Starting phenix.real_space_refine on Tue Dec 31 19:47:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ekt_31176/12_2024/7ekt_31176.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ekt_31176/12_2024/7ekt_31176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ekt_31176/12_2024/7ekt_31176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ekt_31176/12_2024/7ekt_31176.map" model { file = "/net/cci-nas-00/data/ceres_data/7ekt_31176/12_2024/7ekt_31176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ekt_31176/12_2024/7ekt_31176.cif" } resolution = 3.02 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= 0.010 sd= 0.094 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: 5 Type Number sf(0) Gaussians S 120 5.16 5 Cl 10 4.86 5 C 10625 2.51 5 N 2580 2.21 5 O 2860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16195 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3127 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 396, 3120 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Conformer: "B" Number of residues, atoms: 396, 3120 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 bond proxies already assigned to first conformer: 3196 Chain: "B" Number of atoms: 3127 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 396, 3120 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Conformer: "B" Number of residues, atoms: 396, 3120 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 bond proxies already assigned to first conformer: 3196 Chain: "C" Number of atoms: 3127 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 396, 3120 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Conformer: "B" Number of residues, atoms: 396, 3120 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 bond proxies already assigned to first conformer: 3196 Chain: "D" Number of atoms: 3127 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 396, 3120 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Conformer: "B" Number of residues, atoms: 396, 3120 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 bond proxies already assigned to first conformer: 3196 Chain: "E" Number of atoms: 3127 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 396, 3120 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Conformer: "B" Number of residues, atoms: 396, 3120 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 bond proxies already assigned to first conformer: 3196 Chain: "F" 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'CLR': 1, 'I33': 1, 'I34': 1, 'NAG': 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'CLR': 1, 'I33': 1, 'I34': 1, 'NAG': 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'CLR': 1, 'I33': 1, 'I34': 1, 'NAG': 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: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'CLR': 1, 'I33': 1, 'I34': 1, 'NAG': 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: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'CLR': 1, 'I33': 1, 'I34': 1, 'NAG': 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 Time building chain proxies: 17.11, per 1000 atoms: 1.06 Number of scatterers: 16195 At special positions: 0 Unit cell: (94.302, 91.26, 164.268, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 10 17.00 S 120 16.00 O 2860 8.00 N 2580 7.00 C 10625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 213 " distance=2.04 Simple disulfide: pdb=" SG CYS C 150 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 213 " distance=2.04 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 164 " distance=2.04 Simple disulfide: pdb=" SG CYS D 212 " - pdb=" SG CYS D 213 " distance=2.04 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 213 " distance=2.04 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 601 " - " ASN A 46 " " NAG B 603 " - " ASN B 46 " " NAG C 603 " - " ASN C 46 " " NAG D 603 " - " ASN D 46 " " NAG E 603 " - " ASN E 46 " " NAG F 1 " - " ASN A 133 " " NAG G 1 " - " ASN B 133 " " NAG H 1 " - " ASN C 133 " " NAG I 1 " - " ASN D 133 " " NAG J 1 " - " ASN E 133 " Time building additional restraints: 4.16 Conformation dependent library (CDL) restraints added in 4.1 seconds 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3780 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 20 sheets defined 43.0% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 23 through 34 removed outlier: 3.690A pdb=" N VAL A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 247 through 254 removed outlier: 3.677A pdb=" N PHE A 252 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 272 removed outlier: 3.849A pdb=" N THR A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 281 removed outlier: 3.549A pdb=" N GLU A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 319 removed outlier: 3.531A pdb=" N TYR A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 433 through 490 removed outlier: 3.561A pdb=" N VAL A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'B' and resid 24 through 34 removed outlier: 3.691A pdb=" N VAL B 34 " --> pdb=" O TYR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 159 Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 247 through 254 removed outlier: 3.677A pdb=" N PHE B 252 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 272 removed outlier: 3.849A pdb=" N THR B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.549A pdb=" N GLU B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 319 removed outlier: 3.531A pdb=" N TYR B 317 " --> pdb=" O ILE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 433 through 490 removed outlier: 3.560A pdb=" N VAL B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'C' and resid 24 through 34 removed outlier: 3.691A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 159 Processing helix chain 'C' and resid 230 through 237 Processing helix chain 'C' and resid 238 through 246 Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.677A pdb=" N PHE C 252 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 272 removed outlier: 3.850A pdb=" N THR C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 281 removed outlier: 3.549A pdb=" N GLU C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 319 removed outlier: 3.531A pdb=" N TYR C 317 " --> pdb=" O ILE C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 433 through 490 removed outlier: 3.561A pdb=" N VAL C 467 " --> pdb=" O ALA C 463 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 500 Processing helix chain 'D' and resid 24 through 34 removed outlier: 3.690A pdb=" N VAL D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 159 Processing helix chain 'D' and resid 230 through 237 Processing helix chain 'D' and resid 238 through 246 Processing helix chain 'D' and resid 247 through 254 removed outlier: 3.677A pdb=" N PHE D 252 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 272 removed outlier: 3.849A pdb=" N THR D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 281 removed outlier: 3.548A pdb=" N GLU D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 319 removed outlier: 3.532A pdb=" N TYR D 317 " --> pdb=" O ILE D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 335 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 433 through 490 removed outlier: 3.561A pdb=" N VAL D 467 " --> pdb=" O ALA D 463 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'E' and resid 24 through 34 removed outlier: 3.691A pdb=" N VAL E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 159 Processing helix chain 'E' and resid 230 through 237 Processing helix chain 'E' and resid 238 through 246 Processing helix chain 'E' and resid 247 through 254 removed outlier: 3.677A pdb=" N PHE E 252 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 272 removed outlier: 3.849A pdb=" N THR E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 281 removed outlier: 3.548A pdb=" N GLU E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 319 removed outlier: 3.531A pdb=" N TYR E 317 " --> pdb=" O ILE E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 335 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 433 through 490 removed outlier: 3.561A pdb=" N VAL E 467 " --> pdb=" O ALA E 463 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA E 490 " --> pdb=" O ILE E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 500 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.510A pdb=" N VAL A 100 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.510A pdb=" N VAL A 100 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A 71 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASP A 64 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR A 73 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ILE A 62 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN A 75 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A 79 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR A 83 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR A 52 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU A 51 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN A 181 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 53 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 114 removed outlier: 3.531A pdb=" N GLY A 169 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR A 225 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 114 removed outlier: 3.531A pdb=" N GLY A 169 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 208 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 102 removed outlier: 3.510A pdb=" N VAL B 100 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 102 removed outlier: 3.510A pdb=" N VAL B 100 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL B 71 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASP B 64 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR B 73 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ILE B 62 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN B 75 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN B 79 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR B 83 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR B 52 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU B 51 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLN B 181 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 53 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 113 through 114 removed outlier: 3.532A pdb=" N GLY B 169 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR B 225 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 113 through 114 removed outlier: 3.532A pdb=" N GLY B 169 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 208 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.511A pdb=" N VAL C 100 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.511A pdb=" N VAL C 100 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C 71 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ASP C 64 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN C 75 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 79 " --> pdb=" O SER C 56 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR C 83 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR C 52 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU C 51 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLN C 181 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL C 53 " --> pdb=" O GLN C 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 113 through 114 removed outlier: 3.531A pdb=" N GLY C 169 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR C 225 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 113 through 114 removed outlier: 3.531A pdb=" N GLY C 169 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG C 208 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 100 through 102 removed outlier: 3.510A pdb=" N VAL D 100 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 100 through 102 removed outlier: 3.510A pdb=" N VAL D 100 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL D 71 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASP D 64 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR D 73 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ILE D 62 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN D 75 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN D 79 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR D 83 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR D 52 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU D 51 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN D 181 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL D 53 " --> pdb=" O GLN D 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 113 through 114 removed outlier: 3.531A pdb=" N GLY D 169 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR D 225 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 113 through 114 removed outlier: 3.531A pdb=" N GLY D 169 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG D 208 " --> pdb=" O TYR D 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 100 through 102 removed outlier: 3.510A pdb=" N VAL E 100 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 102 removed outlier: 3.510A pdb=" N VAL E 100 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL E 71 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASP E 64 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN E 75 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN E 79 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR E 83 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR E 52 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU E 51 " --> pdb=" O ASP E 179 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLN E 181 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL E 53 " --> pdb=" O GLN E 181 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 113 through 114 removed outlier: 3.532A pdb=" N GLY E 169 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR E 225 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 113 through 114 removed outlier: 3.532A pdb=" N GLY E 169 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG E 208 " --> pdb=" O TYR E 217 " (cutoff:3.500A) 866 hydrogen bonds defined for protein. 2448 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: 5.77 Time building geometry restraints manager: 4.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2485 1.31 - 1.44: 4745 1.44 - 1.57: 9190 1.57 - 1.71: 55 1.71 - 1.84: 190 Bond restraints: 16665 Sorted by residual: bond pdb=" C02 I33 E 601 " pdb=" N13 I33 E 601 " ideal model delta sigma weight residual 1.339 1.452 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C02 I33 C 601 " pdb=" N13 I33 C 601 " ideal model delta sigma weight residual 1.339 1.451 -0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C02 I33 B 601 " pdb=" N13 I33 B 601 " ideal model delta sigma weight residual 1.339 1.451 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C02 I33 D 601 " pdb=" N13 I33 D 601 " ideal model delta sigma weight residual 1.339 1.451 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C02 I33 A 603 " pdb=" N13 I33 A 603 " ideal model delta sigma weight residual 1.339 1.451 -0.112 2.00e-02 2.50e+03 3.12e+01 ... (remaining 16660 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 22427 2.55 - 5.10: 246 5.10 - 7.65: 97 7.65 - 10.20: 20 10.20 - 12.75: 5 Bond angle restraints: 22795 Sorted by residual: angle pdb=" C02 I33 D 601 " pdb=" C03 I33 D 601 " pdb=" S12 I33 D 601 " ideal model delta sigma weight residual 115.03 127.78 -12.75 3.00e+00 1.11e-01 1.81e+01 angle pdb=" C02 I33 E 601 " pdb=" C03 I33 E 601 " pdb=" S12 I33 E 601 " ideal model delta sigma weight residual 115.03 127.74 -12.71 3.00e+00 1.11e-01 1.80e+01 angle pdb=" C02 I33 C 601 " pdb=" C03 I33 C 601 " pdb=" S12 I33 C 601 " ideal model delta sigma weight residual 115.03 127.73 -12.70 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C02 I33 B 601 " pdb=" C03 I33 B 601 " pdb=" S12 I33 B 601 " ideal model delta sigma weight residual 115.03 127.73 -12.70 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C02 I33 A 603 " pdb=" C03 I33 A 603 " pdb=" S12 I33 A 603 " ideal model delta sigma weight residual 115.03 127.70 -12.67 3.00e+00 1.11e-01 1.78e+01 ... (remaining 22790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.14: 8886 11.14 - 22.28: 839 22.28 - 33.43: 335 33.43 - 44.57: 95 44.57 - 55.71: 35 Dihedral angle restraints: 10190 sinusoidal: 4345 harmonic: 5845 Sorted by residual: dihedral pdb=" CB CYS D 150 " pdb=" SG CYS D 150 " pdb=" SG CYS D 164 " pdb=" CB CYS D 164 " ideal model delta sinusoidal sigma weight residual 93.00 48.98 44.02 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CB CYS B 150 " pdb=" SG CYS B 150 " pdb=" SG CYS B 164 " pdb=" CB CYS B 164 " ideal model delta sinusoidal sigma weight residual 93.00 48.98 44.02 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CB CYS C 150 " pdb=" SG CYS C 150 " pdb=" SG CYS C 164 " pdb=" CB CYS C 164 " ideal model delta sinusoidal sigma weight residual 93.00 48.98 44.02 1 1.00e+01 1.00e-02 2.70e+01 ... (remaining 10187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 2585 0.121 - 0.241: 15 0.241 - 0.362: 10 0.362 - 0.482: 5 0.482 - 0.603: 20 Chirality restraints: 2635 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN E 133 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.08e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 133 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.98e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 133 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.98e+00 ... (remaining 2632 not shown) Planarity restraints: 2785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 321 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO E 322 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO E 322 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 322 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 321 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO C 322 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 322 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 322 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 321 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO A 322 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " -0.033 5.00e-02 4.00e+02 ... (remaining 2782 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 5952 2.89 - 3.39: 14768 3.39 - 3.89: 25767 3.89 - 4.40: 29375 4.40 - 4.90: 52067 Nonbonded interactions: 127929 Sorted by model distance: nonbonded pdb=" NH1 ARG A 446 " pdb=" OD1 ASP B 451 " model vdw 2.385 3.120 nonbonded pdb=" NH1 ARG D 446 " pdb=" OD1 ASP E 451 " model vdw 2.390 3.120 nonbonded pdb=" OE2 GLU D 67 " pdb=" NH2 ARG D 228 " model vdw 2.399 3.120 nonbonded pdb=" OE2 GLU E 67 " pdb=" NH2 ARG E 228 " model vdw 2.399 3.120 nonbonded pdb=" OE2 GLU A 67 " pdb=" NH2 ARG A 228 " model vdw 2.399 3.120 ... (remaining 127924 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 23 through 136 or resid 138 through 502)) selection = (chain 'B' and (resid 23 through 136 or resid 138 through 502)) selection = (chain 'C' and (resid 23 through 136 or resid 138 through 502)) selection = (chain 'D' and (resid 23 through 136 or resid 138 through 502)) selection = (chain 'E' and (resid 23 through 136 or resid 138 through 502)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 11.460 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 46.860 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 : 0.008 0.113 16665 Z= 0.511 Angle : 0.785 12.747 22795 Z= 0.350 Chirality : 0.069 0.603 2635 Planarity : 0.004 0.061 2775 Dihedral : 11.100 55.708 6380 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.30 % Allowed : 1.18 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.97 (0.18), residues: 1965 helix: -0.94 (0.18), residues: 765 sheet: -0.85 (0.26), residues: 430 loop : -1.81 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 156 HIS 0.002 0.001 HIS C 127 PHE 0.004 0.001 PHE C 146 TYR 0.011 0.001 TYR E 140 ARG 0.007 0.001 ARG D 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 206 time to evaluate : 1.889 Fit side-chains REVERT: A 470 LEU cc_start: 0.7845 (tt) cc_final: 0.7640 (tt) outliers start: 5 outliers final: 1 residues processed: 211 average time/residue: 0.2513 time to fit residues: 83.0428 Evaluate side-chains 167 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.0270 chunk 147 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16665 Z= 0.241 Angle : 0.689 10.519 22795 Z= 0.334 Chirality : 0.048 0.463 2635 Planarity : 0.005 0.056 2775 Dihedral : 7.414 66.915 2882 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.41 % Allowed : 4.56 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.16 (0.18), residues: 1965 helix: 0.53 (0.18), residues: 775 sheet: -0.64 (0.26), residues: 430 loop : -2.20 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 320 PHE 0.021 0.001 PHE E 342 TYR 0.014 0.001 TYR B 140 ARG 0.004 0.001 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 186 time to evaluate : 1.913 Fit side-chains REVERT: E 332 ARG cc_start: 0.8406 (tpt90) cc_final: 0.8119 (tpp80) outliers start: 7 outliers final: 1 residues processed: 192 average time/residue: 0.2366 time to fit residues: 72.7615 Evaluate side-chains 164 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 191 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 60 optimal weight: 0.0470 chunk 142 optimal weight: 5.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16665 Z= 0.203 Angle : 0.618 10.277 22795 Z= 0.300 Chirality : 0.047 0.458 2635 Planarity : 0.004 0.053 2775 Dihedral : 7.494 82.817 2880 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.30 % Allowed : 6.63 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.84 (0.19), residues: 1965 helix: 1.01 (0.19), residues: 790 sheet: -0.65 (0.26), residues: 430 loop : -2.25 (0.19), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 82 HIS 0.003 0.001 HIS B 320 PHE 0.014 0.001 PHE A 342 TYR 0.013 0.001 TYR B 140 ARG 0.007 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 2.087 Fit side-chains REVERT: B 342 PHE cc_start: 0.8465 (t80) cc_final: 0.8208 (t80) REVERT: C 301 MET cc_start: 0.7401 (mtm) cc_final: 0.7141 (mtp) REVERT: E 332 ARG cc_start: 0.8465 (tpt90) cc_final: 0.8186 (tpp80) outliers start: 5 outliers final: 4 residues processed: 179 average time/residue: 0.2502 time to fit residues: 71.8569 Evaluate side-chains 165 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 161 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 497 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 0.9980 chunk 133 optimal weight: 0.0170 chunk 92 optimal weight: 0.0770 chunk 19 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 119 optimal weight: 0.0870 chunk 178 optimal weight: 0.8980 chunk 188 optimal weight: 0.0010 chunk 93 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16665 Z= 0.146 Angle : 0.569 9.379 22795 Z= 0.273 Chirality : 0.044 0.419 2635 Planarity : 0.004 0.048 2775 Dihedral : 7.423 81.830 2880 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.47 % Allowed : 8.05 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.19), residues: 1965 helix: 1.37 (0.19), residues: 795 sheet: -0.59 (0.26), residues: 415 loop : -1.90 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 82 HIS 0.003 0.001 HIS C 318 PHE 0.013 0.001 PHE A 342 TYR 0.012 0.001 TYR C 140 ARG 0.007 0.000 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 204 time to evaluate : 1.885 Fit side-chains REVERT: B 342 PHE cc_start: 0.8550 (t80) cc_final: 0.8245 (t80) REVERT: B 488 MET cc_start: 0.7405 (tpp) cc_final: 0.7049 (mmm) REVERT: E 187 ILE cc_start: 0.8332 (pt) cc_final: 0.8099 (mm) REVERT: E 332 ARG cc_start: 0.8275 (tpt90) cc_final: 0.8057 (tpp80) outliers start: 8 outliers final: 6 residues processed: 205 average time/residue: 0.2652 time to fit residues: 86.2862 Evaluate side-chains 185 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 179 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 277 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 chunk 140 optimal weight: 5.9990 chunk 77 optimal weight: 0.2980 chunk 160 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16665 Z= 0.194 Angle : 0.597 10.524 22795 Z= 0.289 Chirality : 0.046 0.442 2635 Planarity : 0.004 0.048 2775 Dihedral : 7.214 74.934 2880 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.59 % Allowed : 9.64 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.19), residues: 1965 helix: 1.57 (0.19), residues: 775 sheet: -0.61 (0.26), residues: 415 loop : -1.74 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 341 HIS 0.003 0.001 HIS C 320 PHE 0.008 0.001 PHE E 342 TYR 0.012 0.001 TYR D 140 ARG 0.006 0.000 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 1.997 Fit side-chains REVERT: B 342 PHE cc_start: 0.8504 (t80) cc_final: 0.8300 (t80) REVERT: B 488 MET cc_start: 0.7477 (tpp) cc_final: 0.7106 (mmm) REVERT: C 301 MET cc_start: 0.7659 (mtp) cc_final: 0.7262 (mtp) REVERT: E 276 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7293 (mtp) REVERT: E 332 ARG cc_start: 0.8272 (tpt90) cc_final: 0.8068 (tpp80) outliers start: 10 outliers final: 5 residues processed: 189 average time/residue: 0.2500 time to fit residues: 76.2803 Evaluate side-chains 185 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 179 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 188 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16665 Z= 0.225 Angle : 0.602 10.715 22795 Z= 0.292 Chirality : 0.047 0.463 2635 Planarity : 0.004 0.048 2775 Dihedral : 7.082 89.240 2880 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.83 % Allowed : 9.59 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.19), residues: 1965 helix: 1.60 (0.19), residues: 775 sheet: -0.64 (0.26), residues: 415 loop : -1.78 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 341 HIS 0.003 0.001 HIS B 320 PHE 0.008 0.001 PHE B 297 TYR 0.011 0.001 TYR C 140 ARG 0.007 0.000 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 1.973 Fit side-chains REVERT: B 342 PHE cc_start: 0.8477 (t80) cc_final: 0.8269 (t80) REVERT: C 301 MET cc_start: 0.7628 (mtp) cc_final: 0.7363 (mtp) outliers start: 14 outliers final: 11 residues processed: 181 average time/residue: 0.2601 time to fit residues: 75.2067 Evaluate side-chains 182 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16665 Z= 0.213 Angle : 0.593 10.737 22795 Z= 0.288 Chirality : 0.046 0.448 2635 Planarity : 0.003 0.047 2775 Dihedral : 6.690 86.856 2880 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.83 % Allowed : 9.88 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.19), residues: 1965 helix: 1.61 (0.19), residues: 780 sheet: -0.66 (0.26), residues: 415 loop : -1.79 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 341 HIS 0.003 0.001 HIS E 320 PHE 0.007 0.001 PHE D 275 TYR 0.011 0.001 TYR A 296 ARG 0.007 0.000 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 1.859 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 181 average time/residue: 0.2677 time to fit residues: 76.3527 Evaluate side-chains 182 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 170 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16665 Z= 0.345 Angle : 0.663 11.520 22795 Z= 0.324 Chirality : 0.049 0.498 2635 Planarity : 0.004 0.050 2775 Dihedral : 6.523 82.314 2880 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.77 % Allowed : 10.00 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.50 (0.19), residues: 1965 helix: 1.38 (0.19), residues: 785 sheet: -0.65 (0.26), residues: 430 loop : -2.03 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 341 HIS 0.006 0.002 HIS C 319 PHE 0.011 0.001 PHE B 126 TYR 0.013 0.002 TYR B 190 ARG 0.007 0.001 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 1.763 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 171 average time/residue: 0.2531 time to fit residues: 68.3011 Evaluate side-chains 168 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 272 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 1.9990 chunk 164 optimal weight: 0.5980 chunk 175 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 165 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16665 Z= 0.203 Angle : 0.599 10.916 22795 Z= 0.290 Chirality : 0.046 0.450 2635 Planarity : 0.003 0.047 2775 Dihedral : 6.344 75.294 2880 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.89 % Allowed : 10.00 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.19), residues: 1965 helix: 1.60 (0.19), residues: 780 sheet: -0.68 (0.26), residues: 415 loop : -1.87 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 341 HIS 0.003 0.001 HIS B 320 PHE 0.007 0.001 PHE A 342 TYR 0.011 0.001 TYR A 140 ARG 0.007 0.000 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 1.926 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 175 average time/residue: 0.2557 time to fit residues: 70.8552 Evaluate side-chains 179 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16665 Z= 0.219 Angle : 0.610 10.852 22795 Z= 0.296 Chirality : 0.046 0.460 2635 Planarity : 0.003 0.048 2775 Dihedral : 6.261 74.664 2880 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.89 % Allowed : 10.12 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.19), residues: 1965 helix: 1.58 (0.19), residues: 780 sheet: -0.67 (0.27), residues: 415 loop : -1.87 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 341 HIS 0.003 0.001 HIS A 163 PHE 0.023 0.001 PHE D 342 TYR 0.011 0.001 TYR B 296 ARG 0.007 0.000 ARG C 332 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 1.970 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 174 average time/residue: 0.2436 time to fit residues: 67.8369 Evaluate side-chains 180 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.117009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.095503 restraints weight = 37923.851| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.07 r_work: 0.2984 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16665 Z= 0.178 Angle : 0.592 10.375 22795 Z= 0.287 Chirality : 0.045 0.444 2635 Planarity : 0.003 0.046 2775 Dihedral : 6.121 69.387 2880 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.95 % Allowed : 10.12 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.19), residues: 1965 helix: 1.76 (0.19), residues: 770 sheet: -0.66 (0.27), residues: 415 loop : -1.69 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 341 HIS 0.002 0.001 HIS A 163 PHE 0.007 0.001 PHE A 342 TYR 0.012 0.001 TYR A 296 ARG 0.007 0.000 ARG C 332 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2952.03 seconds wall clock time: 55 minutes 49.81 seconds (3349.81 seconds total)