Starting phenix.real_space_refine on Sat Jun 14 12:02:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsv_32768/06_2025/7wsv_32768.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsv_32768/06_2025/7wsv_32768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wsv_32768/06_2025/7wsv_32768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsv_32768/06_2025/7wsv_32768.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsv_32768/06_2025/7wsv_32768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsv_32768/06_2025/7wsv_32768.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 10934 2.51 5 N 2555 2.21 5 O 2877 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16443 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2349 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2349 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2349 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2349 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2349 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2349 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2349 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 9.79, per 1000 atoms: 0.60 Number of scatterers: 16443 At special positions: 0 Unit cell: (109.648, 109.648, 123.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 77 16.00 O 2877 8.00 N 2555 7.00 C 10934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.04 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.04 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.04 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.04 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.04 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.04 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.04 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.61 Conformation dependent library (CDL) restraints added in 2.1 seconds 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3990 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 7 sheets defined 69.6% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 33 through 61 Proline residue: A 46 - end of helix removed outlier: 3.817A pdb=" N SER A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE A 60 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 100 through 129 Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 158 removed outlier: 3.673A pdb=" N ALA A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.794A pdb=" N ASN A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 236 removed outlier: 4.061A pdb=" N LYS A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.011A pdb=" N ARG A 254 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A 255 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 296 Proline residue: A 289 - end of helix removed outlier: 3.665A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 338 removed outlier: 3.824A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'B' and resid 33 through 61 Proline residue: B 46 - end of helix removed outlier: 3.816A pdb=" N SER B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE B 60 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 Processing helix chain 'B' and resid 100 through 129 Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 158 removed outlier: 3.672A pdb=" N ALA B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS B 158 " --> pdb=" O ILE B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.794A pdb=" N ASN B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 236 removed outlier: 4.060A pdb=" N LYS B 212 " --> pdb=" O ASN B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 4.011A pdb=" N ARG B 254 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN B 255 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 296 Proline residue: B 289 - end of helix removed outlier: 3.666A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 338 removed outlier: 3.824A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 356 Processing helix chain 'C' and resid 33 through 61 Proline residue: C 46 - end of helix removed outlier: 3.817A pdb=" N SER C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE C 60 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 87 Processing helix chain 'C' and resid 100 through 129 Proline residue: C 110 - end of helix Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 158 removed outlier: 3.672A pdb=" N ALA C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.794A pdb=" N ASN C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 236 removed outlier: 4.061A pdb=" N LYS C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 4.011A pdb=" N ARG C 254 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN C 255 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 296 Proline residue: C 289 - end of helix removed outlier: 3.666A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 338 removed outlier: 3.825A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 356 Processing helix chain 'D' and resid 33 through 61 Proline residue: D 46 - end of helix removed outlier: 3.816A pdb=" N SER D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE D 60 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 87 Processing helix chain 'D' and resid 100 through 129 Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 158 removed outlier: 3.672A pdb=" N ALA D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS D 158 " --> pdb=" O ILE D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.793A pdb=" N ASN D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 236 removed outlier: 4.061A pdb=" N LYS D 212 " --> pdb=" O ASN D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 4.011A pdb=" N ARG D 254 " --> pdb=" O GLY D 251 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN D 255 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 296 Proline residue: D 289 - end of helix removed outlier: 3.666A pdb=" N PHE D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 338 removed outlier: 3.825A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 356 Processing helix chain 'E' and resid 33 through 61 Proline residue: E 46 - end of helix removed outlier: 3.816A pdb=" N SER E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE E 60 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 87 Processing helix chain 'E' and resid 100 through 129 Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 158 removed outlier: 3.673A pdb=" N ALA E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS E 158 " --> pdb=" O ILE E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.793A pdb=" N ASN E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER E 206 " --> pdb=" O THR E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 236 removed outlier: 4.060A pdb=" N LYS E 212 " --> pdb=" O ASN E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 255 removed outlier: 4.011A pdb=" N ARG E 254 " --> pdb=" O GLY E 251 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN E 255 " --> pdb=" O ILE E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 296 Proline residue: E 289 - end of helix removed outlier: 3.666A pdb=" N PHE E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 338 removed outlier: 3.824A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 356 Processing helix chain 'F' and resid 33 through 61 Proline residue: F 46 - end of helix removed outlier: 3.816A pdb=" N SER F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE F 60 " --> pdb=" O GLN F 56 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 87 Processing helix chain 'F' and resid 100 through 129 Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 158 removed outlier: 3.672A pdb=" N ALA F 157 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS F 158 " --> pdb=" O ILE F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.795A pdb=" N ASN F 205 " --> pdb=" O LYS F 201 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER F 206 " --> pdb=" O THR F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 236 removed outlier: 4.060A pdb=" N LYS F 212 " --> pdb=" O ASN F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 255 removed outlier: 4.011A pdb=" N ARG F 254 " --> pdb=" O GLY F 251 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN F 255 " --> pdb=" O ILE F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 296 Proline residue: F 289 - end of helix removed outlier: 3.665A pdb=" N PHE F 296 " --> pdb=" O VAL F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 338 removed outlier: 3.825A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 356 Processing helix chain 'G' and resid 33 through 61 Proline residue: G 46 - end of helix removed outlier: 3.817A pdb=" N SER G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE G 60 " --> pdb=" O GLN G 56 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY G 61 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 87 Processing helix chain 'G' and resid 100 through 129 Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 158 removed outlier: 3.673A pdb=" N ALA G 157 " --> pdb=" O ALA G 153 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS G 158 " --> pdb=" O ILE G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.794A pdb=" N ASN G 205 " --> pdb=" O LYS G 201 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER G 206 " --> pdb=" O THR G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 236 removed outlier: 4.060A pdb=" N LYS G 212 " --> pdb=" O ASN G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 255 removed outlier: 4.011A pdb=" N ARG G 254 " --> pdb=" O GLY G 251 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN G 255 " --> pdb=" O ILE G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 296 Proline residue: G 289 - end of helix removed outlier: 3.666A pdb=" N PHE G 296 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 338 removed outlier: 3.825A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 356 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 3.591A pdb=" N PHE A 244 " --> pdb=" O CYS A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 removed outlier: 3.591A pdb=" N PHE B 244 " --> pdb=" O CYS B 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 removed outlier: 3.592A pdb=" N PHE C 244 " --> pdb=" O CYS C 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 removed outlier: 3.592A pdb=" N PHE D 244 " --> pdb=" O CYS D 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 removed outlier: 3.592A pdb=" N PHE E 244 " --> pdb=" O CYS E 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 removed outlier: 3.591A pdb=" N PHE F 244 " --> pdb=" O CYS F 265 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 removed outlier: 3.591A pdb=" N PHE G 244 " --> pdb=" O CYS G 265 " (cutoff:3.500A) 1022 hydrogen bonds defined for protein. 3024 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: 6.56 Time building geometry restraints manager: 5.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4897 1.35 - 1.47: 4119 1.47 - 1.59: 7700 1.59 - 1.71: 0 1.71 - 1.83: 91 Bond restraints: 16807 Sorted by residual: bond pdb=" CD GLU C 144 " pdb=" OE1 GLU C 144 " ideal model delta sigma weight residual 1.249 1.230 0.019 1.90e-02 2.77e+03 9.71e-01 bond pdb=" CA LEU C 318 " pdb=" CB LEU C 318 " ideal model delta sigma weight residual 1.527 1.552 -0.024 2.48e-02 1.63e+03 9.66e-01 bond pdb=" CA LEU G 318 " pdb=" CB LEU G 318 " ideal model delta sigma weight residual 1.527 1.551 -0.024 2.48e-02 1.63e+03 9.24e-01 bond pdb=" CA LEU E 318 " pdb=" CB LEU E 318 " ideal model delta sigma weight residual 1.527 1.551 -0.024 2.48e-02 1.63e+03 9.14e-01 bond pdb=" CA LEU F 318 " pdb=" CB LEU F 318 " ideal model delta sigma weight residual 1.527 1.551 -0.024 2.48e-02 1.63e+03 9.13e-01 ... (remaining 16802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 21942 1.57 - 3.15: 644 3.15 - 4.72: 96 4.72 - 6.30: 89 6.30 - 7.87: 28 Bond angle restraints: 22799 Sorted by residual: angle pdb=" CA LYS C 307 " pdb=" CB LYS C 307 " pdb=" CG LYS C 307 " ideal model delta sigma weight residual 114.10 120.96 -6.86 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CA LYS D 307 " pdb=" CB LYS D 307 " pdb=" CG LYS D 307 " ideal model delta sigma weight residual 114.10 120.95 -6.85 2.00e+00 2.50e-01 1.17e+01 angle pdb=" CA LYS A 307 " pdb=" CB LYS A 307 " pdb=" CG LYS A 307 " ideal model delta sigma weight residual 114.10 120.95 -6.85 2.00e+00 2.50e-01 1.17e+01 angle pdb=" CA LYS F 307 " pdb=" CB LYS F 307 " pdb=" CG LYS F 307 " ideal model delta sigma weight residual 114.10 120.94 -6.84 2.00e+00 2.50e-01 1.17e+01 angle pdb=" CA LYS G 307 " pdb=" CB LYS G 307 " pdb=" CG LYS G 307 " ideal model delta sigma weight residual 114.10 120.94 -6.84 2.00e+00 2.50e-01 1.17e+01 ... (remaining 22794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.29: 8912 14.29 - 28.59: 755 28.59 - 42.88: 350 42.88 - 57.18: 70 57.18 - 71.47: 14 Dihedral angle restraints: 10101 sinusoidal: 3976 harmonic: 6125 Sorted by residual: dihedral pdb=" CA ALA G 269 " pdb=" C ALA G 269 " pdb=" N VAL G 270 " pdb=" CA VAL G 270 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ALA B 269 " pdb=" C ALA B 269 " pdb=" N VAL B 270 " pdb=" CA VAL B 270 " ideal model delta harmonic sigma weight residual -180.00 -159.45 -20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA ALA E 269 " pdb=" C ALA E 269 " pdb=" N VAL E 270 " pdb=" CA VAL E 270 " ideal model delta harmonic sigma weight residual -180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 10098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1687 0.032 - 0.064: 649 0.064 - 0.095: 277 0.095 - 0.127: 82 0.127 - 0.159: 21 Chirality restraints: 2716 Sorted by residual: chirality pdb=" CA GLU G 144 " pdb=" N GLU G 144 " pdb=" C GLU G 144 " pdb=" CB GLU G 144 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA GLU D 144 " pdb=" N GLU D 144 " pdb=" C GLU D 144 " pdb=" CB GLU D 144 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA GLU C 144 " pdb=" N GLU C 144 " pdb=" C GLU C 144 " pdb=" CB GLU C 144 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 ... (remaining 2713 not shown) Planarity restraints: 2751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 123 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO A 124 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 123 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO D 124 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 124 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 124 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 123 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO G 124 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO G 124 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 124 " -0.022 5.00e-02 4.00e+02 ... (remaining 2748 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3923 2.79 - 3.32: 16765 3.32 - 3.85: 27275 3.85 - 4.37: 27251 4.37 - 4.90: 48664 Nonbonded interactions: 123878 Sorted by model distance: nonbonded pdb=" OD2 ASP F 138 " pdb=" OH TYR F 331 " model vdw 2.263 3.040 nonbonded pdb=" OD2 ASP G 138 " pdb=" OH TYR G 331 " model vdw 2.263 3.040 nonbonded pdb=" OD2 ASP C 138 " pdb=" OH TYR C 331 " model vdw 2.264 3.040 nonbonded pdb=" OD2 ASP D 138 " pdb=" OH TYR D 331 " model vdw 2.264 3.040 nonbonded pdb=" OD2 ASP A 138 " pdb=" OH TYR A 331 " model vdw 2.264 3.040 ... (remaining 123873 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.290 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: 0.710 Check model and map are aligned: 0.140 Set scattering table: 0.150 Process input model: 41.430 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.003 0.047 16821 Z= 0.142 Angle : 0.740 7.869 22827 Z= 0.366 Chirality : 0.042 0.159 2716 Planarity : 0.004 0.038 2751 Dihedral : 13.526 71.473 6069 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 2009 helix: 1.66 (0.14), residues: 1407 sheet: -2.55 (0.45), residues: 84 loop : -2.37 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 127 HIS 0.001 0.000 HIS C 134 PHE 0.010 0.001 PHE F 273 TYR 0.019 0.001 TYR C 345 ARG 0.001 0.000 ARG G 152 Details of bonding type rmsd hydrogen bonds : bond 0.06682 ( 1022) hydrogen bonds : angle 3.76853 ( 3024) SS BOND : bond 0.00337 ( 14) SS BOND : angle 1.16558 ( 28) covalent geometry : bond 0.00305 (16807) covalent geometry : angle 0.73907 (22799) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 121 TYR cc_start: 0.8485 (t80) cc_final: 0.7692 (t80) REVERT: A 140 LYS cc_start: 0.7065 (mmtt) cc_final: 0.6749 (mmtt) REVERT: A 143 MET cc_start: 0.8314 (ppp) cc_final: 0.7553 (ppp) REVERT: A 307 LYS cc_start: 0.8804 (tptp) cc_final: 0.8591 (tptp) REVERT: A 327 ASP cc_start: 0.7441 (m-30) cc_final: 0.7134 (m-30) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1210 time to fit residues: 17.2089 Evaluate side-chains 101 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 82 optimal weight: 0.0020 chunk 159 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 overall best weight: 2.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.169220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.138345 restraints weight = 3955.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.142301 restraints weight = 2624.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.145060 restraints weight = 1918.813| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16821 Z= 0.135 Angle : 0.610 6.750 22827 Z= 0.299 Chirality : 0.039 0.123 2716 Planarity : 0.004 0.034 2751 Dihedral : 3.604 16.680 2184 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.38 % Allowed : 4.91 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.19), residues: 2009 helix: 2.28 (0.14), residues: 1365 sheet: -2.82 (0.44), residues: 84 loop : -2.68 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 127 HIS 0.000 0.000 HIS G 134 PHE 0.014 0.001 PHE A 273 TYR 0.011 0.001 TYR C 111 ARG 0.006 0.001 ARG E 75 Details of bonding type rmsd hydrogen bonds : bond 0.03017 ( 1022) hydrogen bonds : angle 3.46233 ( 3024) SS BOND : bond 0.00433 ( 14) SS BOND : angle 0.76988 ( 28) covalent geometry : bond 0.00311 (16807) covalent geometry : angle 0.61010 (22799) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 39 THR cc_start: 0.9395 (p) cc_final: 0.9141 (t) REVERT: A 121 TYR cc_start: 0.8486 (t80) cc_final: 0.7855 (t80) REVERT: A 143 MET cc_start: 0.8338 (ppp) cc_final: 0.7882 (ppp) REVERT: A 339 ILE cc_start: 0.9099 (tt) cc_final: 0.8740 (tt) REVERT: A 345 TYR cc_start: 0.7984 (t80) cc_final: 0.7641 (t80) outliers start: 1 outliers final: 1 residues processed: 133 average time/residue: 0.1181 time to fit residues: 18.7059 Evaluate side-chains 103 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 103 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 149 optimal weight: 0.0020 chunk 77 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 144 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 7 optimal weight: 0.1980 chunk 125 optimal weight: 0.0980 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.171490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.141458 restraints weight = 3968.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.145455 restraints weight = 2552.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.148414 restraints weight = 1835.627| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16821 Z= 0.112 Angle : 0.625 6.792 22827 Z= 0.304 Chirality : 0.039 0.129 2716 Planarity : 0.003 0.036 2751 Dihedral : 3.572 19.178 2184 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.20), residues: 2009 helix: 2.41 (0.14), residues: 1365 sheet: -2.73 (0.44), residues: 84 loop : -2.44 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 74 HIS 0.001 0.001 HIS D 134 PHE 0.008 0.001 PHE F 72 TYR 0.011 0.001 TYR G 111 ARG 0.001 0.000 ARG G 75 Details of bonding type rmsd hydrogen bonds : bond 0.02793 ( 1022) hydrogen bonds : angle 3.37624 ( 3024) SS BOND : bond 0.00260 ( 14) SS BOND : angle 1.89096 ( 28) covalent geometry : bond 0.00245 (16807) covalent geometry : angle 0.62234 (22799) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 39 THR cc_start: 0.9435 (p) cc_final: 0.9135 (t) REVERT: A 56 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8193 (tm-30) REVERT: A 121 TYR cc_start: 0.8476 (t80) cc_final: 0.7820 (t80) REVERT: A 140 LYS cc_start: 0.6278 (mmtt) cc_final: 0.5254 (mmtt) REVERT: A 143 MET cc_start: 0.8340 (ppp) cc_final: 0.8006 (ppp) REVERT: A 305 VAL cc_start: 0.7329 (t) cc_final: 0.7078 (t) REVERT: A 307 LYS cc_start: 0.8719 (tptp) cc_final: 0.8507 (tptp) REVERT: A 339 ILE cc_start: 0.9104 (tt) cc_final: 0.8795 (tt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1137 time to fit residues: 17.0101 Evaluate side-chains 103 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 122 optimal weight: 0.4980 chunk 182 optimal weight: 0.4980 chunk 161 optimal weight: 0.9990 chunk 165 optimal weight: 0.0670 chunk 86 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.167498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.136236 restraints weight = 4005.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140463 restraints weight = 2548.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.143565 restraints weight = 1815.996| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16821 Z= 0.113 Angle : 0.635 7.436 22827 Z= 0.301 Chirality : 0.039 0.125 2716 Planarity : 0.004 0.036 2751 Dihedral : 3.557 19.961 2184 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.20), residues: 2009 helix: 2.37 (0.14), residues: 1372 sheet: -2.60 (0.47), residues: 84 loop : -2.42 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 74 HIS 0.001 0.001 HIS D 134 PHE 0.011 0.001 PHE G 334 TYR 0.010 0.001 TYR G 111 ARG 0.004 0.000 ARG F 254 Details of bonding type rmsd hydrogen bonds : bond 0.02742 ( 1022) hydrogen bonds : angle 3.38742 ( 3024) SS BOND : bond 0.00299 ( 14) SS BOND : angle 1.74874 ( 28) covalent geometry : bond 0.00241 (16807) covalent geometry : angle 0.63239 (22799) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 39 THR cc_start: 0.9424 (p) cc_final: 0.9139 (t) REVERT: A 56 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8153 (tm-30) REVERT: A 121 TYR cc_start: 0.8486 (t80) cc_final: 0.7808 (t80) REVERT: A 140 LYS cc_start: 0.6351 (mmtt) cc_final: 0.4875 (mttm) REVERT: A 143 MET cc_start: 0.8344 (ppp) cc_final: 0.7966 (ppp) REVERT: A 245 VAL cc_start: 0.9618 (m) cc_final: 0.9365 (p) REVERT: A 307 LYS cc_start: 0.8756 (tptp) cc_final: 0.8430 (tptp) REVERT: A 339 ILE cc_start: 0.9055 (tt) cc_final: 0.8760 (tt) REVERT: A 349 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8440 (mmmt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1791 time to fit residues: 25.9508 Evaluate side-chains 108 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 184 optimal weight: 8.9990 chunk 161 optimal weight: 0.9990 chunk 115 optimal weight: 0.0770 chunk 59 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 51 optimal weight: 0.0470 chunk 111 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.166908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.135728 restraints weight = 4064.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.140120 restraints weight = 2549.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.143218 restraints weight = 1796.257| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16821 Z= 0.113 Angle : 0.635 6.973 22827 Z= 0.304 Chirality : 0.040 0.128 2716 Planarity : 0.004 0.037 2751 Dihedral : 3.581 20.268 2184 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.20), residues: 2009 helix: 2.30 (0.14), residues: 1372 sheet: -2.51 (0.50), residues: 84 loop : -2.21 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 74 HIS 0.001 0.001 HIS D 134 PHE 0.008 0.001 PHE C 273 TYR 0.013 0.001 TYR C 345 ARG 0.006 0.001 ARG F 254 Details of bonding type rmsd hydrogen bonds : bond 0.02686 ( 1022) hydrogen bonds : angle 3.41195 ( 3024) SS BOND : bond 0.00221 ( 14) SS BOND : angle 1.60672 ( 28) covalent geometry : bond 0.00253 (16807) covalent geometry : angle 0.63260 (22799) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.269 Fit side-chains REVERT: A 39 THR cc_start: 0.9411 (p) cc_final: 0.9115 (t) REVERT: A 121 TYR cc_start: 0.8496 (t80) cc_final: 0.7831 (t80) REVERT: A 245 VAL cc_start: 0.9577 (m) cc_final: 0.9347 (p) REVERT: A 305 VAL cc_start: 0.7293 (t) cc_final: 0.7049 (t) REVERT: A 307 LYS cc_start: 0.8717 (tptp) cc_final: 0.8451 (tptp) REVERT: A 327 ASP cc_start: 0.7421 (m-30) cc_final: 0.7191 (m-30) REVERT: A 339 ILE cc_start: 0.9046 (tt) cc_final: 0.8773 (tt) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1218 time to fit residues: 17.1328 Evaluate side-chains 109 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 84 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 131 optimal weight: 0.0270 chunk 95 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 48 optimal weight: 0.0170 chunk 122 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 82 optimal weight: 8.9990 chunk 187 optimal weight: 0.4980 chunk 105 optimal weight: 0.0470 overall best weight: 0.2374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.169905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.139492 restraints weight = 4003.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.143907 restraints weight = 2528.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.146896 restraints weight = 1774.780| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16821 Z= 0.114 Angle : 0.627 7.251 22827 Z= 0.300 Chirality : 0.040 0.133 2716 Planarity : 0.004 0.037 2751 Dihedral : 3.595 21.533 2184 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.20), residues: 2009 helix: 2.27 (0.14), residues: 1372 sheet: -2.61 (0.51), residues: 84 loop : -2.12 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 74 HIS 0.001 0.000 HIS D 134 PHE 0.009 0.001 PHE E 273 TYR 0.010 0.001 TYR B 111 ARG 0.002 0.000 ARG E 254 Details of bonding type rmsd hydrogen bonds : bond 0.02648 ( 1022) hydrogen bonds : angle 3.53174 ( 3024) SS BOND : bond 0.00410 ( 14) SS BOND : angle 1.36328 ( 28) covalent geometry : bond 0.00244 (16807) covalent geometry : angle 0.62570 (22799) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 39 THR cc_start: 0.9385 (p) cc_final: 0.9094 (t) REVERT: A 56 GLN cc_start: 0.8338 (tm-30) cc_final: 0.8005 (tp40) REVERT: A 76 GLN cc_start: 0.8233 (mt0) cc_final: 0.7894 (mt0) REVERT: A 121 TYR cc_start: 0.8542 (t80) cc_final: 0.7771 (t80) REVERT: A 245 VAL cc_start: 0.9556 (m) cc_final: 0.9316 (p) REVERT: A 254 ARG cc_start: 0.8360 (mmm160) cc_final: 0.7937 (tpp80) REVERT: A 307 LYS cc_start: 0.8754 (tptp) cc_final: 0.8525 (tptp) REVERT: A 327 ASP cc_start: 0.7404 (m-30) cc_final: 0.7143 (m-30) REVERT: A 332 ASN cc_start: 0.9081 (m110) cc_final: 0.8840 (m110) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2149 time to fit residues: 30.0768 Evaluate side-chains 107 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 131 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 150 optimal weight: 0.5980 chunk 140 optimal weight: 0.0370 chunk 33 optimal weight: 0.0050 chunk 55 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 197 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 overall best weight: 0.6674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.167836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.137776 restraints weight = 4073.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.142224 restraints weight = 2530.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.145104 restraints weight = 1760.058| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16821 Z= 0.113 Angle : 0.667 7.530 22827 Z= 0.310 Chirality : 0.041 0.131 2716 Planarity : 0.004 0.038 2751 Dihedral : 3.616 21.858 2184 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.20), residues: 2009 helix: 2.31 (0.14), residues: 1365 sheet: -2.49 (0.51), residues: 84 loop : -1.83 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 74 HIS 0.000 0.000 HIS A 134 PHE 0.010 0.001 PHE A 273 TYR 0.019 0.001 TYR D 345 ARG 0.002 0.000 ARG B 254 Details of bonding type rmsd hydrogen bonds : bond 0.02647 ( 1022) hydrogen bonds : angle 3.49138 ( 3024) SS BOND : bond 0.00155 ( 14) SS BOND : angle 1.38923 ( 28) covalent geometry : bond 0.00247 (16807) covalent geometry : angle 0.66572 (22799) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 THR cc_start: 0.9384 (p) cc_final: 0.9079 (t) REVERT: A 56 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8174 (tp40) REVERT: A 74 TRP cc_start: 0.7669 (t60) cc_final: 0.7401 (t60) REVERT: A 76 GLN cc_start: 0.8249 (mt0) cc_final: 0.8035 (mt0) REVERT: A 121 TYR cc_start: 0.8565 (t80) cc_final: 0.7839 (t80) REVERT: A 143 MET cc_start: 0.8706 (ptm) cc_final: 0.8502 (ppp) REVERT: A 245 VAL cc_start: 0.9560 (m) cc_final: 0.9321 (p) REVERT: A 254 ARG cc_start: 0.8470 (mmm160) cc_final: 0.7853 (tpp80) REVERT: A 305 VAL cc_start: 0.7133 (t) cc_final: 0.6867 (t) REVERT: A 307 LYS cc_start: 0.8737 (tptp) cc_final: 0.8466 (tptp) REVERT: A 327 ASP cc_start: 0.7435 (m-30) cc_final: 0.7215 (m-30) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1158 time to fit residues: 15.4747 Evaluate side-chains 107 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 85 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 191 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.164829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.135114 restraints weight = 4018.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.139071 restraints weight = 2561.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.142012 restraints weight = 1821.136| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16821 Z= 0.153 Angle : 0.691 6.743 22827 Z= 0.333 Chirality : 0.042 0.161 2716 Planarity : 0.004 0.036 2751 Dihedral : 3.768 17.701 2184 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.20), residues: 2009 helix: 2.33 (0.14), residues: 1358 sheet: -0.91 (0.76), residues: 49 loop : -1.69 (0.28), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 74 HIS 0.001 0.000 HIS B 134 PHE 0.009 0.001 PHE D 273 TYR 0.016 0.001 TYR C 111 ARG 0.003 0.001 ARG E 29 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 1022) hydrogen bonds : angle 3.68629 ( 3024) SS BOND : bond 0.00388 ( 14) SS BOND : angle 1.80150 ( 28) covalent geometry : bond 0.00359 (16807) covalent geometry : angle 0.68892 (22799) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 39 THR cc_start: 0.9395 (p) cc_final: 0.9086 (t) REVERT: A 56 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8239 (tp40) REVERT: A 76 GLN cc_start: 0.8263 (mt0) cc_final: 0.7874 (mt0) REVERT: A 121 TYR cc_start: 0.8615 (t80) cc_final: 0.7875 (t80) REVERT: A 254 ARG cc_start: 0.8741 (mmm160) cc_final: 0.8437 (mmm160) REVERT: A 327 ASP cc_start: 0.7579 (m-30) cc_final: 0.7245 (m-30) REVERT: A 332 ASN cc_start: 0.9224 (m110) cc_final: 0.8997 (m110) REVERT: A 349 LYS cc_start: 0.8608 (mtpt) cc_final: 0.8382 (mtpt) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1446 time to fit residues: 19.7097 Evaluate side-chains 96 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 83 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 154 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.162171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.133725 restraints weight = 3698.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.137688 restraints weight = 2332.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140403 restraints weight = 1642.881| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16821 Z= 0.126 Angle : 0.703 7.067 22827 Z= 0.335 Chirality : 0.042 0.166 2716 Planarity : 0.004 0.038 2751 Dihedral : 3.837 21.049 2184 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.20), residues: 2009 helix: 2.39 (0.14), residues: 1365 sheet: -2.34 (0.51), residues: 84 loop : -1.68 (0.30), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 74 HIS 0.001 0.000 HIS E 134 PHE 0.009 0.001 PHE E 235 TYR 0.013 0.001 TYR D 111 ARG 0.008 0.001 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.03082 ( 1022) hydrogen bonds : angle 3.58366 ( 3024) SS BOND : bond 0.00253 ( 14) SS BOND : angle 1.51273 ( 28) covalent geometry : bond 0.00292 (16807) covalent geometry : angle 0.70158 (22799) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 THR cc_start: 0.9410 (p) cc_final: 0.9072 (t) REVERT: A 56 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8343 (tp40) REVERT: A 76 GLN cc_start: 0.8192 (mt0) cc_final: 0.7881 (mt0) REVERT: A 121 TYR cc_start: 0.8639 (t80) cc_final: 0.7875 (t80) REVERT: A 143 MET cc_start: 0.8838 (ptm) cc_final: 0.7816 (ppp) REVERT: A 305 VAL cc_start: 0.7402 (t) cc_final: 0.6223 (t) REVERT: A 327 ASP cc_start: 0.7607 (m-30) cc_final: 0.7241 (m-30) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1669 time to fit residues: 24.2898 Evaluate side-chains 107 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 148 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 150 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 3 optimal weight: 0.0010 chunk 14 optimal weight: 0.0030 chunk 190 optimal weight: 1.9990 chunk 172 optimal weight: 7.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.168890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.140036 restraints weight = 3874.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144033 restraints weight = 2457.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.146829 restraints weight = 1745.576| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16821 Z= 0.121 Angle : 0.693 7.347 22827 Z= 0.327 Chirality : 0.042 0.152 2716 Planarity : 0.004 0.037 2751 Dihedral : 3.847 22.527 2184 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.20), residues: 2009 helix: 2.40 (0.14), residues: 1365 sheet: -2.51 (0.49), residues: 84 loop : -1.79 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 74 HIS 0.002 0.001 HIS G 134 PHE 0.010 0.001 PHE E 273 TYR 0.015 0.001 TYR D 234 ARG 0.003 0.001 ARG F 29 Details of bonding type rmsd hydrogen bonds : bond 0.02849 ( 1022) hydrogen bonds : angle 3.56570 ( 3024) SS BOND : bond 0.00298 ( 14) SS BOND : angle 1.41976 ( 28) covalent geometry : bond 0.00267 (16807) covalent geometry : angle 0.69177 (22799) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.534 Fit side-chains revert: symmetry clash REVERT: A 39 THR cc_start: 0.9376 (p) cc_final: 0.9051 (t) REVERT: A 56 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8122 (tp40) REVERT: A 121 TYR cc_start: 0.8641 (t80) cc_final: 0.7856 (t80) REVERT: A 279 ILE cc_start: 0.9009 (tt) cc_final: 0.8790 (tt) REVERT: A 305 VAL cc_start: 0.7448 (t) cc_final: 0.6728 (t) REVERT: A 327 ASP cc_start: 0.7521 (m-30) cc_final: 0.7308 (m-30) REVERT: A 341 GLU cc_start: 0.4282 (tt0) cc_final: 0.4002 (tt0) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1546 time to fit residues: 22.5886 Evaluate side-chains 110 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 87 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 142 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 181 optimal weight: 0.0670 chunk 117 optimal weight: 8.9990 chunk 176 optimal weight: 0.0970 overall best weight: 1.0918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.166749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.137801 restraints weight = 3794.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.141674 restraints weight = 2390.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144417 restraints weight = 1695.731| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16821 Z= 0.123 Angle : 0.702 7.580 22827 Z= 0.333 Chirality : 0.042 0.154 2716 Planarity : 0.005 0.059 2751 Dihedral : 3.833 21.812 2184 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.20), residues: 2009 helix: 2.33 (0.14), residues: 1365 sheet: -2.42 (0.47), residues: 84 loop : -1.77 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 74 HIS 0.001 0.000 HIS G 134 PHE 0.010 0.001 PHE E 273 TYR 0.013 0.001 TYR A 331 ARG 0.003 0.000 ARG G 254 Details of bonding type rmsd hydrogen bonds : bond 0.02883 ( 1022) hydrogen bonds : angle 3.54267 ( 3024) SS BOND : bond 0.00342 ( 14) SS BOND : angle 1.46282 ( 28) covalent geometry : bond 0.00279 (16807) covalent geometry : angle 0.70097 (22799) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3210.17 seconds wall clock time: 60 minutes 45.69 seconds (3645.69 seconds total)