Starting phenix.real_space_refine on Thu Feb 15 23:10:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fh1_31584/02_2024/7fh1_31584.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fh1_31584/02_2024/7fh1_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_31584/02_2024/7fh1_31584.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fh1_31584/02_2024/7fh1_31584.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fh1_31584/02_2024/7fh1_31584.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fh1_31584/02_2024/7fh1_31584.pdb" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.62, per 1000 atoms: 0.56 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: 5.88 Conformation dependent library (CDL) restraints added in 2.5 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: 1.53 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: 4.04 Time building geometry restraints manager: 6.24 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 - 26.91: 7869 26.91 - 53.82: 485 53.82 - 80.73: 91 80.73 - 107.63: 42 107.63 - 134.54: 35 Dihedral angle restraints: 8522 sinusoidal: 3420 harmonic: 5102 Sorted by residual: dihedral pdb=" C PHE B 758 " pdb=" N PHE B 758 " pdb=" CA PHE B 758 " pdb=" CB PHE B 758 " ideal model delta harmonic sigma weight residual -122.60 -93.04 -29.56 0 2.50e+00 1.60e-01 1.40e+02 dihedral pdb=" C PHE A 758 " pdb=" N PHE A 758 " pdb=" CA PHE A 758 " pdb=" CB PHE A 758 " ideal model delta harmonic sigma weight residual -122.60 -93.05 -29.55 0 2.50e+00 1.60e-01 1.40e+02 dihedral pdb=" N PHE A 758 " pdb=" C PHE A 758 " pdb=" CA PHE A 758 " pdb=" CB PHE A 758 " ideal model delta harmonic sigma weight residual 122.80 95.48 27.32 0 2.50e+00 1.60e-01 1.19e+02 ... (remaining 8519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 2208 0.163 - 0.327: 26 0.327 - 0.490: 2 0.490 - 0.654: 3 0.654 - 0.817: 3 Chirality restraints: 2242 Sorted by residual: chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-02 2.50e+03 1.67e+03 chirality pdb=" C1 BMA J 5 " pdb=" O6 BMA J 3 " pdb=" C2 BMA J 5 " pdb=" O5 BMA J 5 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-02 2.50e+03 1.43e+03 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.63e+02 ... (remaining 2239 not shown) Planarity restraints: 2374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.354 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG D 1 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.106 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.348 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG H 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.161 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.340 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG E 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.054 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.517 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.200 2.00e-02 2.50e+03 ... (remaining 2371 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1772 2.74 - 3.28: 13660 3.28 - 3.82: 20522 3.82 - 4.36: 24304 4.36 - 4.90: 43090 Nonbonded interactions: 103348 Sorted by model distance: nonbonded pdb=" C VAL B 613 " pdb=" CG1 VAL B 613 " model vdw 2.200 2.952 nonbonded pdb=" C VAL A 613 " pdb=" CG1 VAL A 613 " model vdw 2.201 2.952 nonbonded pdb=" ND2 ASN B 242 " pdb=" C1 NAG J 1 " model vdw 2.206 3.550 nonbonded pdb=" O GLY A 91 " pdb=" OD1 ASN B 242 " model vdw 2.212 3.040 nonbonded pdb=" OD1 ASN A 242 " pdb=" O GLY B 91 " model vdw 2.214 3.040 ... (remaining 103343 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.600 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: 3.730 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 38.560 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.130 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.000 ------------------------------------------------------------------------------- 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 : 21.248 134.542 5158 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 % 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 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 346 HIS 0.007 0.002 HIS A 473 PHE 0.027 0.002 PHE B 895 TYR 0.020 0.002 TYR B 932 ARG 0.008 0.001 ARG A 975 *********************** 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 : 1.549 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: 0.6802 (OUTLIER) cc_final: 0.6470 (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: 0.7349 (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: 0.2816 time to fit residues: 81.7939 Evaluate side-chains 132 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 101 time to evaluate : 1.620 ------------------------------------------------------------------------------- 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 146 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 158 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 179 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13992 Z= 0.269 Angle : 0.844 16.728 19034 Z= 0.400 Chirality : 0.050 0.410 2242 Planarity : 0.006 0.099 2374 Dihedral : 18.436 108.240 2392 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 2.29 % Allowed : 11.17 % Favored : 86.53 % 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: -2.85 (0.19), residues: 1728 helix: -0.22 (0.21), residues: 650 sheet: -2.41 (0.28), residues: 238 loop : -3.19 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 346 HIS 0.004 0.001 HIS B 133 PHE 0.021 0.002 PHE B 637 TYR 0.018 0.002 TYR A 932 ARG 0.003 0.000 ARG A 669 *********************** 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 146 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 114 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 775 ILE cc_start: 0.7651 (mm) cc_final: 0.7432 (tp) REVERT: B 363 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7648 (mmt90) REVERT: B 775 ILE cc_start: 0.7637 (mm) cc_final: 0.7431 (tp) outliers start: 32 outliers final: 20 residues processed: 137 average time/residue: 0.2196 time to fit residues: 46.9901 Evaluate side-chains 126 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR 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 632 ILE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 938 THR 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 756 GLU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 938 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 0.0070 chunk 49 optimal weight: 7.9990 chunk 131 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 171 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 126 optimal weight: 0.0060 overall best weight: 0.4814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 480 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2583 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= 0.163 Angle : 0.702 10.662 19034 Z= 0.329 Chirality : 0.046 0.296 2242 Planarity : 0.005 0.098 2374 Dihedral : 14.946 105.125 2345 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 1.86 % Allowed : 13.90 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (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: -2.01 (0.20), residues: 1728 helix: 0.64 (0.21), residues: 652 sheet: -1.57 (0.30), residues: 232 loop : -3.00 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 346 HIS 0.003 0.001 HIS B 626 PHE 0.013 0.001 PHE B 919 TYR 0.013 0.001 TYR A 932 ARG 0.007 0.000 ARG B 182 *********************** 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 142 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 1.467 Fit side-chains REVERT: A 775 ILE cc_start: 0.7803 (mm) cc_final: 0.7571 (tp) REVERT: B 775 ILE cc_start: 0.7782 (mm) cc_final: 0.7551 (tp) outliers start: 26 outliers final: 18 residues processed: 136 average time/residue: 0.2000 time to fit residues: 44.0558 Evaluate side-chains 119 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 612 TYR 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 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 612 TYR Chi-restraints excluded: chain B residue 751 PHE 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 156 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 ASN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN B 678 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13992 Z= 0.414 Angle : 0.774 12.292 19034 Z= 0.373 Chirality : 0.049 0.384 2242 Planarity : 0.005 0.099 2374 Dihedral : 13.336 106.281 2328 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 2.87 % Allowed : 15.83 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (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: -1.89 (0.20), residues: 1728 helix: 0.78 (0.21), residues: 658 sheet: -1.79 (0.30), residues: 244 loop : -2.91 (0.19), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 290 HIS 0.004 0.001 HIS B 626 PHE 0.019 0.002 PHE B 609 TYR 0.017 0.002 TYR B 843 ARG 0.011 0.001 ARG A 182 *********************** 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 140 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 100 time to evaluate : 1.491 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 22 residues processed: 135 average time/residue: 0.1966 time to fit residues: 42.9990 Evaluate side-chains 117 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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 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 938 THR 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 938 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 0.0770 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 678 ASN A 878 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3080 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= 0.209 Angle : 0.703 11.211 19034 Z= 0.328 Chirality : 0.046 0.325 2242 Planarity : 0.005 0.096 2374 Dihedral : 12.150 103.509 2328 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.22 % Allowed : 17.19 % Favored : 80.59 % 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: -1.61 (0.20), residues: 1728 helix: 1.11 (0.21), residues: 654 sheet: -1.39 (0.32), residues: 230 loop : -2.89 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 346 HIS 0.005 0.001 HIS A 626 PHE 0.012 0.001 PHE A 672 TYR 0.013 0.001 TYR B 932 ARG 0.009 0.000 ARG A 182 *********************** 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 129 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 98 time to evaluate : 1.627 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 27 residues processed: 121 average time/residue: 0.2120 time to fit residues: 41.2513 Evaluate side-chains 122 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 1.591 ------------------------------------------------------------------------------- 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 278 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 835 ILE 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 278 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 775 ILE Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 938 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 41 optimal weight: 0.2980 chunk 168 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 GLN B 408 GLN B 878 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3289 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= 0.256 Angle : 0.703 11.401 19034 Z= 0.332 Chirality : 0.046 0.311 2242 Planarity : 0.005 0.099 2374 Dihedral : 11.033 101.003 2324 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 2.29 % Allowed : 18.34 % Favored : 79.37 % 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: -1.49 (0.20), residues: 1728 helix: 1.30 (0.21), residues: 654 sheet: -1.55 (0.32), residues: 240 loop : -2.84 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 346 HIS 0.004 0.001 HIS B 626 PHE 0.017 0.001 PHE B 884 TYR 0.012 0.001 TYR B 932 ARG 0.010 0.000 ARG A 182 *********************** 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 129 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 97 time to evaluate : 1.807 Fit side-chains outliers start: 32 outliers final: 25 residues processed: 125 average time/residue: 0.2279 time to fit residues: 44.1435 Evaluate side-chains 119 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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 278 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 835 ILE 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 18 optimal weight: 0.0770 chunk 95 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 167 optimal weight: 20.0000 chunk 104 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 77 optimal weight: 30.0000 chunk 103 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3452 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= 0.207 Angle : 0.679 10.974 19034 Z= 0.319 Chirality : 0.045 0.291 2242 Planarity : 0.005 0.095 2374 Dihedral : 10.258 97.198 2324 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 2.44 % Allowed : 18.27 % 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 (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: -1.33 (0.20), residues: 1728 helix: 1.45 (0.21), residues: 652 sheet: -1.17 (0.33), residues: 230 loop : -2.85 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 346 HIS 0.004 0.001 HIS B 626 PHE 0.018 0.001 PHE B 884 TYR 0.012 0.001 TYR A 932 ARG 0.011 0.000 ARG B 182 *********************** 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 136 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 102 time to evaluate : 1.649 Fit side-chains outliers start: 34 outliers final: 26 residues processed: 131 average time/residue: 0.2601 time to fit residues: 51.1881 Evaluate side-chains 119 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 93 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 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 100 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 131 optimal weight: 0.0020 chunk 152 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- 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 878 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13992 Z= 0.249 Angle : 0.695 11.195 19034 Z= 0.328 Chirality : 0.045 0.294 2242 Planarity : 0.005 0.098 2374 Dihedral : 9.801 94.057 2324 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 2.44 % Allowed : 18.98 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (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: -1.23 (0.20), residues: 1728 helix: 1.54 (0.21), residues: 654 sheet: -1.09 (0.33), residues: 230 loop : -2.83 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 346 HIS 0.004 0.001 HIS B 626 PHE 0.016 0.001 PHE A 884 TYR 0.023 0.001 TYR A 874 ARG 0.012 0.000 ARG A 182 *********************** 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 133 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 99 time to evaluate : 1.451 Fit side-chains outliers start: 34 outliers final: 26 residues processed: 128 average time/residue: 0.2199 time to fit residues: 44.6364 Evaluate side-chains 121 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 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 156 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 878 ASN B 878 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3640 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= 0.246 Angle : 0.689 11.127 19034 Z= 0.327 Chirality : 0.045 0.289 2242 Planarity : 0.005 0.095 2374 Dihedral : 9.381 88.527 2324 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 2.01 % Allowed : 19.20 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (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: -1.18 (0.20), residues: 1728 helix: 1.61 (0.21), residues: 658 sheet: -1.04 (0.33), residues: 230 loop : -2.84 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 346 HIS 0.004 0.001 HIS B 626 PHE 0.016 0.001 PHE A 884 TYR 0.013 0.001 TYR B 932 ARG 0.002 0.000 ARG A 684 *********************** 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 127 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 1.530 Fit side-chains outliers start: 28 outliers final: 26 residues processed: 121 average time/residue: 0.2215 time to fit residues: 42.1051 Evaluate side-chains 123 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 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 100 optimal weight: 3.9990 chunk 78 optimal weight: 0.1980 chunk 114 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 878 ASN B 878 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3710 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= 0.249 Angle : 0.686 11.176 19034 Z= 0.326 Chirality : 0.045 0.284 2242 Planarity : 0.005 0.097 2374 Dihedral : 8.913 78.308 2324 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 2.08 % Allowed : 19.20 % Favored : 78.72 % 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: -1.07 (0.21), residues: 1728 helix: 1.85 (0.21), residues: 646 sheet: -1.04 (0.34), residues: 230 loop : -2.84 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 668 HIS 0.004 0.001 HIS B 626 PHE 0.017 0.001 PHE A 884 TYR 0.028 0.001 TYR B 874 ARG 0.016 0.001 ARG A 182 ********************** 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 130 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 101 time to evaluate : 1.495 Fit side-chains REVERT: A 884 PHE cc_start: 0.7328 (t80) cc_final: 0.7080 (t80) REVERT: B 884 PHE cc_start: 0.7365 (t80) cc_final: 0.7112 (t80) outliers start: 29 outliers final: 27 residues processed: 124 average time/residue: 0.2293 time to fit residues: 44.9198 Evaluate side-chains 126 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 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 42 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 878 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.113936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.072606 restraints weight = 23369.854| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.61 r_work: 0.2698 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3853 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= 0.185 Angle : 0.657 10.857 19034 Z= 0.311 Chirality : 0.044 0.270 2242 Planarity : 0.005 0.095 2374 Dihedral : 8.006 58.568 2324 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.22 % Allowed : 19.20 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.21), residues: 1728 helix: 2.02 (0.21), residues: 644 sheet: -0.94 (0.34), residues: 230 loop : -2.80 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 346 HIS 0.007 0.001 HIS A 842 PHE 0.016 0.001 PHE A 884 TYR 0.024 0.001 TYR A 843 ARG 0.002 0.000 ARG A 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2745.80 seconds wall clock time: 50 minutes 36.53 seconds (3036.53 seconds total)