Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 03:31:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fh1_31584/07_2023/7fh1_31584.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fh1_31584/07_2023/7fh1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fh1_31584/07_2023/7fh1_31584.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fh1_31584/07_2023/7fh1_31584.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fh1_31584/07_2023/7fh1_31584.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fh1_31584/07_2023/7fh1_31584.pdb" } 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 ------------------------------------------------------------------------------- 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 Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 207": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A ARG 451": "NH1" <-> "NH2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A ASP 496": "OD1" <-> "OD2" Residue "A TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A ARG 549": "NH1" <-> "NH2" Residue "A TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 732": "NH1" <-> "NH2" Residue "A GLU 756": "OE1" <-> "OE2" Residue "A PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "A ARG 840": "NH1" <-> "NH2" Residue "A TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 886": "OD1" <-> "OD2" Residue "A PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 903": "OE1" <-> "OE2" Residue "A ARG 904": "NH1" <-> "NH2" Residue "A PHE 910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 969": "OE1" <-> "OE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 139": "OD1" <-> "OD2" Residue "B PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 359": "OD1" <-> "OD2" Residue "B TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 441": "NH1" <-> "NH2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 494": "OD1" <-> "OD2" Residue "B ASP 496": "OD1" <-> "OD2" Residue "B TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 548": "NH1" <-> "NH2" Residue "B ARG 549": "NH1" <-> "NH2" Residue "B TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 608": "NH1" <-> "NH2" Residue "B PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 732": "NH1" <-> "NH2" Residue "B GLU 756": "OE1" <-> "OE2" Residue "B PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 792": "NH1" <-> "NH2" Residue "B ARG 840": "NH1" <-> "NH2" Residue "B TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 886": "OD1" <-> "OD2" Residue "B PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 903": "OE1" <-> "OE2" Residue "B ARG 904": "NH1" <-> "NH2" Residue "B PHE 910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 969": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/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, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 2, 'GLU:plan': 16, '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, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 2, 'GLU:plan': 16, '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: 7.09, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 6.26 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 0.71 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: 4.28 Time building geometry restraints manager: 6.47 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: 87.15 - 99.13: 13 99.13 - 111.11: 5809 111.11 - 123.09: 12427 123.09 - 135.07: 783 135.07 - 147.06: 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 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: 0.810 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: 4.240 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 36.650 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.061 13992 Z= 0.593 Angle : 1.203 32.967 19034 Z= 0.702 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 : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.24 % Favored : 85.76 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 fitting. rotamer outliers: 44 poor density : 170 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 25 residues processed: 205 average time/residue: 0.2871 time to fit residues: 83.6071 Evaluate side-chains 128 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 1.640 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 25 outliers final: 1 residues processed: 25 average time/residue: 0.1737 time to fit residues: 9.0311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 158 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN A 242 ASN A 875 HIS ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 242 ASN B 875 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 13992 Z= 0.247 Angle : 0.811 16.879 19034 Z= 0.389 Chirality : 0.049 0.335 2242 Planarity : 0.006 0.100 2374 Dihedral : 5.844 38.372 1868 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.19), residues: 1728 helix: -0.18 (0.21), residues: 644 sheet: -2.37 (0.28), residues: 238 loop : -3.18 (0.19), residues: 846 *********************** 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 154 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 146 average time/residue: 0.2456 time to fit residues: 54.6796 Evaluate side-chains 120 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 1.561 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1215 time to fit residues: 4.6280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 0.0770 chunk 49 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 158 optimal weight: 20.0000 chunk 171 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN B 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 13992 Z= 0.174 Angle : 0.680 14.584 19034 Z= 0.328 Chirality : 0.045 0.461 2242 Planarity : 0.005 0.098 2374 Dihedral : 5.286 36.550 1868 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.20), residues: 1728 helix: 0.47 (0.21), residues: 656 sheet: -1.87 (0.29), residues: 242 loop : -2.98 (0.19), residues: 830 *********************** 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 131 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.623 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 127 average time/residue: 0.2107 time to fit residues: 43.1573 Evaluate side-chains 116 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 1.627 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1247 time to fit residues: 3.7699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 chunk 168 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 ASN B 318 ASN B 678 ASN B 935 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 13992 Z= 0.340 Angle : 0.724 14.477 19034 Z= 0.353 Chirality : 0.047 0.475 2242 Planarity : 0.005 0.098 2374 Dihedral : 5.331 36.456 1868 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.20), residues: 1728 helix: 0.76 (0.21), residues: 654 sheet: -1.76 (0.30), residues: 244 loop : -2.93 (0.19), residues: 830 *********************** 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 139 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 11 residues processed: 131 average time/residue: 0.2177 time to fit residues: 45.7690 Evaluate side-chains 113 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.698 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1247 time to fit residues: 4.7124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 125 optimal weight: 0.4980 chunk 69 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 878 ASN A 935 ASN B 480 ASN B 935 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 13992 Z= 0.233 Angle : 0.684 12.463 19034 Z= 0.328 Chirality : 0.045 0.450 2242 Planarity : 0.005 0.096 2374 Dihedral : 5.154 35.585 1868 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.20), residues: 1728 helix: 1.04 (0.21), residues: 654 sheet: -1.62 (0.31), residues: 240 loop : -2.90 (0.19), residues: 834 *********************** 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 116 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 108 average time/residue: 0.2597 time to fit residues: 42.7544 Evaluate side-chains 109 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.670 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1400 time to fit residues: 3.8821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 77 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 162 optimal weight: 30.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 678 ASN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.046 13992 Z= 0.438 Angle : 0.756 12.374 19034 Z= 0.372 Chirality : 0.049 0.476 2242 Planarity : 0.005 0.098 2374 Dihedral : 5.412 36.110 1868 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.20), residues: 1728 helix: 0.99 (0.21), residues: 660 sheet: -1.73 (0.31), residues: 240 loop : -2.92 (0.19), residues: 828 *********************** 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 118 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 1.636 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 111 average time/residue: 0.2431 time to fit residues: 42.0082 Evaluate side-chains 102 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 2.008 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1443 time to fit residues: 3.4682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 167 optimal weight: 0.0010 chunk 104 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 30.0000 chunk 103 optimal weight: 0.7980 chunk 66 optimal weight: 0.0010 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 13992 Z= 0.157 Angle : 0.648 10.815 19034 Z= 0.311 Chirality : 0.044 0.421 2242 Planarity : 0.005 0.094 2374 Dihedral : 5.032 35.660 1868 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.20), residues: 1728 helix: 1.32 (0.21), residues: 654 sheet: -1.26 (0.32), residues: 234 loop : -2.88 (0.19), residues: 840 *********************** 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 117 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 1.677 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 112 average time/residue: 0.2308 time to fit residues: 41.1375 Evaluate side-chains 98 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 1.597 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2316 time to fit residues: 3.7896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 131 optimal weight: 0.0010 chunk 152 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 overall best weight: 1.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A 878 ASN B 90 ASN B 878 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 13992 Z= 0.274 Angle : 0.675 11.363 19034 Z= 0.325 Chirality : 0.046 0.433 2242 Planarity : 0.005 0.095 2374 Dihedral : 5.022 36.188 1868 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.20), residues: 1728 helix: 1.36 (0.21), residues: 662 sheet: -1.19 (0.33), residues: 230 loop : -2.85 (0.19), residues: 836 *********************** 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 112 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 1.649 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 108 average time/residue: 0.2356 time to fit residues: 40.1497 Evaluate side-chains 101 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.610 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2587 time to fit residues: 4.0714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 147 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 165 optimal weight: 20.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 13992 Z= 0.199 Angle : 0.656 10.803 19034 Z= 0.314 Chirality : 0.044 0.421 2242 Planarity : 0.005 0.094 2374 Dihedral : 4.879 35.272 1868 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.20), residues: 1728 helix: 1.63 (0.21), residues: 644 sheet: -1.07 (0.33), residues: 230 loop : -2.84 (0.19), residues: 854 *********************** 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 100 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 1.440 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 99 average time/residue: 0.2733 time to fit residues: 42.6128 Evaluate side-chains 94 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 1.621 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1231 time to fit residues: 2.8674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 138 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 84 optimal weight: 0.0770 chunk 109 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 overall best weight: 2.1144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 842 HIS ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 13992 Z= 0.304 Angle : 0.690 11.436 19034 Z= 0.333 Chirality : 0.046 0.431 2242 Planarity : 0.005 0.095 2374 Dihedral : 5.009 35.888 1868 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.20), residues: 1728 helix: 1.62 (0.21), residues: 650 sheet: -1.12 (0.34), residues: 230 loop : -2.81 (0.19), residues: 848 ********************** 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 96 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 1.623 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.2260 time to fit residues: 34.6148 Evaluate side-chains 94 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.588 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 20 optimal weight: 0.0020 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 842 HIS A 878 ASN ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.072787 restraints weight = 23212.132| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.72 r_work: 0.2689 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 13992 Z= 0.166 Angle : 0.651 10.690 19034 Z= 0.309 Chirality : 0.044 0.415 2242 Planarity : 0.005 0.094 2374 Dihedral : 4.807 34.892 1868 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.21), residues: 1728 helix: 1.81 (0.21), residues: 648 sheet: -1.00 (0.33), residues: 230 loop : -2.75 (0.19), residues: 850 =============================================================================== Job complete usr+sys time: 2386.39 seconds wall clock time: 44 minutes 32.95 seconds (2672.95 seconds total)