Starting phenix.real_space_refine on Mon May 19 05:43:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szh_40916/05_2025/8szh_40916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szh_40916/05_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_40916/05_2025/8szh_40916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szh_40916/05_2025/8szh_40916.map" model { file = "/net/cci-nas-00/data/ceres_data/8szh_40916/05_2025/8szh_40916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szh_40916/05_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-5687/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: 11.72, per 1000 atoms: 0.65 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: 4.85 Conformation dependent library (CDL) restraints added in 2.4 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: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 64 through 83 removed outlier: 3.704A pdb=" N MET A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.526A pdb=" N ALA A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.512A pdb=" N ASP A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.722A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.632A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.625A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 4.026A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 272 through 287 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 329 through 335 removed outlier: 3.592A pdb=" N PHE A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.581A pdb=" N ASN A 419 " --> pdb=" O ARG A 415 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.638A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 610 through 637 removed outlier: 4.248A pdb=" N ALA A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 646 removed outlier: 3.824A pdb=" N THR A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 664 Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.627A pdb=" N PHE A 668 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 669 " --> pdb=" O LEU A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 669' Processing helix chain 'A' and resid 675 through 707 removed outlier: 5.576A pdb=" N GLN A 681 " --> pdb=" O CYS A 677 " (cutoff:3.500A) Proline residue: A 682 - end of helix removed outlier: 3.909A pdb=" N CYS A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 719 Processing helix chain 'A' and resid 722 through 746 removed outlier: 3.807A pdb=" N LEU A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 793 removed outlier: 3.964A pdb=" N LEU A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 788 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 821 removed outlier: 3.957A pdb=" N THR A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 809 " --> pdb=" O LYS A 805 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 813 " --> pdb=" O PHE A 809 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 814 " --> pdb=" O SER A 810 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 821 " --> pdb=" O VAL A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 828 Processing helix chain 'A' and resid 831 through 862 removed outlier: 3.915A pdb=" N ALA A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 858 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 877 removed outlier: 4.001A pdb=" N VAL A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 873 " --> pdb=" O ILE A 869 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N CYS A 874 " --> pdb=" O GLU A 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 83 removed outlier: 3.683A pdb=" N LEU B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 113 removed outlier: 3.846A pdb=" N SER B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.680A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.572A pdb=" N LEU B 174 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 218 through 233 removed outlier: 3.962A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 260 removed outlier: 3.563A pdb=" N VAL B 258 " --> pdb=" O HIS B 254 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 416 through 436 removed outlier: 3.606A pdb=" N VAL B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.991A pdb=" N VAL B 455 " --> pdb=" O ILE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.517A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 610 through 637 removed outlier: 3.820A pdb=" N LEU B 616 " --> pdb=" O PHE B 612 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 619 " --> pdb=" O ALA B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 646 removed outlier: 3.679A pdb=" N THR B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 664 removed outlier: 3.935A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 669 removed outlier: 3.523A pdb=" N PHE B 668 " --> pdb=" O SER B 665 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 669 " --> pdb=" O LEU B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 665 through 669' Processing helix chain 'B' and resid 679 through 699 removed outlier: 3.972A pdb=" N ALA B 683 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS B 698 " --> pdb=" O CYS B 694 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 699 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 4.217A pdb=" N LEU B 703 " --> pdb=" O THR B 699 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU B 704 " --> pdb=" O ASN B 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 699 through 704' Processing helix chain 'B' and resid 724 through 746 removed outlier: 3.993A pdb=" N MET B 734 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 793 removed outlier: 3.939A pdb=" N LEU B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE B 775 " --> pdb=" O MET B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 827 removed outlier: 3.963A pdb=" N PHE B 806 " --> pdb=" O ASN B 802 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 807 " --> pdb=" O GLU B 803 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR B 808 " --> pdb=" O ALA B 804 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 832 through 861 removed outlier: 3.608A pdb=" N ILE B 839 " --> pdb=" O ALA B 835 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA B 840 " --> pdb=" O VAL B 836 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE B 841 " --> pdb=" O GLU B 837 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 858 " --> pdb=" O PHE B 854 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 859 " --> pdb=" O ASN B 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 31 Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 207 through 216 removed outlier: 3.587A pdb=" N LYS C 210 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C 215 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 231 removed outlier: 4.134A pdb=" N ASP C 231 " --> pdb=" O SER C 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 228 through 231' Processing helix chain 'C' and resid 241 through 255 removed outlier: 3.563A pdb=" N LYS C 248 " --> pdb=" O HIS C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.769A pdb=" N PHE C 274 " --> pdb=" O LYS C 270 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.820A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'D' and resid 4 through 26 removed outlier: 3.945A pdb=" N ALA D 24 " --> pdb=" O ASP D 20 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 35 removed outlier: 3.780A pdb=" N ILE D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'E' and resid 8 through 24 removed outlier: 3.663A pdb=" N ASN E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 removed outlier: 3.548A pdb=" N ALA E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.512A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE A 33 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N VAL A 142 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLY A 35 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N VAL A 165 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 243 removed outlier: 8.095A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.550A pdb=" N PHE A 469 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 550 through 552 Processing sheet with id=AA5, first strand: chain 'A' and resid 572 through 573 Processing sheet with id=AA6, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AA7, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.370A pdb=" N GLU A 602 " --> pdb=" O ILE A 761 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE A 763 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLU A 604 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N CYS A 765 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 27 removed outlier: 6.238A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE B 33 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA B 140 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 37 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N VAL B 165 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 236 through 243 removed outlier: 8.055A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE B 491 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AB2, first strand: chain 'B' and resid 550 through 553 Processing sheet with id=AB3, first strand: chain 'B' and resid 572 through 573 Processing sheet with id=AB4, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AB5, first strand: chain 'B' and resid 602 through 604 removed outlier: 6.204A pdb=" N GLU B 602 " --> pdb=" O ILE B 761 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE B 763 " --> pdb=" O GLU B 602 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU B 604 " --> pdb=" O ILE B 763 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 186 through 190 removed outlier: 3.567A pdb=" N PHE C 189 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 268 " --> pdb=" O HIS C 322 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 46 through 51 removed outlier: 3.630A pdb=" N ARG D 46 " --> pdb=" O ASN D 340 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS D 317 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 58 through 61 removed outlier: 6.814A pdb=" N ALA D 73 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 104 through 105 removed outlier: 3.618A pdb=" N VAL D 112 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR D 124 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N CYS D 121 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU D 138 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE D 123 " --> pdb=" O SER D 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 146 through 151 removed outlier: 4.158A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.731A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D 209 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.754A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG D 251 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.650A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) 731 hydrogen bonds defined for protein. 2097 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.52 Time building geometry restraints manager: 5.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2908 1.32 - 1.45: 5213 1.45 - 1.58: 10195 1.58 - 1.71: 18 1.71 - 1.84: 136 Bond restraints: 18470 Sorted by residual: bond pdb=" C31 PCW B1403 " pdb=" O2 PCW B1403 " ideal model delta sigma weight residual 1.333 1.488 -0.155 2.00e-02 2.50e+03 6.03e+01 bond pdb=" C31 PCW A 902 " pdb=" O2 PCW A 902 " ideal model delta sigma weight residual 1.333 1.484 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" C31 PCW B1403 " pdb=" C32 PCW B1403 " ideal model delta sigma weight residual 1.502 1.604 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C31 PCW A 902 " pdb=" C32 PCW A 902 " ideal model delta sigma weight residual 1.502 1.601 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C16 PCW B1403 " pdb=" C17 PCW B1403 " ideal model delta sigma weight residual 1.523 1.622 -0.099 2.00e-02 2.50e+03 2.44e+01 ... (remaining 18465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.04: 24959 5.04 - 10.08: 56 10.08 - 15.12: 7 15.12 - 20.16: 3 20.16 - 25.20: 2 Bond angle restraints: 25027 Sorted by residual: angle pdb=" N ARG A 866 " pdb=" CA ARG A 866 " pdb=" C ARG A 866 " ideal model delta sigma weight residual 113.23 95.26 17.97 1.22e+00 6.72e-01 2.17e+02 angle pdb=" N ILE A 869 " pdb=" CA ILE A 869 " pdb=" C ILE A 869 " ideal model delta sigma weight residual 112.83 104.47 8.36 9.90e-01 1.02e+00 7.13e+01 angle pdb=" C18 PCW B1403 " pdb=" C19 PCW B1403 " pdb=" C20 PCW B1403 " ideal model delta sigma weight residual 127.82 153.02 -25.20 3.00e+00 1.11e-01 7.05e+01 angle pdb=" C18 PCW A 902 " pdb=" C19 PCW A 902 " pdb=" C20 PCW A 902 " ideal model delta sigma weight residual 127.82 152.59 -24.77 3.00e+00 1.11e-01 6.82e+01 angle pdb=" CA PHE A 862 " pdb=" C PHE A 862 " pdb=" O PHE A 862 " ideal model delta sigma weight residual 121.78 111.37 10.41 1.28e+00 6.10e-01 6.62e+01 ... (remaining 25022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.04: 10156 20.04 - 40.08: 794 40.08 - 60.11: 112 60.11 - 80.15: 24 80.15 - 100.19: 14 Dihedral angle restraints: 11100 sinusoidal: 4505 harmonic: 6595 Sorted by residual: dihedral pdb=" CB CYS A 585 " pdb=" SG CYS A 585 " pdb=" SG CYS A 598 " pdb=" CB CYS A 598 " ideal model delta sinusoidal sigma weight residual -86.00 -172.13 86.13 1 1.00e+01 1.00e-02 8.95e+01 dihedral pdb=" CB CYS A 437 " pdb=" SG CYS A 437 " pdb=" SG CYS A 449 " pdb=" CB CYS A 449 " ideal model delta sinusoidal sigma weight residual 93.00 171.14 -78.14 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS B 677 " pdb=" SG CYS B 677 " pdb=" SG CYS B 765 " pdb=" CB CYS B 765 " ideal model delta sinusoidal sigma weight residual -86.00 -41.20 -44.80 1 1.00e+01 1.00e-02 2.79e+01 ... (remaining 11097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.032: 2823 1.032 - 2.064: 0 2.064 - 3.095: 0 3.095 - 4.127: 0 4.127 - 5.159: 1 Chirality restraints: 2824 Sorted by residual: chirality pdb=" C2 PCW A 902 " pdb=" C1 PCW A 902 " pdb=" C3 PCW A 902 " pdb=" O2 PCW A 902 " both_signs ideal model delta sigma weight residual False -2.32 2.84 -5.16 2.00e-01 2.50e+01 6.65e+02 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 6.24e+00 chirality pdb=" C2 PCW B1403 " pdb=" C1 PCW B1403 " pdb=" C3 PCW B1403 " pdb=" O2 PCW B1403 " both_signs ideal model delta sigma weight residual False -2.32 -2.81 0.49 2.00e-01 2.50e+01 6.02e+00 ... (remaining 2821 not shown) Planarity restraints: 3148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.198 2.00e-02 2.50e+03 1.63e-01 3.32e+02 pdb=" C7 NAG H 2 " -0.052 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.143 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.265 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 541 " -0.063 2.00e-02 2.50e+03 6.88e-02 5.92e+01 pdb=" CG ASN B 541 " 0.122 2.00e-02 2.50e+03 pdb=" OD1 ASN B 541 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN B 541 " 0.029 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 541 " -0.031 2.00e-02 2.50e+03 6.44e-02 4.15e+01 pdb=" CG ASN B 541 " 0.111 2.00e-02 2.50e+03 pdb=" OD1 ASN B 541 " -0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN B 541 " -0.035 2.00e-02 2.50e+03 ... (remaining 3145 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1158 2.74 - 3.28: 16843 3.28 - 3.82: 27590 3.82 - 4.36: 33265 4.36 - 4.90: 59263 Nonbonded interactions: 138119 Sorted by model distance: nonbonded pdb=" OG SER D 331 " pdb=" OD1 ASP D 333 " model vdw 2.196 3.040 nonbonded pdb=" OD2 ASP A 238 " pdb=" OG SER A 262 " model vdw 2.208 3.040 nonbonded pdb=" O PHE B 668 " pdb=" OG SER B 834 " model vdw 2.220 3.040 nonbonded pdb=" O LEU B 87 " pdb=" NE2 GLN B 432 " model vdw 2.227 3.120 nonbonded pdb=" OE1 GLN B 253 " pdb=" NH2 ARG B 286 " model vdw 2.250 3.120 ... (remaining 138114 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 131 or (resid 132 through 135 and (name N or na \ me CA or name C or name O or name CB )) or resid 136 through 362 or resid 392 th \ rough 516 or (resid 517 and (name N or name CA or name C or name O or name CB )) \ or resid 518 through 586 or (resid 587 and (name N or name CA or name C or name \ O or name CB )) or resid 588 through 700 or (resid 701 and (name N or name CA o \ r name C or name O or name CB )) or resid 702 or (resid 703 and (name N or name \ CA or name C or name O or name CB )) or resid 704 through 706 or (resid 707 thro \ ugh 709 and (name N or name CA or name C or name O or name CB )) or resid 722 th \ rough 798 or (resid 799 and (name N or name CA or name C or name O or name CB )) \ or resid 800 through 861 or (resid 862 through 863 and (name N or name CA or na \ me C or name O or name CB )) or resid 864 through 865 or (resid 866 through 868 \ and (name N or name CA or name C or name O or name CB )) or resid 869 through 87 \ 0 or (resid 871 through 873 and (name N or name CA or name C or name O or name C \ B )) or resid 874 through 876 or resid 903 through 909)) selection = (chain 'B' and (resid 20 through 47 or (resid 48 and (name N or name CA or name \ C or name O or name CB )) or resid 49 through 124 or (resid 125 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 131 through 135 and (name N o \ r name CA or name C or name O or name CB )) or resid 136 through 361 or (resid 3 \ 62 and (name N or name CA or name C or name O or name CB )) or resid 392 through \ 498 or (resid 499 through 500 and (name N or name CA or name C or name O or nam \ e CB )) or resid 501 through 591 or (resid 592 and (name N or name CA or name C \ or name O or name CB )) or resid 593 through 867 or (resid 868 and (name N or na \ me CA or name C or name O or name CB )) or resid 869 through 876 or resid 1405 t \ hrough 1411)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 43.510 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.500 ------------------------------------------------------------------------------- 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 : 1.937 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: 0.3329 time to fit residues: 125.4844 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 : 2.032 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.075349 restraints weight = 37100.680| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.03 r_work: 0.3036 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- 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 2.10160 ( 18) link_BETA1-4 : bond 0.00266 ( 3) link_BETA1-4 : angle 1.17733 ( 9) hydrogen bonds : bond 0.05118 ( 731) hydrogen bonds : angle 4.37130 ( 2097) SS BOND : bond 0.00149 ( 18) SS BOND : angle 0.94561 ( 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 : 1.918 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: 0.8258 (t80) cc_final: 0.8040 (t80) REVERT: B 336 LYS cc_start: 0.8589 (mmtm) cc_final: 0.8377 (mptt) REVERT: B 558 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7646 (mp0) REVERT: B 612 PHE cc_start: 0.7437 (t80) cc_final: 0.7195 (t80) REVERT: D 197 ARG cc_start: 0.8639 (ttp-110) cc_final: 0.8208 (mtp85) REVERT: D 292 PHE cc_start: 0.7913 (m-80) cc_final: 0.7480 (m-80) outliers start: 16 outliers final: 8 residues processed: 215 average time/residue: 0.3245 time to fit residues: 102.9584 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 : 2.131 ------------------------------------------------------------------------------- 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: 5.9990 chunk 15 optimal weight: 0.7980 chunk 221 optimal weight: 0.7980 chunk 223 optimal weight: 0.4980 chunk 170 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.0870 chunk 88 optimal weight: 2.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.088899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.073355 restraints weight = 37089.709| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.02 r_work: 0.2990 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18497 Z= 0.137 Angle : 0.516 6.330 25090 Z= 0.277 Chirality : 0.043 0.178 2824 Planarity : 0.004 0.047 3142 Dihedral : 8.239 90.282 2833 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.28 % Allowed : 9.24 % Favored : 89.48 % 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: 1.38 (0.18), residues: 898 sheet: -0.49 (0.27), residues: 371 loop : -1.13 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 719 HIS 0.004 0.001 HIS B 766 PHE 0.018 0.001 PHE B 814 TYR 0.013 0.001 TYR A 421 ARG 0.002 0.000 ARG B 551 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 6) link_NAG-ASN : angle 2.09872 ( 18) link_BETA1-4 : bond 0.00455 ( 3) link_BETA1-4 : angle 1.25701 ( 9) hydrogen bonds : bond 0.05488 ( 731) hydrogen bonds : angle 4.18581 ( 2097) SS BOND : bond 0.00246 ( 18) SS BOND : angle 0.99738 ( 36) covalent geometry : bond 0.00312 (18470) covalent geometry : angle 0.51119 (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 222 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 2.243 Fit side-chains revert: symmetry clash REVERT: B 336 LYS cc_start: 0.8627 (mmtm) cc_final: 0.8405 (mptt) REVERT: B 558 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7622 (mp0) REVERT: B 609 THR cc_start: 0.8863 (m) cc_final: 0.8444 (p) REVERT: B 753 ASN cc_start: 0.8053 (t0) cc_final: 0.7568 (t0) outliers start: 24 outliers final: 18 residues processed: 212 average time/residue: 0.3301 time to fit residues: 102.4436 Evaluate side-chains 206 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 760 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 24 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 141 optimal weight: 0.0980 chunk 170 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 26 optimal weight: 0.0570 chunk 181 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.089162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.073619 restraints weight = 37125.741| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.03 r_work: 0.2996 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18497 Z= 0.124 Angle : 0.492 5.813 25090 Z= 0.264 Chirality : 0.042 0.172 2824 Planarity : 0.004 0.047 3142 Dihedral : 7.921 87.182 2833 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.39 % Allowed : 11.00 % Favored : 87.61 % 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: 1.49 (0.18), residues: 892 sheet: -0.53 (0.27), residues: 373 loop : -1.15 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 719 HIS 0.004 0.001 HIS B 429 PHE 0.018 0.001 PHE A 789 TYR 0.015 0.001 TYR C 230 ARG 0.005 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 6) link_NAG-ASN : angle 1.96840 ( 18) link_BETA1-4 : bond 0.00266 ( 3) link_BETA1-4 : angle 1.26202 ( 9) hydrogen bonds : bond 0.04992 ( 731) hydrogen bonds : angle 4.04369 ( 2097) SS BOND : bond 0.00184 ( 18) SS BOND : angle 0.93818 ( 36) covalent geometry : bond 0.00284 (18470) covalent geometry : angle 0.48751 (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 224 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 1.999 Fit side-chains revert: symmetry clash REVERT: A 789 PHE cc_start: 0.8289 (t80) cc_final: 0.7981 (t80) REVERT: B 117 GLN cc_start: 0.7321 (tm130) cc_final: 0.7005 (tm-30) REVERT: B 336 LYS cc_start: 0.8616 (mmtm) cc_final: 0.8381 (mptt) REVERT: B 558 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7620 (mp0) REVERT: B 609 THR cc_start: 0.8875 (m) cc_final: 0.8388 (p) REVERT: B 753 ASN cc_start: 0.8061 (t0) cc_final: 0.7668 (t0) outliers start: 26 outliers final: 20 residues processed: 214 average time/residue: 0.3320 time to fit residues: 104.3504 Evaluate side-chains 215 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 1.970 ------------------------------------------------------------------------------- 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 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 B residue 760 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 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: 7.9990 chunk 190 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 205 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 222 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS D 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.089131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.073619 restraints weight = 37456.478| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.03 r_work: 0.2994 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18497 Z= 0.122 Angle : 0.493 6.709 25090 Z= 0.264 Chirality : 0.042 0.171 2824 Planarity : 0.004 0.051 3142 Dihedral : 7.794 85.614 2833 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.19 % Allowed : 11.05 % Favored : 86.76 % 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: 1.56 (0.18), residues: 891 sheet: -0.52 (0.27), residues: 373 loop : -1.14 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 818 HIS 0.003 0.001 HIS B 429 PHE 0.018 0.001 PHE A 444 TYR 0.015 0.001 TYR C 230 ARG 0.006 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 6) link_NAG-ASN : angle 1.93437 ( 18) link_BETA1-4 : bond 0.00285 ( 3) link_BETA1-4 : angle 1.24967 ( 9) hydrogen bonds : bond 0.04908 ( 731) hydrogen bonds : angle 3.99042 ( 2097) SS BOND : bond 0.00189 ( 18) SS BOND : angle 1.18679 ( 36) covalent geometry : bond 0.00278 (18470) covalent geometry : angle 0.48789 (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 242 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 2.081 Fit side-chains revert: symmetry clash REVERT: B 117 GLN cc_start: 0.7327 (tm130) cc_final: 0.7003 (tm-30) REVERT: B 336 LYS cc_start: 0.8619 (mmtm) cc_final: 0.8383 (mptt) REVERT: B 558 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7617 (mp0) REVERT: B 609 THR cc_start: 0.8879 (m) cc_final: 0.8398 (p) REVERT: B 753 ASN cc_start: 0.8046 (t0) cc_final: 0.6941 (t0) REVERT: B 876 THR cc_start: 0.5367 (OUTLIER) cc_final: 0.4971 (m) outliers start: 41 outliers final: 28 residues processed: 224 average time/residue: 0.3201 time to fit residues: 107.1228 Evaluate side-chains 224 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 2.194 ------------------------------------------------------------------------------- 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 449 CYS 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 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 44 GLN 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: 2.9990 chunk 129 optimal weight: 0.0470 chunk 56 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN C 333 GLN D 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.087282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.071751 restraints weight = 37421.235| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.02 r_work: 0.2950 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 18497 Z= 0.197 Angle : 0.577 7.374 25090 Z= 0.308 Chirality : 0.045 0.194 2824 Planarity : 0.004 0.057 3142 Dihedral : 8.004 87.097 2833 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.14 % Allowed : 11.85 % Favored : 86.01 % 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: -0.18 (0.18), residues: 2243 helix: 1.31 (0.18), residues: 895 sheet: -0.68 (0.27), residues: 369 loop : -1.24 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 818 HIS 0.006 0.001 HIS B 429 PHE 0.026 0.002 PHE D 235 TYR 0.021 0.002 TYR B 751 ARG 0.006 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 6) link_NAG-ASN : angle 2.26070 ( 18) link_BETA1-4 : bond 0.00372 ( 3) link_BETA1-4 : angle 1.43436 ( 9) hydrogen bonds : bond 0.06104 ( 731) hydrogen bonds : angle 4.17963 ( 2097) SS BOND : bond 0.00281 ( 18) SS BOND : angle 1.40820 ( 36) covalent geometry : bond 0.00480 (18470) covalent geometry : angle 0.57188 (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 225 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 2.112 Fit side-chains revert: symmetry clash REVERT: B 117 GLN cc_start: 0.7346 (tm130) cc_final: 0.7025 (tm-30) REVERT: B 336 LYS cc_start: 0.8635 (mmtm) cc_final: 0.8398 (mptt) REVERT: B 558 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7642 (mp0) REVERT: B 609 THR cc_start: 0.8912 (m) cc_final: 0.8430 (p) REVERT: B 697 VAL cc_start: 0.7569 (t) cc_final: 0.7287 (t) REVERT: B 876 THR cc_start: 0.5316 (OUTLIER) cc_final: 0.4932 (m) REVERT: D 235 PHE cc_start: 0.8152 (t80) cc_final: 0.7657 (t80) outliers start: 40 outliers final: 29 residues processed: 208 average time/residue: 0.3317 time to fit residues: 102.6292 Evaluate side-chains 212 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 1.966 ------------------------------------------------------------------------------- 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 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 612 PHE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 760 ILE 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: 0.6980 chunk 159 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 158 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN C 333 GLN D 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.088463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.073018 restraints weight = 36941.450| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.02 r_work: 0.2980 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18497 Z= 0.128 Angle : 0.505 8.353 25090 Z= 0.271 Chirality : 0.042 0.172 2824 Planarity : 0.004 0.055 3142 Dihedral : 7.751 85.312 2833 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.98 % Allowed : 12.76 % Favored : 85.26 % 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: -0.08 (0.18), residues: 2243 helix: 1.45 (0.18), residues: 895 sheet: -0.60 (0.28), residues: 363 loop : -1.25 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 818 HIS 0.003 0.001 HIS B 429 PHE 0.020 0.001 PHE D 235 TYR 0.014 0.001 TYR B 751 ARG 0.007 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 6) link_NAG-ASN : angle 2.02486 ( 18) link_BETA1-4 : bond 0.00278 ( 3) link_BETA1-4 : angle 1.31400 ( 9) hydrogen bonds : bond 0.05136 ( 731) hydrogen bonds : angle 4.04103 ( 2097) SS BOND : bond 0.00203 ( 18) SS BOND : angle 1.12208 ( 36) covalent geometry : bond 0.00293 (18470) covalent geometry : angle 0.49979 (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 219 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 2.321 Fit side-chains revert: symmetry clash REVERT: B 117 GLN cc_start: 0.7413 (tm130) cc_final: 0.7091 (tm-30) REVERT: B 336 LYS cc_start: 0.8609 (mmtm) cc_final: 0.8374 (mptt) REVERT: B 558 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7620 (mp0) REVERT: B 609 THR cc_start: 0.8917 (m) cc_final: 0.8442 (p) REVERT: B 876 THR cc_start: 0.5237 (OUTLIER) cc_final: 0.4877 (m) REVERT: C 291 THR cc_start: 0.8056 (t) cc_final: 0.7840 (t) outliers start: 37 outliers final: 30 residues processed: 200 average time/residue: 0.3299 time to fit residues: 97.7951 Evaluate side-chains 210 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 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 32 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 760 ILE 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 44 GLN 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 267 ASP 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: 0.0570 chunk 169 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 180 optimal weight: 0.2980 chunk 115 optimal weight: 2.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN D 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.088328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.072835 restraints weight = 37070.380| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.02 r_work: 0.2977 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18497 Z= 0.137 Angle : 0.514 8.650 25090 Z= 0.276 Chirality : 0.043 0.176 2824 Planarity : 0.004 0.053 3142 Dihedral : 7.686 85.159 2833 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.08 % Allowed : 13.08 % Favored : 84.84 % 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: -0.09 (0.18), residues: 2243 helix: 1.43 (0.18), residues: 898 sheet: -0.63 (0.28), residues: 364 loop : -1.25 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 818 HIS 0.004 0.001 HIS B 429 PHE 0.024 0.001 PHE D 235 TYR 0.013 0.001 TYR A 421 ARG 0.007 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 6) link_NAG-ASN : angle 2.02887 ( 18) link_BETA1-4 : bond 0.00309 ( 3) link_BETA1-4 : angle 1.33050 ( 9) hydrogen bonds : bond 0.05212 ( 731) hydrogen bonds : angle 4.03144 ( 2097) SS BOND : bond 0.00207 ( 18) SS BOND : angle 1.11629 ( 36) covalent geometry : bond 0.00322 (18470) covalent geometry : angle 0.50907 (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 214 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 2.067 Fit side-chains revert: symmetry clash REVERT: B 117 GLN cc_start: 0.7417 (tm130) cc_final: 0.7093 (tm-30) REVERT: B 336 LYS cc_start: 0.8602 (mmtm) cc_final: 0.8362 (mptt) REVERT: B 558 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7633 (mp0) REVERT: B 609 THR cc_start: 0.8923 (m) cc_final: 0.8456 (p) REVERT: B 876 THR cc_start: 0.5213 (OUTLIER) cc_final: 0.4859 (m) REVERT: D 17 GLN cc_start: 0.7593 (tm-30) cc_final: 0.7384 (tt0) outliers start: 39 outliers final: 32 residues processed: 196 average time/residue: 0.3284 time to fit residues: 95.0874 Evaluate side-chains 208 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 1.879 ------------------------------------------------------------------------------- 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 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 760 ILE 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 44 GLN 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: 0.0970 chunk 152 optimal weight: 0.0470 chunk 44 optimal weight: 0.6980 chunk 222 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 214 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 148 optimal weight: 0.0270 chunk 5 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN B 463 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 = 0.3447 r_free = 0.3447 target = 0.090108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.074703 restraints weight = 37302.647| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.02 r_work: 0.3020 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1614 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= 0.095 Angle : 0.464 9.206 25090 Z= 0.250 Chirality : 0.041 0.154 2824 Planarity : 0.004 0.052 3142 Dihedral : 7.353 82.998 2833 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.66 % Allowed : 13.51 % Favored : 84.84 % 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: 0.15 (0.18), residues: 2243 helix: 1.67 (0.18), residues: 896 sheet: -0.54 (0.28), residues: 363 loop : -1.13 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 299 HIS 0.002 0.001 HIS A 463 PHE 0.022 0.001 PHE D 235 TYR 0.011 0.001 TYR B 751 ARG 0.007 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 6) link_NAG-ASN : angle 1.73352 ( 18) link_BETA1-4 : bond 0.00378 ( 3) link_BETA1-4 : angle 1.24087 ( 9) hydrogen bonds : bond 0.04168 ( 731) hydrogen bonds : angle 3.85643 ( 2097) SS BOND : bond 0.00146 ( 18) SS BOND : angle 0.90251 ( 36) covalent geometry : bond 0.00203 (18470) covalent geometry : angle 0.46047 (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 219 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 1.949 Fit side-chains revert: symmetry clash REVERT: B 336 LYS cc_start: 0.8579 (mmtm) cc_final: 0.8350 (mptt) REVERT: B 558 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7604 (mp0) REVERT: B 609 THR cc_start: 0.8907 (m) cc_final: 0.8445 (p) REVERT: B 876 THR cc_start: 0.5281 (OUTLIER) cc_final: 0.4916 (m) REVERT: D 197 ARG cc_start: 0.8379 (ttp80) cc_final: 0.8177 (ttm-80) REVERT: D 235 PHE cc_start: 0.8006 (t80) cc_final: 0.7557 (t80) outliers start: 31 outliers final: 24 residues processed: 206 average time/residue: 0.3254 time to fit residues: 99.0096 Evaluate side-chains 211 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 1.891 ------------------------------------------------------------------------------- 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 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 712 THR 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 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 44 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 27 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 169 optimal weight: 0.0040 chunk 18 optimal weight: 0.8980 chunk 180 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 753 ASN D 44 GLN 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 = 0.088587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.073066 restraints weight = 37171.045| |-----------------------------------------------------------------------------| 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: 4.34 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18497 Z= 0.142 Angle : 0.516 9.040 25090 Z= 0.276 Chirality : 0.043 0.179 2824 Planarity : 0.004 0.052 3142 Dihedral : 7.472 83.864 2833 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.49 % Allowed : 13.99 % 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: 1.50 (0.18), residues: 899 sheet: -0.56 (0.28), residues: 362 loop : -1.18 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 818 HIS 0.004 0.001 HIS B 429 PHE 0.024 0.001 PHE D 235 TYR 0.013 0.001 TYR A 421 ARG 0.008 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 6) link_NAG-ASN : angle 1.97457 ( 18) link_BETA1-4 : bond 0.00412 ( 3) link_BETA1-4 : angle 1.30688 ( 9) hydrogen bonds : bond 0.05107 ( 731) hydrogen bonds : angle 3.96976 ( 2097) SS BOND : bond 0.00205 ( 18) SS BOND : angle 1.07081 ( 36) covalent geometry : bond 0.00336 (18470) covalent geometry : angle 0.51161 (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 215 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 2.207 Fit side-chains revert: symmetry clash REVERT: A 286 ARG cc_start: 0.7802 (mtt180) cc_final: 0.7550 (mtt180) REVERT: B 117 GLN cc_start: 0.7414 (tm-30) cc_final: 0.7119 (tm-30) REVERT: B 336 LYS cc_start: 0.8614 (mmtm) cc_final: 0.8382 (mptt) REVERT: B 558 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7629 (mp0) REVERT: B 609 THR cc_start: 0.8918 (m) cc_final: 0.8454 (p) REVERT: B 697 VAL cc_start: 0.7634 (t) cc_final: 0.7302 (t) REVERT: B 876 THR cc_start: 0.5198 (OUTLIER) cc_final: 0.4845 (m) REVERT: D 197 ARG cc_start: 0.8322 (ttp80) cc_final: 0.8022 (ttp80) outliers start: 28 outliers final: 24 residues processed: 203 average time/residue: 0.3297 time to fit residues: 99.0240 Evaluate side-chains 210 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 44 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 148 optimal weight: 0.0570 chunk 222 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 220 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 overall best weight: 1.0500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN B 446 ASN D 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.088131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.072615 restraints weight = 37157.301| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.03 r_work: 0.2971 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18497 Z= 0.157 Angle : 0.531 8.996 25090 Z= 0.284 Chirality : 0.043 0.181 2824 Planarity : 0.004 0.053 3142 Dihedral : 7.542 84.216 2833 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.76 % Allowed : 13.83 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 2243 helix: 1.42 (0.18), residues: 899 sheet: -0.61 (0.28), residues: 360 loop : -1.22 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 818 HIS 0.004 0.001 HIS B 429 PHE 0.025 0.002 PHE D 235 TYR 0.013 0.001 TYR A 421 ARG 0.008 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 6) link_NAG-ASN : angle 2.05259 ( 18) link_BETA1-4 : bond 0.00241 ( 3) link_BETA1-4 : angle 1.35100 ( 9) hydrogen bonds : bond 0.05393 ( 731) hydrogen bonds : angle 4.02147 ( 2097) SS BOND : bond 0.00229 ( 18) SS BOND : angle 1.12821 ( 36) covalent geometry : bond 0.00376 (18470) covalent geometry : angle 0.52640 (25027) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9297.47 seconds wall clock time: 161 minutes 40.42 seconds (9700.42 seconds total)