nonbonded pdb=" OH TYR A 63 " pdb=" O GLY A1011 " model vdw 2.216 2.440 nonbonded pdb=" O THR A 123 " pdb=" OG1 THR A 123 " model vdw 2.225 2.440 nonbonded pdb=" O SER B 928 " pdb=" OG SER B 928 " model vdw 2.262 2.440 nonbonded pdb=" O ARG B 870 " pdb=" ND1 HIS B 936 " model vdw 2.304 2.520 ... (remaining 134086 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.010 Extract box with map and model: 10.680 Check model and map are aligned: 0.270 Set scattering table: 0.150 Process input model: 47.560 Find NCS groups from input model: 0.920 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:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 : 0.010 0.230 17598 Z= 0.648 Angle : 1.155 16.190 24104 Z= 0.672 Chirality : 0.070 0.785 2770 Planarity : 0.010 0.072 3074 Dihedral : 10.107 78.620 6218 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.51 % Favored : 92.27 % Rotamer: Outliers : 0.28 % Allowed : 1.79 % Favored : 97.93 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -4.01 (0.14), residues: 2224 helix: -2.30 (0.12), residues: 936 sheet: -2.13 (0.32), residues: 232 loop : -3.13 (0.15), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP B 636 HIS 0.008 0.002 HIS B 235 PHE 0.044 0.004 PHE B 303 TYR 0.032 0.004 TYR B1028 ARG 0.013 0.001 ARG A1062 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 234 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 THR cc_start: 0.8866 (p) cc_final: 0.8631 (t) REVERT: A 847 ARG cc_start: 0.7185 (ttm110) cc_final: 0.6832 (mtt90) REVERT: A 870 ARG cc_start: 0.6632 (ttt180) cc_final: 0.6295 (mtm180) REVERT: A 924 ARG cc_start: 0.7649 (ttp-170) cc_final: 0.7411 (ttm170) REVERT: B 28 LEU cc_start: 0.7984 (mp) cc_final: 0.7700 (mp) REVERT: B 110 GLU cc_start: 0.7126 (tt0) cc_final: 0.6737 (tt0) REVERT: B 427 THR cc_start: 0.8892 (p) cc_final: 0.8662 (t) REVERT: B 847 ARG cc_start: 0.7160 (ttm110) cc_final: 0.6783 (mtt90) REVERT: B 870 ARG cc_start: 0.6216 (ttt180) cc_final: 0.5922 (mtm-85) REVERT: B 924 ARG cc_start: 0.7630 (ttp-170) cc_final: 0.7384 (ttm170) outliers start: 5 outliers final: 1 residues processed: 238 average time/residue: 1.6278 time to fit residues: 422.2810 Evaluate side-chains 144 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 926 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 199 GLN A 604 ASN A 740 GLN A 743 ASN A 885 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1001 ASN B 146 HIS B 199 GLN B 604 ASN B 723 ASN B 740 GLN B 743 ASN B 885 GLN B 936 HIS B1001 ASN C 50 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17598 Z= 0.240 Angle : 0.634 7.846 24104 Z= 0.322 Chirality : 0.044 0.192 2770 Planarity : 0.006 0.064 3074 Dihedral : 6.804 72.537 2457 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.49 % Favored : 94.42 % Rotamer: Outliers : 1.23 % Allowed : 8.80 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -2.29 (0.17), residues: 2224 helix: -0.38 (0.16), residues: 942 sheet: -1.81 (0.33), residues: 244 loop : -2.57 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 320 HIS 0.003 0.001 HIS B 146 PHE 0.021 0.002 PHE A 303 TYR 0.018 0.002 TYR A 299 ARG 0.006 0.001 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 164 time to evaluate : 1.987 Fit side-chains REVERT: A 28 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7672 (mp) REVERT: A 552 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6855 (mtt90) REVERT: A 870 ARG cc_start: 0.7230 (ttt180) cc_final: 0.6259 (mtm180) REVERT: B 28 LEU cc_start: 0.7865 (mp) cc_final: 0.7538 (mp) REVERT: B 110 GLU cc_start: 0.7156 (tt0) cc_final: 0.6747 (tt0) REVERT: B 552 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6864 (mtt90) REVERT: B 847 ARG cc_start: 0.6696 (ttm110) cc_final: 0.6451 (mtt90) REVERT: B 870 ARG cc_start: 0.6782 (ttt180) cc_final: 0.5987 (mtm180) REVERT: D 50 GLN cc_start: 0.7826 (mm110) cc_final: 0.7623 (mt0) outliers start: 22 outliers final: 7 residues processed: 175 average time/residue: 1.4234 time to fit residues: 276.3910 Evaluate side-chains 139 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 552 ARG Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 940 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 137 optimal weight: 0.0170 chunk 55 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 chunk 179 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 710 ASN ** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 GLN A 935 GLN B 245 HIS B 723 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17598 Z= 0.202 Angle : 0.587 8.869 24104 Z= 0.291 Chirality : 0.042 0.192 2770 Planarity : 0.005 0.055 3074 Dihedral : 6.044 64.023 2456 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.98 % Favored : 93.93 % Rotamer: Outliers : 1.79 % Allowed : 9.92 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -1.45 (0.18), residues: 2224 helix: 0.48 (0.18), residues: 928 sheet: -1.61 (0.33), residues: 242 loop : -2.18 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 343 HIS 0.004 0.001 HIS A 245 PHE 0.017 0.001 PHE A 303 TYR 0.015 0.001 TYR B 282 ARG 0.003 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 1.919 Fit side-chains REVERT: A 28 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7600 (mp) REVERT: A 507 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7636 (mtt180) REVERT: A 552 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6706 (mtt90) REVERT: A 847 ARG cc_start: 0.6779 (ttm110) cc_final: 0.6488 (mtt90) REVERT: A 870 ARG cc_start: 0.7153 (ttt180) cc_final: 0.6225 (mtm180) REVERT: B 28 LEU cc_start: 0.7815 (mp) cc_final: 0.7498 (mp) REVERT: B 110 GLU cc_start: 0.7143 (tt0) cc_final: 0.6698 (tt0) REVERT: B 552 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6702 (mtt90) REVERT: B 847 ARG cc_start: 0.6725 (ttm110) cc_final: 0.6431 (mtt90) REVERT: B 870 ARG cc_start: 0.6814 (ttt180) cc_final: 0.5970 (mtm180) REVERT: B 924 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7185 (ttm170) outliers start: 32 outliers final: 15 residues processed: 169 average time/residue: 1.4796 time to fit residues: 276.6347 Evaluate side-chains 156 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 552 ARG Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 924 ARG Chi-restraints excluded: chain B residue 940 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 202 optimal weight: 3.9990 chunk 214 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 192 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS A 740 GLN ** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 292 HIS B 740 GLN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17598 Z= 0.174 Angle : 0.553 7.531 24104 Z= 0.272 Chirality : 0.041 0.192 2770 Planarity : 0.005 0.048 3074 Dihedral : 5.543 45.672 2456 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 1.74 % Allowed : 11.27 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -1.04 (0.18), residues: 2224 helix: 0.89 (0.18), residues: 928 sheet: -1.51 (0.33), residues: 246 loop : -1.99 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 343 HIS 0.004 0.001 HIS B 936 PHE 0.013 0.001 PHE A 303 TYR 0.013 0.001 TYR B 282 ARG 0.002 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 1.938 Fit side-chains REVERT: A 28 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7575 (mp) REVERT: A 151 THR cc_start: 0.7510 (OUTLIER) cc_final: 0.7239 (m) REVERT: A 507 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7645 (mtt180) REVERT: A 552 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6698 (mtt90) REVERT: A 847 ARG cc_start: 0.6796 (ttm110) cc_final: 0.6504 (mtt90) REVERT: A 870 ARG cc_start: 0.7145 (ttt180) cc_final: 0.6267 (mtm180) REVERT: B 28 LEU cc_start: 0.7795 (mp) cc_final: 0.7483 (mp) REVERT: B 110 GLU cc_start: 0.7148 (tt0) cc_final: 0.6740 (tt0) REVERT: B 507 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7561 (mtt180) REVERT: B 552 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6731 (mtt90) REVERT: B 847 ARG cc_start: 0.6722 (ttm110) cc_final: 0.6462 (mtt90) REVERT: B 870 ARG cc_start: 0.6841 (ttt180) cc_final: 0.5990 (mtm180) REVERT: C 44 MET cc_start: 0.7437 (tpp) cc_final: 0.7182 (mpp) outliers start: 31 outliers final: 10 residues processed: 157 average time/residue: 1.5056 time to fit residues: 260.5153 Evaluate side-chains 149 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 552 ARG Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 940 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 20.0000 chunk 121 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 183 optimal weight: 50.0000 chunk 148 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 682 GLN ** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 54 GLN B 682 GLN B 710 ASN B 879 GLN B 936 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.066 17598 Z= 0.567 Angle : 0.755 9.436 24104 Z= 0.382 Chirality : 0.051 0.225 2770 Planarity : 0.006 0.052 3074 Dihedral : 6.295 50.734 2456 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.28 % Favored : 92.67 % Rotamer: Outliers : 2.80 % Allowed : 10.59 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -1.45 (0.18), residues: 2224 helix: 0.33 (0.17), residues: 926 sheet: -1.51 (0.33), residues: 236 loop : -2.04 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 343 HIS 0.008 0.002 HIS A 271 PHE 0.019 0.002 PHE A 303 TYR 0.022 0.003 TYR B 712 ARG 0.005 0.001 ARG A 520 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 148 time to evaluate : 2.084 Fit side-chains REVERT: A 28 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7664 (mp) REVERT: A 507 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7688 (mtt180) REVERT: A 552 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.6856 (mtt90) REVERT: A 847 ARG cc_start: 0.6780 (ttm110) cc_final: 0.6467 (mtt90) REVERT: A 870 ARG cc_start: 0.7055 (ttt180) cc_final: 0.6109 (mtm-85) REVERT: A 924 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7490 (ttm170) REVERT: B 28 LEU cc_start: 0.7863 (mp) cc_final: 0.7556 (mp) REVERT: B 110 GLU cc_start: 0.7294 (tt0) cc_final: 0.6847 (tt0) REVERT: B 552 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6859 (mtt90) REVERT: B 847 ARG cc_start: 0.6798 (ttm110) cc_final: 0.6470 (mtt90) REVERT: B 870 ARG cc_start: 0.6855 (ttt180) cc_final: 0.5919 (mtm-85) REVERT: B 924 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7287 (ttm170) REVERT: D 50 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7420 (mt0) outliers start: 50 outliers final: 31 residues processed: 180 average time/residue: 1.5423 time to fit residues: 305.1583 Evaluate side-chains 178 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 140 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 924 ARG Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 552 ARG Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 769 ASN Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 924 ARG Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain D residue 50 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 214 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 769 ASN ** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 936 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17598 Z= 0.205 Angle : 0.592 10.789 24104 Z= 0.291 Chirality : 0.042 0.193 2770 Planarity : 0.005 0.047 3074 Dihedral : 5.732 50.040 2456 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.21 % Favored : 93.75 % Rotamer: Outliers : 2.30 % Allowed : 12.16 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -0.98 (0.18), residues: 2224 helix: 0.84 (0.18), residues: 926 sheet: -1.29 (0.33), residues: 234 loop : -1.89 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 343 HIS 0.004 0.001 HIS B 936 PHE 0.011 0.001 PHE A 154 TYR 0.016 0.001 TYR B 712 ARG 0.003 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 142 time to evaluate : 2.179 Fit side-chains REVERT: A 24 LEU cc_start: 0.7833 (mt) cc_final: 0.7554 (mm) REVERT: A 28 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7592 (mp) REVERT: A 266 MET cc_start: 0.7891 (mmp) cc_final: 0.7676 (mmm) REVERT: A 552 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6678 (mtt90) REVERT: A 847 ARG cc_start: 0.6811 (ttm110) cc_final: 0.6532 (mtt90) REVERT: A 870 ARG cc_start: 0.7064 (ttt180) cc_final: 0.6132 (mtm-85) REVERT: B 28 LEU cc_start: 0.7800 (mp) cc_final: 0.7474 (mp) REVERT: B 110 GLU cc_start: 0.7213 (tt0) cc_final: 0.6770 (tt0) REVERT: B 552 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6667 (mtt90) REVERT: B 847 ARG cc_start: 0.6793 (ttm110) cc_final: 0.6497 (mtt90) REVERT: B 870 ARG cc_start: 0.6793 (ttt180) cc_final: 0.5851 (mtm-85) outliers start: 41 outliers final: 20 residues processed: 166 average time/residue: 1.5220 time to fit residues: 279.4095 Evaluate side-chains 152 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 552 ARG Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1007 TYR Chi-restraints excluded: chain C residue 14 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 180 optimal weight: 0.1980 chunk 119 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 936 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17598 Z= 0.188 Angle : 0.578 9.754 24104 Z= 0.283 Chirality : 0.042 0.233 2770 Planarity : 0.005 0.045 3074 Dihedral : 5.532 50.831 2456 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.12 % Favored : 93.84 % Rotamer: Outliers : 2.02 % Allowed : 13.06 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -0.73 (0.18), residues: 2224 helix: 1.08 (0.18), residues: 922 sheet: -1.11 (0.34), residues: 234 loop : -1.80 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 343 HIS 0.004 0.001 HIS B 936 PHE 0.010 0.001 PHE A 154 TYR 0.014 0.001 TYR A1007 ARG 0.004 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 134 time to evaluate : 1.982 Fit side-chains REVERT: A 24 LEU cc_start: 0.7813 (mt) cc_final: 0.7533 (mm) REVERT: A 28 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7598 (mp) REVERT: A 171 ARG cc_start: 0.7606 (mtm-85) cc_final: 0.7244 (mtp-110) REVERT: A 266 MET cc_start: 0.7924 (mmp) cc_final: 0.7701 (mmm) REVERT: A 552 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6710 (mtt90) REVERT: A 847 ARG cc_start: 0.6756 (ttm110) cc_final: 0.6507 (mtt90) REVERT: A 870 ARG cc_start: 0.7052 (ttt180) cc_final: 0.6130 (mtm180) REVERT: B 28 LEU cc_start: 0.7773 (mp) cc_final: 0.7460 (mp) REVERT: B 110 GLU cc_start: 0.7148 (tt0) cc_final: 0.6720 (tt0) REVERT: B 552 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6715 (mtt90) REVERT: B 847 ARG cc_start: 0.6801 (ttm110) cc_final: 0.6479 (mtt90) REVERT: B 870 ARG cc_start: 0.6777 (ttt180) cc_final: 0.5845 (mtm180) REVERT: B 924 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7152 (ttp-170) outliers start: 36 outliers final: 24 residues processed: 155 average time/residue: 1.5727 time to fit residues: 268.0256 Evaluate side-chains 161 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 552 ARG Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 924 ARG Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1007 TYR Chi-restraints excluded: chain C residue 14 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 1.9990 chunk 85 optimal weight: 0.0030 chunk 127 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 145 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 936 HIS C 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17598 Z= 0.164 Angle : 0.554 9.277 24104 Z= 0.271 Chirality : 0.041 0.189 2770 Planarity : 0.005 0.044 3074 Dihedral : 5.248 51.156 2456 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.53 % Favored : 94.42 % Rotamer: Outliers : 1.96 % Allowed : 13.40 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -0.54 (0.19), residues: 2224 helix: 1.27 (0.18), residues: 920 sheet: -1.06 (0.34), residues: 242 loop : -1.71 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 343 HIS 0.005 0.001 HIS B 936 PHE 0.009 0.001 PHE A 154 TYR 0.013 0.001 TYR A1007 ARG 0.010 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 140 time to evaluate : 2.085 Fit side-chains REVERT: A 24 LEU cc_start: 0.7800 (mt) cc_final: 0.7507 (mm) REVERT: A 28 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7586 (mp) REVERT: A 54 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.6796 (tm-30) REVERT: A 171 ARG cc_start: 0.7552 (mtm-85) cc_final: 0.7288 (mtp-110) REVERT: A 266 MET cc_start: 0.7885 (mmp) cc_final: 0.7675 (mmm) REVERT: A 552 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6783 (mtt90) REVERT: A 847 ARG cc_start: 0.6773 (ttm110) cc_final: 0.6520 (mtt90) REVERT: A 870 ARG cc_start: 0.7029 (ttt180) cc_final: 0.6129 (mtm180) REVERT: A 935 GLN cc_start: 0.6529 (OUTLIER) cc_final: 0.6137 (pp30) REVERT: B 24 LEU cc_start: 0.7731 (mt) cc_final: 0.7402 (mm) REVERT: B 28 LEU cc_start: 0.7787 (mp) cc_final: 0.7471 (mp) REVERT: B 110 GLU cc_start: 0.7101 (tt0) cc_final: 0.6653 (tt0) REVERT: B 552 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6795 (mtt90) REVERT: B 847 ARG cc_start: 0.6795 (ttm110) cc_final: 0.6509 (mtt90) REVERT: B 870 ARG cc_start: 0.6753 (ttt180) cc_final: 0.5832 (mtm180) outliers start: 35 outliers final: 22 residues processed: 162 average time/residue: 1.5007 time to fit residues: 268.7900 Evaluate side-chains 157 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 552 ARG Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1007 TYR Chi-restraints excluded: chain C residue 14 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 0.9980 chunk 204 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 156 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 198 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 936 HIS C 50 GLN D 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17598 Z= 0.237 Angle : 0.582 8.970 24104 Z= 0.286 Chirality : 0.042 0.194 2770 Planarity : 0.005 0.061 3074 Dihedral : 5.297 52.952 2456 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.12 % Favored : 93.84 % Rotamer: Outliers : 1.91 % Allowed : 13.79 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -0.58 (0.18), residues: 2224 helix: 1.21 (0.18), residues: 918 sheet: -0.96 (0.33), residues: 258 loop : -1.74 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 343 HIS 0.008 0.001 HIS A 936 PHE 0.009 0.001 PHE A 154 TYR 0.014 0.001 TYR A1007 ARG 0.013 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 1.972 Fit side-chains REVERT: A 24 LEU cc_start: 0.7806 (mt) cc_final: 0.7527 (mm) REVERT: A 28 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7590 (mp) REVERT: A 54 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.6774 (tm-30) REVERT: A 110 GLU cc_start: 0.8406 (pm20) cc_final: 0.8201 (pm20) REVERT: A 171 ARG cc_start: 0.7600 (mtm-85) cc_final: 0.7249 (mtp-110) REVERT: A 266 MET cc_start: 0.7910 (mmp) cc_final: 0.7709 (mmm) REVERT: A 847 ARG cc_start: 0.6788 (ttm110) cc_final: 0.6519 (mtt90) REVERT: A 870 ARG cc_start: 0.7064 (ttt180) cc_final: 0.6160 (mtm180) REVERT: B 28 LEU cc_start: 0.7819 (mp) cc_final: 0.7485 (mp) REVERT: B 54 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.6773 (tm-30) REVERT: B 110 GLU cc_start: 0.7144 (tt0) cc_final: 0.6703 (tt0) REVERT: B 139 ARG cc_start: 0.6424 (mtt90) cc_final: 0.6219 (mtm110) REVERT: B 552 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6833 (mtt90) REVERT: B 847 ARG cc_start: 0.6816 (ttm110) cc_final: 0.6487 (mtt90) REVERT: B 870 ARG cc_start: 0.6759 (ttt180) cc_final: 0.5830 (mtm180) REVERT: B 924 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7193 (ttm170) REVERT: C 44 MET cc_start: 0.7442 (mpp) cc_final: 0.7128 (mmp) REVERT: D 44 MET cc_start: 0.7411 (mpp) cc_final: 0.7205 (mmp) outliers start: 34 outliers final: 23 residues processed: 162 average time/residue: 1.6186 time to fit residues: 287.4606 Evaluate side-chains 161 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 54 GLN Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 552 ARG Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 924 ARG Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1007 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 0.7980 chunk 210 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 221 optimal weight: 0.4980 chunk 203 optimal weight: 0.6980 chunk 176 optimal weight: 8.9990 chunk 18 optimal weight: 0.0670 chunk 136 optimal weight: 1.9990 chunk 107 optimal weight: 0.0570 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 199 GLN B 936 HIS C 50 GLN D 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 17598 Z= 0.149 Angle : 0.542 8.806 24104 Z= 0.265 Chirality : 0.040 0.187 2770 Planarity : 0.005 0.058 3074 Dihedral : 5.088 52.076 2456 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.57 % Allowed : 14.13 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -0.34 (0.19), residues: 2224 helix: 1.45 (0.18), residues: 920 sheet: -0.87 (0.34), residues: 242 loop : -1.63 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 343 HIS 0.018 0.001 HIS A 936 PHE 0.009 0.001 PHE A 154 TYR 0.012 0.001 TYR A1007 ARG 0.014 0.000 ARG B 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.978 Fit side-chains REVERT: A 24 LEU cc_start: 0.7770 (mt) cc_final: 0.7483 (mm) REVERT: A 28 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7582 (mp) REVERT: A 54 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.6783 (tm-30) REVERT: A 110 GLU cc_start: 0.8355 (pm20) cc_final: 0.8128 (pm20) REVERT: A 171 ARG cc_start: 0.7541 (mtm-85) cc_final: 0.7199 (mtp-110) REVERT: A 266 MET cc_start: 0.7804 (mmp) cc_final: 0.7588 (mmm) REVERT: A 847 ARG cc_start: 0.6778 (ttm110) cc_final: 0.6519 (mtt90) REVERT: A 870 ARG cc_start: 0.7011 (ttt180) cc_final: 0.6127 (mtm180) REVERT: A 935 GLN cc_start: 0.6760 (OUTLIER) cc_final: 0.6275 (pp30) REVERT: B 24 LEU cc_start: 0.7752 (mt) cc_final: 0.7409 (mm) REVERT: B 28 LEU cc_start: 0.7835 (mp) cc_final: 0.7491 (mp) REVERT: B 54 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.6780 (tm-30) REVERT: B 110 GLU cc_start: 0.7101 (tt0) cc_final: 0.6680 (tt0) REVERT: B 139 ARG cc_start: 0.6478 (mtt90) cc_final: 0.6229 (mtm110) REVERT: B 151 THR cc_start: 0.7612 (OUTLIER) cc_final: 0.7412 (p) REVERT: B 847 ARG cc_start: 0.6791 (ttm110) cc_final: 0.6514 (mtt90) REVERT: B 870 ARG cc_start: 0.6722 (ttt180) cc_final: 0.5819 (mtm180) REVERT: C 44 MET cc_start: 0.7413 (mpp) cc_final: 0.7057 (mmp) outliers start: 28 outliers final: 19 residues processed: 155 average time/residue: 1.5099 time to fit residues: 257.9296 Evaluate side-chains 158 residues out of total 1786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain B residue 54 GLN Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 769 ASN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1007 TYR Chi-restraints excluded: chain B residue 1032 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 0.0970 chunk 187 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 48 optimal weight: 0.0370 chunk 176 optimal weight: 6.9990 chunk 73 optimal weight: 0.0270 chunk 181 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 overall best weight: 0.3314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 936 HIS C 50 GLN D 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.158688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.115357 restraints weight = 19921.623| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.27 r_work: 0.3203 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17598 Z= 0.139 Angle : 0.532 8.821 24104 Z= 0.259 Chirality : 0.040 0.186 2770 Planarity : 0.005 0.060 3074 Dihedral : 4.961 51.911 2456 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.29 % Allowed : 14.46 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -0.22 (0.19), residues: 2224 helix: 1.53 (0.18), residues: 918 sheet: -0.70 (0.34), residues: 240 loop : -1.58 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 343 HIS 0.013 0.001 HIS A 936 PHE 0.008 0.001 PHE A 154 TYR 0.012 0.001 TYR A1007 ARG 0.014 0.000 ARG B 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5717.96 seconds wall clock time: 101 minutes 29.18 seconds (6089.18 seconds total)