Starting phenix.real_space_refine on Mon Jun 16 02:32:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szh_40916/06_2025/8szh_40916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szh_40916/06_2025/8szh_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/cci-nas-00/data/ceres_data/8szh_40916/06_2025/8szh_40916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szh_40916/06_2025/8szh_40916.map" model { file = "/net/cci-nas-00/data/ceres_data/8szh_40916/06_2025/8szh_40916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szh_40916/06_2025/8szh_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.74, per 1000 atoms: 0.76 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: 4.72 Conformation dependent library (CDL) restraints added in 2.5 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: 2.26 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: 7.15 Time building geometry restraints manager: 5.70 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: 0.010 Normalize map: mean=0, sd=1: 9.470 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: 0.180 Process input model: 48.080 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.970 ------------------------------------------------------------------------------- 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 18497 Z= 0.313 Angle : 0.792 25.195 25090 Z= 0.442 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00459 ( 6) link_NAG-ASN : angle 4.66294 ( 18) link_BETA1-4 : bond 0.00415 ( 3) link_BETA1-4 : angle 2.57737 ( 9) hydrogen bonds : bond 0.18210 ( 731) hydrogen bonds : angle 5.87086 ( 2097) SS BOND : bond 0.00151 ( 18) SS BOND : angle 0.87724 ( 36) covalent geometry : bond 0.00577 (18470) covalent geometry : angle 0.78035 (25027) *********************** 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 to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 2.177 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: 0.4280 time to fit residues: 161.5154 Evaluate side-chains 196 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 2.224 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.090759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.075360 restraints weight = 37100.713| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.02 r_work: 0.3036 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 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 18497 Z= 0.106 Angle : 0.498 6.527 25090 Z= 0.269 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 6) link_NAG-ASN : angle 2.10157 ( 18) link_BETA1-4 : bond 0.00265 ( 3) link_BETA1-4 : angle 1.17740 ( 9) hydrogen bonds : bond 0.05118 ( 731) hydrogen bonds : angle 4.37130 ( 2097) SS BOND : bond 0.00149 ( 18) SS BOND : angle 0.94556 ( 36) covalent geometry : bond 0.00212 (18470) covalent geometry : angle 0.49360 (25027) *********************** 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 to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 2.553 Fit side-chains revert: symmetry clash REVERT: A 231 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7523 (mt-10) REVERT: A 789 PHE cc_start: 0.8261 (t80) cc_final: 0.8042 (t80) REVERT: B 336 LYS cc_start: 0.8589 (mmtm) cc_final: 0.8376 (mptt) REVERT: B 558 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7645 (mp0) REVERT: B 612 PHE cc_start: 0.7437 (t80) cc_final: 0.7195 (t80) REVERT: D 197 ARG cc_start: 0.8643 (ttp-110) cc_final: 0.8211 (mtp85) REVERT: D 292 PHE cc_start: 0.7916 (m-80) cc_final: 0.7481 (m-80) outliers start: 16 outliers final: 8 residues processed: 215 average time/residue: 0.4529 time to fit residues: 148.0861 Evaluate side-chains 200 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 192 time to evaluate : 1.998 ------------------------------------------------------------------------------- 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 159 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 221 optimal weight: 0.4980 chunk 223 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.088540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.072974 restraints weight = 37112.466| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.03 r_work: 0.2981 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18497 Z= 0.152 Angle : 0.532 6.242 25090 Z= 0.286 Chirality : 0.043 0.182 2824 Planarity : 0.004 0.048 3142 Dihedral : 8.322 90.678 2833 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.28 % Allowed : 9.40 % Favored : 89.32 % 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: 1.33 (0.18), residues: 898 sheet: -0.51 (0.27), residues: 371 loop : -1.16 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 719 HIS 0.005 0.001 HIS B 429 PHE 0.019 0.002 PHE B 814 TYR 0.013 0.001 TYR A 421 ARG 0.003 0.000 ARG B 551 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 6) link_NAG-ASN : angle 2.17125 ( 18) link_BETA1-4 : bond 0.00420 ( 3) link_BETA1-4 : angle 1.26373 ( 9) hydrogen bonds : bond 0.05728 ( 731) hydrogen bonds : angle 4.23355 ( 2097) SS BOND : bond 0.00246 ( 18) SS BOND : angle 1.05694 ( 36) covalent geometry : bond 0.00357 (18470) covalent geometry : angle 0.52782 (25027) *********************** 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 220 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 1.943 Fit side-chains revert: symmetry clash REVERT: B 336 LYS cc_start: 0.8635 (mmtm) cc_final: 0.8411 (mptt) REVERT: B 558 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7634 (mp0) REVERT: B 609 THR cc_start: 0.8861 (m) cc_final: 0.8440 (p) REVERT: B 753 ASN cc_start: 0.8059 (t0) cc_final: 0.7570 (t0) outliers start: 24 outliers final: 18 residues processed: 209 average time/residue: 0.3526 time to fit residues: 107.8721 Evaluate side-chains 204 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 2.020 ------------------------------------------------------------------------------- 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 394 LEU 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 B residue 760 ILE Chi-restraints excluded: chain C residue 249 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 24 optimal weight: 4.9990 chunk 53 optimal weight: 0.3980 chunk 168 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 181 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.087876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.072322 restraints weight = 37121.721| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.02 r_work: 0.2965 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18497 Z= 0.165 Angle : 0.542 5.994 25090 Z= 0.290 Chirality : 0.044 0.185 2824 Planarity : 0.004 0.048 3142 Dihedral : 8.155 88.789 2833 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.71 % Allowed : 10.62 % Favored : 87.67 % 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: 1.29 (0.18), residues: 896 sheet: -0.64 (0.27), residues: 371 loop : -1.25 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 818 HIS 0.005 0.001 HIS B 429 PHE 0.019 0.002 PHE A 789 TYR 0.014 0.001 TYR C 230 ARG 0.005 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 6) link_NAG-ASN : angle 2.23599 ( 18) link_BETA1-4 : bond 0.00317 ( 3) link_BETA1-4 : angle 1.37358 ( 9) hydrogen bonds : bond 0.05817 ( 731) hydrogen bonds : angle 4.20433 ( 2097) SS BOND : bond 0.00262 ( 18) SS BOND : angle 1.12952 ( 36) covalent geometry : bond 0.00395 (18470) covalent geometry : angle 0.53703 (25027) *********************** 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 226 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 2.154 Fit side-chains revert: symmetry clash REVERT: B 117 GLN cc_start: 0.7349 (tm130) cc_final: 0.7035 (tm-30) REVERT: B 336 LYS cc_start: 0.8630 (mmtm) cc_final: 0.8388 (mptt) REVERT: B 558 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7627 (mp0) REVERT: B 609 THR cc_start: 0.8885 (m) cc_final: 0.8402 (p) REVERT: B 753 ASN cc_start: 0.8101 (t0) cc_final: 0.7092 (t0) outliers start: 32 outliers final: 20 residues processed: 214 average time/residue: 0.3574 time to fit residues: 112.9222 Evaluate side-chains 208 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 1.997 ------------------------------------------------------------------------------- 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 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 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 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 54 optimal weight: 6.9990 chunk 190 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 205 optimal weight: 0.0870 chunk 22 optimal weight: 0.1980 chunk 57 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.089182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.073695 restraints weight = 37422.510| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.03 r_work: 0.2997 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18497 Z= 0.110 Angle : 0.486 7.335 25090 Z= 0.261 Chirality : 0.042 0.164 2824 Planarity : 0.004 0.050 3142 Dihedral : 7.843 86.098 2833 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.60 % Allowed : 12.12 % Favored : 86.28 % 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: -0.02 (0.18), residues: 2243 helix: 1.51 (0.18), residues: 891 sheet: -0.57 (0.27), residues: 376 loop : -1.21 (0.18), residues: 976 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 0.012 0.001 TYR A 421 ARG 0.005 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 6) link_NAG-ASN : angle 1.90512 ( 18) link_BETA1-4 : bond 0.00309 ( 3) link_BETA1-4 : angle 1.26584 ( 9) hydrogen bonds : bond 0.04775 ( 731) hydrogen bonds : angle 4.01233 ( 2097) SS BOND : bond 0.00192 ( 18) SS BOND : angle 1.16783 ( 36) covalent geometry : bond 0.00241 (18470) covalent geometry : angle 0.48082 (25027) *********************** 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 to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 2.140 Fit side-chains revert: symmetry clash REVERT: B 117 GLN cc_start: 0.7315 (tm130) cc_final: 0.6999 (tm-30) REVERT: B 336 LYS cc_start: 0.8606 (mmtm) cc_final: 0.8368 (mptt) REVERT: B 558 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7614 (mp0) REVERT: B 609 THR cc_start: 0.8892 (m) cc_final: 0.8407 (p) REVERT: B 876 THR cc_start: 0.5338 (OUTLIER) cc_final: 0.4948 (m) outliers start: 30 outliers final: 21 residues processed: 209 average time/residue: 0.3381 time to fit residues: 104.2058 Evaluate side-chains 207 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 1.959 ------------------------------------------------------------------------------- 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 A residue 599 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 486 VAL 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 307 PHE 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 262 MET Chi-restraints excluded: chain D residue 267 ASP 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 66 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 200 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS C 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.087477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.071973 restraints weight = 37359.154| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.02 r_work: 0.2956 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18497 Z= 0.182 Angle : 0.559 7.264 25090 Z= 0.299 Chirality : 0.044 0.189 2824 Planarity : 0.004 0.053 3142 Dihedral : 7.980 87.495 2833 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.87 % Allowed : 12.60 % Favored : 85.53 % 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: 1.32 (0.18), residues: 894 sheet: -0.64 (0.28), residues: 360 loop : -1.28 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 818 HIS 0.005 0.001 HIS B 429 PHE 0.024 0.002 PHE D 235 TYR 0.015 0.001 TYR B 751 ARG 0.006 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 6) link_NAG-ASN : angle 2.21900 ( 18) link_BETA1-4 : bond 0.00363 ( 3) link_BETA1-4 : angle 1.42537 ( 9) hydrogen bonds : bond 0.05906 ( 731) hydrogen bonds : angle 4.14878 ( 2097) SS BOND : bond 0.00262 ( 18) SS BOND : angle 1.37644 ( 36) covalent geometry : bond 0.00440 (18470) covalent geometry : angle 0.55331 (25027) *********************** 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 215 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 1.886 Fit side-chains revert: symmetry clash REVERT: B 117 GLN cc_start: 0.7336 (tm130) cc_final: 0.7017 (tm-30) REVERT: B 336 LYS cc_start: 0.8628 (mmtm) cc_final: 0.8387 (mptt) REVERT: B 558 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7632 (mp0) REVERT: B 609 THR cc_start: 0.8911 (m) cc_final: 0.8431 (p) REVERT: B 876 THR cc_start: 0.5238 (OUTLIER) cc_final: 0.4848 (m) outliers start: 35 outliers final: 27 residues processed: 201 average time/residue: 0.3435 time to fit residues: 102.4309 Evaluate side-chains 207 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 1.868 ------------------------------------------------------------------------------- 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 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 B residue 27 GLN Chi-restraints excluded: chain B residue 486 VAL 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 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 262 MET 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 94 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN C 188 HIS C 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.085398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.070023 restraints weight = 37088.140| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.98 r_work: 0.2913 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 18497 Z= 0.292 Angle : 0.689 8.023 25090 Z= 0.365 Chirality : 0.049 0.219 2824 Planarity : 0.005 0.055 3142 Dihedral : 8.449 87.242 2833 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.24 % Allowed : 12.76 % Favored : 85.00 % 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: -0.62 (0.17), residues: 2243 helix: 0.90 (0.18), residues: 899 sheet: -0.81 (0.27), residues: 373 loop : -1.48 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 299 HIS 0.009 0.002 HIS B 429 PHE 0.038 0.003 PHE A 634 TYR 0.025 0.002 TYR B 751 ARG 0.006 0.001 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 6) link_NAG-ASN : angle 2.73886 ( 18) link_BETA1-4 : bond 0.00456 ( 3) link_BETA1-4 : angle 1.77362 ( 9) hydrogen bonds : bond 0.07563 ( 731) hydrogen bonds : angle 4.48932 ( 2097) SS BOND : bond 0.00400 ( 18) SS BOND : angle 1.67772 ( 36) covalent geometry : bond 0.00723 (18470) covalent geometry : angle 0.68172 (25027) *********************** 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 222 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 2.138 Fit side-chains revert: symmetry clash REVERT: A 285 ARG cc_start: 0.8797 (ttp80) cc_final: 0.8595 (ttt-90) REVERT: A 576 GLU cc_start: 0.7743 (mp0) cc_final: 0.7350 (mm-30) REVERT: A 734 MET cc_start: 0.8329 (mmt) cc_final: 0.8046 (mmp) REVERT: B 117 GLN cc_start: 0.7524 (tm130) cc_final: 0.7219 (tm-30) REVERT: B 349 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7631 (mmtt) REVERT: B 558 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7769 (mm-30) REVERT: B 609 THR cc_start: 0.8952 (m) cc_final: 0.8511 (p) REVERT: B 696 LEU cc_start: 0.8299 (tt) cc_final: 0.8081 (tp) REVERT: B 697 VAL cc_start: 0.7607 (t) cc_final: 0.7333 (t) REVERT: B 876 THR cc_start: 0.5307 (OUTLIER) cc_final: 0.4912 (m) outliers start: 42 outliers final: 30 residues processed: 202 average time/residue: 0.3337 time to fit residues: 100.8959 Evaluate side-chains 206 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 1.885 ------------------------------------------------------------------------------- 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 642 ILE Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 349 LYS 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 307 PHE Chi-restraints excluded: chain D residue 15 LYS 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 262 MET 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 156 optimal weight: 0.5980 chunk 169 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 647 ASN B 753 ASN C 188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.087800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.072333 restraints weight = 37054.852| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.03 r_work: 0.2966 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18497 Z= 0.130 Angle : 0.523 8.973 25090 Z= 0.282 Chirality : 0.043 0.170 2824 Planarity : 0.004 0.053 3142 Dihedral : 7.928 84.857 2833 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.82 % Allowed : 13.40 % 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: -0.28 (0.18), residues: 2243 helix: 1.30 (0.18), residues: 887 sheet: -0.72 (0.28), residues: 361 loop : -1.36 (0.18), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 299 HIS 0.003 0.001 HIS B 429 PHE 0.023 0.001 PHE D 235 TYR 0.017 0.001 TYR B 751 ARG 0.005 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 6) link_NAG-ASN : angle 2.15445 ( 18) link_BETA1-4 : bond 0.00259 ( 3) link_BETA1-4 : angle 1.35541 ( 9) hydrogen bonds : bond 0.05385 ( 731) hydrogen bonds : angle 4.16130 ( 2097) SS BOND : bond 0.00218 ( 18) SS BOND : angle 1.17328 ( 36) covalent geometry : bond 0.00296 (18470) covalent geometry : angle 0.51803 (25027) *********************** 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 215 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 1.894 Fit side-chains revert: symmetry clash REVERT: A 285 ARG cc_start: 0.8739 (ttp80) cc_final: 0.8522 (ttt-90) REVERT: A 734 MET cc_start: 0.8233 (mmt) cc_final: 0.7948 (mmp) REVERT: B 117 GLN cc_start: 0.7415 (tm130) cc_final: 0.7105 (tm-30) REVERT: B 349 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7521 (mmtt) REVERT: B 558 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7539 (mp0) REVERT: B 609 THR cc_start: 0.8947 (m) cc_final: 0.8530 (p) REVERT: B 696 LEU cc_start: 0.8223 (tt) cc_final: 0.8004 (tp) REVERT: B 876 THR cc_start: 0.5281 (OUTLIER) cc_final: 0.4894 (m) outliers start: 34 outliers final: 27 residues processed: 201 average time/residue: 0.3309 time to fit residues: 99.2327 Evaluate side-chains 206 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 223 ILE 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 A residue 712 THR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 349 LYS 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 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 262 MET 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 118 optimal weight: 0.0050 chunk 152 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 173 optimal weight: 0.0670 chunk 214 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 overall best weight: 0.2730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.090370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.075145 restraints weight = 37262.340| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.99 r_work: 0.3030 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18497 Z= 0.092 Angle : 0.459 10.035 25090 Z= 0.247 Chirality : 0.041 0.154 2824 Planarity : 0.004 0.051 3142 Dihedral : 7.344 83.231 2833 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.71 % Allowed : 13.61 % Favored : 84.68 % 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: 1.57 (0.18), residues: 893 sheet: -0.62 (0.28), residues: 365 loop : -1.18 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 299 HIS 0.002 0.001 HIS B 766 PHE 0.021 0.001 PHE D 235 TYR 0.017 0.001 TYR B 751 ARG 0.006 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 6) link_NAG-ASN : angle 1.71443 ( 18) link_BETA1-4 : bond 0.00334 ( 3) link_BETA1-4 : angle 1.18936 ( 9) hydrogen bonds : bond 0.03967 ( 731) hydrogen bonds : angle 3.85608 ( 2097) SS BOND : bond 0.00245 ( 18) SS BOND : angle 0.96263 ( 36) covalent geometry : bond 0.00192 (18470) covalent geometry : angle 0.45559 (25027) *********************** 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 222 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 1.995 Fit side-chains revert: symmetry clash REVERT: A 285 ARG cc_start: 0.8745 (ttp80) cc_final: 0.8531 (ttt-90) REVERT: A 789 PHE cc_start: 0.8241 (t80) cc_final: 0.7908 (t80) REVERT: B 336 LYS cc_start: 0.8560 (mmtm) cc_final: 0.8318 (mptt) REVERT: B 349 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7546 (mmtt) REVERT: B 544 ARG cc_start: 0.7861 (mmt-90) cc_final: 0.7632 (tpp-160) REVERT: B 558 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7588 (mp0) REVERT: B 609 THR cc_start: 0.8932 (m) cc_final: 0.8523 (p) REVERT: B 697 VAL cc_start: 0.7630 (t) cc_final: 0.7246 (t) REVERT: B 876 THR cc_start: 0.5389 (OUTLIER) cc_final: 0.4999 (m) REVERT: C 291 THR cc_start: 0.8035 (t) cc_final: 0.7831 (t) outliers start: 32 outliers final: 20 residues processed: 210 average time/residue: 0.3593 time to fit residues: 111.1689 Evaluate side-chains 212 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 223 ILE 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 A residue 712 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 349 LYS 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 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 27 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 169 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 180 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 199 optimal weight: 0.0020 chunk 129 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN B 463 HIS C 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.090008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.074731 restraints weight = 37145.224| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.99 r_work: 0.3019 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18497 Z= 0.101 Angle : 0.474 9.675 25090 Z= 0.254 Chirality : 0.041 0.162 2824 Planarity : 0.004 0.051 3142 Dihedral : 7.303 82.568 2833 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.28 % Allowed : 13.99 % Favored : 84.73 % 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: 1.60 (0.18), residues: 895 sheet: -0.56 (0.28), residues: 363 loop : -1.17 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 299 HIS 0.003 0.001 HIS B 766 PHE 0.022 0.001 PHE D 235 TYR 0.014 0.001 TYR B 751 ARG 0.008 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 6) link_NAG-ASN : angle 1.75340 ( 18) link_BETA1-4 : bond 0.00335 ( 3) link_BETA1-4 : angle 1.17571 ( 9) hydrogen bonds : bond 0.04218 ( 731) hydrogen bonds : angle 3.82653 ( 2097) SS BOND : bond 0.00148 ( 18) SS BOND : angle 0.96035 ( 36) covalent geometry : bond 0.00222 (18470) covalent geometry : angle 0.46991 (25027) ********************** 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 218 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 2.129 Fit side-chains revert: symmetry clash REVERT: A 285 ARG cc_start: 0.8746 (ttp80) cc_final: 0.8533 (ttt-90) REVERT: A 286 ARG cc_start: 0.7790 (mtt180) cc_final: 0.7511 (mtt180) REVERT: B 336 LYS cc_start: 0.8573 (mmtm) cc_final: 0.8334 (mptt) REVERT: B 349 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7562 (mmtt) REVERT: B 558 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7627 (mp0) REVERT: B 609 THR cc_start: 0.8936 (m) cc_final: 0.8491 (p) REVERT: B 697 VAL cc_start: 0.7619 (t) cc_final: 0.7237 (t) REVERT: B 751 TYR cc_start: 0.8105 (t80) cc_final: 0.7872 (t80) REVERT: B 876 THR cc_start: 0.5349 (OUTLIER) cc_final: 0.4963 (m) REVERT: C 291 THR cc_start: 0.8033 (t) cc_final: 0.7808 (t) REVERT: D 17 GLN cc_start: 0.7682 (tm-30) cc_final: 0.7394 (tt0) REVERT: D 235 PHE cc_start: 0.8057 (t80) cc_final: 0.7679 (t80) outliers start: 24 outliers final: 22 residues processed: 211 average time/residue: 0.3523 time to fit residues: 112.1114 Evaluate side-chains 217 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 1.947 ------------------------------------------------------------------------------- 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 223 ILE 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 A residue 712 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 463 HIS 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 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 148 optimal weight: 0.0870 chunk 222 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN C 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.089014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.073555 restraints weight = 37161.358| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.03 r_work: 0.2994 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18497 Z= 0.128 Angle : 0.503 9.574 25090 Z= 0.269 Chirality : 0.042 0.174 2824 Planarity : 0.004 0.053 3142 Dihedral : 7.394 83.055 2833 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.44 % Allowed : 14.04 % 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: 0.01 (0.18), residues: 2243 helix: 1.52 (0.18), residues: 896 sheet: -0.59 (0.28), residues: 362 loop : -1.19 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 818 HIS 0.005 0.001 HIS B 463 PHE 0.023 0.001 PHE D 235 TYR 0.014 0.001 TYR B 751 ARG 0.008 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 6) link_NAG-ASN : angle 1.88260 ( 18) link_BETA1-4 : bond 0.00320 ( 3) link_BETA1-4 : angle 1.25491 ( 9) hydrogen bonds : bond 0.04744 ( 731) hydrogen bonds : angle 3.89189 ( 2097) SS BOND : bond 0.00182 ( 18) SS BOND : angle 1.03920 ( 36) covalent geometry : bond 0.00300 (18470) covalent geometry : angle 0.49869 (25027) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10076.04 seconds wall clock time: 175 minutes 13.72 seconds (10513.72 seconds total)