Starting phenix.real_space_refine on Fri Jul 3 22:05:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ekt_31176/07_2026/7ekt_31176.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ekt_31176/07_2026/7ekt_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ekt_31176/07_2026/7ekt_31176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ekt_31176/07_2026/7ekt_31176.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ekt_31176/07_2026/7ekt_31176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ekt_31176/07_2026/7ekt_31176.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ekt_31176/07_2026/7ekt_31176.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ekt_31176/07_2026/7ekt_31176.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'ASP:plan': 4, 'GLU:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} 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: {'ASP:plan': 4, 'GLU:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} 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: {'ASP:plan': 4, 'GLU:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} 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: {'ASP:plan': 4, 'GLU:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} 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: {'ASP:plan': 4, 'GLU:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} 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: {'ASP:plan': 4, 'GLU:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} 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: {'ASP:plan': 4, 'GLU:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} 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: {'ASP:plan': 4, 'GLU:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} 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: {'ASP:plan': 4, 'GLU:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} 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: {'ASP:plan': 4, 'GLU:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} 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 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 chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 chiralities: 1 Time building chain proxies: 6.65, per 1000 atoms: 0.41 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: 1.79 Conformation dependent library (CDL) restraints added in 1.4 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: 0.48 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: 2.88 Time building geometry restraints manager: 2.18 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: 8381 11.14 - 22.28: 749 22.28 - 33.43: 285 33.43 - 44.57: 95 44.57 - 55.71: 25 Dihedral angle restraints: 9535 sinusoidal: 3690 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 9532 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: 0.01 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: 1.390 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.810 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 16690 Z= 0.387 Angle : 0.835 15.507 22860 Z= 0.363 Chirality : 0.069 0.603 2635 Planarity : 0.004 0.061 2775 Dihedral : 11.003 55.708 5725 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.14 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (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 ARG 0.007 0.001 ARG D 205 TYR 0.011 0.001 TYR E 140 PHE 0.004 0.001 PHE C 146 TRP 0.007 0.001 TRP C 156 HIS 0.002 0.001 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00766 / 0.39 (16665) covalent geometry : angle 0.78469 / 0.35 (22795) SS BOND : bond 0.00845 / 0.55 ( 10) SS BOND : angle 1.63703 / 1.06 ( 20) hydrogen bonds : bond 0.26718 / 17.73 ( 776) hydrogen bonds : angle 8.69604 / 6.01 ( 2448) link_BETA1-4 : bond 0.00233 / 0.15 ( 5) link_BETA1-4 : angle 3.40882 / 2.00 ( 15) link_NAG-ASN : bond 0.00310 / 0.20 ( 10) link_NAG-ASN : angle 7.46842 / 4.52 ( 30) *********************** 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 : 0.621 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: 0.1122 time to fit residues: 38.0068 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 : 0.628 ------------------------------------------------------------------------------- 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 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 ASN B 492 ASN C 492 ASN D 492 ASN E 492 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.114973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.090500 restraints weight = 45386.023| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.97 r_work: 0.2871 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16690 Z= 0.149 Angle : 0.703 12.533 22860 Z= 0.330 Chirality : 0.045 0.399 2635 Planarity : 0.005 0.055 2775 Dihedral : 5.606 57.937 2227 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.65 % Allowed : 4.67 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.18), residues: 1965 helix: 0.56 (0.18), residues: 780 sheet: -0.54 (0.26), residues: 430 loop : -2.09 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 332 TYR 0.013 0.001 TYR B 140 PHE 0.021 0.001 PHE E 342 TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (16665) covalent geometry : angle 0.66753 / 0.32 (22795) SS BOND : bond 0.00832 / 0.54 ( 10) SS BOND : angle 1.37190 / 0.90 ( 20) hydrogen bonds : bond 0.07343 / 4.76 ( 776) hydrogen bonds : angle 5.43665 / 3.81 ( 2448) link_BETA1-4 : bond 0.00832 / 0.53 ( 5) link_BETA1-4 : angle 1.22622 / 0.75 ( 15) link_NAG-ASN : bond 0.00255 / 0.17 ( 10) link_NAG-ASN : angle 6.00131 / 3.63 ( 30) *********************** 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 203 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 0.616 Fit side-chains REVERT: D 204 LYS cc_start: 0.7446 (tttt) cc_final: 0.7163 (tttp) REVERT: E 332 ARG cc_start: 0.8389 (tpt90) cc_final: 0.8028 (tpp80) outliers start: 11 outliers final: 2 residues processed: 202 average time/residue: 0.1090 time to fit residues: 35.7837 Evaluate side-chains 169 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 492 ASN 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 118 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.111098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.086828 restraints weight = 45584.671| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.92 r_work: 0.2805 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16690 Z= 0.181 Angle : 0.691 12.364 22860 Z= 0.328 Chirality : 0.047 0.416 2635 Planarity : 0.004 0.055 2775 Dihedral : 5.992 86.311 2225 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.59 % Allowed : 6.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.19), residues: 1965 helix: 0.96 (0.19), residues: 785 sheet: -0.63 (0.26), residues: 430 loop : -2.21 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 332 TYR 0.013 0.001 TYR B 140 PHE 0.014 0.001 PHE E 342 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (16665) covalent geometry : angle 0.65750 / 0.32 (22795) SS BOND : bond 0.00760 / 0.49 ( 10) SS BOND : angle 1.39231 / 0.92 ( 20) hydrogen bonds : bond 0.06515 / 4.27 ( 776) hydrogen bonds : angle 4.97471 / 3.48 ( 2448) link_BETA1-4 : bond 0.00216 / 0.12 ( 5) link_BETA1-4 : angle 1.13010 / 0.67 ( 15) link_NAG-ASN : bond 0.00116 / 0.08 ( 10) link_NAG-ASN : angle 5.80149 / 3.50 ( 30) *********************** 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 174 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 0.521 Fit side-chains REVERT: C 301 MET cc_start: 0.7605 (mtp) cc_final: 0.7346 (mtp) REVERT: D 204 LYS cc_start: 0.7584 (tttt) cc_final: 0.7230 (tttp) REVERT: E 332 ARG cc_start: 0.8518 (tpt90) cc_final: 0.8166 (tpp80) outliers start: 10 outliers final: 7 residues processed: 172 average time/residue: 0.1097 time to fit residues: 30.5445 Evaluate side-chains 160 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 170 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.109075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.085442 restraints weight = 44197.443| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.86 r_work: 0.2781 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16690 Z= 0.211 Angle : 0.714 12.198 22860 Z= 0.340 Chirality : 0.049 0.437 2635 Planarity : 0.004 0.055 2775 Dihedral : 6.174 83.216 2225 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.89 % Allowed : 7.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.19), residues: 1965 helix: 1.00 (0.19), residues: 790 sheet: -0.74 (0.26), residues: 430 loop : -2.29 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 332 TYR 0.013 0.002 TYR C 190 PHE 0.028 0.002 PHE B 342 TRP 0.012 0.001 TRP E 82 HIS 0.005 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.21 (16665) covalent geometry : angle 0.68267 / 0.33 (22795) SS BOND : bond 0.00715 / 0.46 ( 10) SS BOND : angle 1.40438 / 0.93 ( 20) hydrogen bonds : bond 0.06255 / 4.08 ( 776) hydrogen bonds : angle 4.88029 / 3.42 ( 2448) link_BETA1-4 : bond 0.00092 / 0.05 ( 5) link_BETA1-4 : angle 1.02064 / 0.61 ( 15) link_NAG-ASN : bond 0.00162 / 0.11 ( 10) link_NAG-ASN : angle 5.70835 / 3.44 ( 30) *********************** 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 162 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.625 Fit side-chains REVERT: A 276 MET cc_start: 0.7647 (mtm) cc_final: 0.7262 (mtt) REVERT: D 204 LYS cc_start: 0.8046 (tttt) cc_final: 0.7661 (tttp) REVERT: E 332 ARG cc_start: 0.8487 (tpt90) cc_final: 0.8145 (tpp80) outliers start: 15 outliers final: 7 residues processed: 159 average time/residue: 0.1160 time to fit residues: 29.6259 Evaluate side-chains 155 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain C residue 226 MET 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 E residue 276 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 148 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 194 optimal weight: 0.3980 chunk 44 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.090505 restraints weight = 34931.679| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.39 r_work: 0.2874 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16690 Z= 0.124 Angle : 0.634 13.312 22860 Z= 0.297 Chirality : 0.044 0.369 2635 Planarity : 0.004 0.050 2775 Dihedral : 5.699 76.990 2225 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.59 % Allowed : 8.88 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.19), residues: 1965 helix: 1.28 (0.19), residues: 795 sheet: -1.08 (0.24), residues: 465 loop : -2.04 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 332 TYR 0.012 0.001 TYR B 140 PHE 0.010 0.001 PHE C 342 TRP 0.009 0.001 TRP E 82 HIS 0.003 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (16665) covalent geometry : angle 0.60497 / 0.29 (22795) SS BOND : bond 0.00764 / 0.50 ( 10) SS BOND : angle 1.39694 / 0.92 ( 20) hydrogen bonds : bond 0.05367 / 3.50 ( 776) hydrogen bonds : angle 4.46891 / 3.13 ( 2448) link_BETA1-4 : bond 0.00307 / 0.19 ( 5) link_BETA1-4 : angle 0.96913 / 0.58 ( 15) link_NAG-ASN : bond 0.00360 / 0.23 ( 10) link_NAG-ASN : angle 5.14674 / 3.12 ( 30) *********************** 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 183 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 0.663 Fit side-chains REVERT: A 301 MET cc_start: 0.7523 (mtp) cc_final: 0.7210 (mtp) REVERT: C 301 MET cc_start: 0.7545 (mtp) cc_final: 0.7289 (mtp) REVERT: D 204 LYS cc_start: 0.8144 (tttt) cc_final: 0.7813 (ttpp) REVERT: E 332 ARG cc_start: 0.8375 (tpt90) cc_final: 0.8085 (tpp80) outliers start: 10 outliers final: 6 residues processed: 177 average time/residue: 0.1169 time to fit residues: 33.3806 Evaluate side-chains 169 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 163 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 277 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 145 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.112204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.088490 restraints weight = 44417.501| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.88 r_work: 0.2826 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16690 Z= 0.147 Angle : 0.656 13.191 22860 Z= 0.307 Chirality : 0.045 0.381 2635 Planarity : 0.004 0.050 2775 Dihedral : 5.654 80.360 2225 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.77 % Allowed : 9.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.19), residues: 1965 helix: 1.30 (0.19), residues: 795 sheet: -0.74 (0.26), residues: 415 loop : -2.07 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 332 TYR 0.012 0.001 TYR B 140 PHE 0.008 0.001 PHE E 342 TRP 0.011 0.001 TRP E 82 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (16665) covalent geometry : angle 0.62871 / 0.30 (22795) SS BOND : bond 0.00754 / 0.49 ( 10) SS BOND : angle 1.40822 / 0.94 ( 20) hydrogen bonds : bond 0.05363 / 3.50 ( 776) hydrogen bonds : angle 4.43047 / 3.10 ( 2448) link_BETA1-4 : bond 0.00134 / 0.08 ( 5) link_BETA1-4 : angle 1.08798 / 0.65 ( 15) link_NAG-ASN : bond 0.00123 / 0.08 ( 10) link_NAG-ASN : angle 5.06654 / 3.06 ( 30) *********************** 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 185 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.619 Fit side-chains REVERT: A 301 MET cc_start: 0.7716 (mtp) cc_final: 0.7424 (mtp) REVERT: C 276 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.6527 (mtm) REVERT: D 204 LYS cc_start: 0.8148 (tttt) cc_final: 0.7862 (ttpp) REVERT: E 332 ARG cc_start: 0.8353 (tpt90) cc_final: 0.8059 (tpp80) outliers start: 13 outliers final: 9 residues processed: 177 average time/residue: 0.1151 time to fit residues: 32.6785 Evaluate side-chains 175 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 C residue 272 LEU Chi-restraints excluded: chain C residue 276 MET 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 235 LEU Chi-restraints excluded: chain E residue 277 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 131 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.088639 restraints weight = 39828.376| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.68 r_work: 0.2849 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16690 Z= 0.155 Angle : 0.648 12.015 22860 Z= 0.305 Chirality : 0.045 0.386 2635 Planarity : 0.004 0.050 2775 Dihedral : 5.476 67.738 2225 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.83 % Allowed : 9.82 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.19), residues: 1965 helix: 1.36 (0.19), residues: 795 sheet: -0.75 (0.26), residues: 415 loop : -2.08 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 332 TYR 0.011 0.001 TYR B 296 PHE 0.008 0.001 PHE B 275 TRP 0.010 0.001 TRP E 82 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (16665) covalent geometry : angle 0.62022 / 0.30 (22795) SS BOND : bond 0.00737 / 0.48 ( 10) SS BOND : angle 1.42371 / 0.94 ( 20) hydrogen bonds : bond 0.05358 / 3.49 ( 776) hydrogen bonds : angle 4.41952 / 3.09 ( 2448) link_BETA1-4 : bond 0.00160 / 0.10 ( 5) link_BETA1-4 : angle 1.05674 / 0.63 ( 15) link_NAG-ASN : bond 0.00103 / 0.07 ( 10) link_NAG-ASN : angle 5.08142 / 3.07 ( 30) *********************** 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 179 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 301 MET cc_start: 0.7744 (mtp) cc_final: 0.7440 (mtp) REVERT: C 276 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.6556 (mtm) REVERT: E 332 ARG cc_start: 0.8346 (tpt90) cc_final: 0.8056 (tpp80) outliers start: 14 outliers final: 12 residues processed: 173 average time/residue: 0.1093 time to fit residues: 30.5733 Evaluate side-chains 177 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 276 MET 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 235 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 186 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.089559 restraints weight = 39253.379| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.66 r_work: 0.2860 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16690 Z= 0.136 Angle : 0.632 13.161 22860 Z= 0.297 Chirality : 0.045 0.371 2635 Planarity : 0.003 0.049 2775 Dihedral : 5.332 67.084 2225 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.83 % Allowed : 10.00 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.19), residues: 1965 helix: 1.44 (0.19), residues: 795 sheet: -0.75 (0.26), residues: 415 loop : -2.06 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 332 TYR 0.012 0.001 TYR D 296 PHE 0.007 0.001 PHE A 342 TRP 0.009 0.001 TRP E 341 HIS 0.003 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (16665) covalent geometry : angle 0.60495 / 0.29 (22795) SS BOND : bond 0.00750 / 0.49 ( 10) SS BOND : angle 1.42581 / 0.95 ( 20) hydrogen bonds : bond 0.05158 / 3.36 ( 776) hydrogen bonds : angle 4.33738 / 3.03 ( 2448) link_BETA1-4 : bond 0.00213 / 0.14 ( 5) link_BETA1-4 : angle 1.03942 / 0.62 ( 15) link_NAG-ASN : bond 0.00196 / 0.13 ( 10) link_NAG-ASN : angle 4.93869 / 2.99 ( 30) *********************** 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 185 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: C 276 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.6520 (mtm) REVERT: E 332 ARG cc_start: 0.8318 (tpt90) cc_final: 0.8033 (tpp80) outliers start: 14 outliers final: 11 residues processed: 177 average time/residue: 0.1127 time to fit residues: 32.3569 Evaluate side-chains 178 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 276 MET 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 277 LEU Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 173 optimal weight: 6.9990 chunk 144 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.112222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.088047 restraints weight = 53333.014| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 4.22 r_work: 0.2804 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16690 Z= 0.152 Angle : 0.653 11.664 22860 Z= 0.307 Chirality : 0.045 0.374 2635 Planarity : 0.004 0.049 2775 Dihedral : 5.382 67.251 2225 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.19), residues: 1965 helix: 1.40 (0.19), residues: 795 sheet: -0.73 (0.27), residues: 415 loop : -2.09 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 332 TYR 0.012 0.001 TYR D 296 PHE 0.007 0.001 PHE D 126 TRP 0.010 0.001 TRP E 341 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (16665) covalent geometry : angle 0.62704 / 0.30 (22795) SS BOND : bond 0.00739 / 0.48 ( 10) SS BOND : angle 1.43351 / 0.95 ( 20) hydrogen bonds : bond 0.05234 / 3.41 ( 776) hydrogen bonds : angle 4.37014 / 3.06 ( 2448) link_BETA1-4 : bond 0.00138 / 0.09 ( 5) link_BETA1-4 : angle 1.05458 / 0.63 ( 15) link_NAG-ASN : bond 0.00096 / 0.06 ( 10) link_NAG-ASN : angle 4.94362 / 2.99 ( 30) *********************** 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 : 0.521 Fit side-chains REVERT: A 276 MET cc_start: 0.7403 (mtm) cc_final: 0.6921 (mtt) REVERT: E 332 ARG cc_start: 0.8328 (tpt90) cc_final: 0.8041 (tpp80) outliers start: 15 outliers final: 12 residues processed: 176 average time/residue: 0.1073 time to fit residues: 30.6197 Evaluate side-chains 178 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 299 SER Chi-restraints excluded: chain C residue 272 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 235 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 6 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 104 optimal weight: 0.0870 chunk 171 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 152 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.113928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.090697 restraints weight = 39592.282| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.61 r_work: 0.2867 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16690 Z= 0.126 Angle : 0.637 16.187 22860 Z= 0.300 Chirality : 0.044 0.363 2635 Planarity : 0.003 0.048 2775 Dihedral : 5.235 65.000 2225 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.19), residues: 1965 helix: 1.61 (0.19), residues: 780 sheet: -0.72 (0.27), residues: 415 loop : -1.92 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 332 TYR 0.012 0.001 TYR D 296 PHE 0.009 0.001 PHE B 297 TRP 0.010 0.001 TRP E 341 HIS 0.003 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (16665) covalent geometry : angle 0.61121 / 0.29 (22795) SS BOND : bond 0.00763 / 0.50 ( 10) SS BOND : angle 1.43859 / 0.95 ( 20) hydrogen bonds : bond 0.04960 / 3.23 ( 776) hydrogen bonds : angle 4.25657 / 2.98 ( 2448) link_BETA1-4 : bond 0.00277 / 0.18 ( 5) link_BETA1-4 : angle 1.04691 / 0.62 ( 15) link_NAG-ASN : bond 0.00273 / 0.18 ( 10) link_NAG-ASN : angle 4.81401 / 2.92 ( 30) ********************** 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 198 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.630 Fit side-chains REVERT: E 332 ARG cc_start: 0.8228 (tpt90) cc_final: 0.7952 (tpp80) outliers start: 15 outliers final: 14 residues processed: 192 average time/residue: 0.1072 time to fit residues: 32.9554 Evaluate side-chains 184 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain B residue 299 SER 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 235 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 178 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 175 optimal weight: 0.0070 chunk 68 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 31 optimal weight: 0.2980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.115307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.092331 restraints weight = 37905.132| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.55 r_work: 0.2894 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16690 Z= 0.115 Angle : 0.610 9.995 22860 Z= 0.288 Chirality : 0.044 0.343 2635 Planarity : 0.003 0.047 2775 Dihedral : 4.996 59.761 2225 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.53 % Allowed : 11.18 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.19), residues: 1965 helix: 1.69 (0.19), residues: 780 sheet: -0.55 (0.27), residues: 405 loop : -1.91 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 332 TYR 0.011 0.001 TYR A 140 PHE 0.009 0.001 PHE D 275 TRP 0.010 0.001 TRP E 341 HIS 0.002 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (16665) covalent geometry : angle 0.58542 / 0.28 (22795) SS BOND : bond 0.00781 / 0.51 ( 10) SS BOND : angle 1.44910 / 0.96 ( 20) hydrogen bonds : bond 0.04613 / 3.01 ( 776) hydrogen bonds : angle 4.07488 / 2.85 ( 2448) link_BETA1-4 : bond 0.00220 / 0.14 ( 5) link_BETA1-4 : angle 1.08908 / 0.65 ( 15) link_NAG-ASN : bond 0.00326 / 0.21 ( 10) link_NAG-ASN : angle 4.63022 / 2.81 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3503.96 seconds wall clock time: 60 minutes 56.19 seconds (3656.19 seconds total)