Starting phenix.real_space_refine on Sat Sep 28 03:22:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szh_40916/09_2024/8szh_40916.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szh_40916/09_2024/8szh_40916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szh_40916/09_2024/8szh_40916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szh_40916/09_2024/8szh_40916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szh_40916/09_2024/8szh_40916.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szh_40916/09_2024/8szh_40916.cif" } resolution = 3.1 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= 0.051 sd= 0.156 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 4 5.49 5 S 108 5.16 5 C 11657 2.51 5 N 2968 2.21 5 O 3315 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18062 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6579 Classifications: {'peptide': 835} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 32, 'TRANS': 802} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 5, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 6385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6385 Classifications: {'peptide': 812} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 31, 'TRANS': 780} Chain breaks: 3 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1770 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2505 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ASN:plan1': 5, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 84 Chain: "E" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 408 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 144 Unusual residues: {' CA': 2, 'NAG': 1, 'PCW': 1, 'PO4': 1, 'SPM': 2, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A 906 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 187 Unusual residues: {' CA': 2, 'CLR': 1, 'NAG': 2, 'PCW': 1, 'PO4': 1, 'SPM': 2, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B1408 "'] Classifications: {'peptide': 1, 'undetermined': 10, 'water': 1} Modifications used: {'COO': 1} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.29, per 1000 atoms: 0.68 Number of scatterers: 18062 At special positions: 0 Unit cell: (91.9762, 114.536, 253.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 108 16.00 P 4 15.00 F 6 9.00 O 3315 8.00 N 2968 7.00 C 11657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 903 " - " ASN A 468 " " NAG B1404 " - " ASN B 468 " " NAG B1405 " - " ASN B 488 " " NAG F 1 " - " ASN A 488 " " NAG G 1 " - " ASN A 541 " " NAG H 1 " - " ASN B 541 " Time building additional restraints: 4.71 Conformation dependent library (CDL) restraints added in 2.2 seconds 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4270 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 22 sheets defined 42.9% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 64 through 83 removed outlier: 3.704A pdb=" N MET A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.526A pdb=" N ALA A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.512A pdb=" N ASP A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.722A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.632A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.625A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 4.026A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 272 through 287 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 329 through 335 removed outlier: 3.592A pdb=" N PHE A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.581A pdb=" N ASN A 419 " --> pdb=" O ARG A 415 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.638A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 610 through 637 removed outlier: 4.248A pdb=" N ALA A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 646 removed outlier: 3.824A pdb=" N THR A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 664 Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.627A pdb=" N PHE A 668 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 669 " --> pdb=" O LEU A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 669' Processing helix chain 'A' and resid 675 through 707 removed outlier: 5.576A pdb=" N GLN A 681 " --> pdb=" O CYS A 677 " (cutoff:3.500A) Proline residue: A 682 - end of helix removed outlier: 3.909A pdb=" N CYS A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 719 Processing helix chain 'A' and resid 722 through 746 removed outlier: 3.807A pdb=" N LEU A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 793 removed outlier: 3.964A pdb=" N LEU A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 788 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 821 removed outlier: 3.957A pdb=" N THR A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 809 " --> pdb=" O LYS A 805 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 813 " --> pdb=" O PHE A 809 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 814 " --> pdb=" O SER A 810 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 821 " --> pdb=" O VAL A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 828 Processing helix chain 'A' and resid 831 through 862 removed outlier: 3.915A pdb=" N ALA A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 858 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 877 removed outlier: 4.001A pdb=" N VAL A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 873 " --> pdb=" O ILE A 869 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N CYS A 874 " --> pdb=" O GLU A 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 83 removed outlier: 3.683A pdb=" N LEU B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 113 removed outlier: 3.846A pdb=" N SER B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.680A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.572A pdb=" N LEU B 174 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 218 through 233 removed outlier: 3.962A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 260 removed outlier: 3.563A pdb=" N VAL B 258 " --> pdb=" O HIS B 254 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 416 through 436 removed outlier: 3.606A pdb=" N VAL B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.991A pdb=" N VAL B 455 " --> pdb=" O ILE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.517A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 610 through 637 removed outlier: 3.820A pdb=" N LEU B 616 " --> pdb=" O PHE B 612 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 619 " --> pdb=" O ALA B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 646 removed outlier: 3.679A pdb=" N THR B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 664 removed outlier: 3.935A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 669 removed outlier: 3.523A pdb=" N PHE B 668 " --> pdb=" O SER B 665 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 669 " --> pdb=" O LEU B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 665 through 669' Processing helix chain 'B' and resid 679 through 699 removed outlier: 3.972A pdb=" N ALA B 683 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS B 698 " --> pdb=" O CYS B 694 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 699 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 4.217A pdb=" N LEU B 703 " --> pdb=" O THR B 699 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU B 704 " --> pdb=" O ASN B 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 699 through 704' Processing helix chain 'B' and resid 724 through 746 removed outlier: 3.993A pdb=" N MET B 734 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 793 removed outlier: 3.939A pdb=" N LEU B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE B 775 " --> pdb=" O MET B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 827 removed outlier: 3.963A pdb=" N PHE B 806 " --> pdb=" O ASN B 802 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 807 " --> pdb=" O GLU B 803 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR B 808 " --> pdb=" O ALA B 804 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 832 through 861 removed outlier: 3.608A pdb=" N ILE B 839 " --> pdb=" O ALA B 835 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA B 840 " --> pdb=" O VAL B 836 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE B 841 " --> pdb=" O GLU B 837 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 858 " --> pdb=" O PHE B 854 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 859 " --> pdb=" O ASN B 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 31 Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 207 through 216 removed outlier: 3.587A pdb=" N LYS C 210 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C 215 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 231 removed outlier: 4.134A pdb=" N ASP C 231 " --> pdb=" O SER C 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 228 through 231' Processing helix chain 'C' and resid 241 through 255 removed outlier: 3.563A pdb=" N LYS C 248 " --> pdb=" O HIS C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.769A pdb=" N PHE C 274 " --> pdb=" O LYS C 270 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.820A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'D' and resid 4 through 26 removed outlier: 3.945A pdb=" N ALA D 24 " --> pdb=" O ASP D 20 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 35 removed outlier: 3.780A pdb=" N ILE D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'E' and resid 8 through 24 removed outlier: 3.663A pdb=" N ASN E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 removed outlier: 3.548A pdb=" N ALA E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.512A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE A 33 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N VAL A 142 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLY A 35 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N VAL A 165 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 243 removed outlier: 8.095A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.550A pdb=" N PHE A 469 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 550 through 552 Processing sheet with id=AA5, first strand: chain 'A' and resid 572 through 573 Processing sheet with id=AA6, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AA7, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.370A pdb=" N GLU A 602 " --> pdb=" O ILE A 761 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE A 763 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLU A 604 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N CYS A 765 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 27 removed outlier: 6.238A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE B 33 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA B 140 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 37 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N VAL B 165 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 236 through 243 removed outlier: 8.055A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE B 491 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AB2, first strand: chain 'B' and resid 550 through 553 Processing sheet with id=AB3, first strand: chain 'B' and resid 572 through 573 Processing sheet with id=AB4, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AB5, first strand: chain 'B' and resid 602 through 604 removed outlier: 6.204A pdb=" N GLU B 602 " --> pdb=" O ILE B 761 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE B 763 " --> pdb=" O GLU B 602 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU B 604 " --> pdb=" O ILE B 763 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 186 through 190 removed outlier: 3.567A pdb=" N PHE C 189 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 268 " --> pdb=" O HIS C 322 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 46 through 51 removed outlier: 3.630A pdb=" N ARG D 46 " --> pdb=" O ASN D 340 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS D 317 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 58 through 61 removed outlier: 6.814A pdb=" N ALA D 73 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 104 through 105 removed outlier: 3.618A pdb=" N VAL D 112 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR D 124 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N CYS D 121 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU D 138 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE D 123 " --> pdb=" O SER D 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 146 through 151 removed outlier: 4.158A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.731A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D 209 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.754A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG D 251 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.650A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) 731 hydrogen bonds defined for protein. 2097 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: 6.32 Time building geometry restraints manager: 5.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2908 1.32 - 1.45: 5213 1.45 - 1.58: 10195 1.58 - 1.71: 18 1.71 - 1.84: 136 Bond restraints: 18470 Sorted by residual: bond pdb=" C31 PCW B1403 " pdb=" O2 PCW B1403 " ideal model delta sigma weight residual 1.333 1.488 -0.155 2.00e-02 2.50e+03 6.03e+01 bond pdb=" C31 PCW A 902 " pdb=" O2 PCW A 902 " ideal model delta sigma weight residual 1.333 1.484 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" C31 PCW B1403 " pdb=" C32 PCW B1403 " ideal model delta sigma weight residual 1.502 1.604 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C31 PCW A 902 " pdb=" C32 PCW A 902 " ideal model delta sigma weight residual 1.502 1.601 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C16 PCW B1403 " pdb=" C17 PCW B1403 " ideal model delta sigma weight residual 1.523 1.622 -0.099 2.00e-02 2.50e+03 2.44e+01 ... (remaining 18465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.04: 24959 5.04 - 10.08: 56 10.08 - 15.12: 7 15.12 - 20.16: 3 20.16 - 25.20: 2 Bond angle restraints: 25027 Sorted by residual: angle pdb=" N ARG A 866 " pdb=" CA ARG A 866 " pdb=" C ARG A 866 " ideal model delta sigma weight residual 113.23 95.26 17.97 1.22e+00 6.72e-01 2.17e+02 angle pdb=" N ILE A 869 " pdb=" CA ILE A 869 " pdb=" C ILE A 869 " ideal model delta sigma weight residual 112.83 104.47 8.36 9.90e-01 1.02e+00 7.13e+01 angle pdb=" C18 PCW B1403 " pdb=" C19 PCW B1403 " pdb=" C20 PCW B1403 " ideal model delta sigma weight residual 127.82 153.02 -25.20 3.00e+00 1.11e-01 7.05e+01 angle pdb=" C18 PCW A 902 " pdb=" C19 PCW A 902 " pdb=" C20 PCW A 902 " ideal model delta sigma weight residual 127.82 152.59 -24.77 3.00e+00 1.11e-01 6.82e+01 angle pdb=" CA PHE A 862 " pdb=" C PHE A 862 " pdb=" O PHE A 862 " ideal model delta sigma weight residual 121.78 111.37 10.41 1.28e+00 6.10e-01 6.62e+01 ... (remaining 25022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.04: 10156 20.04 - 40.08: 794 40.08 - 60.11: 112 60.11 - 80.15: 24 80.15 - 100.19: 14 Dihedral angle restraints: 11100 sinusoidal: 4505 harmonic: 6595 Sorted by residual: dihedral pdb=" CB CYS A 585 " pdb=" SG CYS A 585 " pdb=" SG CYS A 598 " pdb=" CB CYS A 598 " ideal model delta sinusoidal sigma weight residual -86.00 -172.13 86.13 1 1.00e+01 1.00e-02 8.95e+01 dihedral pdb=" CB CYS A 437 " pdb=" SG CYS A 437 " pdb=" SG CYS A 449 " pdb=" CB CYS A 449 " ideal model delta sinusoidal sigma weight residual 93.00 171.14 -78.14 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS B 677 " pdb=" SG CYS B 677 " pdb=" SG CYS B 765 " pdb=" CB CYS B 765 " ideal model delta sinusoidal sigma weight residual -86.00 -41.20 -44.80 1 1.00e+01 1.00e-02 2.79e+01 ... (remaining 11097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.032: 2823 1.032 - 2.064: 0 2.064 - 3.095: 0 3.095 - 4.127: 0 4.127 - 5.159: 1 Chirality restraints: 2824 Sorted by residual: chirality pdb=" C2 PCW A 902 " pdb=" C1 PCW A 902 " pdb=" C3 PCW A 902 " pdb=" O2 PCW A 902 " both_signs ideal model delta sigma weight residual False -2.32 2.84 -5.16 2.00e-01 2.50e+01 6.65e+02 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 6.24e+00 chirality pdb=" C2 PCW B1403 " pdb=" C1 PCW B1403 " pdb=" C3 PCW B1403 " pdb=" O2 PCW B1403 " both_signs ideal model delta sigma weight residual False -2.32 -2.81 0.49 2.00e-01 2.50e+01 6.02e+00 ... (remaining 2821 not shown) Planarity restraints: 3148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.198 2.00e-02 2.50e+03 1.63e-01 3.32e+02 pdb=" C7 NAG H 2 " -0.052 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.143 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.265 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 541 " -0.063 2.00e-02 2.50e+03 6.88e-02 5.92e+01 pdb=" CG ASN B 541 " 0.122 2.00e-02 2.50e+03 pdb=" OD1 ASN B 541 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN B 541 " 0.029 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 541 " -0.031 2.00e-02 2.50e+03 6.44e-02 4.15e+01 pdb=" CG ASN B 541 " 0.111 2.00e-02 2.50e+03 pdb=" OD1 ASN B 541 " -0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN B 541 " -0.035 2.00e-02 2.50e+03 ... (remaining 3145 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1158 2.74 - 3.28: 16843 3.28 - 3.82: 27590 3.82 - 4.36: 33265 4.36 - 4.90: 59263 Nonbonded interactions: 138119 Sorted by model distance: nonbonded pdb=" OG SER D 331 " pdb=" OD1 ASP D 333 " model vdw 2.196 3.040 nonbonded pdb=" OD2 ASP A 238 " pdb=" OG SER A 262 " model vdw 2.208 3.040 nonbonded pdb=" O PHE B 668 " pdb=" OG SER B 834 " model vdw 2.220 3.040 nonbonded pdb=" O LEU B 87 " pdb=" NE2 GLN B 432 " model vdw 2.227 3.120 nonbonded pdb=" OE1 GLN B 253 " pdb=" NH2 ARG B 286 " model vdw 2.250 3.120 ... (remaining 138114 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 20 through 131 or (resid 132 through 135 and (name N or na \ me CA or name C or name O or name CB )) or resid 136 through 362 or resid 392 th \ rough 516 or (resid 517 and (name N or name CA or name C or name O or name CB )) \ or resid 518 through 586 or (resid 587 and (name N or name CA or name C or name \ O or name CB )) or resid 588 through 700 or (resid 701 and (name N or name CA o \ r name C or name O or name CB )) or resid 702 or (resid 703 and (name N or name \ CA or name C or name O or name CB )) or resid 704 through 706 or (resid 707 thro \ ugh 709 and (name N or name CA or name C or name O or name CB )) or resid 722 th \ rough 798 or (resid 799 and (name N or name CA or name C or name O or name CB )) \ or resid 800 through 861 or (resid 862 through 863 and (name N or name CA or na \ me C or name O or name CB )) or resid 864 through 865 or (resid 866 through 868 \ and (name N or name CA or name C or name O or name CB )) or resid 869 through 87 \ 0 or (resid 871 through 873 and (name N or name CA or name C or name O or name C \ B )) or resid 874 through 876 or resid 903 through 909)) selection = (chain 'B' and (resid 20 through 47 or (resid 48 and (name N or name CA or name \ C or name O or name CB )) or resid 49 through 124 or (resid 125 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 131 through 135 and (name N o \ r name CA or name C or name O or name CB )) or resid 136 through 361 or (resid 3 \ 62 and (name N or name CA or name C or name O or name CB )) or resid 392 through \ 498 or (resid 499 through 500 and (name N or name CA or name C or name O or nam \ e CB )) or resid 501 through 591 or (resid 592 and (name N or name CA or name C \ or name O or name CB )) or resid 593 through 867 or (resid 868 and (name N or na \ me CA or name C or name O or name CB )) or resid 869 through 876 or resid 1405 t \ hrough 1411)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 8.610 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: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 43.610 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.155 18470 Z= 0.383 Angle : 0.780 25.195 25027 Z= 0.440 Chirality : 0.110 5.159 2824 Planarity : 0.005 0.163 3142 Dihedral : 14.616 100.191 6776 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.18), residues: 2243 helix: 0.97 (0.18), residues: 882 sheet: -0.52 (0.27), residues: 379 loop : -1.16 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 719 HIS 0.006 0.001 HIS A 715 PHE 0.045 0.001 PHE B 612 TYR 0.042 0.002 TYR C 354 ARG 0.015 0.000 ARG A 886 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.903 Fit side-chains revert: symmetry clash REVERT: A 231 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7601 (mt-10) REVERT: B 336 LYS cc_start: 0.8430 (mmtm) cc_final: 0.8224 (mptt) REVERT: B 558 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7617 (mp0) REVERT: B 609 THR cc_start: 0.8789 (m) cc_final: 0.8389 (p) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.3343 time to fit residues: 125.9276 Evaluate side-chains 196 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.0970 chunk 169 optimal weight: 0.0980 chunk 94 optimal weight: 0.0570 chunk 57 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 203 optimal weight: 0.3980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN B 117 GLN C 188 HIS C 255 ASN D 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18470 Z= 0.136 Angle : 0.494 6.527 25027 Z= 0.268 Chirality : 0.042 0.202 2824 Planarity : 0.004 0.046 3142 Dihedral : 8.786 90.566 2833 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.85 % Allowed : 6.19 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2243 helix: 1.41 (0.18), residues: 891 sheet: -0.45 (0.27), residues: 372 loop : -1.07 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 719 HIS 0.006 0.001 HIS B 766 PHE 0.014 0.001 PHE B 814 TYR 0.014 0.001 TYR A 829 ARG 0.005 0.000 ARG D 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 205 time to evaluate : 1.855 Fit side-chains revert: symmetry clash REVERT: A 231 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7501 (mt-10) REVERT: B 336 LYS cc_start: 0.8438 (mmtm) cc_final: 0.8230 (mptt) REVERT: B 558 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7613 (mp0) REVERT: B 612 PHE cc_start: 0.7449 (t80) cc_final: 0.7153 (t80) REVERT: D 197 ARG cc_start: 0.8192 (ttp-110) cc_final: 0.7826 (mtp85) REVERT: D 292 PHE cc_start: 0.7857 (m-80) cc_final: 0.7457 (m-80) outliers start: 16 outliers final: 8 residues processed: 215 average time/residue: 0.3224 time to fit residues: 102.5602 Evaluate side-chains 200 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 192 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 169 optimal weight: 0.0570 chunk 138 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 203 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 181 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN B 802 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18470 Z= 0.179 Angle : 0.491 6.594 25027 Z= 0.266 Chirality : 0.042 0.173 2824 Planarity : 0.004 0.047 3142 Dihedral : 8.176 90.804 2833 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.28 % Allowed : 8.70 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.18), residues: 2243 helix: 1.44 (0.18), residues: 898 sheet: -0.46 (0.28), residues: 371 loop : -1.10 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 719 HIS 0.004 0.001 HIS B 766 PHE 0.017 0.001 PHE B 814 TYR 0.013 0.001 TYR A 421 ARG 0.002 0.000 ARG B 551 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 203 time to evaluate : 1.980 Fit side-chains revert: symmetry clash REVERT: B 336 LYS cc_start: 0.8467 (mmtm) cc_final: 0.8239 (mptt) REVERT: B 558 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7601 (mp0) REVERT: B 609 THR cc_start: 0.8871 (m) cc_final: 0.8497 (p) REVERT: B 753 ASN cc_start: 0.7863 (t0) cc_final: 0.7421 (t0) REVERT: D 197 ARG cc_start: 0.8184 (ttp-110) cc_final: 0.7876 (mtp85) outliers start: 24 outliers final: 17 residues processed: 217 average time/residue: 0.3607 time to fit residues: 117.0262 Evaluate side-chains 210 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN C 188 HIS D 44 GLN D 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 18470 Z= 0.414 Angle : 0.642 6.243 25027 Z= 0.343 Chirality : 0.048 0.211 2824 Planarity : 0.005 0.053 3142 Dihedral : 8.499 88.874 2833 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.08 % Allowed : 10.57 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2243 helix: 1.03 (0.18), residues: 895 sheet: -0.72 (0.27), residues: 368 loop : -1.35 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 818 HIS 0.009 0.002 HIS B 429 PHE 0.030 0.002 PHE A 634 TYR 0.019 0.002 TYR D 105 ARG 0.005 0.001 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 189 time to evaluate : 1.906 Fit side-chains revert: symmetry clash REVERT: B 117 GLN cc_start: 0.7359 (tm130) cc_final: 0.7109 (tm-30) REVERT: B 558 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7617 (mp0) REVERT: B 609 THR cc_start: 0.8920 (m) cc_final: 0.8455 (p) REVERT: B 697 VAL cc_start: 0.7605 (t) cc_final: 0.7358 (t) REVERT: B 753 ASN cc_start: 0.7974 (t0) cc_final: 0.6907 (t0) REVERT: D 234 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.8436 (m-10) outliers start: 39 outliers final: 25 residues processed: 213 average time/residue: 0.3317 time to fit residues: 105.8019 Evaluate side-chains 210 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 184 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 859 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 161 optimal weight: 0.9980 chunk 89 optimal weight: 0.0040 chunk 184 optimal weight: 0.5980 chunk 149 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN C 188 HIS C 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18470 Z= 0.157 Angle : 0.490 6.711 25027 Z= 0.266 Chirality : 0.042 0.163 2824 Planarity : 0.004 0.052 3142 Dihedral : 8.014 85.883 2833 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.76 % Allowed : 11.91 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2243 helix: 1.41 (0.18), residues: 888 sheet: -0.60 (0.27), residues: 374 loop : -1.26 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 818 HIS 0.003 0.001 HIS B 766 PHE 0.023 0.001 PHE D 235 TYR 0.014 0.001 TYR A 421 ARG 0.003 0.000 ARG D 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 186 time to evaluate : 2.156 Fit side-chains revert: symmetry clash REVERT: B 117 GLN cc_start: 0.7358 (tm130) cc_final: 0.7110 (tm-30) REVERT: B 336 LYS cc_start: 0.8470 (mmtm) cc_final: 0.8233 (mptt) REVERT: B 558 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7630 (mp0) REVERT: B 609 THR cc_start: 0.8929 (m) cc_final: 0.8484 (p) REVERT: B 876 THR cc_start: 0.6144 (OUTLIER) cc_final: 0.5715 (m) outliers start: 33 outliers final: 19 residues processed: 207 average time/residue: 0.3282 time to fit residues: 100.6930 Evaluate side-chains 197 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 177 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 216 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN C 188 HIS C 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18470 Z= 0.248 Angle : 0.534 7.076 25027 Z= 0.287 Chirality : 0.044 0.182 2824 Planarity : 0.004 0.053 3142 Dihedral : 7.969 86.773 2833 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.76 % Allowed : 13.03 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 2243 helix: 1.33 (0.18), residues: 893 sheet: -0.67 (0.28), residues: 361 loop : -1.27 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 818 HIS 0.004 0.001 HIS B 429 PHE 0.023 0.002 PHE D 235 TYR 0.014 0.001 TYR A 421 ARG 0.006 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 177 time to evaluate : 2.001 Fit side-chains revert: symmetry clash REVERT: B 117 GLN cc_start: 0.7377 (tm130) cc_final: 0.7113 (tm-30) REVERT: B 336 LYS cc_start: 0.8497 (mmtm) cc_final: 0.8249 (mptt) REVERT: B 558 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7607 (mp0) REVERT: B 609 THR cc_start: 0.8936 (m) cc_final: 0.8499 (p) REVERT: B 876 THR cc_start: 0.6050 (OUTLIER) cc_final: 0.5632 (m) outliers start: 33 outliers final: 25 residues processed: 197 average time/residue: 0.3395 time to fit residues: 98.6846 Evaluate side-chains 201 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 175 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 0.0980 chunk 24 optimal weight: 3.9990 chunk 123 optimal weight: 0.3980 chunk 158 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN C 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18470 Z= 0.176 Angle : 0.488 8.273 25027 Z= 0.264 Chirality : 0.042 0.169 2824 Planarity : 0.004 0.053 3142 Dihedral : 7.695 85.449 2833 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.71 % Allowed : 13.51 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.18), residues: 2243 helix: 1.49 (0.18), residues: 890 sheet: -0.64 (0.28), residues: 363 loop : -1.22 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 818 HIS 0.003 0.001 HIS C 213 PHE 0.022 0.001 PHE D 235 TYR 0.023 0.001 TYR B 751 ARG 0.007 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 184 time to evaluate : 2.030 Fit side-chains revert: symmetry clash REVERT: A 285 ARG cc_start: 0.8513 (ttp80) cc_final: 0.8300 (ttt-90) REVERT: B 117 GLN cc_start: 0.7263 (tm130) cc_final: 0.7000 (tm-30) REVERT: B 336 LYS cc_start: 0.8472 (mmtm) cc_final: 0.8229 (mptt) REVERT: B 558 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7579 (mp0) REVERT: B 609 THR cc_start: 0.8935 (m) cc_final: 0.8498 (p) REVERT: B 697 VAL cc_start: 0.7710 (t) cc_final: 0.7346 (t) REVERT: B 876 THR cc_start: 0.6040 (OUTLIER) cc_final: 0.5635 (m) outliers start: 32 outliers final: 24 residues processed: 205 average time/residue: 0.3505 time to fit residues: 106.8265 Evaluate side-chains 203 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 178 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.8980 chunk 86 optimal weight: 0.0030 chunk 128 optimal weight: 3.9990 chunk 65 optimal weight: 0.0770 chunk 42 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.5348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 647 ASN B 463 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18470 Z= 0.154 Angle : 0.477 8.612 25027 Z= 0.257 Chirality : 0.041 0.164 2824 Planarity : 0.004 0.053 3142 Dihedral : 7.465 83.977 2833 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.87 % Allowed : 13.67 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2243 helix: 1.56 (0.18), residues: 896 sheet: -0.60 (0.28), residues: 363 loop : -1.18 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 818 HIS 0.003 0.001 HIS C 213 PHE 0.022 0.001 PHE D 235 TYR 0.016 0.001 TYR B 751 ARG 0.007 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 186 time to evaluate : 1.934 Fit side-chains revert: symmetry clash REVERT: A 285 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8297 (ttt-90) REVERT: B 336 LYS cc_start: 0.8461 (mmtm) cc_final: 0.8221 (mptt) REVERT: B 558 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7591 (mp0) REVERT: B 609 THR cc_start: 0.8938 (m) cc_final: 0.8502 (p) REVERT: B 697 VAL cc_start: 0.7694 (t) cc_final: 0.7297 (t) REVERT: B 876 THR cc_start: 0.6054 (OUTLIER) cc_final: 0.5655 (m) outliers start: 35 outliers final: 26 residues processed: 204 average time/residue: 0.3276 time to fit residues: 99.0920 Evaluate side-chains 209 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 182 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 188 optimal weight: 0.1980 chunk 201 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 157 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 190 optimal weight: 0.1980 chunk 200 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 753 ASN C 188 HIS D 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18470 Z= 0.151 Angle : 0.472 8.635 25027 Z= 0.254 Chirality : 0.041 0.164 2824 Planarity : 0.004 0.053 3142 Dihedral : 7.364 82.840 2833 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.71 % Allowed : 13.77 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.18), residues: 2243 helix: 1.59 (0.18), residues: 896 sheet: -0.57 (0.28), residues: 361 loop : -1.16 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 818 HIS 0.003 0.001 HIS B 766 PHE 0.022 0.001 PHE D 235 TYR 0.015 0.001 TYR B 751 ARG 0.007 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 189 time to evaluate : 1.978 Fit side-chains revert: symmetry clash REVERT: A 285 ARG cc_start: 0.8524 (ttp80) cc_final: 0.8298 (ttt-90) REVERT: B 117 GLN cc_start: 0.7368 (tm-30) cc_final: 0.7134 (tm-30) REVERT: B 336 LYS cc_start: 0.8447 (mmtm) cc_final: 0.8215 (mptt) REVERT: B 558 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7592 (mp0) REVERT: B 609 THR cc_start: 0.8942 (m) cc_final: 0.8508 (p) REVERT: B 697 VAL cc_start: 0.7708 (t) cc_final: 0.7312 (t) REVERT: B 876 THR cc_start: 0.6048 (OUTLIER) cc_final: 0.5652 (m) REVERT: D 235 PHE cc_start: 0.7953 (t80) cc_final: 0.7494 (t80) outliers start: 32 outliers final: 28 residues processed: 206 average time/residue: 0.3351 time to fit residues: 102.3790 Evaluate side-chains 214 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 185 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.5980 chunk 212 optimal weight: 4.9990 chunk 129 optimal weight: 0.0370 chunk 100 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 205 optimal weight: 0.5980 chunk 177 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN B 446 ASN C 188 HIS D 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18470 Z= 0.200 Angle : 0.505 8.687 25027 Z= 0.272 Chirality : 0.042 0.175 2824 Planarity : 0.004 0.054 3142 Dihedral : 7.426 83.729 2833 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.66 % Allowed : 13.93 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.18), residues: 2243 helix: 1.51 (0.18), residues: 898 sheet: -0.64 (0.28), residues: 362 loop : -1.17 (0.18), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 818 HIS 0.004 0.001 HIS B 429 PHE 0.023 0.001 PHE D 235 TYR 0.015 0.001 TYR B 751 ARG 0.008 0.000 ARG B 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 185 time to evaluate : 2.145 Fit side-chains revert: symmetry clash REVERT: A 285 ARG cc_start: 0.8536 (ttp80) cc_final: 0.8306 (ttt-90) REVERT: A 286 ARG cc_start: 0.7660 (mtt180) cc_final: 0.7417 (mtt180) REVERT: B 117 GLN cc_start: 0.7376 (tm-30) cc_final: 0.7137 (tm-30) REVERT: B 336 LYS cc_start: 0.8475 (mmtm) cc_final: 0.8237 (mptt) REVERT: B 558 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7599 (mp0) REVERT: B 609 THR cc_start: 0.8951 (m) cc_final: 0.8530 (p) REVERT: B 697 VAL cc_start: 0.7749 (t) cc_final: 0.7355 (t) REVERT: B 876 THR cc_start: 0.6090 (OUTLIER) cc_final: 0.5699 (m) REVERT: D 17 GLN cc_start: 0.7604 (tm-30) cc_final: 0.7348 (tt0) REVERT: D 197 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7555 (ttp80) REVERT: D 235 PHE cc_start: 0.8021 (t80) cc_final: 0.7624 (t80) outliers start: 31 outliers final: 28 residues processed: 202 average time/residue: 0.3411 time to fit residues: 102.0611 Evaluate side-chains 213 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 184 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.7980 chunk 189 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 163 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.088934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.073555 restraints weight = 37094.877| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.99 r_work: 0.2994 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18470 Z= 0.182 Angle : 0.493 8.984 25027 Z= 0.266 Chirality : 0.042 0.171 2824 Planarity : 0.004 0.053 3142 Dihedral : 7.379 83.496 2833 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.60 % Allowed : 14.04 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2243 helix: 1.55 (0.18), residues: 896 sheet: -0.60 (0.28), residues: 361 loop : -1.18 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 818 HIS 0.003 0.001 HIS B 766 PHE 0.023 0.001 PHE D 235 TYR 0.028 0.001 TYR B 751 ARG 0.008 0.000 ARG B 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4016.12 seconds wall clock time: 72 minutes 46.60 seconds (4366.60 seconds total)