Starting phenix.real_space_refine (version: dev) on Sat May 14 03:10:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsv_32768/05_2022/7wsv_32768.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsv_32768/05_2022/7wsv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsv_32768/05_2022/7wsv_32768.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsv_32768/05_2022/7wsv_32768.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsv_32768/05_2022/7wsv_32768.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsv_32768/05_2022/7wsv_32768.pdb" } resolution = 4.5 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 31": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 316": "OD1" <-> "OD2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 316": "OD1" <-> "OD2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 316": "OD1" <-> "OD2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 316": "OD1" <-> "OD2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 316": "OD1" <-> "OD2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 316": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: 9.38, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 7.31 Conformation dependent library (CDL) restraints added in 2.6 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: 0.58 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: 4.59 Time building geometry restraints manager: 7.76 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: 100.95 - 107.62: 448 107.62 - 114.29: 9900 114.29 - 120.96: 8237 120.96 - 127.63: 4074 127.63 - 134.30: 140 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 2.440 nonbonded pdb=" OD2 ASP G 138 " pdb=" OH TYR G 331 " model vdw 2.263 2.440 nonbonded pdb=" OD2 ASP C 138 " pdb=" OH TYR C 331 " model vdw 2.264 2.440 nonbonded pdb=" OD2 ASP D 138 " pdb=" OH TYR D 331 " model vdw 2.264 2.440 nonbonded pdb=" OD2 ASP A 138 " pdb=" OH TYR A 331 " model vdw 2.264 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set refine NCS operators NCS operators will be refined. 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. 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: 0.180 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: 2.590 Check model and map are aligned: 0.240 Convert atoms to be neutral: 0.140 Process input model: 44.350 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 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 16807 Z= 0.195 Angle : 0.739 7.869 22799 Z= 0.365 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 : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.00 % 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.302 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1273 time to fit residues: 17.9537 Evaluate side-chains 101 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.274 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3805 ------------------------------------------------------------------------------- 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: 9.9990 chunk 153 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 159 optimal weight: 0.0670 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 16807 Z= 0.227 Angle : 0.623 6.631 22799 Z= 0.306 Chirality : 0.039 0.128 2716 Planarity : 0.004 0.032 2751 Dihedral : 3.621 16.170 2184 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.38 % 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: 1.17 (0.20), residues: 2009 helix: 2.28 (0.14), residues: 1365 sheet: -2.80 (0.43), residues: 84 loop : -2.67 (0.24), residues: 560 *********************** 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 129 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 0.322 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.1240 time to fit residues: 18.8497 Evaluate side-chains 106 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.281 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0251 time to fit residues: 0.4295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 153 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 183 optimal weight: 0.4980 chunk 62 optimal weight: 0.0040 chunk 148 optimal weight: 0.0170 overall best weight: 0.5034 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 16807 Z= 0.163 Angle : 0.619 6.576 22799 Z= 0.299 Chirality : 0.039 0.128 2716 Planarity : 0.004 0.037 2751 Dihedral : 3.569 20.142 2184 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.00 % 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: 1.43 (0.20), residues: 2009 helix: 2.42 (0.14), residues: 1372 sheet: -2.70 (0.45), residues: 84 loop : -2.46 (0.25), residues: 553 *********************** 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 124 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.303 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1145 time to fit residues: 16.9464 Evaluate side-chains 105 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.291 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 88 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 185 optimal weight: 5.9990 chunk 196 optimal weight: 0.7980 chunk 96 optimal weight: 0.0030 chunk 175 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 16807 Z= 0.153 Angle : 0.637 7.711 22799 Z= 0.303 Chirality : 0.039 0.129 2716 Planarity : 0.004 0.035 2751 Dihedral : 3.530 20.107 2184 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.00 % 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: 1.37 (0.20), residues: 2009 helix: 2.34 (0.14), residues: 1372 sheet: -2.41 (0.50), residues: 84 loop : -2.41 (0.25), residues: 553 *********************** 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 115 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.278 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1133 time to fit residues: 15.5943 Evaluate side-chains 94 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.278 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 135 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 176 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 16807 Z= 0.180 Angle : 0.650 6.746 22799 Z= 0.313 Chirality : 0.039 0.125 2716 Planarity : 0.004 0.035 2751 Dihedral : 3.655 19.527 2184 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 0.00 % 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: 1.54 (0.20), residues: 2009 helix: 2.41 (0.14), residues: 1365 sheet: -2.26 (0.53), residues: 84 loop : -2.13 (0.25), residues: 560 *********************** 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 118 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.288 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1133 time to fit residues: 16.2712 Evaluate side-chains 99 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.284 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 196 optimal weight: 0.5980 chunk 163 optimal weight: 5.9990 chunk 90 optimal weight: 0.0370 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 0.3980 chunk 103 optimal weight: 2.9990 overall best weight: 0.6062 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 16807 Z= 0.177 Angle : 0.674 7.040 22799 Z= 0.324 Chirality : 0.040 0.135 2716 Planarity : 0.004 0.040 2751 Dihedral : 3.660 21.348 2184 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 0.00 % 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: 1.34 (0.20), residues: 2009 helix: 2.24 (0.14), residues: 1365 sheet: -2.45 (0.53), residues: 84 loop : -2.15 (0.26), residues: 560 *********************** 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 117 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.303 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1099 time to fit residues: 15.5030 Evaluate side-chains 99 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.295 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 111 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 165 optimal weight: 4.9990 chunk 109 optimal weight: 0.0570 chunk 195 optimal weight: 2.9990 chunk 122 optimal weight: 0.0000 chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 16807 Z= 0.176 Angle : 0.688 7.625 22799 Z= 0.325 Chirality : 0.042 0.133 2716 Planarity : 0.004 0.036 2751 Dihedral : 3.696 21.182 2184 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.00 % 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: 1.47 (0.20), residues: 2009 helix: 2.34 (0.14), residues: 1365 sheet: -2.31 (0.50), residues: 84 loop : -2.11 (0.26), residues: 560 *********************** 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 113 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.288 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1070 time to fit residues: 14.6994 Evaluate side-chains 99 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.288 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.0970 chunk 124 optimal weight: 0.7980 chunk 133 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 177 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 16807 Z= 0.177 Angle : 0.688 7.084 22799 Z= 0.327 Chirality : 0.041 0.138 2716 Planarity : 0.004 0.036 2751 Dihedral : 3.653 21.992 2184 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.00 % 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: 1.42 (0.20), residues: 2009 helix: 2.32 (0.14), residues: 1365 sheet: -2.27 (0.50), residues: 84 loop : -2.20 (0.26), residues: 560 *********************** 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 110 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.321 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1020 time to fit residues: 13.6919 Evaluate side-chains 97 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 182 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 16807 Z= 0.247 Angle : 0.723 6.686 22799 Z= 0.354 Chirality : 0.043 0.176 2716 Planarity : 0.006 0.084 2751 Dihedral : 3.859 18.028 2184 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 0.00 % 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: 1.42 (0.20), residues: 2009 helix: 2.26 (0.14), residues: 1365 sheet: -1.20 (0.71), residues: 49 loop : -2.18 (0.24), residues: 595 *********************** 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 115 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.354 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.0953 time to fit residues: 13.5376 Evaluate side-chains 97 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.254 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 0.0370 chunk 117 optimal weight: 4.9990 chunk 91 optimal weight: 0.3980 chunk 134 optimal weight: 0.8980 chunk 202 optimal weight: 4.9990 chunk 186 optimal weight: 8.9990 chunk 161 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 16807 Z= 0.181 Angle : 0.702 6.956 22799 Z= 0.334 Chirality : 0.041 0.146 2716 Planarity : 0.006 0.080 2751 Dihedral : 3.821 22.517 2184 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.00 % 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: 2.36 (0.14), residues: 1365 sheet: -2.53 (0.48), residues: 84 loop : -2.33 (0.24), residues: 560 ********************** 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 116 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.302 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1055 time to fit residues: 14.8171 Evaluate side-chains 108 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 6.9990 chunk 49 optimal weight: 0.0470 chunk 148 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 67 optimal weight: 0.0270 chunk 165 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.165216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.137230 restraints weight = 3868.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141199 restraints weight = 2436.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.143923 restraints weight = 1717.452| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 16807 Z= 0.178 Angle : 0.701 6.952 22799 Z= 0.334 Chirality : 0.041 0.135 2716 Planarity : 0.006 0.078 2751 Dihedral : 3.757 22.051 2184 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.00 % 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: 1.32 (0.20), residues: 2009 helix: 2.26 (0.14), residues: 1365 sheet: -2.46 (0.46), residues: 84 loop : -2.26 (0.25), residues: 560 =============================================================================== Job complete usr+sys time: 1929.89 seconds wall clock time: 36 minutes 48.05 seconds (2208.05 seconds total)