Starting phenix.real_space_refine on Mon May 19 13:58:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bqi_44800/05_2025/9bqi_44800_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bqi_44800/05_2025/9bqi_44800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bqi_44800/05_2025/9bqi_44800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bqi_44800/05_2025/9bqi_44800.map" model { file = "/net/cci-nas-00/data/ceres_data/9bqi_44800/05_2025/9bqi_44800_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bqi_44800/05_2025/9bqi_44800_trim.cif" } resolution = 2.55 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= 0.012 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: 6 Type Number sf(0) Gaussians S 69 5.16 5 Cl 3 4.86 5 C 6021 2.51 5 N 1509 2.21 5 O 1950 1.98 5 H 8589 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18141 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 374, 5787 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Conformer: "B" Number of residues, atoms: 374, 5787 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 bond proxies already assigned to first conformer: 5851 Chain: "C" Number of atoms: 5788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 374, 5787 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Conformer: "B" Number of residues, atoms: 374, 5787 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 bond proxies already assigned to first conformer: 5851 Chain: "B" Number of atoms: 5788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 374, 5787 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Conformer: "B" Number of residues, atoms: 374, 5787 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 bond proxies already assigned to first conformer: 5851 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: "K" 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: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'LMT': 2, 'NAG': 1, 'P6E': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'LMT': 2, 'NAG': 1, 'P6E': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'LMT': 2, 'NAG': 1, 'P6E': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Time building chain proxies: 18.20, per 1000 atoms: 1.00 Number of scatterers: 18141 At special positions: 0 Unit cell: (92.016, 88.128, 132.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 3 17.00 S 69 16.00 O 1950 8.00 N 1509 7.00 C 6021 6.00 H 8589 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 227 " distance=2.04 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 227 " distance=2.04 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 270 " distance=2.04 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 227 " distance=2.04 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 270 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " 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 I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A 404 " - " ASN A 199 " " NAG B 404 " - " ASN B 199 " " NAG C 404 " - " ASN C 199 " " NAG D 1 " - " ASN A 75 " " NAG E 1 " - " ASN A 184 " " NAG F 1 " - " ASN A 208 " " NAG G 1 " - " ASN C 75 " " NAG H 1 " - " ASN C 184 " " NAG I 1 " - " ASN C 208 " " NAG J 1 " - " ASN B 75 " " NAG K 1 " - " ASN B 184 " " NAG L 1 " - " ASN B 208 " Time building additional restraints: 5.05 Conformation dependent library (CDL) restraints added in 2.5 seconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 21 sheets defined 29.5% alpha, 50.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 25 through 46 Processing helix chain 'A' and resid 85 through 90 removed outlier: 3.514A pdb=" N VAL A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.560A pdb=" N ALA A 182 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 183 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 removed outlier: 3.549A pdb=" N LYS A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.785A pdb=" N VAL A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.630A pdb=" N CYS A 270 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 346 removed outlier: 3.770A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 removed outlier: 4.196A pdb=" N THR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'C' and resid 4 through 13 Processing helix chain 'C' and resid 25 through 46 Processing helix chain 'C' and resid 85 through 90 removed outlier: 3.514A pdb=" N VAL C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.560A pdb=" N ALA C 182 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 183 " --> pdb=" O LYS C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.550A pdb=" N LYS C 215 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.784A pdb=" N VAL C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 removed outlier: 3.629A pdb=" N CYS C 270 " --> pdb=" O ALA C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 346 removed outlier: 3.770A pdb=" N THR C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 360 removed outlier: 4.197A pdb=" N THR C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 Processing helix chain 'B' and resid 4 through 13 Processing helix chain 'B' and resid 25 through 46 Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.514A pdb=" N VAL B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.560A pdb=" N ALA B 182 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 183 " --> pdb=" O LYS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 215 removed outlier: 3.550A pdb=" N LYS B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.784A pdb=" N VAL B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.627A pdb=" N CYS B 270 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 removed outlier: 3.769A pdb=" N THR B 335 " --> pdb=" O ASP B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 360 removed outlier: 4.197A pdb=" N THR B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 18 removed outlier: 4.274A pdb=" N ARG B 24 " --> pdb=" O VAL C 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 14 through 18 removed outlier: 6.646A pdb=" N ILE A 20 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL B 375 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU A 22 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 59 Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 69 Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 69 Processing sheet with id=AA6, first strand: chain 'A' and resid 72 through 76 removed outlier: 3.770A pdb=" N THR A 76 " --> pdb=" O GLY A 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 144 through 151 removed outlier: 9.123A pdb=" N VAL A 144 " --> pdb=" O TRP A 164 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N TRP A 164 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N THR A 146 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ALA A 162 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ARG A 148 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR A 315 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 105 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS A 313 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU A 107 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU A 311 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N MET A 109 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG A 309 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN A 111 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU A 307 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 144 through 151 removed outlier: 9.123A pdb=" N VAL A 144 " --> pdb=" O TRP A 164 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N TRP A 164 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N THR A 146 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ALA A 162 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ARG A 148 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR A 315 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 105 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS A 313 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU A 107 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU A 311 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N MET A 109 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG A 309 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN A 111 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU A 307 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 372 through 375 removed outlier: 4.278A pdb=" N ARG C 24 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 55 through 59 Processing sheet with id=AB2, first strand: chain 'C' and resid 61 through 69 Processing sheet with id=AB3, first strand: chain 'C' and resid 61 through 69 Processing sheet with id=AB4, first strand: chain 'C' and resid 72 through 76 removed outlier: 3.769A pdb=" N THR C 76 " --> pdb=" O GLY C 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 144 through 151 removed outlier: 9.123A pdb=" N VAL C 144 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N TRP C 164 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR C 146 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ALA C 162 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ARG C 148 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR C 315 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL C 105 " --> pdb=" O LYS C 313 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS C 313 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU C 107 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU C 311 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N MET C 109 " --> pdb=" O ARG C 309 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG C 309 " --> pdb=" O MET C 109 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN C 111 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLU C 307 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 144 through 151 removed outlier: 9.123A pdb=" N VAL C 144 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N TRP C 164 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR C 146 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ALA C 162 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ARG C 148 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR C 315 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL C 105 " --> pdb=" O LYS C 313 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS C 313 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU C 107 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU C 311 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N MET C 109 " --> pdb=" O ARG C 309 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG C 309 " --> pdb=" O MET C 109 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN C 111 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLU C 307 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 55 through 59 Processing sheet with id=AB8, first strand: chain 'B' and resid 61 through 69 Processing sheet with id=AB9, first strand: chain 'B' and resid 61 through 69 Processing sheet with id=AC1, first strand: chain 'B' and resid 72 through 76 removed outlier: 3.769A pdb=" N THR B 76 " --> pdb=" O GLY B 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 144 through 151 removed outlier: 9.122A pdb=" N VAL B 144 " --> pdb=" O TRP B 164 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N TRP B 164 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR B 146 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ALA B 162 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ARG B 148 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR B 315 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL B 105 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS B 313 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU B 107 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU B 311 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N MET B 109 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG B 309 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN B 111 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU B 307 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 144 through 151 removed outlier: 9.122A pdb=" N VAL B 144 " --> pdb=" O TRP B 164 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N TRP B 164 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR B 146 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ALA B 162 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ARG B 148 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR B 315 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL B 105 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS B 313 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU B 107 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU B 311 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N MET B 109 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG B 309 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN B 111 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU B 307 " --> pdb=" O GLN B 111 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1263 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: 7.29 Time building geometry restraints manager: 5.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8574 1.03 - 1.23: 141 1.23 - 1.43: 3906 1.43 - 1.62: 5475 1.62 - 1.82: 96 Bond restraints: 18192 Sorted by residual: bond pdb=" C LYS B 67 " pdb=" O LYS B 67 " ideal model delta sigma weight residual 1.234 1.194 0.040 1.18e-02 7.18e+03 1.15e+01 bond pdb=" C LYS C 67 " pdb=" O LYS C 67 " ideal model delta sigma weight residual 1.234 1.194 0.040 1.18e-02 7.18e+03 1.15e+01 bond pdb=" C LYS A 67 " pdb=" O LYS A 67 " ideal model delta sigma weight residual 1.234 1.195 0.039 1.18e-02 7.18e+03 1.08e+01 bond pdb=" N LYS A 363 " pdb=" CA LYS A 363 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.10e-02 8.26e+03 8.21e+00 bond pdb=" N LYS B 363 " pdb=" CA LYS B 363 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 7.74e+00 ... (remaining 18187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 31990 1.88 - 3.77: 428 3.77 - 5.65: 51 5.65 - 7.53: 21 7.53 - 9.41: 15 Bond angle restraints: 32505 Sorted by residual: angle pdb=" N LEU B 365 " pdb=" CA LEU B 365 " pdb=" C LEU B 365 " ideal model delta sigma weight residual 112.90 108.41 4.49 1.31e+00 5.83e-01 1.18e+01 angle pdb=" N LEU C 365 " pdb=" CA LEU C 365 " pdb=" C LEU C 365 " ideal model delta sigma weight residual 112.90 108.42 4.48 1.31e+00 5.83e-01 1.17e+01 angle pdb=" N LEU A 365 " pdb=" CA LEU A 365 " pdb=" C LEU A 365 " ideal model delta sigma weight residual 112.90 108.44 4.46 1.31e+00 5.83e-01 1.16e+01 angle pdb=" CA LYS C 373 " pdb=" C LYS C 373 " pdb=" O LYS C 373 " ideal model delta sigma weight residual 120.32 116.63 3.69 1.10e+00 8.26e-01 1.12e+01 angle pdb=" CA THR B 210 " pdb=" C THR B 210 " pdb=" O THR B 210 " ideal model delta sigma weight residual 121.89 117.97 3.92 1.17e+00 7.31e-01 1.12e+01 ... (remaining 32500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.88: 8635 21.88 - 43.77: 426 43.77 - 65.65: 143 65.65 - 87.54: 30 87.54 - 109.42: 15 Dihedral angle restraints: 9249 sinusoidal: 5352 harmonic: 3897 Sorted by residual: dihedral pdb=" CB CYS C 261 " pdb=" SG CYS C 261 " pdb=" SG CYS C 270 " pdb=" CB CYS C 270 " ideal model delta sinusoidal sigma weight residual -86.00 -53.23 -32.77 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CB CYS A 261 " pdb=" SG CYS A 261 " pdb=" SG CYS A 270 " pdb=" CB CYS A 270 " ideal model delta sinusoidal sigma weight residual -86.00 -53.23 -32.77 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CB CYS B 261 " pdb=" SG CYS B 261 " pdb=" SG CYS B 270 " pdb=" CB CYS B 270 " ideal model delta sinusoidal sigma weight residual -86.00 -53.26 -32.74 1 1.00e+01 1.00e-02 1.52e+01 ... (remaining 9246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1232 0.054 - 0.109: 206 0.109 - 0.163: 110 0.163 - 0.218: 12 0.218 - 0.272: 6 Chirality restraints: 1566 Sorted by residual: chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1563 not shown) Planarity restraints: 2661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 365 " 0.015 2.00e-02 2.50e+03 2.79e-02 7.79e+00 pdb=" N TYR C 366 " -0.048 2.00e-02 2.50e+03 pdb=" CA TYR C 366 " 0.012 2.00e-02 2.50e+03 pdb=" H TYR C 366 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 365 " 0.015 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" N TYR A 366 " -0.048 2.00e-02 2.50e+03 pdb=" CA TYR A 366 " 0.012 2.00e-02 2.50e+03 pdb=" H TYR A 366 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 365 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" N TYR B 366 " -0.048 2.00e-02 2.50e+03 pdb=" CA TYR B 366 " 0.012 2.00e-02 2.50e+03 pdb=" H TYR B 366 " 0.021 2.00e-02 2.50e+03 ... (remaining 2658 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 607 2.17 - 2.78: 33941 2.78 - 3.38: 47326 3.38 - 3.99: 66430 3.99 - 4.60: 100791 Nonbonded interactions: 249095 Sorted by model distance: nonbonded pdb=" HH TYR C 299 " pdb=" OD1 ASP B 88 " model vdw 1.562 2.450 nonbonded pdb=" OD1 ASP A 88 " pdb=" HH TYR B 299 " model vdw 1.570 2.450 nonbonded pdb=" HH TYR A 299 " pdb=" OD1 ASP C 88 " model vdw 1.572 2.450 nonbonded pdb=" O GLY C 70 " pdb=" HH TYR C 89 " model vdw 1.701 2.450 nonbonded pdb=" O GLY B 70 " pdb=" HH TYR B 89 " model vdw 1.702 2.450 ... (remaining 249090 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 253 or resid 255 through 376)) selection = (chain 'B' and (resid 3 through 253 or resid 255 through 376)) selection = (chain 'C' and (resid 3 through 253 or resid 255 through 376)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' } 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=0.50 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: 17.210 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: 0.310 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 49.990 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 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:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 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 : 0.006 0.050 9636 Z= 0.301 Angle : 0.798 9.413 13125 Z= 0.371 Chirality : 0.055 0.272 1566 Planarity : 0.005 0.080 1578 Dihedral : 15.816 109.419 4128 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1116 helix: 0.18 (0.31), residues: 324 sheet: 0.40 (0.27), residues: 348 loop : -0.95 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 259 HIS 0.002 0.000 HIS C 286 PHE 0.013 0.001 PHE B 178 TYR 0.009 0.001 TYR B 213 ARG 0.003 0.000 ARG B 277 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 12) link_NAG-ASN : angle 2.31752 ( 36) link_BETA1-4 : bond 0.00509 ( 12) link_BETA1-4 : angle 1.90590 ( 36) hydrogen bonds : bond 0.17871 ( 382) hydrogen bonds : angle 7.81106 ( 1263) SS BOND : bond 0.00362 ( 9) SS BOND : angle 1.10444 ( 18) covalent geometry : bond 0.00581 ( 9603) covalent geometry : angle 0.78401 (13035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8221 (t0) cc_final: 0.7876 (t0) REVERT: A 197 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7969 (ttmt) REVERT: A 246 MET cc_start: 0.8485 (ttt) cc_final: 0.8240 (ttt) REVERT: C 159 CYS cc_start: 0.7720 (p) cc_final: 0.7386 (p) REVERT: C 234 LYS cc_start: 0.8114 (tttt) cc_final: 0.7873 (ttpp) REVERT: C 320 ASP cc_start: 0.7341 (m-30) cc_final: 0.7127 (m-30) REVERT: B 107 LEU cc_start: 0.8537 (mt) cc_final: 0.8328 (mp) REVERT: B 168 GLU cc_start: 0.7464 (tt0) cc_final: 0.7254 (tt0) REVERT: B 220 ASP cc_start: 0.7782 (t0) cc_final: 0.7490 (t70) outliers start: 0 outliers final: 1 residues processed: 283 average time/residue: 2.6391 time to fit residues: 795.5937 Evaluate side-chains 262 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.128614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.108971 restraints weight = 34218.304| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.27 r_work: 0.3307 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9636 Z= 0.250 Angle : 0.636 5.370 13125 Z= 0.328 Chirality : 0.048 0.220 1566 Planarity : 0.004 0.028 1578 Dihedral : 12.347 70.425 2135 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.84 % Allowed : 9.92 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1116 helix: 0.12 (0.30), residues: 327 sheet: 0.73 (0.29), residues: 330 loop : -0.80 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 259 HIS 0.002 0.001 HIS C 286 PHE 0.012 0.002 PHE B 178 TYR 0.013 0.002 TYR B 292 ARG 0.005 0.001 ARG A 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 12) link_NAG-ASN : angle 1.64725 ( 36) link_BETA1-4 : bond 0.00517 ( 12) link_BETA1-4 : angle 2.13099 ( 36) hydrogen bonds : bond 0.05194 ( 382) hydrogen bonds : angle 5.59487 ( 1263) SS BOND : bond 0.00458 ( 9) SS BOND : angle 1.47335 ( 18) covalent geometry : bond 0.00601 ( 9603) covalent geometry : angle 0.61950 (13035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 284 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 276 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8412 (t0) cc_final: 0.8135 (t0) REVERT: A 69 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8297 (mtmm) REVERT: A 82 ARG cc_start: 0.7922 (mtp85) cc_final: 0.7719 (mtp-110) REVERT: A 112 THR cc_start: 0.8653 (p) cc_final: 0.8441 (m) REVERT: A 308 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7883 (mm-40) REVERT: C 13 PHE cc_start: 0.8644 (m-80) cc_final: 0.8279 (m-80) REVERT: B 69 LYS cc_start: 0.8832 (mtpp) cc_final: 0.8339 (mtmm) outliers start: 8 outliers final: 4 residues processed: 278 average time/residue: 2.6993 time to fit residues: 798.8474 Evaluate side-chains 273 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 268 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 320 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 0.9990 chunk 38 optimal weight: 0.0470 chunk 2 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 chunk 70 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN C 262 ASN ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.128697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109033 restraints weight = 33620.937| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.24 r_work: 0.3312 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9636 Z= 0.169 Angle : 0.578 4.853 13125 Z= 0.297 Chirality : 0.046 0.253 1566 Planarity : 0.003 0.028 1578 Dihedral : 10.236 56.978 2135 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.95 % Allowed : 12.55 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1116 helix: 0.15 (0.30), residues: 327 sheet: 0.73 (0.29), residues: 330 loop : -0.84 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 259 HIS 0.003 0.001 HIS C 286 PHE 0.011 0.001 PHE B 11 TYR 0.011 0.001 TYR A 89 ARG 0.003 0.000 ARG A 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 12) link_NAG-ASN : angle 1.76814 ( 36) link_BETA1-4 : bond 0.00464 ( 12) link_BETA1-4 : angle 2.07988 ( 36) hydrogen bonds : bond 0.04658 ( 382) hydrogen bonds : angle 5.16551 ( 1263) SS BOND : bond 0.00429 ( 9) SS BOND : angle 1.30884 ( 18) covalent geometry : bond 0.00397 ( 9603) covalent geometry : angle 0.56015 (13035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 277 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7644 (mtp-110) REVERT: A 112 THR cc_start: 0.8662 (p) cc_final: 0.8453 (m) REVERT: A 308 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7951 (mm-40) REVERT: A 363 LYS cc_start: 0.8400 (mtpt) cc_final: 0.8051 (mmpt) REVERT: C 159 CYS cc_start: 0.8552 (p) cc_final: 0.8269 (m) REVERT: C 273 ARG cc_start: 0.8114 (mmt180) cc_final: 0.7878 (mmt180) REVERT: B 69 LYS cc_start: 0.8822 (mtpp) cc_final: 0.8346 (mtmm) REVERT: B 168 GLU cc_start: 0.7895 (tt0) cc_final: 0.7670 (tt0) REVERT: B 307 GLU cc_start: 0.7486 (tt0) cc_final: 0.7180 (tt0) outliers start: 9 outliers final: 5 residues processed: 279 average time/residue: 2.7303 time to fit residues: 810.5278 Evaluate side-chains 278 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 272 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 179 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 76 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.0020 chunk 96 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 109 optimal weight: 0.2980 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN C 97 ASN C 262 ASN B 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.128808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.108952 restraints weight = 34102.264| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.27 r_work: 0.3298 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9636 Z= 0.145 Angle : 0.544 4.620 13125 Z= 0.281 Chirality : 0.045 0.242 1566 Planarity : 0.003 0.052 1578 Dihedral : 9.139 56.179 2135 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.05 % Allowed : 14.24 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1116 helix: 0.25 (0.30), residues: 327 sheet: 0.48 (0.28), residues: 360 loop : -0.86 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 259 HIS 0.002 0.001 HIS C 286 PHE 0.010 0.001 PHE B 11 TYR 0.011 0.001 TYR A 89 ARG 0.008 0.001 ARG C 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 12) link_NAG-ASN : angle 1.77327 ( 36) link_BETA1-4 : bond 0.00387 ( 12) link_BETA1-4 : angle 1.94545 ( 36) hydrogen bonds : bond 0.04208 ( 382) hydrogen bonds : angle 4.93439 ( 1263) SS BOND : bond 0.00419 ( 9) SS BOND : angle 1.23466 ( 18) covalent geometry : bond 0.00341 ( 9603) covalent geometry : angle 0.52632 (13035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 276 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 THR cc_start: 0.8633 (p) cc_final: 0.8423 (m) REVERT: A 363 LYS cc_start: 0.8407 (mtpt) cc_final: 0.8048 (mmpt) REVERT: C 159 CYS cc_start: 0.8521 (p) cc_final: 0.8259 (m) REVERT: C 273 ARG cc_start: 0.8108 (mmt180) cc_final: 0.7859 (mmt180) REVERT: C 308 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7962 (mt0) REVERT: B 69 LYS cc_start: 0.8812 (mtpp) cc_final: 0.8312 (mtmm) REVERT: B 170 ASP cc_start: 0.8132 (p0) cc_final: 0.7894 (p0) outliers start: 10 outliers final: 6 residues processed: 278 average time/residue: 2.7585 time to fit residues: 816.8765 Evaluate side-chains 278 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 272 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 179 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 ASN C 262 ASN B 110 ASN B 308 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.127708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107958 restraints weight = 34686.389| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.26 r_work: 0.3269 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 9636 Z= 0.297 Angle : 0.643 5.216 13125 Z= 0.330 Chirality : 0.049 0.264 1566 Planarity : 0.004 0.053 1578 Dihedral : 9.244 55.282 2135 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.05 % Allowed : 15.08 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1116 helix: 0.10 (0.30), residues: 324 sheet: 0.66 (0.28), residues: 354 loop : -0.93 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 259 HIS 0.004 0.001 HIS C 286 PHE 0.014 0.002 PHE B 11 TYR 0.018 0.002 TYR B 89 ARG 0.008 0.001 ARG C 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 12) link_NAG-ASN : angle 2.01643 ( 36) link_BETA1-4 : bond 0.00387 ( 12) link_BETA1-4 : angle 2.28625 ( 36) hydrogen bonds : bond 0.04975 ( 382) hydrogen bonds : angle 5.15984 ( 1263) SS BOND : bond 0.00559 ( 9) SS BOND : angle 1.75205 ( 18) covalent geometry : bond 0.00725 ( 9603) covalent geometry : angle 0.62209 (13035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 282 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 272 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8811 (mtpp) cc_final: 0.8237 (mtmm) REVERT: A 363 LYS cc_start: 0.8477 (mtpt) cc_final: 0.8112 (mmpt) REVERT: C 69 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8405 (mtmm) REVERT: C 273 ARG cc_start: 0.8131 (mmt180) cc_final: 0.7903 (mmt180) REVERT: C 308 GLN cc_start: 0.8296 (mm-40) cc_final: 0.8001 (mt0) REVERT: B 69 LYS cc_start: 0.8801 (mtpp) cc_final: 0.8298 (mtmm) outliers start: 10 outliers final: 5 residues processed: 276 average time/residue: 2.6602 time to fit residues: 781.1340 Evaluate side-chains 276 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 271 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 363 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 86 optimal weight: 0.0010 chunk 80 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 108 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 82 optimal weight: 0.0770 chunk 67 optimal weight: 0.9980 overall best weight: 0.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.128599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.108957 restraints weight = 34667.635| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.26 r_work: 0.3288 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9636 Z= 0.166 Angle : 0.556 5.538 13125 Z= 0.289 Chirality : 0.045 0.217 1566 Planarity : 0.004 0.044 1578 Dihedral : 8.591 55.915 2133 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.53 % Allowed : 16.24 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1116 helix: 0.19 (0.30), residues: 324 sheet: 0.51 (0.28), residues: 360 loop : -0.85 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 259 HIS 0.003 0.001 HIS C 286 PHE 0.010 0.001 PHE B 11 TYR 0.011 0.001 TYR A 89 ARG 0.006 0.000 ARG C 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 12) link_NAG-ASN : angle 1.62572 ( 36) link_BETA1-4 : bond 0.00421 ( 12) link_BETA1-4 : angle 1.95110 ( 36) hydrogen bonds : bond 0.04263 ( 382) hydrogen bonds : angle 4.93204 ( 1263) SS BOND : bond 0.00482 ( 9) SS BOND : angle 1.40566 ( 18) covalent geometry : bond 0.00395 ( 9603) covalent geometry : angle 0.53894 (13035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 279 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 274 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 LYS cc_start: 0.8411 (mtpt) cc_final: 0.8017 (mmpt) REVERT: C 273 ARG cc_start: 0.8125 (mmt180) cc_final: 0.7896 (mmt180) REVERT: B 69 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8287 (mtmm) outliers start: 5 outliers final: 4 residues processed: 275 average time/residue: 2.6695 time to fit residues: 780.5455 Evaluate side-chains 274 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 270 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 179 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 17 optimal weight: 0.0980 chunk 4 optimal weight: 0.2980 chunk 101 optimal weight: 0.7980 chunk 94 optimal weight: 0.0970 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN C 97 ASN C 238 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.129134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.109655 restraints weight = 34282.357| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.24 r_work: 0.3301 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9636 Z= 0.134 Angle : 0.537 6.247 13125 Z= 0.277 Chirality : 0.044 0.191 1566 Planarity : 0.003 0.046 1578 Dihedral : 8.176 56.096 2133 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.42 % Allowed : 16.14 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1116 helix: 0.29 (0.30), residues: 324 sheet: 0.56 (0.28), residues: 360 loop : -0.84 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 259 HIS 0.002 0.001 HIS C 286 PHE 0.010 0.001 PHE B 11 TYR 0.011 0.001 TYR A 89 ARG 0.008 0.000 ARG C 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 12) link_NAG-ASN : angle 1.49610 ( 36) link_BETA1-4 : bond 0.00402 ( 12) link_BETA1-4 : angle 1.81012 ( 36) hydrogen bonds : bond 0.03940 ( 382) hydrogen bonds : angle 4.80792 ( 1263) SS BOND : bond 0.00425 ( 9) SS BOND : angle 1.25058 ( 18) covalent geometry : bond 0.00315 ( 9603) covalent geometry : angle 0.52231 (13035) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 280 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 276 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8802 (mtpp) cc_final: 0.8276 (mtmm) REVERT: A 363 LYS cc_start: 0.8377 (mtpt) cc_final: 0.8028 (mmpt) REVERT: C 273 ARG cc_start: 0.8107 (mmt180) cc_final: 0.7868 (mmt180) REVERT: B 69 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8280 (mtmm) outliers start: 4 outliers final: 3 residues processed: 278 average time/residue: 2.7711 time to fit residues: 818.0430 Evaluate side-chains 276 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 273 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 355 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 87 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 110 optimal weight: 0.3980 chunk 19 optimal weight: 0.1980 chunk 107 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN C 110 ASN C 262 ASN C 308 GLN B 110 ASN B 308 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.128238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.108553 restraints weight = 34491.151| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.25 r_work: 0.3281 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9636 Z= 0.208 Angle : 0.574 6.484 13125 Z= 0.296 Chirality : 0.045 0.189 1566 Planarity : 0.004 0.060 1578 Dihedral : 8.244 55.726 2133 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.42 % Allowed : 16.46 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.25), residues: 1116 helix: 0.20 (0.30), residues: 324 sheet: 0.57 (0.28), residues: 360 loop : -0.83 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 259 HIS 0.003 0.001 HIS B 286 PHE 0.011 0.002 PHE B 11 TYR 0.014 0.002 TYR A 89 ARG 0.010 0.001 ARG A 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 12) link_NAG-ASN : angle 1.62432 ( 36) link_BETA1-4 : bond 0.00382 ( 12) link_BETA1-4 : angle 1.88448 ( 36) hydrogen bonds : bond 0.04350 ( 382) hydrogen bonds : angle 4.92763 ( 1263) SS BOND : bond 0.00497 ( 9) SS BOND : angle 1.50027 ( 18) covalent geometry : bond 0.00508 ( 9603) covalent geometry : angle 0.55765 (13035) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 272 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8791 (mtpp) cc_final: 0.8214 (mtmm) REVERT: A 148 ARG cc_start: 0.6697 (ttp-110) cc_final: 0.6303 (ttp-110) REVERT: A 363 LYS cc_start: 0.8418 (mtpt) cc_final: 0.8023 (mmpt) REVERT: C 273 ARG cc_start: 0.8114 (mmt180) cc_final: 0.7879 (mmt180) REVERT: B 69 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8286 (mtmm) REVERT: B 170 ASP cc_start: 0.8184 (p0) cc_final: 0.7971 (p0) outliers start: 4 outliers final: 4 residues processed: 274 average time/residue: 2.7496 time to fit residues: 800.7143 Evaluate side-chains 275 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 271 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 149 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 11 optimal weight: 0.2980 chunk 73 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 54 optimal weight: 0.0370 chunk 81 optimal weight: 0.7980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN C 238 ASN C 308 GLN B 308 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108796 restraints weight = 34632.295| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.26 r_work: 0.3286 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9636 Z= 0.165 Angle : 0.556 6.534 13125 Z= 0.288 Chirality : 0.044 0.183 1566 Planarity : 0.004 0.076 1578 Dihedral : 8.103 55.898 2133 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.63 % Allowed : 16.24 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1116 helix: 0.22 (0.30), residues: 324 sheet: 0.56 (0.28), residues: 360 loop : -0.83 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 259 HIS 0.003 0.001 HIS C 286 PHE 0.011 0.001 PHE B 11 TYR 0.012 0.001 TYR A 89 ARG 0.012 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 12) link_NAG-ASN : angle 1.54290 ( 36) link_BETA1-4 : bond 0.00382 ( 12) link_BETA1-4 : angle 1.78561 ( 36) hydrogen bonds : bond 0.04113 ( 382) hydrogen bonds : angle 4.87088 ( 1263) SS BOND : bond 0.00462 ( 9) SS BOND : angle 1.33336 ( 18) covalent geometry : bond 0.00394 ( 9603) covalent geometry : angle 0.54150 (13035) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 272 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.6688 (ttp-110) cc_final: 0.6433 (ttp-110) REVERT: A 363 LYS cc_start: 0.8403 (mtpt) cc_final: 0.8009 (mmpt) REVERT: C 273 ARG cc_start: 0.8114 (mmt180) cc_final: 0.7883 (mmt180) REVERT: B 69 LYS cc_start: 0.8785 (mtpp) cc_final: 0.8285 (mtmm) outliers start: 6 outliers final: 4 residues processed: 275 average time/residue: 2.7206 time to fit residues: 794.8541 Evaluate side-chains 275 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 271 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 149 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 0.2980 chunk 95 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 68 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 308 GLN C 308 GLN B 308 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.128513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108887 restraints weight = 34365.588| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.24 r_work: 0.3288 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9636 Z= 0.165 Angle : 0.547 6.247 13125 Z= 0.284 Chirality : 0.044 0.176 1566 Planarity : 0.004 0.073 1578 Dihedral : 8.003 55.773 2133 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.63 % Allowed : 16.14 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1116 helix: 0.24 (0.30), residues: 324 sheet: 0.57 (0.28), residues: 360 loop : -0.83 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 259 HIS 0.003 0.001 HIS C 286 PHE 0.010 0.001 PHE B 11 TYR 0.012 0.001 TYR A 89 ARG 0.011 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 12) link_NAG-ASN : angle 1.54493 ( 36) link_BETA1-4 : bond 0.00382 ( 12) link_BETA1-4 : angle 1.73979 ( 36) hydrogen bonds : bond 0.04091 ( 382) hydrogen bonds : angle 4.85956 ( 1263) SS BOND : bond 0.00445 ( 9) SS BOND : angle 1.31602 ( 18) covalent geometry : bond 0.00394 ( 9603) covalent geometry : angle 0.53331 (13035) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 270 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8782 (mtpp) cc_final: 0.8213 (mtmm) REVERT: A 148 ARG cc_start: 0.6721 (ttp-110) cc_final: 0.6398 (ttp-110) REVERT: A 363 LYS cc_start: 0.8395 (mtpt) cc_final: 0.8040 (mmpt) REVERT: C 273 ARG cc_start: 0.8121 (mmt180) cc_final: 0.7893 (mmt180) REVERT: B 69 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8289 (mtmm) outliers start: 6 outliers final: 6 residues processed: 272 average time/residue: 2.7505 time to fit residues: 794.5706 Evaluate side-chains 275 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 269 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 149 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 57 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 85 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN C 97 ASN C 238 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.108090 restraints weight = 34302.679| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.24 r_work: 0.3274 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9636 Z= 0.225 Angle : 0.587 6.064 13125 Z= 0.304 Chirality : 0.046 0.182 1566 Planarity : 0.004 0.071 1578 Dihedral : 8.165 57.698 2133 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.63 % Allowed : 16.35 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.25), residues: 1116 helix: 0.15 (0.30), residues: 324 sheet: 0.69 (0.28), residues: 354 loop : -0.87 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 259 HIS 0.003 0.001 HIS C 286 PHE 0.013 0.002 PHE B 11 TYR 0.014 0.002 TYR A 89 ARG 0.011 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 12) link_NAG-ASN : angle 1.67640 ( 36) link_BETA1-4 : bond 0.00375 ( 12) link_BETA1-4 : angle 1.82841 ( 36) hydrogen bonds : bond 0.04456 ( 382) hydrogen bonds : angle 4.97427 ( 1263) SS BOND : bond 0.00515 ( 9) SS BOND : angle 1.52259 ( 18) covalent geometry : bond 0.00548 ( 9603) covalent geometry : angle 0.57146 (13035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18279.40 seconds wall clock time: 313 minutes 12.98 seconds (18792.98 seconds total)