Starting phenix.real_space_refine on Sun Jun 29 20:37:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h08_34411/06_2025/8h08_34411_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h08_34411/06_2025/8h08_34411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h08_34411/06_2025/8h08_34411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h08_34411/06_2025/8h08_34411.map" model { file = "/net/cci-nas-00/data/ceres_data/8h08_34411/06_2025/8h08_34411_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h08_34411/06_2025/8h08_34411_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4614 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 19833 2.51 5 N 5334 2.21 5 O 5999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31277 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7138 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 53, 'TRANS': 894} Chain breaks: 10 Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 8, 'ASN:plan1': 7, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 125 Chain: "B" Number of atoms: 7024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 933, 7024 Classifications: {'peptide': 933} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 50, 'TRANS': 882} Chain breaks: 14 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 406 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 6, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 136 Chain: "C" Number of atoms: 7125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7125 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 53, 'TRANS': 894} Chain breaks: 11 Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 245 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 132 Chain: "D" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 839 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 738 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 794 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 839 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 738 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 794 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 839 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 738 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "Q" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 794 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 18.85, per 1000 atoms: 0.60 Number of scatterers: 31277 At special positions: 0 Unit cell: (161.99, 172.66, 226.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 5999 8.00 N 5334 7.00 C 19833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=1.29 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.06 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.76 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=1.96 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=1.97 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.01 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.97 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.08 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.07 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.07 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 NAG-ASN " NAG A1401 " - " ASN A 343 " " NAG B1401 " - " ASN B 343 " " NAG C1401 " - " ASN C 343 " Time building additional restraints: 7.99 Conformation dependent library (CDL) restraints added in 4.5 seconds 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7714 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 76 sheets defined 17.4% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.16 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.547A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.968A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.501A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.635A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.567A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 880 removed outlier: 3.507A pdb=" N THR A 874 " --> pdb=" O ILE A 870 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 890 removed outlier: 4.127A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.648A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.599A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.544A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.724A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1022 removed outlier: 3.581A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.587A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.548A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.969A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.548A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.561A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 771 removed outlier: 3.552A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 782 removed outlier: 3.529A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.855A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.802A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 901 Processing helix chain 'B' and resid 905 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.664A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.793A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.600A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.672A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.016A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.548A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.969A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.209A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 774 Processing helix chain 'C' and resid 776 through 783 removed outlier: 3.879A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 827 Processing helix chain 'C' and resid 866 through 878 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.874A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 4.172A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.523A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 4.087A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.553A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1022 removed outlier: 3.718A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.113A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.540A pdb=" N THR N 91 " --> pdb=" O ALA N 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.536A pdb=" N PHE O 83 " --> pdb=" O PRO O 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.539A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.536A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 91 removed outlier: 3.539A pdb=" N THR Q 91 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.536A pdb=" N PHE R 83 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.426A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.747A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA5, first strand: chain 'A' and resid 89 through 92 removed outlier: 4.146A pdb=" N PHE A 92 " --> pdb=" O PHE A 192 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 89 through 92 removed outlier: 4.146A pdb=" N PHE A 92 " --> pdb=" O PHE A 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA9, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AB1, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.956A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP A 574 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.132A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 399 through 403 removed outlier: 3.590A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.049A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 715 through 722 removed outlier: 6.422A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 715 through 722 removed outlier: 6.422A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.564A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1076 through 1077 removed outlier: 3.824A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.328A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.843A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.930A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 90 through 94 removed outlier: 3.825A pdb=" N PHE B 92 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.548A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.101A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 326 through 327 removed outlier: 4.880A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 399 through 403 removed outlier: 3.591A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.908A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 703 through 704 removed outlier: 7.129A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.733A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 717 through 720 removed outlier: 7.083A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.631A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.600A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.934A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.626A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.562A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 190 through 195 removed outlier: 5.509A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 313 Processing sheet with id=AE6, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE7, first strand: chain 'C' and resid 324 through 327 removed outlier: 4.270A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 399 through 403 removed outlier: 3.590A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.985A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 720 removed outlier: 3.617A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C 723 " --> pdb=" O HIS C1064 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 720 removed outlier: 3.617A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF8, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AF9, first strand: chain 'D' and resid 55 through 57 removed outlier: 5.145A pdb=" N CYS D 45 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ARG D 36 " --> pdb=" O CYS D 45 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER D 47 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET D 32 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AG2, first strand: chain 'J' and resid 45 through 46 removed outlier: 3.855A pdb=" N ALA J 34 " --> pdb=" O GLN J 89 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 18 through 22 removed outlier: 3.591A pdb=" N LEU N 81 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR N 69 " --> pdb=" O GLN N 82 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.294A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N MET N 34 " --> pdb=" O PHE N 50 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR N 94 " --> pdb=" O THR N 116 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 4 through 6 removed outlier: 3.510A pdb=" N ILE O 21 " --> pdb=" O LEU O 73 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.224A pdb=" N LEU O 11 " --> pdb=" O ASP O 105 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN O 38 " --> pdb=" O THR O 85 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AG8, first strand: chain 'F' and resid 55 through 57 removed outlier: 5.146A pdb=" N CYS F 45 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ARG F 36 " --> pdb=" O CYS F 45 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER F 47 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET F 32 " --> pdb=" O ILE F 49 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AH1, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.855A pdb=" N ALA H 34 " --> pdb=" O GLN H 89 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 18 through 22 removed outlier: 3.592A pdb=" N LEU I 81 " --> pdb=" O LEU I 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL I 79 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR I 69 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.295A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N MET I 34 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR I 94 " --> pdb=" O THR I 116 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.510A pdb=" N ILE K 21 " --> pdb=" O LEU K 73 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.226A pdb=" N LEU K 11 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN K 38 " --> pdb=" O THR K 85 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AH7, first strand: chain 'L' and resid 55 through 57 removed outlier: 5.145A pdb=" N CYS L 45 " --> pdb=" O ARG L 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ARG L 36 " --> pdb=" O CYS L 45 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER L 47 " --> pdb=" O TRP L 34 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET L 32 " --> pdb=" O ILE L 49 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'P' and resid 5 through 7 Processing sheet with id=AH9, first strand: chain 'P' and resid 45 through 46 removed outlier: 3.855A pdb=" N ALA P 34 " --> pdb=" O GLN P 89 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Q' and resid 18 through 22 removed outlier: 3.592A pdb=" N LEU Q 81 " --> pdb=" O LEU Q 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL Q 79 " --> pdb=" O CYS Q 22 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR Q 69 " --> pdb=" O GLN Q 82 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.294A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N PHE Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N MET Q 34 " --> pdb=" O PHE Q 50 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR Q 94 " --> pdb=" O THR Q 116 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'R' and resid 4 through 6 removed outlier: 3.511A pdb=" N ILE R 21 " --> pdb=" O LEU R 73 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.226A pdb=" N LEU R 11 " --> pdb=" O ASP R 105 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN R 38 " --> pdb=" O THR R 85 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) 1023 hydrogen bonds defined for protein. 2649 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: 14.24 Time building geometry restraints manager: 8.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.30: 5131 1.30 - 1.44: 9129 1.44 - 1.59: 17604 1.59 - 1.73: 0 1.73 - 1.88: 147 Bond restraints: 32011 Sorted by residual: bond pdb=" C ASN I 57 " pdb=" N TYR I 58 " ideal model delta sigma weight residual 1.331 1.485 -0.155 1.32e-02 5.74e+03 1.37e+02 bond pdb=" C ASN N 57 " pdb=" N TYR N 58 " ideal model delta sigma weight residual 1.331 1.485 -0.154 1.32e-02 5.74e+03 1.37e+02 bond pdb=" C ASN Q 57 " pdb=" N TYR Q 58 " ideal model delta sigma weight residual 1.331 1.484 -0.154 1.32e-02 5.74e+03 1.35e+02 bond pdb=" C TYR N 58 " pdb=" N TYR N 59 " ideal model delta sigma weight residual 1.331 1.483 -0.152 1.55e-02 4.16e+03 9.59e+01 bond pdb=" C TYR Q 58 " pdb=" N TYR Q 59 " ideal model delta sigma weight residual 1.331 1.483 -0.152 1.55e-02 4.16e+03 9.59e+01 ... (remaining 32006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 40711 3.69 - 7.38: 2684 7.38 - 11.08: 175 11.08 - 14.77: 22 14.77 - 18.46: 1 Bond angle restraints: 43593 Sorted by residual: angle pdb=" N PRO B 812 " pdb=" CA PRO B 812 " pdb=" C PRO B 812 " ideal model delta sigma weight residual 113.47 95.01 18.46 1.43e+00 4.89e-01 1.67e+02 angle pdb=" N ILE A 909 " pdb=" CA ILE A 909 " pdb=" C ILE A 909 " ideal model delta sigma weight residual 113.10 104.63 8.47 9.70e-01 1.06e+00 7.63e+01 angle pdb=" C ILE P 29 " pdb=" N SER P 30 " pdb=" CA SER P 30 " ideal model delta sigma weight residual 122.30 110.53 11.77 1.35e+00 5.49e-01 7.61e+01 angle pdb=" N PRO A 337 " pdb=" CA PRO A 337 " pdb=" C PRO A 337 " ideal model delta sigma weight residual 112.48 124.25 -11.77 1.35e+00 5.49e-01 7.60e+01 angle pdb=" C ILE H 29 " pdb=" N SER H 30 " pdb=" CA SER H 30 " ideal model delta sigma weight residual 122.30 110.57 11.73 1.35e+00 5.49e-01 7.55e+01 ... (remaining 43588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 17216 17.71 - 35.43: 1334 35.43 - 53.14: 284 53.14 - 70.85: 57 70.85 - 88.56: 17 Dihedral angle restraints: 18908 sinusoidal: 6875 harmonic: 12033 Sorted by residual: dihedral pdb=" C TYR K 94 " pdb=" N TYR K 94 " pdb=" CA TYR K 94 " pdb=" CB TYR K 94 " ideal model delta harmonic sigma weight residual -122.60 -153.55 30.95 0 2.50e+00 1.60e-01 1.53e+02 dihedral pdb=" C TYR R 94 " pdb=" N TYR R 94 " pdb=" CA TYR R 94 " pdb=" CB TYR R 94 " ideal model delta harmonic sigma weight residual -122.60 -153.51 30.91 0 2.50e+00 1.60e-01 1.53e+02 dihedral pdb=" C TYR O 94 " pdb=" N TYR O 94 " pdb=" CA TYR O 94 " pdb=" CB TYR O 94 " ideal model delta harmonic sigma weight residual -122.60 -153.49 30.89 0 2.50e+00 1.60e-01 1.53e+02 ... (remaining 18905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.267: 4553 0.267 - 0.535: 298 0.535 - 0.802: 10 0.802 - 1.070: 0 1.070 - 1.337: 3 Chirality restraints: 4864 Sorted by residual: chirality pdb=" CA TYR K 94 " pdb=" N TYR K 94 " pdb=" C TYR K 94 " pdb=" CB TYR K 94 " both_signs ideal model delta sigma weight residual False 2.51 1.17 1.34 2.00e-01 2.50e+01 4.47e+01 chirality pdb=" CA TYR R 94 " pdb=" N TYR R 94 " pdb=" C TYR R 94 " pdb=" CB TYR R 94 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.34 2.00e-01 2.50e+01 4.46e+01 chirality pdb=" CA TYR O 94 " pdb=" N TYR O 94 " pdb=" C TYR O 94 " pdb=" CB TYR O 94 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.45e+01 ... (remaining 4861 not shown) Planarity restraints: 5698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 107 " -0.018 2.00e-02 2.50e+03 2.29e-02 1.31e+01 pdb=" CG TRP L 107 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP L 107 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP L 107 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP L 107 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP L 107 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 107 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 107 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 107 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP L 107 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 107 " 0.018 2.00e-02 2.50e+03 2.28e-02 1.29e+01 pdb=" CG TRP D 107 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP D 107 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP D 107 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 107 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP D 107 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 107 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 107 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 107 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 107 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 107 " -0.018 2.00e-02 2.50e+03 2.28e-02 1.29e+01 pdb=" CG TRP F 107 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP F 107 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP F 107 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP F 107 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP F 107 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 107 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 107 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 107 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 107 " -0.000 2.00e-02 2.50e+03 ... (remaining 5695 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.19: 4 2.19 - 2.87: 12219 2.87 - 3.55: 40255 3.55 - 4.22: 69859 4.22 - 4.90: 121541 Nonbonded interactions: 243878 Sorted by model distance: nonbonded pdb=" OE1 GLN B 965 " pdb=" OG SER B1003 " model vdw 1.518 3.040 nonbonded pdb=" CG1 VAL A 483 " pdb=" OD1 ASN L 54 " model vdw 2.107 3.460 nonbonded pdb=" CG1 VAL B 483 " pdb=" OD1 ASN F 54 " model vdw 2.107 3.460 nonbonded pdb=" CG1 VAL C 483 " pdb=" OD1 ASN D 54 " model vdw 2.107 3.460 nonbonded pdb=" O ASP B 574 " pdb=" OD1 ASP B 586 " model vdw 2.229 3.040 ... (remaining 243873 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 29 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 40 or (resid 41 through 43 and (na \ me N or name CA or name C or name O or name CB )) or resid 44 through 46 or (res \ id 47 and (name N or name CA or name C or name O or name CB )) or resid 48 throu \ gh 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) or r \ esid 55 or (resid 56 and (name N or name CA or name C or name O or name CB )) or \ resid 57 through 61 or (resid 62 through 63 and (name N or name CA or name C or \ name O or name CB )) or resid 64 through 65 or resid 88 through 89 or (resid 90 \ and (name N or name CA or name C or name O or name CB )) or resid 91 through 94 \ or (resid 95 and (name N or name CA or name C or name O or name CB )) or (resid \ 100 and (name N or name CA or name C or name O or name CB )) or resid 101 or (r \ esid 102 and (name N or name CA or name C or name O or name CB )) or resid 103 t \ hrough 107 or (resid 121 and (name N or name CA or name C or name O or name CB ) \ ) or resid 126 or (resid 127 and (name N or name CA or name C or name O or name \ CB )) or resid 128 through 130 or (resid 189 through 191 and (name N or name CA \ or name C or name O or name CB )) or resid 192 through 194 or (resid 195 through \ 196 and (name N or name CA or name C or name O or name CB )) or resid 201 throu \ gh 208 or resid 220 through 222 or (resid 223 and (name N or name CA or name C o \ r name O or name CB )) or resid 224 through 230 or resid 236 through 240 or (res \ id 241 through 242 and (name N or name CA or name C or name O or name CB )) or r \ esid 265 or (resid 266 through 267 and (name N or name CA or name C or name O or \ name CB )) or resid 268 or (resid 269 and (name N or name CA or name C or name \ O or name CB )) or resid 270 through 285 or (resid 286 and (name N or name CA or \ name C or name O or name CB )) or resid 287 through 290 or (resid 291 through 2 \ 92 and (name N or name CA or name C or name O or name CB )) or resid 293 through \ 300 or (resid 301 and (name N or name CA or name C or name O or name CB )) or r \ esid 302 through 307 or (resid 308 and (name N or name CA or name C or name O or \ name CB )) or resid 309 or (resid 310 and (name N or name CA or name C or name \ O or name CB )) or resid 311 through 318 or (resid 319 and (name N or name CA or \ name C or name O or name CB )) or resid 320 through 530 or (resid 531 and (name \ N or name CA or name C or name O or name CB )) or resid 532 or (resid 533 and ( \ name N or name CA or name C or name O or name CB )) or resid 534 through 548 or \ (resid 549 and (name N or name CA or name C or name O or name CB )) or resid 550 \ through 564 or (resid 565 and (name N or name CA or name C or name O or name CB \ )) or resid 566 through 567 or (resid 568 and (name N or name CA or name C or n \ ame O or name CB )) or resid 569 through 577 or (resid 578 and (name N or name C \ A or name C or name O or name CB )) or resid 579 through 582 or (resid 583 throu \ gh 584 and (name N or name CA or name C or name O or name CB )) or resid 585 thr \ ough 590 or (resid 591 through 592 and (name N or name CA or name C or name O or \ name CB )) or resid 593 through 594 or (resid 595 and (name N or name CA or nam \ e C or name O or name CB )) or resid 596 or (resid 597 through 598 and (name N o \ r name CA or name C or name O or name CB )) or resid 599 through 601 or (resid 6 \ 02 and (name N or name CA or name C or name O or name CB )) or resid 603 through \ 605 or (resid 606 and (name N or name CA or name C or name O or name CB )) or r \ esid 607 through 609 or (resid 610 and (name N or name CA or name C or name O or \ name CB )) or resid 611 through 621 or resid 641 through 644 or (resid 645 and \ (name N or name CA or name C or name O or name CB )) or resid 646 through 659 or \ (resid 660 and (name N or name CA or name C or name O or name CB )) or resid 66 \ 1 through 662 or (resid 663 and (name N or name CA or name C or name O or name C \ B )) or resid 664 through 669 or (resid 670 and (name N or name CA or name C or \ name O or name CB )) or resid 671 through 675 or resid 691 or (resid 692 through \ 694 and (name N or name CA or name C or name O or name CB )) or resid 695 throu \ gh 701 or (resid 702 and (name N or name CA or name C or name O or name CB )) or \ resid 703 through 704 or (resid 705 through 706 and (name N or name CA or name \ C or name O or name CB )) or resid 707 through 721 or (resid 722 and (name N or \ name CA or name C or name O or name CB )) or resid 723 or (resid 724 and (name N \ or name CA or name C or name O or name CB )) or resid 725 through 737 or (resid \ 738 and (name N or name CA or name C or name O or name CB )) or resid 739 throu \ gh 741 or (resid 742 and (name N or name CA or name C or name O or name CB )) or \ resid 743 through 745 or (resid 746 and (name N or name CA or name C or name O \ or name CB )) or resid 747 or (resid 748 and (name N or name CA or name C or nam \ e O or name CB )) or resid 749 through 754 or (resid 755 and (name N or name CA \ or name C or name O or name CB )) or resid 756 through 759 or (resid 760 and (na \ me N or name CA or name C or name O or name CB )) or resid 761 through 790 or (r \ esid 791 and (name N or name CA or name C or name O or name CB )) or resid 792 t \ hrough 812 or (resid 813 through 814 and (name N or name CA or name C or name O \ or name CB )) or resid 815 through 820 or (resid 821 and (name N or name CA or n \ ame C or name O or name CB )) or resid 822 through 825 or (resid 826 through 856 \ and (name N or name CA or name C or name O or name CB )) or resid 857 or (resid \ 858 and (name N or name CA or name C or name O or name CB )) or resid 859 throu \ gh 877 or (resid 878 through 879 and (name N or name CA or name C or name O or n \ ame CB )) or resid 880 through 903 or (resid 904 and (name N or name CA or name \ C or name O or name CB )) or resid 905 through 914 or (resid 915 through 916 and \ (name N or name CA or name C or name O or name CB )) or resid 917 through 920 o \ r (resid 921 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 22 or (resid 923 through 924 and (name N or name CA or name C or name O or name \ CB )) or resid 925 through 930 or (resid 931 and (name N or name CA or name C or \ name O or name CB )) or (resid 932 through 934 and (name N or name CA or name C \ or name O or name CB )) or resid 935 through 940 or resid 944 through 949 or (r \ esid 950 and (name N or name CA or name C or name O or name CB )) or resid 951 t \ hrough 953 or (resid 954 and (name N or name CA or name C or name O or name CB ) \ ) or resid 955 through 964 or (resid 965 and (name N or name CA or name C or nam \ e O or name CB )) or resid 966 through 972 or (resid 973 and (name N or name CA \ or name C or name O or name CB )) or resid 974 through 976 or (resid 977 through \ 980 and (name N or name CA or name C or name O or name CB )) or resid 981 throu \ gh 993 or (resid 994 and (name N or name CA or name C or name O or name CB )) or \ resid 995 or (resid 996 through 997 and (name N or name CA or name C or name O \ or name CB )) or resid 998 through 1017 or (resid 1018 and (name N or name CA or \ name C or name O or name CB )) or resid 1019 through 1071 or (resid 1072 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1073 through 1080 or \ (resid 1081 through 1082 and (name N or name CA or name C or name O or name CB \ )) or resid 1083 through 1091 or (resid 1092 and (name N or name CA or name C or \ name O or name CB )) or resid 1093 or (resid 1094 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1095 through 1103 or (resid 1104 and (name \ N or name CA or name C or name O or name CB )) or resid 1105 through 1110 or (re \ sid 1111 and (name N or name CA or name C or name O or name CB )) or resid 1112 \ through 1121 or (resid 1122 through 1123 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1124 through 1125 or (resid 1126 through 1127 and (na \ me N or name CA or name C or name O or name CB )) or resid 1128 through 1138 or \ (resid 1139 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 40 through 1141 or resid 1401)) selection = (chain 'B' and (resid 29 through 60 or (resid 61 through 63 and (name N or name \ CA or name C or name O or name CB )) or resid 64 through 95 or (resid 100 and (n \ ame N or name CA or name C or name O or name CB )) or resid 101 through 107 or ( \ resid 121 and (name N or name CA or name C or name O or name CB )) or resid 126 \ through 128 or (resid 129 through 130 and (name N or name CA or name C or name O \ or name CB )) or (resid 189 through 191 and (name N or name CA or name C or nam \ e O or name CB )) or resid 192 through 196 or (resid 201 through 203 and (name N \ or name CA or name C or name O or name CB )) or resid 204 or (resid 205 and (na \ me N or name CA or name C or name O or name CB )) or resid 206 through 208 or re \ sid 220 through 226 or (resid 227 and (name N or name CA or name C or name O or \ name CB )) or resid 228 or (resid 229 and (name N or name CA or name C or name O \ or name CB )) or resid 230 or resid 236 through 239 or (resid 240 through 242 a \ nd (name N or name CA or name C or name O or name CB )) or resid 265 through 270 \ or (resid 271 and (name N or name CA or name C or name O or name CB )) or resid \ 272 through 285 or (resid 286 and (name N or name CA or name C or name O or nam \ e CB )) or resid 287 through 318 or (resid 319 and (name N or name CA or name C \ or name O or name CB )) or resid 320 through 323 or (resid 324 and (name N or na \ me CA or name C or name O or name CB )) or resid 325 through 331 or (resid 332 a \ nd (name N or name CA or name C or name O or name CB )) or resid 333 through 527 \ or (resid 528 and (name N or name CA or name C or name O or name CB )) or resid \ 529 through 543 or (resid 544 and (name N or name CA or name C or name O or nam \ e CB )) or resid 545 through 571 or (resid 572 and (name N or name CA or name C \ or name O or name CB )) or resid 573 through 581 or (resid 582 through 584 and ( \ name N or name CA or name C or name O or name CB )) or resid 585 or (resid 586 a \ nd (name N or name CA or name C or name O or name CB )) or resid 587 through 596 \ or (resid 597 through 598 and (name N or name CA or name C or name O or name CB \ )) or resid 599 through 618 or (resid 619 and (name N or name CA or name C or n \ ame O or name CB )) or resid 620 through 621 or resid 641 through 644 or (resid \ 645 and (name N or name CA or name C or name O or name CB )) or resid 646 throug \ h 659 or (resid 660 and (name N or name CA or name C or name O or name CB )) or \ resid 661 through 674 or (resid 675 and (name N or name CA or name C or name O o \ r name CB )) or resid 691 or (resid 692 through 694 and (name N or name CA or na \ me C or name O or name CB )) or resid 695 or (resid 696 and (name N or name CA o \ r name C or name O or name CB )) or resid 697 through 701 or (resid 702 and (nam \ e N or name CA or name C or name O or name CB )) or resid 703 through 709 or (re \ sid 710 and (name N or name CA or name C or name O or name CB )) or resid 711 th \ rough 713 or (resid 714 and (name N or name CA or name C or name O or name CB )) \ or resid 715 through 721 or (resid 722 and (name N or name CA or name C or name \ O or name CB )) or resid 723 through 741 or (resid 742 and (name N or name CA o \ r name C or name O or name CB )) or resid 743 through 752 or (resid 753 through \ 755 and (name N or name CA or name C or name O or name CB )) or resid 756 throug \ h 784 or (resid 785 through 786 and (name N or name CA or name C or name O or na \ me CB )) or resid 787 through 810 or (resid 811 and (name N or name CA or name C \ or name O or name CB )) or resid 812 through 813 or (resid 814 and (name N or n \ ame CA or name C or name O or name CB )) or resid 815 through 819 or (resid 820 \ through 821 and (name N or name CA or name C or name O or name CB )) or resid 82 \ 2 through 824 or (resid 825 through 826 and (name N or name CA or name C or name \ O or name CB )) or (resid 855 through 856 and (name N or name CA or name C or n \ ame O or name CB )) or resid 857 or (resid 858 and (name N or name CA or name C \ or name O or name CB )) or resid 859 through 866 or (resid 867 and (name N or na \ me CA or name C or name O or name CB )) or resid 868 through 883 or (resid 884 a \ nd (name N or name CA or name C or name O or name CB )) or resid 885 through 893 \ or (resid 894 through 895 and (name N or name CA or name C or name O or name CB \ )) or resid 896 through 901 or (resid 902 through 904 and (name N or name CA or \ name C or name O or name CB )) or resid 905 through 913 or (resid 914 through 9 \ 16 and (name N or name CA or name C or name O or name CB )) or resid 917 through \ 932 or (resid 933 through 934 and (name N or name CA or name C or name O or nam \ e CB )) or resid 935 or (resid 936 and (name N or name CA or name C or name O or \ name CB )) or resid 937 through 953 or (resid 954 and (name N or name CA or nam \ e C or name O or name CB )) or resid 955 through 964 or (resid 965 and (name N o \ r name CA or name C or name O or name CB )) or resid 966 through 972 or (resid 9 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 974 through \ 977 or (resid 978 through 980 and (name N or name CA or name C or name O or nam \ e CB )) or resid 981 through 983 or (resid 984 and (name N or name CA or name C \ or name O or name CB )) or resid 985 through 993 or (resid 994 and (name N or na \ me CA or name C or name O or name CB )) or resid 995 or (resid 996 through 997 a \ nd (name N or name CA or name C or name O or name CB )) or resid 998 through 100 \ 9 or (resid 1010 and (name N or name CA or name C or name O or name CB )) or res \ id 1011 through 1028 or (resid 1029 and (name N or name CA or name C or name O o \ r name CB )) or resid 1030 through 1033 or (resid 1034 and (name N or name CA or \ name C or name O or name CB )) or resid 1035 through 1081 or (resid 1082 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1083 through 1103 or \ (resid 1104 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 105 through 1106 or (resid 1107 and (name N or name CA or name C or name O or na \ me CB )) or resid 1108 through 1110 or (resid 1111 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1112 through 1122 or (resid 1123 and (name \ N or name CA or name C or name O or name CB )) or resid 1124 through 1125 or (re \ sid 1126 through 1127 and (name N or name CA or name C or name O or name CB )) o \ r resid 1128 through 1138 or (resid 1139 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1140 through 1141 or resid 1401)) selection = (chain 'C' and (resid 29 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 40 or (resid 41 through 43 and (na \ me N or name CA or name C or name O or name CB )) or resid 44 through 46 or (res \ id 47 and (name N or name CA or name C or name O or name CB )) or resid 48 throu \ gh 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) or r \ esid 55 or (resid 56 and (name N or name CA or name C or name O or name CB )) or \ resid 57 through 60 or (resid 61 through 63 and (name N or name CA or name C or \ name O or name CB )) or resid 64 through 65 or resid 88 through 107 or resid 12 \ 5 through 126 or (resid 127 and (name N or name CA or name C or name O or name C \ B )) or resid 128 through 129 or (resid 130 and (name N or name CA or name C or \ name O or name CB )) or (resid 189 through 191 and (name N or name CA or name C \ or name O or name CB )) or resid 192 through 194 or (resid 195 through 196 and ( \ name N or name CA or name C or name O or name CB )) or (resid 201 through 203 an \ d (name N or name CA or name C or name O or name CB )) or resid 204 or (resid 20 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 206 through \ 208 or resid 220 through 228 or (resid 229 and (name N or name CA or name C or n \ ame O or name CB )) or resid 230 through 237 or (resid 238 through 242 and (name \ N or name CA or name C or name O or name CB )) or resid 265 or (resid 266 throu \ gh 267 and (name N or name CA or name C or name O or name CB )) or resid 268 or \ (resid 269 and (name N or name CA or name C or name O or name CB )) or resid 270 \ or (resid 271 and (name N or name CA or name C or name O or name CB )) or resid \ 272 through 290 or (resid 291 through 292 and (name N or name CA or name C or n \ ame O or name CB )) or resid 293 through 300 or (resid 301 and (name N or name C \ A or name C or name O or name CB )) or resid 302 through 323 or (resid 324 and ( \ name N or name CA or name C or name O or name CB )) or resid 325 through 331 or \ (resid 332 and (name N or name CA or name C or name O or name CB )) or resid 333 \ through 530 or (resid 531 and (name N or name CA or name C or name O or name CB \ )) or resid 532 or (resid 533 and (name N or name CA or name C or name O or nam \ e CB )) or resid 534 through 548 or (resid 549 and (name N or name CA or name C \ or name O or name CB )) or resid 550 through 564 or (resid 565 and (name N or na \ me CA or name C or name O or name CB )) or resid 566 through 567 or (resid 568 a \ nd (name N or name CA or name C or name O or name CB )) or resid 569 through 571 \ or (resid 572 and (name N or name CA or name C or name O or name CB )) or resid \ 573 through 577 or (resid 578 and (name N or name CA or name C or name O or nam \ e CB )) or resid 579 or (resid 580 through 584 and (name N or name CA or name C \ or name O or name CB )) or resid 585 or (resid 586 and (name N or name CA or nam \ e C or name O or name CB )) or resid 587 through 590 or (resid 591 through 592 a \ nd (name N or name CA or name C or name O or name CB )) or resid 593 through 594 \ or (resid 595 and (name N or name CA or name C or name O or name CB )) or resid \ 596 through 605 or (resid 606 and (name N or name CA or name C or name O or nam \ e CB )) or resid 607 or (resid 608 through 610 and (name N or name CA or name C \ or name O or name CB )) or resid 611 through 618 or (resid 619 and (name N or na \ me CA or name C or name O or name CB )) or resid 620 through 662 or (resid 663 a \ nd (name N or name CA or name C or name O or name CB )) or resid 664 through 665 \ or (resid 666 and (name N or name CA or name C or name O or name CB )) or (resi \ d 667 through 670 and (name N or name CA or name C or name O or name CB )) or re \ sid 671 through 704 or (resid 705 through 706 and (name N or name CA or name C o \ r name O or name CB )) or resid 707 through 709 or (resid 710 and (name N or nam \ e CA or name C or name O or name CB )) or resid 711 through 725 or (resid 726 an \ d (name N or name CA or name C or name O or name CB )) or resid 727 through 737 \ or (resid 738 and (name N or name CA or name C or name O or name CB )) or resid \ 739 through 745 or (resid 746 and (name N or name CA or name C or name O or name \ CB )) or resid 747 through 753 or (resid 754 through 755 and (name N or name CA \ or name C or name O or name CB )) or resid 756 through 759 or (resid 760 and (n \ ame N or name CA or name C or name O or name CB )) or resid 761 through 778 or ( \ resid 779 and (name N or name CA or name C or name O or name CB )) or resid 780 \ through 812 or (resid 813 through 814 and (name N or name CA or name C or name O \ or name CB )) or resid 815 through 826 or (resid 855 through 856 and (name N or \ name CA or name C or name O or name CB )) or resid 857 through 866 or (resid 86 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 868 through \ 877 or (resid 878 through 879 and (name N or name CA or name C or name O or name \ CB )) or resid 880 through 882 or (resid 883 through 884 and (name N or name CA \ or name C or name O or name CB )) or resid 885 through 893 or (resid 894 throug \ h 895 and (name N or name CA or name C or name O or name CB )) or resid 896 thro \ ugh 901 or (resid 902 through 904 and (name N or name CA or name C or name O or \ name CB )) or resid 905 through 911 or (resid 912 and (name N or name CA or name \ C or name O or name CB )) or resid 913 or (resid 914 through 916 and (name N or \ name CA or name C or name O or name CB )) or resid 917 through 922 or (resid 92 \ 3 through 924 and (name N or name CA or name C or name O or name CB )) or resid \ 925 through 932 or (resid 933 through 934 and (name N or name CA or name C or na \ me O or name CB )) or resid 935 or (resid 936 and (name N or name CA or name C o \ r name O or name CB )) or resid 937 through 940 or resid 944 through 949 or (res \ id 950 and (name N or name CA or name C or name O or name CB )) or resid 951 thr \ ough 976 or (resid 977 through 980 and (name N or name CA or name C or name O or \ name CB )) or resid 981 through 1009 or (resid 1010 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1011 through 1017 or (resid 1018 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1019 through 1080 or ( \ resid 1081 through 1082 and (name N or name CA or name C or name O or name CB )) \ or resid 1083 through 1091 or (resid 1092 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1093 through 1114 or (resid 1115 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1116 through 1121 or (resid 1122 \ through 1123 and (name N or name CA or name C or name O or name CB )) or resid \ 1124 through 1126 or (resid 1127 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1128 or (resid 1129 and (name N or name CA or name C or name \ O or name CB )) or resid 1130 through 1141 or resid 1401)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'P' } ncs_group { reference = chain 'I' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'K' selection = chain 'O' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.020 Extract box with map and model: 1.260 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 73.270 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.170 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 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 : 0.014 0.742 32047 Z= 1.031 Angle : 2.039 50.828 43668 Z= 1.480 Chirality : 0.150 1.337 4864 Planarity : 0.007 0.059 5695 Dihedral : 13.411 88.564 11095 Min Nonbonded Distance : 1.518 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.13 % Favored : 94.25 % Rotamer: Outliers : 1.16 % Allowed : 12.93 % Favored : 85.92 % Cbeta Deviations : 2.88 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.13), residues: 4073 helix: 0.60 (0.21), residues: 573 sheet: -0.11 (0.16), residues: 1050 loop : -0.92 (0.12), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP L 107 HIS 0.013 0.003 HIS N 104 PHE 0.046 0.004 PHE A1121 TYR 0.046 0.004 TYR C 707 ARG 0.006 0.001 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.05560 ( 3) link_NAG-ASN : angle 7.03025 ( 9) hydrogen bonds : bond 0.25081 ( 1010) hydrogen bonds : angle 10.11067 ( 2649) SS BOND : bond 0.14013 ( 33) SS BOND : angle 9.19836 ( 66) covalent geometry : bond 0.01374 (32011) covalent geometry : angle 2.00682 (43593) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 343 time to evaluate : 3.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7339 (mt0) REVERT: B 347 PHE cc_start: 0.3610 (OUTLIER) cc_final: 0.1577 (m-80) REVERT: C 106 PHE cc_start: 0.5995 (m-80) cc_final: 0.4209 (t80) REVERT: C 759 PHE cc_start: 0.6964 (m-80) cc_final: 0.6737 (m-80) REVERT: J 46 VAL cc_start: 0.4134 (OUTLIER) cc_final: 0.3742 (m) outliers start: 37 outliers final: 9 residues processed: 376 average time/residue: 0.3877 time to fit residues: 244.9729 Evaluate side-chains 209 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain Q residue 104 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 346 optimal weight: 8.9990 chunk 310 optimal weight: 20.0000 chunk 172 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 166 optimal weight: 0.5980 chunk 321 optimal weight: 30.0000 chunk 124 optimal weight: 8.9990 chunk 195 optimal weight: 0.9980 chunk 239 optimal weight: 0.0770 chunk 372 optimal weight: 7.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN A 540 ASN A 907 ASN A 919 ASN A 935 GLN A 965 GLN A1005 GLN A1113 GLN B 49 HIS B 52 GLN B 536 ASN B 751 ASN B 762 GLN B 787 GLN B 992 GLN B1005 GLN B1083 HIS B1088 HIS B1106 GLN C 87 ASN C 207 HIS C 239 GLN C 481 ASN C 658 ASN C 762 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 953 ASN C1002 GLN C1023 ASN C1106 GLN D 79 GLN F 79 GLN L 79 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.231174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.190987 restraints weight = 52871.592| |-----------------------------------------------------------------------------| r_work (start): 0.4399 rms_B_bonded: 3.12 r_work: 0.3688 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32047 Z= 0.145 Angle : 0.668 10.858 43668 Z= 0.359 Chirality : 0.047 0.192 4864 Planarity : 0.005 0.045 5695 Dihedral : 6.202 56.947 4555 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.82 % Favored : 97.08 % Rotamer: Outliers : 2.62 % Allowed : 14.74 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.61 (0.13), residues: 4073 helix: 0.57 (0.21), residues: 617 sheet: -0.06 (0.15), residues: 1165 loop : -0.84 (0.12), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 353 HIS 0.009 0.001 HIS N 104 PHE 0.030 0.002 PHE B 377 TYR 0.034 0.002 TYR K 87 ARG 0.006 0.001 ARG L 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 3) link_NAG-ASN : angle 2.87551 ( 9) hydrogen bonds : bond 0.04361 ( 1010) hydrogen bonds : angle 6.60693 ( 2649) SS BOND : bond 0.00690 ( 33) SS BOND : angle 1.97088 ( 66) covalent geometry : bond 0.00308 (32011) covalent geometry : angle 0.66253 (43593) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 228 time to evaluate : 3.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 CYS cc_start: 0.4281 (OUTLIER) cc_final: 0.2141 (m) REVERT: A 969 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7192 (mmtt) REVERT: B 436 TRP cc_start: 0.6605 (p90) cc_final: 0.6379 (p90) REVERT: C 707 TYR cc_start: 0.7769 (t80) cc_final: 0.7408 (t80) REVERT: J 46 VAL cc_start: 0.4436 (OUTLIER) cc_final: 0.3986 (m) REVERT: N 34 MET cc_start: 0.2226 (tmm) cc_final: 0.1357 (tmm) REVERT: F 80 MET cc_start: -0.2702 (mtp) cc_final: -0.3567 (tpp) REVERT: H 4 MET cc_start: 0.2591 (ttt) cc_final: 0.2202 (ttt) REVERT: I 109 PHE cc_start: 0.7434 (m-80) cc_final: 0.6594 (t80) REVERT: I 112 TRP cc_start: 0.3659 (m-90) cc_final: 0.2334 (m-90) REVERT: P 4 MET cc_start: -0.0148 (tpp) cc_final: -0.0919 (tmm) outliers start: 84 outliers final: 31 residues processed: 299 average time/residue: 0.3796 time to fit residues: 194.8622 Evaluate side-chains 211 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain R residue 38 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 383 optimal weight: 0.0570 chunk 378 optimal weight: 0.9980 chunk 196 optimal weight: 6.9990 chunk 311 optimal weight: 50.0000 chunk 177 optimal weight: 1.9990 chunk 210 optimal weight: 20.0000 chunk 160 optimal weight: 2.9990 chunk 222 optimal weight: 30.0000 chunk 109 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 398 optimal weight: 30.0000 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN B 919 ASN C 87 ASN C 334 ASN C 755 GLN C 762 GLN C 935 GLN C 949 GLN C 953 ASN C1074 ASN I 3 GLN I 57 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.229732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.188088 restraints weight = 53481.718| |-----------------------------------------------------------------------------| r_work (start): 0.4339 rms_B_bonded: 3.23 r_work: 0.3615 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32047 Z= 0.139 Angle : 0.598 10.330 43668 Z= 0.317 Chirality : 0.045 0.209 4864 Planarity : 0.004 0.045 5695 Dihedral : 5.525 57.025 4546 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.71 % Favored : 96.19 % Rotamer: Outliers : 2.75 % Allowed : 14.39 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.69 (0.13), residues: 4073 helix: 0.59 (0.22), residues: 594 sheet: -0.18 (0.15), residues: 1133 loop : -0.86 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 353 HIS 0.008 0.001 HIS B 505 PHE 0.036 0.002 PHE A 565 TYR 0.025 0.001 TYR R 49 ARG 0.004 0.000 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 3) link_NAG-ASN : angle 2.14714 ( 9) hydrogen bonds : bond 0.03762 ( 1010) hydrogen bonds : angle 6.02853 ( 2649) SS BOND : bond 0.00593 ( 33) SS BOND : angle 1.71489 ( 66) covalent geometry : bond 0.00309 (32011) covalent geometry : angle 0.59424 (43593) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 198 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 CYS cc_start: 0.3588 (OUTLIER) cc_final: 0.0987 (m) REVERT: A 563 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7092 (mt0) REVERT: B 714 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7841 (mm) REVERT: C 92 PHE cc_start: 0.6589 (t80) cc_final: 0.6332 (t80) REVERT: C 329 PHE cc_start: 0.7757 (m-80) cc_final: 0.7547 (m-80) REVERT: C 1043 CYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8136 (m) REVERT: N 34 MET cc_start: 0.2211 (tmm) cc_final: 0.1481 (tmm) REVERT: F 80 MET cc_start: -0.2782 (mtp) cc_final: -0.3609 (tpp) REVERT: I 50 PHE cc_start: 0.6652 (t80) cc_final: 0.6320 (t80) REVERT: I 109 PHE cc_start: 0.7569 (m-80) cc_final: 0.6910 (t80) REVERT: I 112 TRP cc_start: 0.3608 (m-90) cc_final: 0.2454 (m-90) REVERT: K 53 ASN cc_start: 0.7368 (t0) cc_final: 0.7102 (t0) REVERT: P 4 MET cc_start: -0.0151 (tpp) cc_final: -0.0990 (tmm) outliers start: 88 outliers final: 48 residues processed: 274 average time/residue: 0.3758 time to fit residues: 179.9170 Evaluate side-chains 231 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 179 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain F residue 32 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain P residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 357 optimal weight: 0.0670 chunk 344 optimal weight: 30.0000 chunk 343 optimal weight: 30.0000 chunk 19 optimal weight: 2.9990 chunk 369 optimal weight: 30.0000 chunk 408 optimal weight: 40.0000 chunk 6 optimal weight: 7.9990 chunk 215 optimal weight: 20.0000 chunk 59 optimal weight: 0.5980 chunk 353 optimal weight: 40.0000 chunk 350 optimal weight: 20.0000 overall best weight: 6.3326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 762 GLN A 926 GLN A 965 GLN A1036 GLN C 87 ASN C 196 ASN C 207 HIS C 414 GLN C 564 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 GLN I 3 GLN ** I 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN K 53 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.219721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.174188 restraints weight = 53211.193| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 3.32 r_work: 0.3507 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.097 32047 Z= 0.445 Angle : 0.819 10.694 43668 Z= 0.440 Chirality : 0.055 0.331 4864 Planarity : 0.006 0.059 5695 Dihedral : 6.292 59.282 4546 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.94 % Rotamer: Outliers : 3.72 % Allowed : 15.20 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 4073 helix: -0.73 (0.20), residues: 606 sheet: -0.59 (0.15), residues: 1221 loop : -1.11 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 886 HIS 0.010 0.002 HIS I 33 PHE 0.033 0.003 PHE A1121 TYR 0.038 0.003 TYR C 707 ARG 0.008 0.001 ARG C1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 3) link_NAG-ASN : angle 2.36583 ( 9) hydrogen bonds : bond 0.05206 ( 1010) hydrogen bonds : angle 6.58568 ( 2649) SS BOND : bond 0.01079 ( 33) SS BOND : angle 2.04598 ( 66) covalent geometry : bond 0.01054 (32011) covalent geometry : angle 0.81479 (43593) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 190 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 CYS cc_start: 0.4275 (OUTLIER) cc_final: 0.1469 (m) REVERT: B 347 PHE cc_start: 0.5864 (OUTLIER) cc_final: 0.3970 (m-80) REVERT: B 772 VAL cc_start: 0.9352 (OUTLIER) cc_final: 0.9109 (p) REVERT: C 452 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6165 (tt) REVERT: C 985 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6821 (m-30) REVERT: D 32 MET cc_start: 0.0554 (pmm) cc_final: 0.0197 (tpp) REVERT: N 34 MET cc_start: 0.2547 (tmm) cc_final: 0.1920 (tmm) REVERT: F 80 MET cc_start: -0.2654 (mtp) cc_final: -0.3563 (tpp) REVERT: H 4 MET cc_start: 0.2381 (tpt) cc_final: 0.2063 (ttt) REVERT: I 109 PHE cc_start: 0.7239 (m-80) cc_final: 0.6871 (t80) REVERT: I 112 TRP cc_start: 0.4298 (m-90) cc_final: 0.3212 (m-90) REVERT: L 80 MET cc_start: -0.1823 (mmt) cc_final: -0.3247 (tpp) REVERT: Q 83 MET cc_start: 0.1498 (mtp) cc_final: 0.1097 (mmp) outliers start: 119 outliers final: 77 residues processed: 295 average time/residue: 0.3638 time to fit residues: 185.4667 Evaluate side-chains 257 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 175 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain Q residue 78 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 88 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 274 optimal weight: 0.8980 chunk 260 optimal weight: 1.9990 chunk 381 optimal weight: 30.0000 chunk 251 optimal weight: 0.8980 chunk 233 optimal weight: 0.7980 chunk 280 optimal weight: 0.9990 chunk 263 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 196 ASN C 955 ASN H 55 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.227388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.182362 restraints weight = 53017.324| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 3.42 r_work: 0.3560 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32047 Z= 0.115 Angle : 0.567 10.111 43668 Z= 0.298 Chirality : 0.044 0.200 4864 Planarity : 0.004 0.051 5695 Dihedral : 5.467 57.873 4546 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.39 % Favored : 96.51 % Rotamer: Outliers : 2.09 % Allowed : 17.11 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.95 (0.13), residues: 4073 helix: 0.12 (0.21), residues: 607 sheet: -0.37 (0.15), residues: 1215 loop : -0.95 (0.13), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K 35 HIS 0.007 0.001 HIS N 104 PHE 0.020 0.001 PHE C 86 TYR 0.021 0.001 TYR C 707 ARG 0.003 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 3) link_NAG-ASN : angle 1.72261 ( 9) hydrogen bonds : bond 0.03279 ( 1010) hydrogen bonds : angle 5.72903 ( 2649) SS BOND : bond 0.00503 ( 33) SS BOND : angle 1.36447 ( 66) covalent geometry : bond 0.00250 (32011) covalent geometry : angle 0.56402 (43593) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 199 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 347 PHE cc_start: 0.5758 (OUTLIER) cc_final: 0.3302 (m-80) REVERT: B 560 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8330 (mp) REVERT: C 92 PHE cc_start: 0.6688 (t80) cc_final: 0.6364 (t80) REVERT: C 1043 CYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8192 (m) REVERT: D 32 MET cc_start: 0.0500 (OUTLIER) cc_final: 0.0189 (tpp) REVERT: J 4 MET cc_start: 0.0638 (pmm) cc_final: 0.0305 (pmm) REVERT: H 4 MET cc_start: 0.1876 (tpt) cc_final: 0.1604 (ttt) REVERT: I 112 TRP cc_start: 0.4130 (m-90) cc_final: 0.3760 (m-90) REVERT: Q 83 MET cc_start: 0.1385 (mtp) cc_final: 0.1011 (mmp) outliers start: 67 outliers final: 48 residues processed: 252 average time/residue: 0.3857 time to fit residues: 164.2658 Evaluate side-chains 237 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 185 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain Q residue 78 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 405 optimal weight: 0.2980 chunk 310 optimal weight: 50.0000 chunk 298 optimal weight: 50.0000 chunk 244 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 257 optimal weight: 0.5980 chunk 372 optimal weight: 40.0000 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN C 196 ASN C 755 GLN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.223220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.178552 restraints weight = 53060.841| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 3.28 r_work: 0.3563 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32047 Z= 0.119 Angle : 0.543 10.152 43668 Z= 0.283 Chirality : 0.044 0.196 4864 Planarity : 0.004 0.050 5695 Dihedral : 5.113 59.063 4546 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.10 % Favored : 95.83 % Rotamer: Outliers : 2.00 % Allowed : 17.23 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.75 (0.13), residues: 4073 helix: 0.40 (0.22), residues: 609 sheet: -0.30 (0.15), residues: 1231 loop : -0.83 (0.13), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 353 HIS 0.006 0.001 HIS N 104 PHE 0.016 0.001 PHE A1121 TYR 0.016 0.001 TYR B1067 ARG 0.005 0.000 ARG F 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 3) link_NAG-ASN : angle 1.51724 ( 9) hydrogen bonds : bond 0.03125 ( 1010) hydrogen bonds : angle 5.47869 ( 2649) SS BOND : bond 0.00483 ( 33) SS BOND : angle 1.11472 ( 66) covalent geometry : bond 0.00267 (32011) covalent geometry : angle 0.54151 (43593) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 205 time to evaluate : 3.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1138 TYR cc_start: 0.6817 (t80) cc_final: 0.6462 (t80) REVERT: B 118 LEU cc_start: 0.8799 (mt) cc_final: 0.8589 (mm) REVERT: B 347 PHE cc_start: 0.5606 (OUTLIER) cc_final: 0.2605 (m-80) REVERT: C 92 PHE cc_start: 0.6911 (t80) cc_final: 0.6641 (t80) REVERT: C 452 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.6111 (tt) REVERT: I 109 PHE cc_start: 0.7468 (m-80) cc_final: 0.6910 (t80) REVERT: I 112 TRP cc_start: 0.3676 (m-90) cc_final: 0.2720 (m-90) REVERT: L 80 MET cc_start: -0.2717 (mmt) cc_final: -0.3427 (tpp) REVERT: Q 83 MET cc_start: 0.1420 (mtp) cc_final: 0.1032 (mmp) outliers start: 64 outliers final: 51 residues processed: 253 average time/residue: 0.3793 time to fit residues: 163.8119 Evaluate side-chains 244 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 191 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain Q residue 78 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 343 optimal weight: 50.0000 chunk 216 optimal weight: 20.0000 chunk 70 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 347 optimal weight: 50.0000 chunk 138 optimal weight: 0.8980 chunk 197 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 217 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS K 53 ASN Q 57 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.223704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.178920 restraints weight = 52701.471| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 3.29 r_work: 0.3575 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32047 Z= 0.114 Angle : 0.532 10.241 43668 Z= 0.276 Chirality : 0.043 0.179 4864 Planarity : 0.004 0.049 5695 Dihedral : 4.844 59.756 4540 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.41 % Favored : 96.51 % Rotamer: Outliers : 2.22 % Allowed : 16.89 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.67 (0.13), residues: 4073 helix: 0.61 (0.22), residues: 604 sheet: -0.32 (0.15), residues: 1207 loop : -0.77 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP F 107 HIS 0.009 0.001 HIS N 104 PHE 0.018 0.001 PHE C 375 TYR 0.017 0.001 TYR B1067 ARG 0.005 0.000 ARG K 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 3) link_NAG-ASN : angle 1.43766 ( 9) hydrogen bonds : bond 0.02991 ( 1010) hydrogen bonds : angle 5.34822 ( 2649) SS BOND : bond 0.00366 ( 33) SS BOND : angle 1.03014 ( 66) covalent geometry : bond 0.00254 (32011) covalent geometry : angle 0.53094 (43593) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 199 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6903 (tp30) REVERT: A 1138 TYR cc_start: 0.6778 (t80) cc_final: 0.6438 (t80) REVERT: B 347 PHE cc_start: 0.5318 (OUTLIER) cc_final: 0.3885 (m-80) REVERT: B 509 ARG cc_start: 0.5431 (mtt180) cc_final: 0.4820 (mtt180) REVERT: C 92 PHE cc_start: 0.6858 (t80) cc_final: 0.6610 (t80) REVERT: C 452 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.6134 (tt) REVERT: C 1043 CYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8286 (m) REVERT: F 80 MET cc_start: -0.2823 (OUTLIER) cc_final: -0.3610 (tmm) REVERT: I 68 PHE cc_start: 0.1699 (m-80) cc_final: 0.1485 (m-80) REVERT: I 83 MET cc_start: 0.3657 (ppp) cc_final: 0.3231 (ttp) REVERT: I 109 PHE cc_start: 0.7528 (m-80) cc_final: 0.6915 (t80) REVERT: I 112 TRP cc_start: 0.3693 (m-90) cc_final: 0.2714 (m-90) REVERT: K 30 SER cc_start: 0.8302 (m) cc_final: 0.8087 (p) REVERT: L 80 MET cc_start: -0.2322 (mmt) cc_final: -0.3206 (tpp) REVERT: Q 83 MET cc_start: 0.1424 (mtp) cc_final: 0.1019 (mmp) outliers start: 71 outliers final: 56 residues processed: 252 average time/residue: 0.3797 time to fit residues: 164.2338 Evaluate side-chains 253 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 192 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain Q residue 78 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 353 optimal weight: 10.0000 chunk 275 optimal weight: 0.2980 chunk 215 optimal weight: 10.0000 chunk 355 optimal weight: 30.0000 chunk 282 optimal weight: 7.9990 chunk 344 optimal weight: 0.6980 chunk 347 optimal weight: 40.0000 chunk 213 optimal weight: 9.9990 chunk 287 optimal weight: 50.0000 chunk 335 optimal weight: 0.0470 chunk 386 optimal weight: 8.9990 overall best weight: 3.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS K 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.225407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.181249 restraints weight = 53045.985| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 3.37 r_work: 0.3536 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 32047 Z= 0.260 Angle : 0.634 14.124 43668 Z= 0.333 Chirality : 0.048 0.277 4864 Planarity : 0.005 0.061 5695 Dihedral : 5.263 59.134 4540 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.18 % Favored : 94.77 % Rotamer: Outliers : 2.37 % Allowed : 17.33 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 4073 helix: -0.02 (0.21), residues: 608 sheet: -0.42 (0.15), residues: 1214 loop : -0.93 (0.13), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 107 HIS 0.009 0.001 HIS N 104 PHE 0.026 0.002 PHE A1121 TYR 0.024 0.002 TYR C 707 ARG 0.006 0.000 ARG I 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 3) link_NAG-ASN : angle 1.50190 ( 9) hydrogen bonds : bond 0.03904 ( 1010) hydrogen bonds : angle 5.78641 ( 2649) SS BOND : bond 0.00686 ( 33) SS BOND : angle 1.41850 ( 66) covalent geometry : bond 0.00610 (32011) covalent geometry : angle 0.63144 (43593) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 186 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 338 PHE cc_start: 0.8560 (m-80) cc_final: 0.8122 (m-10) REVERT: B 347 PHE cc_start: 0.5489 (OUTLIER) cc_final: 0.3572 (m-80) REVERT: B 560 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8400 (mp) REVERT: C 452 LEU cc_start: 0.6370 (OUTLIER) cc_final: 0.6132 (tt) REVERT: F 80 MET cc_start: -0.2857 (OUTLIER) cc_final: -0.3591 (tmm) REVERT: I 83 MET cc_start: 0.3616 (ppp) cc_final: 0.3195 (ttp) REVERT: I 109 PHE cc_start: 0.7506 (m-80) cc_final: 0.6661 (t80) REVERT: L 80 MET cc_start: -0.2092 (mmt) cc_final: -0.3123 (tpp) REVERT: Q 83 MET cc_start: 0.1312 (mtp) cc_final: 0.0891 (mmp) outliers start: 76 outliers final: 63 residues processed: 247 average time/residue: 0.4168 time to fit residues: 177.1414 Evaluate side-chains 243 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 176 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain Q residue 78 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 129 optimal weight: 20.0000 chunk 356 optimal weight: 10.0000 chunk 268 optimal weight: 0.5980 chunk 363 optimal weight: 40.0000 chunk 76 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 316 optimal weight: 5.9990 chunk 357 optimal weight: 40.0000 chunk 3 optimal weight: 9.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 HIS ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS ** R 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.220510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.176693 restraints weight = 52409.820| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 3.33 r_work: 0.3556 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 32047 Z= 0.243 Angle : 0.617 10.403 43668 Z= 0.325 Chirality : 0.047 0.197 4864 Planarity : 0.005 0.058 5695 Dihedral : 5.298 59.641 4540 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.37 % Favored : 95.56 % Rotamer: Outliers : 2.53 % Allowed : 17.39 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 4073 helix: -0.17 (0.21), residues: 626 sheet: -0.47 (0.15), residues: 1220 loop : -1.00 (0.13), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 353 HIS 0.005 0.001 HIS C1048 PHE 0.025 0.002 PHE B1121 TYR 0.022 0.002 TYR C 707 ARG 0.005 0.000 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 3) link_NAG-ASN : angle 1.44122 ( 9) hydrogen bonds : bond 0.03704 ( 1010) hydrogen bonds : angle 5.72544 ( 2649) SS BOND : bond 0.00649 ( 33) SS BOND : angle 1.34142 ( 66) covalent geometry : bond 0.00570 (32011) covalent geometry : angle 0.61474 (43593) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 176 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 338 PHE cc_start: 0.8415 (m-80) cc_final: 0.7958 (m-10) REVERT: B 560 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8375 (mp) REVERT: C 452 LEU cc_start: 0.6289 (OUTLIER) cc_final: 0.6069 (tt) REVERT: C 533 LEU cc_start: 0.8900 (pt) cc_final: 0.8690 (pt) REVERT: N 83 MET cc_start: -0.2509 (mmt) cc_final: -0.3042 (mmt) REVERT: F 80 MET cc_start: -0.2658 (OUTLIER) cc_final: -0.3507 (tmm) REVERT: I 68 PHE cc_start: 0.1438 (m-80) cc_final: 0.1234 (m-80) REVERT: I 83 MET cc_start: 0.3650 (ppp) cc_final: 0.3223 (ttp) REVERT: I 109 PHE cc_start: 0.7304 (m-80) cc_final: 0.6629 (t80) REVERT: L 80 MET cc_start: -0.1882 (mmt) cc_final: -0.2886 (tpp) REVERT: Q 32 TYR cc_start: 0.4727 (OUTLIER) cc_final: 0.4308 (t80) outliers start: 81 outliers final: 60 residues processed: 238 average time/residue: 0.3857 time to fit residues: 160.2283 Evaluate side-chains 240 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 176 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain Q residue 32 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 205 optimal weight: 1.9990 chunk 397 optimal weight: 20.0000 chunk 256 optimal weight: 0.8980 chunk 106 optimal weight: 0.0870 chunk 374 optimal weight: 10.0000 chunk 91 optimal weight: 0.5980 chunk 360 optimal weight: 30.0000 chunk 137 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 505 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS K 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.223427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.181172 restraints weight = 52540.307| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 3.22 r_work: 0.3646 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 32047 Z= 0.098 Angle : 0.531 10.964 43668 Z= 0.274 Chirality : 0.043 0.168 4864 Planarity : 0.004 0.060 5695 Dihedral : 4.805 58.634 4540 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.68 % Favored : 96.24 % Rotamer: Outliers : 1.56 % Allowed : 18.39 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.74 (0.13), residues: 4073 helix: 0.43 (0.21), residues: 625 sheet: -0.27 (0.15), residues: 1222 loop : -0.84 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 436 HIS 0.006 0.001 HIS N 104 PHE 0.016 0.001 PHE C 565 TYR 0.019 0.001 TYR B1067 ARG 0.003 0.000 ARG Q 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 3) link_NAG-ASN : angle 1.26773 ( 9) hydrogen bonds : bond 0.02873 ( 1010) hydrogen bonds : angle 5.25345 ( 2649) SS BOND : bond 0.00307 ( 33) SS BOND : angle 1.02945 ( 66) covalent geometry : bond 0.00216 (32011) covalent geometry : angle 0.52990 (43593) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 193 time to evaluate : 3.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 338 PHE cc_start: 0.8410 (m-80) cc_final: 0.7946 (m-10) REVERT: B 436 TRP cc_start: 0.7375 (p90) cc_final: 0.7140 (p90) REVERT: C 92 PHE cc_start: 0.6748 (t80) cc_final: 0.6469 (t80) REVERT: C 571 ASP cc_start: 0.7908 (m-30) cc_final: 0.7660 (m-30) REVERT: C 762 GLN cc_start: 0.8454 (pt0) cc_final: 0.8135 (pm20) REVERT: F 80 MET cc_start: -0.2721 (OUTLIER) cc_final: -0.3503 (tmm) REVERT: I 68 PHE cc_start: 0.1363 (m-80) cc_final: 0.1152 (m-80) REVERT: I 83 MET cc_start: 0.3575 (ppp) cc_final: 0.3150 (ttp) REVERT: I 109 PHE cc_start: 0.7182 (m-80) cc_final: 0.6485 (t80) REVERT: L 80 MET cc_start: -0.2101 (mmt) cc_final: -0.3016 (tpp) REVERT: Q 32 TYR cc_start: 0.4751 (OUTLIER) cc_final: 0.4478 (t80) outliers start: 50 outliers final: 42 residues processed: 228 average time/residue: 0.3864 time to fit residues: 151.2233 Evaluate side-chains 229 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain Q residue 32 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 267 optimal weight: 6.9990 chunk 298 optimal weight: 9.9990 chunk 237 optimal weight: 0.9990 chunk 308 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 204 optimal weight: 0.6980 chunk 175 optimal weight: 0.6980 chunk 161 optimal weight: 0.1980 chunk 14 optimal weight: 7.9990 chunk 329 optimal weight: 0.7980 chunk 285 optimal weight: 8.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 505 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.224634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.183539 restraints weight = 52460.964| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 3.06 r_work: 0.3663 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.626 32047 Z= 0.241 Angle : 0.723 65.599 43668 Z= 0.370 Chirality : 0.045 0.644 4864 Planarity : 0.005 0.214 5695 Dihedral : 4.807 58.658 4540 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % Rotamer: Outliers : 1.47 % Allowed : 18.70 % Favored : 79.83 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.13), residues: 4073 helix: 0.47 (0.22), residues: 625 sheet: -0.27 (0.15), residues: 1222 loop : -0.84 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 436 HIS 0.362 0.005 HIS B 505 PHE 0.015 0.001 PHE C 565 TYR 0.018 0.001 TYR B1067 ARG 0.035 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 3) link_NAG-ASN : angle 1.27212 ( 9) hydrogen bonds : bond 0.02881 ( 1010) hydrogen bonds : angle 5.25418 ( 2649) SS BOND : bond 0.02925 ( 33) SS BOND : angle 1.58524 ( 66) covalent geometry : bond 0.00532 (32011) covalent geometry : angle 0.72091 (43593) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17856.77 seconds wall clock time: 306 minutes 27.83 seconds (18387.83 seconds total)