Starting phenix.real_space_refine on Sun Mar 17 02:15:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsv_32768/03_2024/7wsv_32768.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsv_32768/03_2024/7wsv_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_32768/03_2024/7wsv_32768.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsv_32768/03_2024/7wsv_32768.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsv_32768/03_2024/7wsv_32768.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsv_32768/03_2024/7wsv_32768.pdb" } 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 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-5265/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: 8.68, per 1000 atoms: 0.53 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: 5.62 Conformation dependent library (CDL) restraints added in 2.2 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: 1.25 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: 4.16 Time building geometry restraints manager: 6.06 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. 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: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.810 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 39.030 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.150 ------------------------------------------------------------------------------- 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 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 : 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 *********************** 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 : 0.231 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: 0.1208 time to fit residues: 17.0975 Evaluate side-chains 101 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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: 9.9990 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: 0.7654 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 0.034 16807 Z= 0.224 Angle : 0.625 6.646 22799 Z= 0.307 Chirality : 0.039 0.115 2716 Planarity : 0.003 0.032 2751 Dihedral : 3.635 16.473 2184 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.42 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 (0.20), residues: 2009 helix: 2.28 (0.14), residues: 1365 sheet: -2.82 (0.43), residues: 84 loop : -2.70 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 74 HIS 0.000 0.000 HIS B 106 PHE 0.016 0.002 PHE F 72 TYR 0.012 0.001 TYR D 345 ARG 0.010 0.001 ARG B 75 *********************** 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 130 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.274 Fit side-chains REVERT: A 39 THR cc_start: 0.9383 (p) cc_final: 0.9125 (t) REVERT: A 121 TYR cc_start: 0.8529 (t80) cc_final: 0.7906 (t80) REVERT: A 143 MET cc_start: 0.8389 (ppp) cc_final: 0.7737 (ppp) REVERT: A 144 GLU cc_start: 0.7305 (mp0) cc_final: 0.7071 (mp0) REVERT: A 220 THR cc_start: 0.9636 (m) cc_final: 0.9431 (m) REVERT: A 284 TYR cc_start: 0.9050 (m-10) cc_final: 0.8831 (m-80) REVERT: A 305 VAL cc_start: 0.7581 (t) cc_final: 0.7349 (t) REVERT: A 327 ASP cc_start: 0.7352 (m-30) cc_final: 0.7044 (m-30) REVERT: A 345 TYR cc_start: 0.7993 (t80) cc_final: 0.7734 (t80) outliers start: 1 outliers final: 1 residues processed: 130 average time/residue: 0.1266 time to fit residues: 19.3572 Evaluate side-chains 113 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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: 0.6980 chunk 153 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 62 optimal weight: 0.0470 chunk 148 optimal weight: 5.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- 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: 0.7595 moved from start: 0.1763 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= 0.162 Angle : 0.616 6.590 22799 Z= 0.294 Chirality : 0.039 0.130 2716 Planarity : 0.003 0.035 2751 Dihedral : 3.576 19.549 2184 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.38 % Allowed : 4.15 % Favored : 95.47 % 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: 2.45 (0.14), residues: 1372 sheet: -2.73 (0.45), residues: 84 loop : -2.53 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 74 HIS 0.001 0.000 HIS D 134 PHE 0.009 0.001 PHE B 273 TYR 0.004 0.001 TYR A 111 ARG 0.001 0.000 ARG G 75 *********************** 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 fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 39 THR cc_start: 0.9420 (p) cc_final: 0.9109 (t) REVERT: A 121 TYR cc_start: 0.8457 (t80) cc_final: 0.7825 (t80) REVERT: A 140 LYS cc_start: 0.6397 (mmtt) cc_final: 0.5409 (mmtt) REVERT: A 143 MET cc_start: 0.8365 (ppp) cc_final: 0.7996 (ppp) REVERT: A 305 VAL cc_start: 0.7327 (t) cc_final: 0.7001 (t) outliers start: 1 outliers final: 1 residues processed: 124 average time/residue: 0.1374 time to fit residues: 20.1059 Evaluate side-chains 106 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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: 0.8980 chunk 138 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 196 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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: 0.7614 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16807 Z= 0.167 Angle : 0.640 7.294 22799 Z= 0.305 Chirality : 0.039 0.128 2716 Planarity : 0.004 0.035 2751 Dihedral : 3.589 19.637 2184 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: 1.44 (0.20), residues: 2009 helix: 2.44 (0.14), residues: 1372 sheet: -2.49 (0.50), residues: 84 loop : -2.53 (0.25), 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 0.008 0.001 PHE C 334 TYR 0.011 0.001 TYR G 111 ARG 0.006 0.001 ARG C 254 *********************** 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 124 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.202 Fit side-chains REVERT: A 39 THR cc_start: 0.9414 (p) cc_final: 0.9114 (t) REVERT: A 121 TYR cc_start: 0.8470 (t80) cc_final: 0.7827 (t80) REVERT: A 140 LYS cc_start: 0.6123 (mmtt) cc_final: 0.5828 (mmtt) REVERT: A 245 VAL cc_start: 0.9617 (m) cc_final: 0.9369 (p) REVERT: A 305 VAL cc_start: 0.7329 (t) cc_final: 0.7109 (t) REVERT: A 327 ASP cc_start: 0.7217 (m-30) cc_final: 0.6693 (m-30) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1110 time to fit residues: 16.4863 Evaluate side-chains 106 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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: 0.8980 chunk 111 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 167 optimal weight: 0.7980 chunk 135 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 176 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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: 0.7587 moved from start: 0.2311 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= 0.162 Angle : 0.633 7.066 22799 Z= 0.301 Chirality : 0.039 0.133 2716 Planarity : 0.004 0.036 2751 Dihedral : 3.651 20.790 2184 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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: 1.29 (0.20), residues: 2009 helix: 2.26 (0.14), residues: 1372 sheet: -2.36 (0.53), residues: 84 loop : -2.41 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 85 HIS 0.001 0.000 HIS B 106 PHE 0.008 0.001 PHE B 273 TYR 0.010 0.001 TYR E 111 ARG 0.002 0.000 ARG F 254 *********************** 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 : 0.239 Fit side-chains REVERT: A 39 THR cc_start: 0.9384 (p) cc_final: 0.9091 (t) REVERT: A 121 TYR cc_start: 0.8503 (t80) cc_final: 0.7875 (t80) REVERT: A 143 MET cc_start: 0.9019 (ptm) cc_final: 0.8584 (ppp) REVERT: A 144 GLU cc_start: 0.7921 (mp0) cc_final: 0.7672 (mp0) REVERT: A 245 VAL cc_start: 0.9582 (m) cc_final: 0.9318 (p) REVERT: A 254 ARG cc_start: 0.8396 (mmm160) cc_final: 0.8006 (tpp80) REVERT: A 349 LYS cc_start: 0.8691 (mtpp) cc_final: 0.8411 (mtpt) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1061 time to fit residues: 15.0555 Evaluate side-chains 101 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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: 0.5980 chunk 176 optimal weight: 0.4980 chunk 38 optimal weight: 0.0870 chunk 115 optimal weight: 7.9990 chunk 48 optimal weight: 0.0870 chunk 196 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 90 optimal weight: 0.0770 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 0.0000 chunk 103 optimal weight: 1.9990 overall best weight: 0.1498 ------------------------------------------------------------------------------- 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: 0.7537 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16807 Z= 0.156 Angle : 0.624 7.097 22799 Z= 0.295 Chirality : 0.039 0.135 2716 Planarity : 0.004 0.037 2751 Dihedral : 3.562 22.069 2184 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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: 2.28 (0.14), residues: 1372 sheet: -2.42 (0.53), residues: 84 loop : -2.39 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 85 HIS 0.002 0.001 HIS D 134 PHE 0.009 0.001 PHE D 273 TYR 0.010 0.001 TYR B 111 ARG 0.001 0.000 ARG D 254 *********************** 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 116 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.274 Fit side-chains REVERT: A 39 THR cc_start: 0.9378 (p) cc_final: 0.9078 (t) REVERT: A 121 TYR cc_start: 0.8563 (t80) cc_final: 0.7817 (t80) REVERT: A 143 MET cc_start: 0.9200 (ptm) cc_final: 0.8950 (ptm) REVERT: A 245 VAL cc_start: 0.9561 (m) cc_final: 0.9314 (p) REVERT: A 254 ARG cc_start: 0.8424 (mmm160) cc_final: 0.8057 (tpp80) REVERT: A 280 ASN cc_start: 0.9093 (t0) cc_final: 0.8893 (t0) REVERT: A 327 ASP cc_start: 0.7562 (m-30) cc_final: 0.7186 (m-30) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1062 time to fit residues: 14.9306 Evaluate side-chains 100 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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: 6.9990 chunk 22 optimal weight: 0.0980 chunk 111 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 165 optimal weight: 0.0170 chunk 109 optimal weight: 0.1980 chunk 195 optimal weight: 0.9990 chunk 122 optimal weight: 0.0870 chunk 119 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.2796 ------------------------------------------------------------------------------- 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: 0.7520 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16807 Z= 0.161 Angle : 0.686 7.947 22799 Z= 0.314 Chirality : 0.041 0.138 2716 Planarity : 0.004 0.037 2751 Dihedral : 3.560 22.436 2184 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.38 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: 1.44 (0.20), residues: 2009 helix: 2.33 (0.14), residues: 1365 sheet: -2.20 (0.52), residues: 84 loop : -2.18 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 127 HIS 0.004 0.001 HIS D 134 PHE 0.011 0.001 PHE G 273 TYR 0.012 0.001 TYR G 345 ARG 0.002 0.000 ARG D 254 *********************** 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 115 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 39 THR cc_start: 0.9359 (p) cc_final: 0.9054 (t) REVERT: A 121 TYR cc_start: 0.8565 (t80) cc_final: 0.7852 (t80) REVERT: A 245 VAL cc_start: 0.9539 (m) cc_final: 0.9298 (p) REVERT: A 254 ARG cc_start: 0.8392 (mmm160) cc_final: 0.7934 (tpp80) REVERT: A 279 ILE cc_start: 0.9125 (tt) cc_final: 0.8915 (tt) REVERT: A 280 ASN cc_start: 0.8943 (t0) cc_final: 0.8739 (t0) REVERT: A 327 ASP cc_start: 0.7553 (m-30) cc_final: 0.7174 (m-30) REVERT: A 332 ASN cc_start: 0.9112 (m110) cc_final: 0.8903 (m110) REVERT: A 339 ILE cc_start: 0.8706 (tp) cc_final: 0.8438 (tp) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1051 time to fit residues: 14.6747 Evaluate side-chains 104 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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: 7.9990 chunk 116 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 177 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.7558 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16807 Z= 0.172 Angle : 0.679 7.316 22799 Z= 0.317 Chirality : 0.040 0.132 2716 Planarity : 0.004 0.037 2751 Dihedral : 3.588 21.160 2184 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.44 (0.20), residues: 2009 helix: 2.38 (0.14), residues: 1358 sheet: -2.10 (0.52), residues: 84 loop : -2.29 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 74 HIS 0.003 0.001 HIS D 134 PHE 0.010 0.001 PHE C 273 TYR 0.011 0.001 TYR G 111 ARG 0.001 0.000 ARG F 254 *********************** 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 107 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 39 THR cc_start: 0.9356 (p) cc_final: 0.9041 (t) REVERT: A 56 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7704 (tm-30) REVERT: A 121 TYR cc_start: 0.8578 (t80) cc_final: 0.7870 (t80) REVERT: A 254 ARG cc_start: 0.8463 (mmm160) cc_final: 0.8022 (tpp80) REVERT: A 305 VAL cc_start: 0.7371 (t) cc_final: 0.6874 (t) REVERT: A 327 ASP cc_start: 0.7612 (m-30) cc_final: 0.7276 (m-30) REVERT: A 332 ASN cc_start: 0.9145 (m110) cc_final: 0.8923 (m110) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1139 time to fit residues: 14.5872 Evaluate side-chains 99 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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: 8.9990 chunk 182 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 143 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 164 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 181 optimal weight: 0.0070 chunk 119 optimal weight: 8.9990 overall best weight: 3.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3130 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= 0.236 Angle : 0.708 6.690 22799 Z= 0.341 Chirality : 0.043 0.169 2716 Planarity : 0.004 0.036 2751 Dihedral : 3.669 18.416 2184 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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: 1.46 (0.20), residues: 2009 helix: 2.43 (0.14), residues: 1358 sheet: -2.14 (0.53), residues: 84 loop : -2.38 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 74 HIS 0.000 0.000 HIS C 134 PHE 0.016 0.002 PHE D 129 TYR 0.016 0.001 TYR A 111 ARG 0.002 0.001 ARG E 75 *********************** 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 113 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.286 Fit side-chains REVERT: A 39 THR cc_start: 0.9332 (p) cc_final: 0.9057 (t) REVERT: A 56 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8181 (tm-30) REVERT: A 121 TYR cc_start: 0.8605 (t80) cc_final: 0.7895 (t80) REVERT: A 143 MET cc_start: 0.9038 (ptm) cc_final: 0.8746 (ptm) REVERT: A 307 LYS cc_start: 0.8581 (tptp) cc_final: 0.8256 (tptp) REVERT: A 327 ASP cc_start: 0.7850 (m-30) cc_final: 0.7533 (m-30) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1134 time to fit residues: 15.4618 Evaluate side-chains 98 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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: 7.9990 chunk 117 optimal weight: 8.9990 chunk 91 optimal weight: 0.0060 chunk 134 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- 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: 0.7669 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16807 Z= 0.191 Angle : 0.693 6.853 22799 Z= 0.331 Chirality : 0.042 0.166 2716 Planarity : 0.004 0.037 2751 Dihedral : 3.748 20.962 2184 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % 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: 1.41 (0.20), residues: 2009 helix: 2.41 (0.14), residues: 1358 sheet: -2.42 (0.49), residues: 84 loop : -2.40 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 74 HIS 0.002 0.001 HIS D 134 PHE 0.019 0.001 PHE A 235 TYR 0.014 0.001 TYR D 111 ARG 0.003 0.000 ARG A 254 ********************** 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 109 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.272 Fit side-chains REVERT: A 39 THR cc_start: 0.9359 (p) cc_final: 0.9041 (t) REVERT: A 56 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8236 (tm-30) REVERT: A 121 TYR cc_start: 0.8646 (t80) cc_final: 0.7928 (t80) REVERT: A 143 MET cc_start: 0.8855 (ptm) cc_final: 0.8602 (ptm) REVERT: A 307 LYS cc_start: 0.8790 (tptp) cc_final: 0.8450 (tptp) REVERT: A 327 ASP cc_start: 0.8035 (m-30) cc_final: 0.7561 (m-30) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1110 time to fit residues: 14.6058 Evaluate side-chains 99 residues out of total 267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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: 10.0000 chunk 49 optimal weight: 0.0970 chunk 148 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 67 optimal weight: 0.2980 chunk 165 optimal weight: 0.0770 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 264 GLN A 274 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.168282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.140874 restraints weight = 3657.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.145002 restraints weight = 2289.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.147812 restraints weight = 1608.214| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16807 Z= 0.170 Angle : 0.692 7.133 22799 Z= 0.322 Chirality : 0.041 0.154 2716 Planarity : 0.004 0.037 2751 Dihedral : 3.669 23.522 2184 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.38 % Allowed : 1.13 % 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: 1.30 (0.20), residues: 2009 helix: 2.28 (0.14), residues: 1365 sheet: -2.60 (0.47), residues: 84 loop : -2.33 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 74 HIS 0.003 0.001 HIS A 134 PHE 0.017 0.001 PHE A 235 TYR 0.011 0.001 TYR F 111 ARG 0.003 0.000 ARG F 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2035.98 seconds wall clock time: 38 minutes 22.50 seconds (2302.50 seconds total)