Starting phenix.real_space_refine on Wed Mar 4 21:22:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ekt_31176/03_2026/7ekt_31176.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ekt_31176/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ekt_31176/03_2026/7ekt_31176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ekt_31176/03_2026/7ekt_31176.map" model { file = "/net/cci-nas-00/data/ceres_data/7ekt_31176/03_2026/7ekt_31176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ekt_31176/03_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-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'CLR': 1, 'I33': 1, 'I34': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'CLR': 1, 'I33': 1, 'I34': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'CLR': 1, 'I33': 1, 'I34': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'CLR': 1, 'I33': 1, 'I34': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'CLR': 1, 'I33': 1, 'I34': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.88, per 1000 atoms: 0.42 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: 1.58 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: 0.59 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: 2.86 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2485 1.31 - 1.44: 4745 1.44 - 1.57: 9190 1.57 - 1.71: 55 1.71 - 1.84: 190 Bond restraints: 16665 Sorted by residual: bond pdb=" C02 I33 E 601 " pdb=" N13 I33 E 601 " ideal model delta sigma weight residual 1.339 1.452 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C02 I33 C 601 " pdb=" N13 I33 C 601 " ideal model delta sigma weight residual 1.339 1.451 -0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C02 I33 B 601 " pdb=" N13 I33 B 601 " ideal model delta sigma weight residual 1.339 1.451 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C02 I33 D 601 " pdb=" N13 I33 D 601 " ideal model delta sigma weight residual 1.339 1.451 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C02 I33 A 603 " pdb=" N13 I33 A 603 " ideal model delta sigma weight residual 1.339 1.451 -0.112 2.00e-02 2.50e+03 3.12e+01 ... (remaining 16660 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 22427 2.55 - 5.10: 246 5.10 - 7.65: 97 7.65 - 10.20: 20 10.20 - 12.75: 5 Bond angle restraints: 22795 Sorted by residual: angle pdb=" C02 I33 D 601 " pdb=" C03 I33 D 601 " pdb=" S12 I33 D 601 " ideal model delta sigma weight residual 115.03 127.78 -12.75 3.00e+00 1.11e-01 1.81e+01 angle pdb=" C02 I33 E 601 " pdb=" C03 I33 E 601 " pdb=" S12 I33 E 601 " ideal model delta sigma weight residual 115.03 127.74 -12.71 3.00e+00 1.11e-01 1.80e+01 angle pdb=" C02 I33 C 601 " pdb=" C03 I33 C 601 " pdb=" S12 I33 C 601 " ideal model delta sigma weight residual 115.03 127.73 -12.70 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C02 I33 B 601 " pdb=" C03 I33 B 601 " pdb=" S12 I33 B 601 " ideal model delta sigma weight residual 115.03 127.73 -12.70 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C02 I33 A 603 " pdb=" C03 I33 A 603 " pdb=" S12 I33 A 603 " ideal model delta sigma weight residual 115.03 127.70 -12.67 3.00e+00 1.11e-01 1.78e+01 ... (remaining 22790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.14: 8886 11.14 - 22.28: 839 22.28 - 33.43: 335 33.43 - 44.57: 95 44.57 - 55.71: 35 Dihedral angle restraints: 10190 sinusoidal: 4345 harmonic: 5845 Sorted by residual: dihedral pdb=" CB CYS D 150 " pdb=" SG CYS D 150 " pdb=" SG CYS D 164 " pdb=" CB CYS D 164 " ideal model delta sinusoidal sigma weight residual 93.00 48.98 44.02 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CB CYS B 150 " pdb=" SG CYS B 150 " pdb=" SG CYS B 164 " pdb=" CB CYS B 164 " ideal model delta sinusoidal sigma weight residual 93.00 48.98 44.02 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CB CYS C 150 " pdb=" SG CYS C 150 " pdb=" SG CYS C 164 " pdb=" CB CYS C 164 " ideal model delta sinusoidal sigma weight residual 93.00 48.98 44.02 1 1.00e+01 1.00e-02 2.70e+01 ... (remaining 10187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 2585 0.121 - 0.241: 15 0.241 - 0.362: 10 0.362 - 0.482: 5 0.482 - 0.603: 20 Chirality restraints: 2635 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN E 133 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.08e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 133 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.98e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 133 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.98e+00 ... (remaining 2632 not shown) Planarity restraints: 2785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 321 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO E 322 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO E 322 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 322 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 321 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO C 322 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 322 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 322 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 321 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO A 322 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " -0.033 5.00e-02 4.00e+02 ... (remaining 2782 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 5952 2.89 - 3.39: 14768 3.39 - 3.89: 25767 3.89 - 4.40: 29375 4.40 - 4.90: 52067 Nonbonded interactions: 127929 Sorted by model distance: nonbonded pdb=" NH1 ARG A 446 " pdb=" OD1 ASP B 451 " model vdw 2.385 3.120 nonbonded pdb=" NH1 ARG D 446 " pdb=" OD1 ASP E 451 " model vdw 2.390 3.120 nonbonded pdb=" OE2 GLU D 67 " pdb=" NH2 ARG D 228 " model vdw 2.399 3.120 nonbonded pdb=" OE2 GLU E 67 " pdb=" NH2 ARG E 228 " model vdw 2.399 3.120 nonbonded pdb=" OE2 GLU A 67 " pdb=" NH2 ARG A 228 " model vdw 2.399 3.120 ... (remaining 127924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.820 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 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:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.113 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 : 11.100 55.708 6380 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 covalent geometry : bond 0.00766 (16665) covalent geometry : angle 0.78469 (22795) SS BOND : bond 0.00845 ( 10) SS BOND : angle 1.63703 ( 20) hydrogen bonds : bond 0.26718 ( 776) hydrogen bonds : angle 8.69604 ( 2448) link_BETA1-4 : bond 0.00233 ( 5) link_BETA1-4 : angle 3.40882 ( 15) link_NAG-ASN : bond 0.00310 ( 10) link_NAG-ASN : angle 7.46842 ( 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 : 0.657 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: 0.1146 time to fit residues: 38.8348 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 : 0.639 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3368 r_free = 0.3368 target = 0.113797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.089783 restraints weight = 45281.599| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.86 r_work: 0.2881 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16690 Z= 0.148 Angle : 0.700 12.621 22860 Z= 0.328 Chirality : 0.047 0.449 2635 Planarity : 0.005 0.055 2775 Dihedral : 7.231 60.203 2882 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.71 % Allowed : 4.62 % 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: -1.07 (0.18), residues: 1965 helix: 0.52 (0.18), residues: 780 sheet: -0.51 (0.26), residues: 425 loop : -2.13 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 332 TYR 0.014 0.001 TYR B 140 PHE 0.021 0.001 PHE E 342 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00301 (16665) covalent geometry : angle 0.66185 (22795) SS BOND : bond 0.00849 ( 10) SS BOND : angle 1.37484 ( 20) hydrogen bonds : bond 0.07324 ( 776) hydrogen bonds : angle 5.38921 ( 2448) link_BETA1-4 : bond 0.00235 ( 5) link_BETA1-4 : angle 1.70427 ( 15) link_NAG-ASN : bond 0.00319 ( 10) link_NAG-ASN : angle 6.15370 ( 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 205 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.681 Fit side-chains REVERT: D 204 LYS cc_start: 0.7518 (tttt) cc_final: 0.7216 (tttp) REVERT: E 332 ARG cc_start: 0.8397 (tpt90) cc_final: 0.8038 (tpp80) outliers start: 12 outliers final: 2 residues processed: 204 average time/residue: 0.1086 time to fit residues: 36.4077 Evaluate side-chains 170 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 168 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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: 0.2980 chunk 42 optimal weight: 3.9990 chunk 124 optimal weight: 0.0050 chunk 141 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 overall best weight: 1.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.112437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.088095 restraints weight = 46321.807| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.96 r_work: 0.2826 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16690 Z= 0.159 Angle : 0.670 12.644 22860 Z= 0.316 Chirality : 0.047 0.461 2635 Planarity : 0.004 0.053 2775 Dihedral : 7.346 79.981 2880 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.59 % Allowed : 6.45 % Favored : 92.96 % 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: -0.79 (0.19), residues: 1965 helix: 1.02 (0.19), residues: 785 sheet: -0.62 (0.26), residues: 430 loop : -2.15 (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 0.015 0.001 PHE A 342 TRP 0.012 0.001 TRP E 82 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00357 (16665) covalent geometry : angle 0.63095 (22795) SS BOND : bond 0.00781 ( 10) SS BOND : angle 1.37355 ( 20) hydrogen bonds : bond 0.06337 ( 776) hydrogen bonds : angle 4.90849 ( 2448) link_BETA1-4 : bond 0.00288 ( 5) link_BETA1-4 : angle 1.78515 ( 15) link_NAG-ASN : bond 0.00206 ( 10) link_NAG-ASN : angle 6.06124 ( 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 181 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 0.636 Fit side-chains REVERT: A 301 MET cc_start: 0.7633 (mtp) cc_final: 0.7325 (mtm) REVERT: C 301 MET cc_start: 0.7569 (mtp) cc_final: 0.7319 (mtp) REVERT: D 204 LYS cc_start: 0.7618 (tttt) cc_final: 0.7217 (tttp) REVERT: E 332 ARG cc_start: 0.8502 (tpt90) cc_final: 0.8138 (tpp80) outliers start: 10 outliers final: 7 residues processed: 179 average time/residue: 0.1097 time to fit residues: 32.0177 Evaluate side-chains 164 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 157 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 113 LEU Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 497 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 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: 0.9980 chunk 48 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.090420 restraints weight = 43436.657| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.21 r_work: 0.2899 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 16690 Z= 0.199 Angle : 0.706 12.804 22860 Z= 0.335 Chirality : 0.050 0.502 2635 Planarity : 0.004 0.053 2775 Dihedral : 7.686 89.033 2880 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.77 % Allowed : 7.75 % 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: -0.83 (0.19), residues: 1965 helix: 1.05 (0.19), residues: 790 sheet: -0.72 (0.26), residues: 430 loop : -2.22 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 332 TYR 0.012 0.002 TYR B 140 PHE 0.027 0.002 PHE B 342 TRP 0.013 0.001 TRP E 82 HIS 0.005 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00477 (16665) covalent geometry : angle 0.66864 (22795) SS BOND : bond 0.00759 ( 10) SS BOND : angle 1.40141 ( 20) hydrogen bonds : bond 0.06147 ( 776) hydrogen bonds : angle 4.81561 ( 2448) link_BETA1-4 : bond 0.00058 ( 5) link_BETA1-4 : angle 1.63923 ( 15) link_NAG-ASN : bond 0.00112 ( 10) link_NAG-ASN : angle 6.08480 ( 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 167 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.642 Fit side-chains REVERT: A 301 MET cc_start: 0.7881 (mtp) cc_final: 0.7515 (mtm) REVERT: B 301 MET cc_start: 0.7899 (mmm) cc_final: 0.7690 (mtp) REVERT: D 204 LYS cc_start: 0.8293 (tttt) cc_final: 0.7932 (tttp) REVERT: E 332 ARG cc_start: 0.8583 (tpt90) cc_final: 0.8246 (tpp80) outliers start: 13 outliers final: 7 residues processed: 164 average time/residue: 0.1161 time to fit residues: 30.7240 Evaluate side-chains 158 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 299 SER Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 148 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 194 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.094346 restraints weight = 35186.863| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.90 r_work: 0.2973 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2169 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= 0.132 Angle : 0.632 11.736 22860 Z= 0.297 Chirality : 0.046 0.450 2635 Planarity : 0.004 0.050 2775 Dihedral : 7.187 82.672 2880 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.59 % Allowed : 9.17 % Favored : 90.24 % 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: -0.63 (0.19), residues: 1965 helix: 1.27 (0.19), residues: 795 sheet: -0.77 (0.26), residues: 415 loop : -2.08 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 332 TYR 0.011 0.001 TYR B 140 PHE 0.010 0.001 PHE E 342 TRP 0.009 0.001 TRP E 82 HIS 0.002 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00290 (16665) covalent geometry : angle 0.59589 (22795) SS BOND : bond 0.00760 ( 10) SS BOND : angle 1.38992 ( 20) hydrogen bonds : bond 0.05386 ( 776) hydrogen bonds : angle 4.46115 ( 2448) link_BETA1-4 : bond 0.00273 ( 5) link_BETA1-4 : angle 1.66068 ( 15) link_NAG-ASN : bond 0.00360 ( 10) link_NAG-ASN : angle 5.65912 ( 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 181 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 0.628 Fit side-chains REVERT: A 276 MET cc_start: 0.7818 (mtm) cc_final: 0.7316 (mtt) REVERT: B 301 MET cc_start: 0.7765 (mmm) cc_final: 0.7371 (mtt) REVERT: C 301 MET cc_start: 0.7782 (mtp) cc_final: 0.7335 (mtp) REVERT: D 204 LYS cc_start: 0.8403 (tttt) cc_final: 0.8087 (ttpp) REVERT: E 332 ARG cc_start: 0.8406 (tpt90) cc_final: 0.8128 (tpp80) outliers start: 10 outliers final: 4 residues processed: 173 average time/residue: 0.1141 time to fit residues: 31.9247 Evaluate side-chains 167 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 163 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 124 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 190 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.116188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.094254 restraints weight = 44657.681| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.33 r_work: 0.2954 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16690 Z= 0.126 Angle : 0.630 11.757 22860 Z= 0.295 Chirality : 0.045 0.444 2635 Planarity : 0.003 0.049 2775 Dihedral : 6.732 76.057 2880 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.77 % Allowed : 9.47 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.39 (0.19), residues: 795 sheet: -0.73 (0.26), residues: 415 loop : -2.01 (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 140 PHE 0.008 0.001 PHE B 297 TRP 0.010 0.001 TRP E 82 HIS 0.002 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00278 (16665) covalent geometry : angle 0.59500 (22795) SS BOND : bond 0.00768 ( 10) SS BOND : angle 1.41465 ( 20) hydrogen bonds : bond 0.05075 ( 776) hydrogen bonds : angle 4.31746 ( 2448) link_BETA1-4 : bond 0.00150 ( 5) link_BETA1-4 : angle 1.78236 ( 15) link_NAG-ASN : bond 0.00305 ( 10) link_NAG-ASN : angle 5.49619 ( 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 193 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: C 276 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.6742 (mtm) REVERT: D 204 LYS cc_start: 0.8382 (tttt) cc_final: 0.8094 (ttpp) REVERT: E 332 ARG cc_start: 0.8395 (tpt90) cc_final: 0.8121 (tpp80) outliers start: 13 outliers final: 10 residues processed: 184 average time/residue: 0.1101 time to fit residues: 32.4219 Evaluate side-chains 183 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 D residue 301 MET Chi-restraints excluded: chain E residue 276 MET 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: 0.5980 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 133 optimal weight: 0.0570 chunk 159 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.117958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.096408 restraints weight = 39933.684| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.15 r_work: 0.2992 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16690 Z= 0.116 Angle : 0.603 10.974 22860 Z= 0.283 Chirality : 0.045 0.432 2635 Planarity : 0.003 0.047 2775 Dihedral : 6.312 68.068 2880 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.71 % Allowed : 9.94 % 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: -0.37 (0.19), residues: 1965 helix: 1.53 (0.19), residues: 795 sheet: -0.68 (0.26), residues: 415 loop : -1.95 (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 0.008 0.001 PHE D 275 TRP 0.008 0.001 TRP E 82 HIS 0.002 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00253 (16665) covalent geometry : angle 0.56816 (22795) SS BOND : bond 0.00770 ( 10) SS BOND : angle 1.44427 ( 20) hydrogen bonds : bond 0.04708 ( 776) hydrogen bonds : angle 4.12325 ( 2448) link_BETA1-4 : bond 0.00133 ( 5) link_BETA1-4 : angle 1.91748 ( 15) link_NAG-ASN : bond 0.00379 ( 10) link_NAG-ASN : angle 5.36416 ( 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 207 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.523 Fit side-chains REVERT: C 301 MET cc_start: 0.7802 (mtp) cc_final: 0.7537 (mtp) REVERT: D 204 LYS cc_start: 0.8413 (tttt) cc_final: 0.8111 (tttp) REVERT: E 332 ARG cc_start: 0.8282 (tpt90) cc_final: 0.7985 (tpp80) outliers start: 12 outliers final: 9 residues processed: 200 average time/residue: 0.1096 time to fit residues: 35.2785 Evaluate side-chains 192 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 183 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 299 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 186 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 170 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 125 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.115995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.094559 restraints weight = 39564.845| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.09 r_work: 0.2967 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16690 Z= 0.141 Angle : 0.633 11.816 22860 Z= 0.299 Chirality : 0.046 0.454 2635 Planarity : 0.003 0.047 2775 Dihedral : 6.261 67.435 2880 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.07 % Allowed : 10.59 % Favored : 88.34 % 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: -0.40 (0.19), residues: 1965 helix: 1.51 (0.19), residues: 795 sheet: -0.70 (0.26), residues: 415 loop : -1.98 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 332 TYR 0.010 0.001 TYR B 140 PHE 0.012 0.001 PHE D 275 TRP 0.012 0.001 TRP E 341 HIS 0.003 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00328 (16665) covalent geometry : angle 0.59965 (22795) SS BOND : bond 0.00756 ( 10) SS BOND : angle 1.44247 ( 20) hydrogen bonds : bond 0.04908 ( 776) hydrogen bonds : angle 4.19829 ( 2448) link_BETA1-4 : bond 0.00073 ( 5) link_BETA1-4 : angle 1.89532 ( 15) link_NAG-ASN : bond 0.00207 ( 10) link_NAG-ASN : angle 5.41401 ( 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 201 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.570 Fit side-chains REVERT: C 276 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.6772 (mtm) REVERT: D 204 LYS cc_start: 0.8422 (tttt) cc_final: 0.8149 (tttp) REVERT: E 332 ARG cc_start: 0.8328 (tpt90) cc_final: 0.8048 (tpp80) outliers start: 18 outliers final: 15 residues processed: 188 average time/residue: 0.1164 time to fit residues: 34.6881 Evaluate side-chains 195 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 226 MET Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B 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 270 LEU Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 173 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 0.0040 chunk 125 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 193 optimal weight: 0.8980 chunk 108 optimal weight: 0.0970 chunk 191 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.118583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.095842 restraints weight = 53399.931| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.70 r_work: 0.2970 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16690 Z= 0.113 Angle : 0.609 11.619 22860 Z= 0.284 Chirality : 0.045 0.435 2635 Planarity : 0.003 0.046 2775 Dihedral : 6.136 62.376 2880 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.83 % Allowed : 10.65 % Favored : 88.52 % 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: -0.14 (0.19), residues: 1965 helix: 1.77 (0.19), residues: 780 sheet: -0.62 (0.26), residues: 415 loop : -1.78 (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 A 140 PHE 0.007 0.001 PHE A 342 TRP 0.010 0.001 TRP E 341 HIS 0.002 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00243 (16665) covalent geometry : angle 0.57536 (22795) SS BOND : bond 0.00783 ( 10) SS BOND : angle 1.46301 ( 20) hydrogen bonds : bond 0.04529 ( 776) hydrogen bonds : angle 4.03963 ( 2448) link_BETA1-4 : bond 0.00176 ( 5) link_BETA1-4 : angle 1.95080 ( 15) link_NAG-ASN : bond 0.00440 ( 10) link_NAG-ASN : angle 5.28588 ( 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 215 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: C 276 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.6841 (mtm) REVERT: D 204 LYS cc_start: 0.8384 (tttt) cc_final: 0.8119 (tttp) REVERT: E 332 ARG cc_start: 0.8221 (tpt90) cc_final: 0.7948 (tpp80) outliers start: 14 outliers final: 8 residues processed: 204 average time/residue: 0.1247 time to fit residues: 39.2029 Evaluate side-chains 194 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 185 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 E residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 6 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 104 optimal weight: 0.0870 chunk 171 optimal weight: 3.9990 chunk 182 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.118428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.096707 restraints weight = 39918.988| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.17 r_work: 0.2995 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16690 Z= 0.117 Angle : 0.615 12.189 22860 Z= 0.287 Chirality : 0.045 0.440 2635 Planarity : 0.003 0.046 2775 Dihedral : 6.011 57.112 2880 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.41 % Allowed : 11.72 % Favored : 87.87 % 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: -0.10 (0.19), residues: 1965 helix: 1.79 (0.19), residues: 780 sheet: -0.55 (0.26), residues: 415 loop : -1.78 (0.20), residues: 770 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 0.024 0.001 PHE D 342 TRP 0.012 0.001 TRP E 341 HIS 0.003 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00261 (16665) covalent geometry : angle 0.58166 (22795) SS BOND : bond 0.00781 ( 10) SS BOND : angle 1.45431 ( 20) hydrogen bonds : bond 0.04472 ( 776) hydrogen bonds : angle 3.99163 ( 2448) link_BETA1-4 : bond 0.00137 ( 5) link_BETA1-4 : angle 2.00254 ( 15) link_NAG-ASN : bond 0.00337 ( 10) link_NAG-ASN : angle 5.24486 ( 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 195 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 188 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: B 207 GLU cc_start: 0.8550 (pt0) cc_final: 0.8212 (pt0) REVERT: C 276 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.6561 (mtm) REVERT: C 301 MET cc_start: 0.7666 (mmm) cc_final: 0.7432 (mtm) REVERT: D 204 LYS cc_start: 0.8406 (tttt) cc_final: 0.8140 (tttp) REVERT: E 332 ARG cc_start: 0.8250 (tpt90) cc_final: 0.7935 (tpp80) REVERT: E 441 ARG cc_start: 0.6721 (mtm-85) cc_final: 0.6450 (mtt180) outliers start: 7 outliers final: 6 residues processed: 191 average time/residue: 0.1162 time to fit residues: 35.3256 Evaluate side-chains 190 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 183 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 178 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 175 optimal weight: 0.1980 chunk 68 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.096783 restraints weight = 38747.146| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.97 r_work: 0.3020 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2659 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= 0.116 Angle : 0.617 11.386 22860 Z= 0.290 Chirality : 0.046 0.444 2635 Planarity : 0.003 0.045 2775 Dihedral : 5.925 55.632 2880 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.71 % Allowed : 11.30 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.05 (0.19), residues: 1965 helix: 1.81 (0.19), residues: 780 sheet: -0.48 (0.27), residues: 415 loop : -1.76 (0.20), residues: 770 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 0.025 0.001 PHE D 342 TRP 0.012 0.001 TRP E 341 HIS 0.002 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00255 (16665) covalent geometry : angle 0.58335 (22795) SS BOND : bond 0.00778 ( 10) SS BOND : angle 1.46149 ( 20) hydrogen bonds : bond 0.04403 ( 776) hydrogen bonds : angle 3.96618 ( 2448) link_BETA1-4 : bond 0.00125 ( 5) link_BETA1-4 : angle 2.02751 ( 15) link_NAG-ASN : bond 0.00357 ( 10) link_NAG-ASN : angle 5.26557 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3628.97 seconds wall clock time: 63 minutes 1.10 seconds (3781.10 seconds total)