Starting phenix.real_space_refine on Fri Jul 3 10:48:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fh1_31584/07_2026/7fh1_31584.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fh1_31584/07_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_31584/07_2026/7fh1_31584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fh1_31584/07_2026/7fh1_31584.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7fh1_31584/07_2026/7fh1_31584.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fh1_31584/07_2026/7fh1_31584.cif" model { file = "/net/cci-nas-00/data/ceres_data/7fh1_31584/07_2026/7fh1_31584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fh1_31584/07_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-6108/lib/python3.11/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 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 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 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 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 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 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 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 chiralities: 5 Time building chain proxies: 2.50, per 1000 atoms: 0.18 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: 0.92 Conformation dependent library (CDL) restraints added in 494.8 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: 0.33 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: 2.22 Time building geometry restraints manager: 1.17 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 - 17.15: 7096 17.15 - 34.31: 757 34.31 - 51.46: 180 51.46 - 68.62: 19 68.62 - 85.77: 20 Dihedral angle restraints: 8072 sinusoidal: 2970 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 8069 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: 0.03 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: 1.060 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.040 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 : 15.239 85.772 4708 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/Z covalent geometry : bond 0.00914 / 0.39 (13992) covalent geometry : angle 1.20330 / 0.70 (19034) SS BOND : bond 0.00507 / 0.29 ( 24) SS BOND : angle 1.70563 / 1.08 ( 48) hydrogen bonds : bond 0.25827 / 17.28 ( 530) hydrogen bonds : angle 8.87909 / 6.13 ( 1506) link_BETA1-3 : bond 0.01176 / 0.62 ( 2) link_BETA1-3 : angle 1.35265 / 0.68 ( 6) link_BETA1-4 : bond 0.00472 / 0.32 ( 10) link_BETA1-4 : angle 2.74868 / 1.63 ( 30) link_BETA1-6 : bond 0.04176 / 1.99 ( 2) link_BETA1-6 : angle 18.90862 / 10.85 ( 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 : 0.437 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: 0.1122 time to fit residues: 32.9026 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 : 0.482 ------------------------------------------------------------------------------- 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... 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 = 0.3559 r_free = 0.3559 target = 0.117330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.075986 restraints weight = 23253.918| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.69 r_work: 0.2744 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1912 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= 0.153 Angle : 0.808 15.554 19124 Z= 0.389 Chirality : 0.049 0.335 2242 Planarity : 0.006 0.100 2374 Dihedral : 8.138 72.202 1942 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 2.51 % Allowed : 11.32 % Favored : 86.17 % 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: -2.85 (0.19), residues: 1728 helix: -0.19 (0.21), residues: 644 sheet: -2.39 (0.28), residues: 242 loop : -3.21 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 208 TYR 0.017 0.001 TYR A 932 PHE 0.021 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/Z covalent geometry : bond 0.00321 / 0.15 (13992) covalent geometry : angle 0.79422 / 0.39 (19034) SS BOND : bond 0.00968 / 0.58 ( 24) SS BOND : angle 1.65760 / 0.98 ( 48) hydrogen bonds : bond 0.05297 / 3.57 ( 530) hydrogen bonds : angle 5.04419 / 3.55 ( 1506) link_BETA1-3 : bond 0.00647 / 0.33 ( 2) link_BETA1-3 : angle 2.22952 / 1.29 ( 6) link_BETA1-4 : bond 0.01233 / 0.85 ( 10) link_BETA1-4 : angle 3.16573 / 1.92 ( 30) link_BETA1-6 : bond 0.00412 / 0.21 ( 2) link_BETA1-6 : angle 2.28060 / 1.18 ( 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 : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 492 TYR cc_start: 0.8777 (m-80) cc_final: 0.8521 (m-80) REVERT: A 877 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8429 (tpt) REVERT: B 363 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7858 (mmt90) REVERT: B 492 TYR cc_start: 0.8770 (m-80) cc_final: 0.8520 (m-80) REVERT: B 877 MET cc_start: 0.8764 (ttm) cc_final: 0.8416 (tpp) outliers start: 35 outliers final: 15 residues processed: 147 average time/residue: 0.0851 time to fit residues: 19.4581 Evaluate side-chains 125 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 A residue 877 MET 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: 0.8980 chunk 91 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 56 optimal weight: 0.2980 chunk 51 optimal weight: 0.0170 chunk 173 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.117646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.076412 restraints weight = 23292.235| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.70 r_work: 0.2754 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2499 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= 0.118 Angle : 0.694 14.626 19124 Z= 0.332 Chirality : 0.046 0.450 2242 Planarity : 0.005 0.099 2374 Dihedral : 5.984 49.354 1888 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 1.72 % Allowed : 13.18 % Favored : 85.10 % 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: -2.15 (0.20), residues: 1728 helix: 0.55 (0.21), residues: 644 sheet: -1.91 (0.29), residues: 242 loop : -2.98 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 182 TYR 0.014 0.001 TYR B 932 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/Z covalent geometry : bond 0.00254 / 0.12 (13992) covalent geometry : angle 0.67874 / 0.33 (19034) SS BOND : bond 0.00242 / 0.15 ( 24) SS BOND : angle 1.43535 / 0.85 ( 48) hydrogen bonds : bond 0.04039 / 2.69 ( 530) hydrogen bonds : angle 4.43073 / 3.12 ( 1506) link_BETA1-3 : bond 0.00714 / 0.36 ( 2) link_BETA1-3 : angle 1.86646 / 1.11 ( 6) link_BETA1-4 : bond 0.01357 / 0.98 ( 10) link_BETA1-4 : angle 3.14151 / 1.92 ( 30) link_BETA1-6 : bond 0.00597 / 0.29 ( 2) link_BETA1-6 : angle 1.69034 / 0.87 ( 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 145 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.518 Fit side-chains REVERT: A 492 TYR cc_start: 0.8722 (m-80) cc_final: 0.8505 (m-80) REVERT: A 746 ILE cc_start: 0.9217 (mm) cc_final: 0.9010 (mt) REVERT: A 877 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8458 (tpt) REVERT: A 884 PHE cc_start: 0.8678 (t80) cc_final: 0.8327 (t80) REVERT: B 161 MET cc_start: 0.8251 (mmt) cc_final: 0.7724 (mmm) REVERT: B 492 TYR cc_start: 0.8739 (m-80) cc_final: 0.8531 (m-80) REVERT: B 746 ILE cc_start: 0.9223 (mm) cc_final: 0.9008 (mt) REVERT: B 877 MET cc_start: 0.8655 (ttm) cc_final: 0.8354 (tpt) REVERT: B 884 PHE cc_start: 0.8677 (t80) cc_final: 0.8342 (t80) outliers start: 24 outliers final: 15 residues processed: 137 average time/residue: 0.0909 time to fit residues: 19.9839 Evaluate side-chains 122 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 369 SER 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 877 MET 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 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: 2.9990 chunk 141 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 173 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN A 878 ASN A 935 ASN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN B 678 ASN B 935 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.111510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.069801 restraints weight = 23505.881| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.69 r_work: 0.2625 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2769 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= 0.219 Angle : 0.759 14.772 19124 Z= 0.367 Chirality : 0.048 0.470 2242 Planarity : 0.005 0.099 2374 Dihedral : 5.736 42.002 1878 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 3.15 % Allowed : 15.19 % 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: -1.91 (0.20), residues: 1728 helix: 0.74 (0.21), residues: 658 sheet: -1.71 (0.31), residues: 244 loop : -2.93 (0.19), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 440 TYR 0.016 0.001 TYR B 932 PHE 0.020 0.002 PHE B 637 TRP 0.012 0.001 TRP A 290 HIS 0.004 0.001 HIS B 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (13992) covalent geometry : angle 0.74201 / 0.36 (19034) SS BOND : bond 0.00244 / 0.15 ( 24) SS BOND : angle 1.72073 / 1.01 ( 48) hydrogen bonds : bond 0.04671 / 3.12 ( 530) hydrogen bonds : angle 4.31139 / 3.04 ( 1506) link_BETA1-3 : bond 0.00897 / 0.46 ( 2) link_BETA1-3 : angle 1.42289 / 0.78 ( 6) link_BETA1-4 : bond 0.01374 / 1.00 ( 10) link_BETA1-4 : angle 3.50304 / 2.11 ( 30) link_BETA1-6 : bond 0.00231 / 0.12 ( 2) link_BETA1-6 : angle 1.75998 / 0.91 ( 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 150 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 0.531 Fit side-chains REVERT: A 675 ASN cc_start: 0.7961 (t0) cc_final: 0.7746 (t0) REVERT: A 746 ILE cc_start: 0.9228 (mm) cc_final: 0.9023 (mt) REVERT: A 877 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8467 (tpt) REVERT: B 675 ASN cc_start: 0.8004 (t0) cc_final: 0.7800 (t0) REVERT: B 746 ILE cc_start: 0.9248 (mm) cc_final: 0.9039 (mt) REVERT: B 925 TYR cc_start: 0.7909 (m-80) cc_final: 0.7553 (m-80) outliers start: 44 outliers final: 28 residues processed: 141 average time/residue: 0.0799 time to fit residues: 18.6561 Evaluate side-chains 129 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS 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 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 877 MET Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain B residue 49 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 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: 3.9990 chunk 26 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 169 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN B 69 GLN B 480 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.072875 restraints weight = 23426.803| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.71 r_work: 0.2686 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3098 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= 0.119 Angle : 0.671 13.797 19124 Z= 0.320 Chirality : 0.045 0.435 2242 Planarity : 0.005 0.096 2374 Dihedral : 5.406 43.729 1878 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.15 % Allowed : 17.12 % Favored : 80.73 % 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: -1.62 (0.20), residues: 1728 helix: 1.08 (0.21), residues: 654 sheet: -1.24 (0.32), residues: 232 loop : -2.94 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 182 TYR 0.016 0.001 TYR B 843 PHE 0.024 0.001 PHE A 637 TRP 0.012 0.001 TRP B 346 HIS 0.005 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (13992) covalent geometry : angle 0.65618 / 0.32 (19034) SS BOND : bond 0.00274 / 0.16 ( 24) SS BOND : angle 1.34238 / 0.79 ( 48) hydrogen bonds : bond 0.03716 / 2.49 ( 530) hydrogen bonds : angle 4.05581 / 2.86 ( 1506) link_BETA1-3 : bond 0.00720 / 0.36 ( 2) link_BETA1-3 : angle 1.74729 / 1.02 ( 6) link_BETA1-4 : bond 0.01370 / 0.99 ( 10) link_BETA1-4 : angle 3.11087 / 1.89 ( 30) link_BETA1-6 : bond 0.00490 / 0.24 ( 2) link_BETA1-6 : angle 1.59814 / 0.82 ( 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 135 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.580 Fit side-chains REVERT: A 359 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8606 (m-30) REVERT: A 785 PHE cc_start: 0.6951 (t80) cc_final: 0.6490 (t80) REVERT: A 877 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8433 (tpt) REVERT: A 914 MET cc_start: 0.8427 (pmm) cc_final: 0.8192 (pmm) REVERT: A 925 TYR cc_start: 0.7908 (m-80) cc_final: 0.7525 (m-80) REVERT: A 965 TYR cc_start: 0.9112 (t80) cc_final: 0.8898 (t80) REVERT: B 69 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8524 (mp10) REVERT: B 914 MET cc_start: 0.8442 (pmm) cc_final: 0.8189 (pmm) REVERT: B 925 TYR cc_start: 0.7865 (m-80) cc_final: 0.7510 (m-80) REVERT: B 965 TYR cc_start: 0.9154 (t80) cc_final: 0.8890 (t80) outliers start: 30 outliers final: 17 residues processed: 128 average time/residue: 0.0937 time to fit residues: 19.6088 Evaluate side-chains 115 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 369 SER 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 877 MET Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 69 GLN 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 751 PHE Chi-restraints excluded: chain B residue 775 ILE Chi-restraints excluded: chain B residue 835 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 162 optimal weight: 20.0000 chunk 54 optimal weight: 0.5980 chunk 69 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.111527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.071047 restraints weight = 23426.446| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.15 r_work: 0.2604 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14030 Z= 0.209 Angle : 0.722 11.704 19124 Z= 0.350 Chirality : 0.047 0.453 2242 Planarity : 0.005 0.099 2374 Dihedral : 5.269 36.065 1874 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 2.22 % Allowed : 17.98 % Favored : 79.80 % 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: -1.59 (0.20), residues: 1728 helix: 1.15 (0.21), residues: 658 sheet: -1.54 (0.32), residues: 240 loop : -2.88 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 182 TYR 0.014 0.001 TYR A 932 PHE 0.017 0.001 PHE B 884 TRP 0.009 0.001 TRP A 346 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.21 (13992) covalent geometry : angle 0.70548 / 0.35 (19034) SS BOND : bond 0.00336 / 0.19 ( 24) SS BOND : angle 1.58797 / 0.93 ( 48) hydrogen bonds : bond 0.04304 / 2.87 ( 530) hydrogen bonds : angle 4.09765 / 2.89 ( 1506) link_BETA1-3 : bond 0.00885 / 0.45 ( 2) link_BETA1-3 : angle 1.42268 / 0.79 ( 6) link_BETA1-4 : bond 0.01314 / 0.95 ( 10) link_BETA1-4 : angle 3.44515 / 2.08 ( 30) link_BETA1-6 : bond 0.00183 / 0.09 ( 2) link_BETA1-6 : angle 1.68613 / 0.87 ( 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 127 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.506 Fit side-chains REVERT: A 877 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8330 (tpt) REVERT: A 878 ASN cc_start: 0.7908 (t160) cc_final: 0.7611 (t0) REVERT: A 925 TYR cc_start: 0.7931 (m-80) cc_final: 0.7533 (m-80) REVERT: B 925 TYR cc_start: 0.7936 (m-80) cc_final: 0.7563 (m-80) REVERT: B 965 TYR cc_start: 0.9209 (t80) cc_final: 0.8942 (t80) outliers start: 31 outliers final: 24 residues processed: 120 average time/residue: 0.0950 time to fit residues: 18.5682 Evaluate side-chains 116 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS 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 431 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 49 CYS 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 564 LEU Chi-restraints excluded: chain B residue 751 PHE 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: 0.0000 chunk 2 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 148 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 7 optimal weight: 0.0170 chunk 131 optimal weight: 2.9990 overall best weight: 0.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 878 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.073901 restraints weight = 23321.937| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.14 r_work: 0.2670 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14030 Z= 0.110 Angle : 0.657 10.787 19124 Z= 0.314 Chirality : 0.044 0.426 2242 Planarity : 0.005 0.095 2374 Dihedral : 5.060 35.362 1874 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.36 % Allowed : 18.77 % Favored : 78.87 % 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: -1.36 (0.20), residues: 1728 helix: 1.38 (0.21), residues: 652 sheet: -1.11 (0.33), residues: 228 loop : -2.86 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 182 TYR 0.010 0.001 TYR A 932 PHE 0.014 0.001 PHE B 637 TRP 0.013 0.001 TRP B 346 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (13992) covalent geometry : angle 0.64209 / 0.31 (19034) SS BOND : bond 0.00278 / 0.17 ( 24) SS BOND : angle 1.25004 / 0.73 ( 48) hydrogen bonds : bond 0.03524 / 2.35 ( 530) hydrogen bonds : angle 3.91830 / 2.76 ( 1506) link_BETA1-3 : bond 0.00698 / 0.35 ( 2) link_BETA1-3 : angle 1.68571 / 0.97 ( 6) link_BETA1-4 : bond 0.01348 / 0.98 ( 10) link_BETA1-4 : angle 3.12167 / 1.89 ( 30) link_BETA1-6 : bond 0.00494 / 0.24 ( 2) link_BETA1-6 : angle 1.56001 / 0.80 ( 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 135 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.541 Fit side-chains REVERT: A 877 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8500 (tpt) REVERT: A 878 ASN cc_start: 0.7925 (t160) cc_final: 0.7691 (t0) REVERT: A 925 TYR cc_start: 0.7984 (m-80) cc_final: 0.7597 (m-80) REVERT: B 925 TYR cc_start: 0.7935 (m-80) cc_final: 0.7564 (m-80) REVERT: B 965 TYR cc_start: 0.9177 (t80) cc_final: 0.8970 (t80) outliers start: 33 outliers final: 22 residues processed: 126 average time/residue: 0.0954 time to fit residues: 18.6869 Evaluate side-chains 117 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 611 THR 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 877 MET Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 49 CYS 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 515 MET 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 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: 0.8980 chunk 107 optimal weight: 0.9990 chunk 152 optimal weight: 8.9990 chunk 120 optimal weight: 0.2980 chunk 156 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 51 optimal weight: 0.0270 chunk 103 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.115029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.074516 restraints weight = 23303.191| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.16 r_work: 0.2690 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14030 Z= 0.110 Angle : 0.643 10.658 19124 Z= 0.310 Chirality : 0.044 0.424 2242 Planarity : 0.005 0.096 2374 Dihedral : 4.877 35.295 1874 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.86 % Allowed : 19.13 % Favored : 79.01 % 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: -1.21 (0.20), residues: 1728 helix: 1.56 (0.21), residues: 646 sheet: -1.02 (0.33), residues: 228 loop : -2.78 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 182 TYR 0.010 0.001 TYR A 932 PHE 0.015 0.001 PHE B 884 TRP 0.012 0.001 TRP B 346 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (13992) covalent geometry : angle 0.62879 / 0.31 (19034) SS BOND : bond 0.00329 / 0.18 ( 24) SS BOND : angle 1.23009 / 0.71 ( 48) hydrogen bonds : bond 0.03331 / 2.21 ( 530) hydrogen bonds : angle 3.83016 / 2.70 ( 1506) link_BETA1-3 : bond 0.00732 / 0.37 ( 2) link_BETA1-3 : angle 1.62041 / 0.92 ( 6) link_BETA1-4 : bond 0.01351 / 0.98 ( 10) link_BETA1-4 : angle 3.10667 / 1.88 ( 30) link_BETA1-6 : bond 0.00457 / 0.23 ( 2) link_BETA1-6 : angle 1.53987 / 0.78 ( 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 119 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.609 Fit side-chains REVERT: A 359 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8719 (m-30) REVERT: A 877 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8574 (tpt) REVERT: A 878 ASN cc_start: 0.7950 (t160) cc_final: 0.7727 (t0) REVERT: A 925 TYR cc_start: 0.7948 (m-80) cc_final: 0.7587 (m-80) REVERT: B 925 TYR cc_start: 0.7928 (m-80) cc_final: 0.7566 (m-80) outliers start: 26 outliers final: 15 residues processed: 112 average time/residue: 0.0946 time to fit residues: 17.0753 Evaluate side-chains 109 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 CYS 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 772 MET Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 184 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 0.0470 chunk 172 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 167 optimal weight: 10.0000 chunk 154 optimal weight: 0.0670 chunk 71 optimal weight: 0.1980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 878 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.116520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.075014 restraints weight = 23284.414| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.73 r_work: 0.2729 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14030 Z= 0.103 Angle : 0.637 10.563 19124 Z= 0.304 Chirality : 0.043 0.416 2242 Planarity : 0.005 0.095 2374 Dihedral : 4.732 34.613 1874 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.65 % Allowed : 19.05 % 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: -1.08 (0.20), residues: 1728 helix: 1.64 (0.21), residues: 650 sheet: -0.87 (0.33), residues: 224 loop : -2.72 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 548 TYR 0.011 0.001 TYR B 965 PHE 0.014 0.001 PHE B 637 TRP 0.012 0.001 TRP B 346 HIS 0.004 0.001 HIS B 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (13992) covalent geometry : angle 0.62350 / 0.30 (19034) SS BOND : bond 0.00401 / 0.27 ( 24) SS BOND : angle 1.13373 / 0.66 ( 48) hydrogen bonds : bond 0.03105 / 2.04 ( 530) hydrogen bonds : angle 3.75903 / 2.64 ( 1506) link_BETA1-3 : bond 0.00697 / 0.35 ( 2) link_BETA1-3 : angle 1.64636 / 0.94 ( 6) link_BETA1-4 : bond 0.01355 / 0.98 ( 10) link_BETA1-4 : angle 3.01536 / 1.83 ( 30) link_BETA1-6 : bond 0.00510 / 0.25 ( 2) link_BETA1-6 : angle 1.47120 / 0.75 ( 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 124 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.536 Fit side-chains REVERT: A 878 ASN cc_start: 0.7870 (t160) cc_final: 0.7666 (t0) outliers start: 23 outliers final: 19 residues processed: 119 average time/residue: 0.0964 time to fit residues: 18.8452 Evaluate side-chains 112 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 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 772 MET Chi-restraints excluded: chain A residue 775 ILE 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 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 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: 8.9990 chunk 125 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 7 optimal weight: 0.0570 chunk 94 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 878 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.114242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.073507 restraints weight = 23402.188| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 3.08 r_work: 0.2659 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3731 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= 0.146 Angle : 0.658 10.769 19124 Z= 0.318 Chirality : 0.045 0.423 2242 Planarity : 0.005 0.096 2374 Dihedral : 4.820 35.052 1874 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.29 % Allowed : 19.13 % 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: -1.05 (0.20), residues: 1728 helix: 1.69 (0.21), residues: 648 sheet: -0.95 (0.33), residues: 230 loop : -2.70 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 182 TYR 0.012 0.001 TYR A 932 PHE 0.016 0.001 PHE B 884 TRP 0.009 0.001 TRP B 586 HIS 0.004 0.001 HIS B 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 (13992) covalent geometry : angle 0.64286 / 0.31 (19034) SS BOND : bond 0.00333 / 0.21 ( 24) SS BOND : angle 1.35145 / 0.80 ( 48) hydrogen bonds : bond 0.03498 / 2.29 ( 530) hydrogen bonds : angle 3.81149 / 2.67 ( 1506) link_BETA1-3 : bond 0.00792 / 0.40 ( 2) link_BETA1-3 : angle 1.48824 / 0.83 ( 6) link_BETA1-4 : bond 0.01304 / 0.94 ( 10) link_BETA1-4 : angle 3.16406 / 1.92 ( 30) link_BETA1-6 : bond 0.00352 / 0.18 ( 2) link_BETA1-6 : angle 1.49341 / 0.76 ( 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 108 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.544 Fit side-chains outliers start: 18 outliers final: 16 residues processed: 103 average time/residue: 0.0950 time to fit residues: 16.0731 Evaluate side-chains 103 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 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 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 51 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3535 r_free = 0.3535 target = 0.115132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.074846 restraints weight = 23359.636| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.11 r_work: 0.2684 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3827 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= 0.115 Angle : 0.639 10.568 19124 Z= 0.307 Chirality : 0.044 0.419 2242 Planarity : 0.005 0.095 2374 Dihedral : 4.748 34.518 1874 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.43 % Allowed : 19.13 % Favored : 79.44 % 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: -0.91 (0.20), residues: 1728 helix: 1.87 (0.21), residues: 638 sheet: -0.91 (0.33), residues: 230 loop : -2.61 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 975 TYR 0.011 0.001 TYR A 932 PHE 0.015 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/Z covalent geometry : bond 0.00260 / 0.11 (13992) covalent geometry : angle 0.62480 / 0.30 (19034) SS BOND : bond 0.00276 / 0.16 ( 24) SS BOND : angle 1.18988 / 0.70 ( 48) hydrogen bonds : bond 0.03304 / 2.17 ( 530) hydrogen bonds : angle 3.77318 / 2.65 ( 1506) link_BETA1-3 : bond 0.00739 / 0.37 ( 2) link_BETA1-3 : angle 1.54826 / 0.88 ( 6) link_BETA1-4 : bond 0.01309 / 0.95 ( 10) link_BETA1-4 : angle 3.04033 / 1.85 ( 30) link_BETA1-6 : bond 0.00460 / 0.23 ( 2) link_BETA1-6 : angle 1.46109 / 0.74 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2908.67 seconds wall clock time: 50 minutes 35.38 seconds (3035.38 seconds total)