Starting phenix.real_space_refine on Wed Mar 4 12:50:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fh1_31584/03_2026/7fh1_31584.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fh1_31584/03_2026/7fh1_31584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fh1_31584/03_2026/7fh1_31584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fh1_31584/03_2026/7fh1_31584.map" model { file = "/net/cci-nas-00/data/ceres_data/7fh1_31584/03_2026/7fh1_31584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fh1_31584/03_2026/7fh1_31584.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 8834 2.51 5 N 2246 2.21 5 O 2500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13672 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 6691 Classifications: {'peptide': 874} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 30, 'TRANS': 843} Chain breaks: 4 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 16, 'ASP:plan': 18, 'ASN:plan1': 7, 'PHE:plan': 2, 'TRP:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 196 Chain: "B" Number of atoms: 6691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 6691 Classifications: {'peptide': 874} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 30, 'TRANS': 843} Chain breaks: 4 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 16, 'ASP:plan': 18, 'ASN:plan1': 7, 'PHE:plan': 2, 'TRP:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 196 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.22, per 1000 atoms: 0.24 Number of scatterers: 13672 At special positions: 0 Unit cell: (96.743, 79.351, 170.659, 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 92 16.00 O 2500 8.00 N 2246 7.00 C 8834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 97 " distance=2.04 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 150 " distance=2.04 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 173 " - pdb=" SG CYS A 184 " distance=2.04 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 197 " distance=2.03 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 253 " - pdb=" SG CYS A 268 " distance=2.04 Simple disulfide: pdb=" SG CYS A 357 " - pdb=" SG CYS A 378 " distance=2.03 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 62 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 78 " distance=2.03 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 97 " distance=2.04 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 150 " distance=2.04 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 173 " - pdb=" SG CYS B 184 " distance=2.04 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 268 " distance=2.04 Simple disulfide: pdb=" SG CYS B 357 " - pdb=" SG CYS B 378 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " " BMA J 3 " - " BMA J 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " BETA1-6 " BMA F 3 " - " BMA F 5 " " BMA J 3 " - " BMA J 5 " Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 323.3 milliseconds 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3292 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 24 sheets defined 40.1% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 223 through 230 removed outlier: 3.531A pdb=" N ALA A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 239 Processing helix chain 'A' and resid 242 through 256 removed outlier: 3.686A pdb=" N CYS A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.642A pdb=" N LEU A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 518 through 549 removed outlier: 3.981A pdb=" N VAL A 522 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 592 removed outlier: 3.542A pdb=" N VAL A 561 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN A 573 " --> pdb=" O GLY A 569 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL A 574 " --> pdb=" O ASP A 570 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 633 removed outlier: 4.024A pdb=" N CYS A 615 " --> pdb=" O THR A 611 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA A 616 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 680 removed outlier: 5.047A pdb=" N PHE A 672 " --> pdb=" O TRP A 668 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 675 " --> pdb=" O TYR A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 701 removed outlier: 3.578A pdb=" N LEU A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 709 removed outlier: 3.791A pdb=" N LEU A 709 " --> pdb=" O ASN A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 758 removed outlier: 3.648A pdb=" N ALA A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 746 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 749 " --> pdb=" O ILE A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 772 removed outlier: 3.604A pdb=" N ASP A 768 " --> pdb=" O ARG A 764 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 845 removed outlier: 3.543A pdb=" N ARG A 845 " --> pdb=" O GLN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 886 removed outlier: 3.989A pdb=" N MET A 876 " --> pdb=" O LYS A 872 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 882 " --> pdb=" O ASN A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 907 Processing helix chain 'A' and resid 925 through 930 removed outlier: 3.959A pdb=" N VAL A 930 " --> pdb=" O PHE A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 946 removed outlier: 4.182A pdb=" N LEU A 939 " --> pdb=" O ASN A 935 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 954 removed outlier: 3.927A pdb=" N LEU A 952 " --> pdb=" O CYS A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 987 removed outlier: 3.510A pdb=" N LEU A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TYR A 965 " --> pdb=" O SER A 961 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 967 " --> pdb=" O LEU A 963 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 971 " --> pdb=" O GLN A 967 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN A 980 " --> pdb=" O ASN A 976 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 985 " --> pdb=" O LYS A 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 223 through 230 removed outlier: 3.531A pdb=" N ALA B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 239 Processing helix chain 'B' and resid 242 through 256 removed outlier: 3.686A pdb=" N CYS B 246 " --> pdb=" O ASN B 242 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 360 through 366 removed outlier: 3.551A pdb=" N LEU B 364 " --> pdb=" O THR B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 381 through 389 Processing helix chain 'B' and resid 518 through 549 removed outlier: 3.981A pdb=" N VAL B 522 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU B 537 " --> pdb=" O GLY B 533 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 592 removed outlier: 3.542A pdb=" N VAL B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN B 573 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL B 574 " --> pdb=" O ASP B 570 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 633 removed outlier: 4.025A pdb=" N CYS B 615 " --> pdb=" O THR B 611 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA B 616 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 680 removed outlier: 5.047A pdb=" N PHE B 672 " --> pdb=" O TRP B 668 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN B 675 " --> pdb=" O TYR B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 701 removed outlier: 3.578A pdb=" N LEU B 699 " --> pdb=" O VAL B 695 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 700 " --> pdb=" O LEU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 709 removed outlier: 3.791A pdb=" N LEU B 709 " --> pdb=" O ASN B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 758 removed outlier: 3.648A pdb=" N ALA B 737 " --> pdb=" O TYR B 733 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU B 741 " --> pdb=" O ALA B 737 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 746 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 749 " --> pdb=" O ILE B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 772 removed outlier: 3.605A pdb=" N ASP B 768 " --> pdb=" O ARG B 764 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER B 771 " --> pdb=" O VAL B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 845 removed outlier: 3.543A pdb=" N ARG B 845 " --> pdb=" O GLN B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 886 removed outlier: 3.989A pdb=" N MET B 876 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 882 " --> pdb=" O ASN B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 907 Processing helix chain 'B' and resid 925 through 930 removed outlier: 3.959A pdb=" N VAL B 930 " --> pdb=" O PHE B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 946 removed outlier: 4.182A pdb=" N LEU B 939 " --> pdb=" O ASN B 935 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 954 removed outlier: 3.927A pdb=" N LEU B 952 " --> pdb=" O CYS B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 987 removed outlier: 3.510A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR B 965 " --> pdb=" O SER B 961 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN B 967 " --> pdb=" O LEU B 963 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 971 " --> pdb=" O GLN B 967 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN B 980 " --> pdb=" O ASN B 976 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 985 " --> pdb=" O LYS B 981 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 88 removed outlier: 7.032A pdb=" N ILE A 96 " --> pdb=" O ILE A 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 135 Processing sheet with id=AA6, first strand: chain 'A' and resid 162 through 163 Processing sheet with id=AA7, first strand: chain 'A' and resid 191 through 193 Processing sheet with id=AA8, first strand: chain 'A' and resid 213 through 214 removed outlier: 3.557A pdb=" N ARG A 213 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 221 " --> pdb=" O ARG A 213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 332 through 337 Processing sheet with id=AB1, first strand: chain 'A' and resid 375 through 377 Processing sheet with id=AB2, first strand: chain 'A' and resid 445 through 446 removed outlier: 3.530A pdb=" N ARG A 463 " --> pdb=" O ASP A 446 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA A 491 " --> pdb=" O THR A 466 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 635 through 639 removed outlier: 3.768A pdb=" N ASP A 635 " --> pdb=" O LEU A 780 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 831 through 833 removed outlier: 7.325A pdb=" N LYS A 897 " --> pdb=" O ASN A 921 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'B' and resid 69 through 71 Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 88 removed outlier: 7.031A pdb=" N ILE B 96 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 133 through 135 Processing sheet with id=AB9, first strand: chain 'B' and resid 162 through 163 Processing sheet with id=AC1, first strand: chain 'B' and resid 191 through 193 Processing sheet with id=AC2, first strand: chain 'B' and resid 213 through 214 removed outlier: 3.557A pdb=" N ARG B 213 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 221 " --> pdb=" O ARG B 213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 375 through 377 Processing sheet with id=AC4, first strand: chain 'B' and resid 445 through 446 removed outlier: 3.530A pdb=" N ARG B 463 " --> pdb=" O ASP B 446 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA B 491 " --> pdb=" O THR B 466 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 635 through 639 removed outlier: 3.768A pdb=" N ASP B 635 " --> pdb=" O LEU B 780 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 831 through 833 removed outlier: 7.325A pdb=" N LYS B 897 " --> pdb=" O ASN B 921 " (cutoff:3.500A) 530 hydrogen bonds defined for protein. 1506 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: 2.08 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3665 1.33 - 1.45: 2800 1.45 - 1.57: 7402 1.57 - 1.70: 1 1.70 - 1.82: 124 Bond restraints: 13992 Sorted by residual: bond pdb=" C2 BMA F 5 " pdb=" C3 BMA F 5 " ideal model delta sigma weight residual 1.544 1.486 0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.576 -0.057 2.00e-02 2.50e+03 8.09e+00 bond pdb=" C GLN A 747 " pdb=" O GLN A 747 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.17e-02 7.31e+03 5.31e+00 bond pdb=" C GLN B 747 " pdb=" O GLN B 747 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.17e-02 7.31e+03 5.31e+00 bond pdb=" CA VAL B 415 " pdb=" C VAL B 415 " ideal model delta sigma weight residual 1.522 1.546 -0.024 1.21e-02 6.83e+03 3.97e+00 ... (remaining 13987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.59: 18969 6.59 - 13.19: 49 13.19 - 19.78: 12 19.78 - 26.37: 2 26.37 - 32.97: 2 Bond angle restraints: 19034 Sorted by residual: angle pdb=" N PHE A 758 " pdb=" CA PHE A 758 " pdb=" C PHE A 758 " ideal model delta sigma weight residual 114.09 147.06 -32.97 1.55e+00 4.16e-01 4.52e+02 angle pdb=" N PHE B 758 " pdb=" CA PHE B 758 " pdb=" C PHE B 758 " ideal model delta sigma weight residual 114.09 147.00 -32.91 1.55e+00 4.16e-01 4.51e+02 angle pdb=" C PHE B 758 " pdb=" CA PHE B 758 " pdb=" CB PHE B 758 " ideal model delta sigma weight residual 109.80 87.15 22.65 1.61e+00 3.86e-01 1.98e+02 angle pdb=" C PHE A 758 " pdb=" CA PHE A 758 " pdb=" CB PHE A 758 " ideal model delta sigma weight residual 109.80 87.15 22.65 1.61e+00 3.86e-01 1.98e+02 angle pdb=" C VAL B 613 " pdb=" CA VAL B 613 " pdb=" CB VAL B 613 " ideal model delta sigma weight residual 111.65 92.03 19.62 1.41e+00 5.03e-01 1.94e+02 ... (remaining 19029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.91: 7869 26.91 - 53.82: 485 53.82 - 80.73: 91 80.73 - 107.63: 42 107.63 - 134.54: 35 Dihedral angle restraints: 8522 sinusoidal: 3420 harmonic: 5102 Sorted by residual: dihedral pdb=" C PHE B 758 " pdb=" N PHE B 758 " pdb=" CA PHE B 758 " pdb=" CB PHE B 758 " ideal model delta harmonic sigma weight residual -122.60 -93.04 -29.56 0 2.50e+00 1.60e-01 1.40e+02 dihedral pdb=" C PHE A 758 " pdb=" N PHE A 758 " pdb=" CA PHE A 758 " pdb=" CB PHE A 758 " ideal model delta harmonic sigma weight residual -122.60 -93.05 -29.55 0 2.50e+00 1.60e-01 1.40e+02 dihedral pdb=" N PHE A 758 " pdb=" C PHE A 758 " pdb=" CA PHE A 758 " pdb=" CB PHE A 758 " ideal model delta harmonic sigma weight residual 122.80 95.48 27.32 0 2.50e+00 1.60e-01 1.19e+02 ... (remaining 8519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 2208 0.163 - 0.327: 26 0.327 - 0.490: 2 0.490 - 0.654: 3 0.654 - 0.817: 3 Chirality restraints: 2242 Sorted by residual: chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-02 2.50e+03 1.67e+03 chirality pdb=" C1 BMA J 5 " pdb=" O6 BMA J 3 " pdb=" C2 BMA J 5 " pdb=" O5 BMA J 5 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-02 2.50e+03 1.43e+03 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.63e+02 ... (remaining 2239 not shown) Planarity restraints: 2374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.354 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG D 1 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.106 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.348 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG H 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.161 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.340 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG E 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.054 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.517 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.200 2.00e-02 2.50e+03 ... (remaining 2371 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1772 2.74 - 3.28: 13660 3.28 - 3.82: 20522 3.82 - 4.36: 24304 4.36 - 4.90: 43090 Nonbonded interactions: 103348 Sorted by model distance: nonbonded pdb=" C VAL B 613 " pdb=" CG1 VAL B 613 " model vdw 2.200 2.952 nonbonded pdb=" C VAL A 613 " pdb=" CG1 VAL A 613 " model vdw 2.201 2.952 nonbonded pdb=" ND2 ASN B 242 " pdb=" C1 NAG J 1 " model vdw 2.206 3.550 nonbonded pdb=" O GLY A 91 " pdb=" OD1 ASN B 242 " model vdw 2.212 3.040 nonbonded pdb=" OD1 ASN A 242 " pdb=" O GLY B 91 " model vdw 2.214 3.040 ... (remaining 103343 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.790 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 : 0.009 0.061 14030 Z= 0.388 Angle : 1.254 41.948 19124 Z= 0.711 Chirality : 0.069 0.817 2242 Planarity : 0.019 0.305 2374 Dihedral : 21.248 134.542 5158 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.24 % Favored : 85.76 % Rotamer: Outliers : 3.15 % Allowed : 2.22 % Favored : 94.63 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.18), residues: 1728 helix: -1.40 (0.20), residues: 626 sheet: -2.95 (0.29), residues: 232 loop : -3.45 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 975 TYR 0.020 0.002 TYR B 932 PHE 0.027 0.002 PHE B 895 TRP 0.026 0.002 TRP B 346 HIS 0.007 0.002 HIS A 473 Details of bonding type rmsd covalent geometry : bond 0.00914 (13992) covalent geometry : angle 1.20330 (19034) SS BOND : bond 0.00507 ( 24) SS BOND : angle 1.70563 ( 48) hydrogen bonds : bond 0.25827 ( 530) hydrogen bonds : angle 8.87909 ( 1506) link_BETA1-3 : bond 0.01176 ( 2) link_BETA1-3 : angle 1.35265 ( 6) link_BETA1-4 : bond 0.00472 ( 10) link_BETA1-4 : angle 2.74868 ( 30) link_BETA1-6 : bond 0.04176 ( 2) link_BETA1-6 : angle 18.90862 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 604 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7791 (mm) REVERT: A 608 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6471 (tpt-90) REVERT: A 669 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6680 (ptp-110) REVERT: A 775 ILE cc_start: 0.7596 (mm) cc_final: 0.7348 (mm) REVERT: B 604 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7814 (mm) REVERT: B 608 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.6480 (tpt-90) REVERT: B 669 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6601 (ptp-110) REVERT: B 775 ILE cc_start: 0.7576 (mm) cc_final: 0.7342 (mm) outliers start: 44 outliers final: 25 residues processed: 205 average time/residue: 0.1249 time to fit residues: 36.5130 Evaluate side-chains 132 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 669 ARG Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 608 ARG Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 669 ARG Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 869 GLN Chi-restraints excluded: chain B residue 936 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.0670 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 85 GLN A 141 ASN A 179 ASN A 242 ASN ** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS B 69 GLN B 85 GLN B 141 ASN B 242 ASN ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.117528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.076111 restraints weight = 23246.706| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.69 r_work: 0.2745 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14030 Z= 0.153 Angle : 0.860 15.629 19124 Z= 0.402 Chirality : 0.050 0.422 2242 Planarity : 0.006 0.100 2374 Dihedral : 18.072 103.060 2392 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 2.51 % Allowed : 11.25 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.19), residues: 1728 helix: -0.19 (0.21), residues: 644 sheet: -2.38 (0.28), residues: 242 loop : -3.21 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 208 TYR 0.017 0.002 TYR A 932 PHE 0.022 0.002 PHE B 637 TRP 0.014 0.001 TRP A 346 HIS 0.003 0.001 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00325 (13992) covalent geometry : angle 0.83926 (19034) SS BOND : bond 0.00270 ( 24) SS BOND : angle 1.72481 ( 48) hydrogen bonds : bond 0.05301 ( 530) hydrogen bonds : angle 5.04125 ( 1506) link_BETA1-3 : bond 0.00781 ( 2) link_BETA1-3 : angle 3.39739 ( 6) link_BETA1-4 : bond 0.01551 ( 10) link_BETA1-4 : angle 3.60597 ( 30) link_BETA1-6 : bond 0.01203 ( 2) link_BETA1-6 : angle 4.71685 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 492 TYR cc_start: 0.8770 (m-80) cc_final: 0.8519 (m-80) REVERT: B 363 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7877 (mmt90) REVERT: B 492 TYR cc_start: 0.8763 (m-80) cc_final: 0.8518 (m-80) REVERT: B 877 MET cc_start: 0.8753 (ttm) cc_final: 0.8410 (tpp) outliers start: 35 outliers final: 15 residues processed: 147 average time/residue: 0.1045 time to fit residues: 23.3872 Evaluate side-chains 124 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 835 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 101 optimal weight: 0.0570 chunk 91 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 56 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 173 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 39 optimal weight: 0.3980 chunk 98 optimal weight: 9.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN B 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.118418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.077364 restraints weight = 23626.771| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.72 r_work: 0.2770 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14030 Z= 0.122 Angle : 0.719 10.457 19124 Z= 0.336 Chirality : 0.046 0.274 2242 Planarity : 0.005 0.099 2374 Dihedral : 14.560 102.452 2338 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 2.01 % Allowed : 12.75 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.20), residues: 1728 helix: 0.49 (0.21), residues: 656 sheet: -1.65 (0.30), residues: 232 loop : -3.02 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 182 TYR 0.017 0.001 TYR A 733 PHE 0.014 0.001 PHE A 785 TRP 0.013 0.001 TRP B 346 HIS 0.003 0.001 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00256 (13992) covalent geometry : angle 0.69858 (19034) SS BOND : bond 0.00236 ( 24) SS BOND : angle 1.43359 ( 48) hydrogen bonds : bond 0.03840 ( 530) hydrogen bonds : angle 4.38388 ( 1506) link_BETA1-3 : bond 0.01101 ( 2) link_BETA1-3 : angle 1.84390 ( 6) link_BETA1-4 : bond 0.01335 ( 10) link_BETA1-4 : angle 3.62377 ( 30) link_BETA1-6 : bond 0.01043 ( 2) link_BETA1-6 : angle 4.00827 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.368 Fit side-chains REVERT: A 359 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8616 (m-30) REVERT: A 884 PHE cc_start: 0.8667 (t80) cc_final: 0.8310 (t80) REVERT: B 637 PHE cc_start: 0.6747 (t80) cc_final: 0.6539 (t80) REVERT: B 877 MET cc_start: 0.8637 (ttm) cc_final: 0.8350 (tpt) outliers start: 28 outliers final: 15 residues processed: 141 average time/residue: 0.0895 time to fit residues: 20.2939 Evaluate side-chains 119 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 775 ILE Chi-restraints excluded: chain B residue 938 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 24 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 173 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 678 ASN A 878 ASN A 935 ASN B 318 ASN B 678 ASN ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.111910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.070477 restraints weight = 23684.916| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.67 r_work: 0.2637 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14030 Z= 0.215 Angle : 0.783 12.073 19124 Z= 0.371 Chirality : 0.049 0.363 2242 Planarity : 0.005 0.098 2374 Dihedral : 12.725 102.190 2328 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 3.01 % Allowed : 15.33 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.20), residues: 1728 helix: 0.74 (0.21), residues: 660 sheet: -1.69 (0.31), residues: 244 loop : -2.89 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 182 TYR 0.016 0.001 TYR A 932 PHE 0.016 0.002 PHE A 609 TRP 0.013 0.001 TRP A 290 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00521 (13992) covalent geometry : angle 0.76078 (19034) SS BOND : bond 0.00223 ( 24) SS BOND : angle 1.56135 ( 48) hydrogen bonds : bond 0.04630 ( 530) hydrogen bonds : angle 4.27348 ( 1506) link_BETA1-3 : bond 0.01309 ( 2) link_BETA1-3 : angle 1.79991 ( 6) link_BETA1-4 : bond 0.01255 ( 10) link_BETA1-4 : angle 4.12583 ( 30) link_BETA1-6 : bond 0.00828 ( 2) link_BETA1-6 : angle 3.51292 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 0.452 Fit side-chains REVERT: A 925 TYR cc_start: 0.7986 (m-80) cc_final: 0.7616 (m-80) REVERT: B 637 PHE cc_start: 0.6704 (t80) cc_final: 0.6479 (t80) REVERT: B 877 MET cc_start: 0.8652 (ttm) cc_final: 0.8407 (tpt) REVERT: B 925 TYR cc_start: 0.7863 (m-80) cc_final: 0.7496 (m-80) outliers start: 42 outliers final: 25 residues processed: 140 average time/residue: 0.0875 time to fit residues: 20.2134 Evaluate side-chains 121 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 775 ILE Chi-restraints excluded: chain B residue 938 THR Chi-restraints excluded: chain B residue 982 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 120 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 480 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.113729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.072195 restraints weight = 23704.405| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.75 r_work: 0.2678 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14030 Z= 0.132 Angle : 0.706 10.999 19124 Z= 0.329 Chirality : 0.046 0.287 2242 Planarity : 0.005 0.096 2374 Dihedral : 11.501 98.719 2328 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.01 % Allowed : 16.76 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.20), residues: 1728 helix: 1.11 (0.21), residues: 656 sheet: -1.32 (0.32), residues: 230 loop : -2.88 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 548 TYR 0.011 0.001 TYR B 932 PHE 0.013 0.001 PHE B 919 TRP 0.012 0.001 TRP B 346 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00307 (13992) covalent geometry : angle 0.68339 (19034) SS BOND : bond 0.00294 ( 24) SS BOND : angle 1.30189 ( 48) hydrogen bonds : bond 0.03777 ( 530) hydrogen bonds : angle 4.04929 ( 1506) link_BETA1-3 : bond 0.01072 ( 2) link_BETA1-3 : angle 1.79076 ( 6) link_BETA1-4 : bond 0.01252 ( 10) link_BETA1-4 : angle 3.95962 ( 30) link_BETA1-6 : bond 0.01030 ( 2) link_BETA1-6 : angle 3.43077 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.465 Fit side-chains REVERT: A 925 TYR cc_start: 0.7928 (m-80) cc_final: 0.7554 (m-80) REVERT: A 965 TYR cc_start: 0.9135 (t80) cc_final: 0.8900 (t80) REVERT: B 637 PHE cc_start: 0.6569 (t80) cc_final: 0.6310 (t80) REVERT: B 925 TYR cc_start: 0.7908 (m-80) cc_final: 0.7562 (m-80) REVERT: B 965 TYR cc_start: 0.9170 (t80) cc_final: 0.8891 (t80) outliers start: 28 outliers final: 20 residues processed: 123 average time/residue: 0.0875 time to fit residues: 17.6451 Evaluate side-chains 114 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 775 ILE Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 938 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 162 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 39 optimal weight: 0.0010 chunk 78 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 GLN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN B 878 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.071271 restraints weight = 23423.483| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.12 r_work: 0.2624 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14030 Z= 0.189 Angle : 0.745 11.634 19124 Z= 0.353 Chirality : 0.047 0.311 2242 Planarity : 0.005 0.099 2374 Dihedral : 10.517 96.159 2324 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 2.08 % Allowed : 18.19 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.20), residues: 1728 helix: 1.19 (0.21), residues: 660 sheet: -1.51 (0.32), residues: 240 loop : -2.83 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 182 TYR 0.013 0.001 TYR A 932 PHE 0.014 0.001 PHE B 609 TRP 0.009 0.001 TRP B 346 HIS 0.004 0.001 HIS B 626 Details of bonding type rmsd covalent geometry : bond 0.00456 (13992) covalent geometry : angle 0.72129 (19034) SS BOND : bond 0.00299 ( 24) SS BOND : angle 1.43043 ( 48) hydrogen bonds : bond 0.04323 ( 530) hydrogen bonds : angle 4.07403 ( 1506) link_BETA1-3 : bond 0.01123 ( 2) link_BETA1-3 : angle 1.57262 ( 6) link_BETA1-4 : bond 0.01319 ( 10) link_BETA1-4 : angle 4.21107 ( 30) link_BETA1-6 : bond 0.00889 ( 2) link_BETA1-6 : angle 3.58144 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.390 Fit side-chains REVERT: A 182 ARG cc_start: 0.8420 (mmm160) cc_final: 0.8208 (tpm170) REVERT: A 965 TYR cc_start: 0.9171 (t80) cc_final: 0.8955 (t80) REVERT: B 914 MET cc_start: 0.8504 (pmm) cc_final: 0.8294 (pmm) REVERT: B 925 TYR cc_start: 0.7974 (m-80) cc_final: 0.7582 (m-80) REVERT: B 965 TYR cc_start: 0.9210 (t80) cc_final: 0.8961 (t80) outliers start: 29 outliers final: 21 residues processed: 121 average time/residue: 0.1006 time to fit residues: 19.0423 Evaluate side-chains 110 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 878 ASN Chi-restraints excluded: chain B residue 938 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 48 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 878 ASN B 878 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.112962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.071466 restraints weight = 23390.594| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.74 r_work: 0.2663 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14030 Z= 0.131 Angle : 0.694 11.059 19124 Z= 0.327 Chirality : 0.045 0.288 2242 Planarity : 0.005 0.094 2374 Dihedral : 9.920 90.512 2324 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.08 % Allowed : 18.62 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.20), residues: 1728 helix: 1.35 (0.21), residues: 658 sheet: -1.16 (0.33), residues: 230 loop : -2.83 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 182 TYR 0.011 0.001 TYR A 932 PHE 0.014 0.001 PHE B 884 TRP 0.012 0.001 TRP A 346 HIS 0.004 0.001 HIS B 626 Details of bonding type rmsd covalent geometry : bond 0.00301 (13992) covalent geometry : angle 0.67193 (19034) SS BOND : bond 0.00287 ( 24) SS BOND : angle 1.22279 ( 48) hydrogen bonds : bond 0.03794 ( 530) hydrogen bonds : angle 3.95147 ( 1506) link_BETA1-3 : bond 0.01066 ( 2) link_BETA1-3 : angle 1.63322 ( 6) link_BETA1-4 : bond 0.01230 ( 10) link_BETA1-4 : angle 3.96932 ( 30) link_BETA1-6 : bond 0.01120 ( 2) link_BETA1-6 : angle 3.40103 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.630 Fit side-chains REVERT: A 925 TYR cc_start: 0.7982 (m-80) cc_final: 0.7676 (m-80) REVERT: B 914 MET cc_start: 0.8512 (pmm) cc_final: 0.8297 (pmm) REVERT: B 925 TYR cc_start: 0.7942 (m-80) cc_final: 0.7537 (m-80) REVERT: B 965 TYR cc_start: 0.9153 (t80) cc_final: 0.8947 (t80) outliers start: 29 outliers final: 19 residues processed: 117 average time/residue: 0.0926 time to fit residues: 17.4446 Evaluate side-chains 111 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 938 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 9 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 152 optimal weight: 8.9990 chunk 120 optimal weight: 0.3980 chunk 156 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN B 878 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.072602 restraints weight = 23420.829| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.21 r_work: 0.2641 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14030 Z= 0.134 Angle : 0.693 11.057 19124 Z= 0.327 Chirality : 0.045 0.287 2242 Planarity : 0.005 0.097 2374 Dihedral : 9.207 78.982 2324 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 1.86 % Allowed : 18.55 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.20), residues: 1728 helix: 1.55 (0.21), residues: 648 sheet: -1.11 (0.32), residues: 230 loop : -2.83 (0.18), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 182 TYR 0.011 0.001 TYR A 932 PHE 0.016 0.001 PHE B 884 TRP 0.012 0.001 TRP A 346 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00311 (13992) covalent geometry : angle 0.67099 (19034) SS BOND : bond 0.00308 ( 24) SS BOND : angle 1.30191 ( 48) hydrogen bonds : bond 0.03669 ( 530) hydrogen bonds : angle 3.89013 ( 1506) link_BETA1-3 : bond 0.01040 ( 2) link_BETA1-3 : angle 1.61641 ( 6) link_BETA1-4 : bond 0.01198 ( 10) link_BETA1-4 : angle 3.89814 ( 30) link_BETA1-6 : bond 0.01260 ( 2) link_BETA1-6 : angle 3.53277 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.480 Fit side-chains REVERT: B 878 ASN cc_start: 0.7558 (t160) cc_final: 0.7333 (t0) REVERT: B 925 TYR cc_start: 0.7988 (m-80) cc_final: 0.7612 (m-80) outliers start: 26 outliers final: 21 residues processed: 115 average time/residue: 0.1002 time to fit residues: 18.2049 Evaluate side-chains 109 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 938 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 167 optimal weight: 20.0000 chunk 154 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 878 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.070435 restraints weight = 23561.169| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.76 r_work: 0.2650 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14030 Z= 0.158 Angle : 0.703 11.270 19124 Z= 0.332 Chirality : 0.045 0.285 2242 Planarity : 0.005 0.094 2374 Dihedral : 8.621 60.337 2324 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 1.79 % Allowed : 18.34 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.20), residues: 1728 helix: 1.62 (0.21), residues: 648 sheet: -1.08 (0.33), residues: 230 loop : -2.82 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 548 TYR 0.012 0.001 TYR A 932 PHE 0.015 0.001 PHE B 884 TRP 0.011 0.001 TRP B 346 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00376 (13992) covalent geometry : angle 0.68089 (19034) SS BOND : bond 0.00405 ( 24) SS BOND : angle 1.37373 ( 48) hydrogen bonds : bond 0.03834 ( 530) hydrogen bonds : angle 3.89998 ( 1506) link_BETA1-3 : bond 0.01051 ( 2) link_BETA1-3 : angle 1.53476 ( 6) link_BETA1-4 : bond 0.01193 ( 10) link_BETA1-4 : angle 3.85495 ( 30) link_BETA1-6 : bond 0.01260 ( 2) link_BETA1-6 : angle 3.60015 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.335 Fit side-chains REVERT: B 884 PHE cc_start: 0.8607 (t80) cc_final: 0.8251 (t80) outliers start: 25 outliers final: 22 residues processed: 115 average time/residue: 0.0933 time to fit residues: 17.1549 Evaluate side-chains 114 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 938 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 128 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 66 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 878 ASN B 878 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.072927 restraints weight = 23530.325| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.20 r_work: 0.2587 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14030 Z= 0.165 Angle : 0.701 11.487 19124 Z= 0.333 Chirality : 0.045 0.280 2242 Planarity : 0.005 0.097 2374 Dihedral : 7.917 58.671 2324 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 1.72 % Allowed : 18.62 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.20), residues: 1728 helix: 1.81 (0.21), residues: 636 sheet: -1.09 (0.33), residues: 230 loop : -2.74 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 182 TYR 0.015 0.001 TYR B 932 PHE 0.013 0.001 PHE B 884 TRP 0.011 0.001 TRP B 346 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00395 (13992) covalent geometry : angle 0.68065 (19034) SS BOND : bond 0.00322 ( 24) SS BOND : angle 1.35465 ( 48) hydrogen bonds : bond 0.03914 ( 530) hydrogen bonds : angle 3.88266 ( 1506) link_BETA1-3 : bond 0.00985 ( 2) link_BETA1-3 : angle 1.51523 ( 6) link_BETA1-4 : bond 0.01163 ( 10) link_BETA1-4 : angle 3.73175 ( 30) link_BETA1-6 : bond 0.01180 ( 2) link_BETA1-6 : angle 2.96879 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.536 Fit side-chains REVERT: A 182 ARG cc_start: 0.8268 (mmm160) cc_final: 0.8051 (tpm170) REVERT: B 884 PHE cc_start: 0.8635 (t80) cc_final: 0.8270 (t80) REVERT: B 925 TYR cc_start: 0.8021 (m-80) cc_final: 0.7820 (m-10) outliers start: 24 outliers final: 23 residues processed: 115 average time/residue: 0.0881 time to fit residues: 16.3259 Evaluate side-chains 115 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 938 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 51 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 35 optimal weight: 0.0050 chunk 107 optimal weight: 0.5980 chunk 167 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN ** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.114322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.073945 restraints weight = 23458.586| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.31 r_work: 0.2659 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14030 Z= 0.113 Angle : 0.661 10.749 19124 Z= 0.312 Chirality : 0.044 0.263 2242 Planarity : 0.005 0.094 2374 Dihedral : 7.399 58.479 2324 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 1.65 % Allowed : 18.62 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.20), residues: 1728 helix: 2.01 (0.21), residues: 636 sheet: -0.97 (0.34), residues: 210 loop : -2.65 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 182 TYR 0.012 0.001 TYR A 932 PHE 0.015 0.001 PHE B 884 TRP 0.015 0.001 TRP A 346 HIS 0.005 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00251 (13992) covalent geometry : angle 0.64268 (19034) SS BOND : bond 0.00298 ( 24) SS BOND : angle 1.16950 ( 48) hydrogen bonds : bond 0.03399 ( 530) hydrogen bonds : angle 3.77541 ( 1506) link_BETA1-3 : bond 0.00788 ( 2) link_BETA1-3 : angle 1.68089 ( 6) link_BETA1-4 : bond 0.01205 ( 10) link_BETA1-4 : angle 3.55334 ( 30) link_BETA1-6 : bond 0.01239 ( 2) link_BETA1-6 : angle 2.46497 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2858.41 seconds wall clock time: 49 minutes 40.96 seconds (2980.96 seconds total)