Starting phenix.real_space_refine (version: dev) on Wed Dec 14 19:26:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfg_9972/12_2022/6kfg_9972.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfg_9972/12_2022/6kfg_9972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfg_9972/12_2022/6kfg_9972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfg_9972/12_2022/6kfg_9972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfg_9972/12_2022/6kfg_9972.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfg_9972/12_2022/6kfg_9972.pdb" } resolution = 3.8 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= 0.011 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 ARG 123": "NH1" <-> "NH2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B ARG 181": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ASP 249": "OD1" <-> "OD2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C ASP 249": "OD1" <-> "OD2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D ASP 155": "OD1" <-> "OD2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D ASP 249": "OD1" <-> "OD2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 123": "NH1" <-> "NH2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E ASP 155": "OD1" <-> "OD2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E ARG 181": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E ASP 249": "OD1" <-> "OD2" Residue "E PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 123": "NH1" <-> "NH2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F ASP 155": "OD1" <-> "OD2" Residue "F ARG 161": "NH1" <-> "NH2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F ARG 181": "NH1" <-> "NH2" Residue "F ARG 184": "NH1" <-> "NH2" Residue "F ASP 249": "OD1" <-> "OD2" Residue "F PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 123": "NH1" <-> "NH2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G ASP 155": "OD1" <-> "OD2" Residue "G ARG 161": "NH1" <-> "NH2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G ARG 181": "NH1" <-> "NH2" Residue "G ARG 184": "NH1" <-> "NH2" Residue "G ASP 249": "OD1" <-> "OD2" Residue "G PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 123": "NH1" <-> "NH2" Residue "H GLU 150": "OE1" <-> "OE2" Residue "H ASP 155": "OD1" <-> "OD2" Residue "H ARG 161": "NH1" <-> "NH2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "H ARG 181": "NH1" <-> "NH2" Residue "H ARG 184": "NH1" <-> "NH2" Residue "H ASP 249": "OD1" <-> "OD2" Residue "H PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 22264 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2783 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2783 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2783 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2783 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2783 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2783 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2783 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2783 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.59, per 1000 atoms: 0.57 Number of scatterers: 22264 At special positions: 0 Unit cell: (126.896, 126.896, 107.184, 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 96 16.00 O 3832 8.00 N 3632 7.00 C 14704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 265 " distance=2.05 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS B 265 " distance=2.05 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 265 " distance=2.05 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 58 " - pdb=" SG CYS D 265 " distance=2.05 Simple disulfide: pdb=" SG CYS D 76 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 58 " - pdb=" SG CYS E 265 " distance=2.05 Simple disulfide: pdb=" SG CYS E 76 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 58 " - pdb=" SG CYS F 265 " distance=2.05 Simple disulfide: pdb=" SG CYS F 76 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 58 " - pdb=" SG CYS G 265 " distance=2.05 Simple disulfide: pdb=" SG CYS G 76 " - pdb=" SG CYS G 248 " distance=2.03 Simple disulfide: pdb=" SG CYS H 58 " - pdb=" SG CYS H 265 " distance=2.05 Simple disulfide: pdb=" SG CYS H 76 " - pdb=" SG CYS H 248 " 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: 9.31 Conformation dependent library (CDL) restraints added in 3.6 seconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5216 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 8 sheets defined 67.8% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 29 through 47 removed outlier: 4.140A pdb=" N ARG A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.338A pdb=" N GLN A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 134 removed outlier: 4.451A pdb=" N ALA A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Proline residue: A 122 - end of helix removed outlier: 3.505A pdb=" N GLY A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 151 removed outlier: 3.602A pdb=" N ALA A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS A 159 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 182 removed outlier: 3.717A pdb=" N ARG A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Proline residue: A 169 - end of helix removed outlier: 3.780A pdb=" N TYR A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 212 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 269 through 305 removed outlier: 3.737A pdb=" N GLU A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU A 302 " --> pdb=" O TRP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 351 through 365 removed outlier: 3.639A pdb=" N TYR A 356 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 19 Processing helix chain 'B' and resid 29 through 47 removed outlier: 4.141A pdb=" N ARG B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 79 removed outlier: 4.339A pdb=" N GLN B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 134 removed outlier: 4.451A pdb=" N ALA B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Proline residue: B 122 - end of helix removed outlier: 3.504A pdb=" N GLY B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 151 removed outlier: 3.602A pdb=" N ALA B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS B 159 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 182 removed outlier: 3.716A pdb=" N ARG B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Proline residue: B 169 - end of helix removed outlier: 3.780A pdb=" N TYR B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 212 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 269 through 305 removed outlier: 3.737A pdb=" N GLU B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU B 302 " --> pdb=" O TRP B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 326 through 335 Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 351 through 365 removed outlier: 3.640A pdb=" N TYR B 356 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU B 357 " --> pdb=" O PRO B 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 19 Processing helix chain 'C' and resid 29 through 47 removed outlier: 4.140A pdb=" N ARG C 33 " --> pdb=" O ARG C 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 79 removed outlier: 4.339A pdb=" N GLN C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 134 removed outlier: 4.451A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) Proline residue: C 122 - end of helix removed outlier: 3.505A pdb=" N GLY C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 151 removed outlier: 3.602A pdb=" N ALA C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 182 removed outlier: 3.718A pdb=" N ARG C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) Proline residue: C 169 - end of helix removed outlier: 3.781A pdb=" N TYR C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 212 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 269 through 305 removed outlier: 3.737A pdb=" N GLU C 274 " --> pdb=" O ASN C 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS C 275 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE C 282 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU C 302 " --> pdb=" O TRP C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 326 through 335 Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 351 through 365 removed outlier: 3.640A pdb=" N TYR C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU C 357 " --> pdb=" O PRO C 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 19 Processing helix chain 'D' and resid 29 through 47 removed outlier: 4.141A pdb=" N ARG D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 79 removed outlier: 4.338A pdb=" N GLN D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 134 removed outlier: 4.451A pdb=" N ALA D 113 " --> pdb=" O PRO D 109 " (cutoff:3.500A) Proline residue: D 122 - end of helix removed outlier: 3.505A pdb=" N GLY D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 151 removed outlier: 3.601A pdb=" N ALA D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS D 159 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 182 removed outlier: 3.716A pdb=" N ARG D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Proline residue: D 169 - end of helix removed outlier: 3.780A pdb=" N TYR D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 212 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 269 through 305 removed outlier: 3.736A pdb=" N GLU D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE D 279 " --> pdb=" O LYS D 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU D 302 " --> pdb=" O TRP D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 316 Processing helix chain 'D' and resid 326 through 335 Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 351 through 365 removed outlier: 3.639A pdb=" N TYR D 356 " --> pdb=" O ILE D 352 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU D 357 " --> pdb=" O PRO D 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 19 Processing helix chain 'E' and resid 29 through 47 removed outlier: 4.140A pdb=" N ARG E 33 " --> pdb=" O ARG E 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL E 37 " --> pdb=" O ARG E 33 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU E 47 " --> pdb=" O SER E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 79 removed outlier: 4.339A pdb=" N GLN E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 134 removed outlier: 4.451A pdb=" N ALA E 113 " --> pdb=" O PRO E 109 " (cutoff:3.500A) Proline residue: E 122 - end of helix removed outlier: 3.505A pdb=" N GLY E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 151 removed outlier: 3.601A pdb=" N ALA E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 159 removed outlier: 4.083A pdb=" N LYS E 159 " --> pdb=" O ASP E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 182 removed outlier: 3.717A pdb=" N ARG E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) Proline residue: E 169 - end of helix removed outlier: 3.781A pdb=" N TYR E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 212 Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 269 through 305 removed outlier: 3.737A pdb=" N GLU E 274 " --> pdb=" O ASN E 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS E 275 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE E 279 " --> pdb=" O LYS E 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE E 282 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL E 293 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP E 298 " --> pdb=" O ASN E 294 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU E 302 " --> pdb=" O TRP E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 316 Processing helix chain 'E' and resid 326 through 335 Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 351 through 365 removed outlier: 3.639A pdb=" N TYR E 356 " --> pdb=" O ILE E 352 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU E 357 " --> pdb=" O PRO E 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 19 Processing helix chain 'F' and resid 29 through 47 removed outlier: 4.141A pdb=" N ARG F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL F 37 " --> pdb=" O ARG F 33 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU F 47 " --> pdb=" O SER F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 79 removed outlier: 4.339A pdb=" N GLN F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 134 removed outlier: 4.452A pdb=" N ALA F 113 " --> pdb=" O PRO F 109 " (cutoff:3.500A) Proline residue: F 122 - end of helix removed outlier: 3.505A pdb=" N GLY F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 151 removed outlier: 3.602A pdb=" N ALA F 140 " --> pdb=" O ASP F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 182 removed outlier: 3.718A pdb=" N ARG F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) Proline residue: F 169 - end of helix removed outlier: 3.779A pdb=" N TYR F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 212 Processing helix chain 'F' and resid 222 through 231 Processing helix chain 'F' and resid 269 through 305 removed outlier: 3.736A pdb=" N GLU F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS F 275 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE F 279 " --> pdb=" O LYS F 275 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE F 282 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL F 293 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP F 298 " --> pdb=" O ASN F 294 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR F 301 " --> pdb=" O LYS F 297 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU F 302 " --> pdb=" O TRP F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 326 through 335 Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 351 through 365 removed outlier: 3.640A pdb=" N TYR F 356 " --> pdb=" O ILE F 352 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU F 357 " --> pdb=" O PRO F 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 19 Processing helix chain 'G' and resid 29 through 47 removed outlier: 4.141A pdb=" N ARG G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL G 37 " --> pdb=" O ARG G 33 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU G 47 " --> pdb=" O SER G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 79 removed outlier: 4.339A pdb=" N GLN G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 134 removed outlier: 4.451A pdb=" N ALA G 113 " --> pdb=" O PRO G 109 " (cutoff:3.500A) Proline residue: G 122 - end of helix removed outlier: 3.504A pdb=" N GLY G 134 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 151 removed outlier: 3.602A pdb=" N ALA G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS G 159 " --> pdb=" O ASP G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 182 removed outlier: 3.717A pdb=" N ARG G 168 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Proline residue: G 169 - end of helix removed outlier: 3.781A pdb=" N TYR G 172 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS G 182 " --> pdb=" O ARG G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 212 Processing helix chain 'G' and resid 222 through 231 Processing helix chain 'G' and resid 269 through 305 removed outlier: 3.736A pdb=" N GLU G 274 " --> pdb=" O ASN G 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS G 275 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE G 279 " --> pdb=" O LYS G 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE G 282 " --> pdb=" O ILE G 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL G 293 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP G 298 " --> pdb=" O ASN G 294 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR G 301 " --> pdb=" O LYS G 297 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU G 302 " --> pdb=" O TRP G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 316 Processing helix chain 'G' and resid 326 through 335 Processing helix chain 'G' and resid 337 through 349 Processing helix chain 'G' and resid 351 through 365 removed outlier: 3.640A pdb=" N TYR G 356 " --> pdb=" O ILE G 352 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU G 357 " --> pdb=" O PRO G 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 19 Processing helix chain 'H' and resid 29 through 47 removed outlier: 4.141A pdb=" N ARG H 33 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL H 37 " --> pdb=" O ARG H 33 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU H 47 " --> pdb=" O SER H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 79 removed outlier: 4.339A pdb=" N GLN H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 134 removed outlier: 4.452A pdb=" N ALA H 113 " --> pdb=" O PRO H 109 " (cutoff:3.500A) Proline residue: H 122 - end of helix removed outlier: 3.505A pdb=" N GLY H 134 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 151 removed outlier: 3.602A pdb=" N ALA H 140 " --> pdb=" O ASP H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS H 159 " --> pdb=" O ASP H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 182 removed outlier: 3.717A pdb=" N ARG H 168 " --> pdb=" O ALA H 164 " (cutoff:3.500A) Proline residue: H 169 - end of helix removed outlier: 3.780A pdb=" N TYR H 172 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS H 182 " --> pdb=" O ARG H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 212 Processing helix chain 'H' and resid 222 through 231 Processing helix chain 'H' and resid 269 through 305 removed outlier: 3.737A pdb=" N GLU H 274 " --> pdb=" O ASN H 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS H 275 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE H 279 " --> pdb=" O LYS H 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE H 282 " --> pdb=" O ILE H 278 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL H 293 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN H 294 " --> pdb=" O VAL H 290 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP H 298 " --> pdb=" O ASN H 294 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR H 301 " --> pdb=" O LYS H 297 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU H 302 " --> pdb=" O TRP H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 309 through 316 Processing helix chain 'H' and resid 326 through 335 Processing helix chain 'H' and resid 337 through 349 Processing helix chain 'H' and resid 351 through 365 removed outlier: 3.640A pdb=" N TYR H 356 " --> pdb=" O ILE H 352 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU H 357 " --> pdb=" O PRO H 353 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 59 removed outlier: 3.930A pdb=" N LEU A 264 " --> pdb=" O TRP A 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 56 through 59 removed outlier: 3.931A pdb=" N LEU B 264 " --> pdb=" O TRP B 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 56 through 59 removed outlier: 3.930A pdb=" N LEU C 264 " --> pdb=" O TRP C 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 56 through 59 removed outlier: 3.931A pdb=" N LEU D 264 " --> pdb=" O TRP D 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 56 through 59 removed outlier: 3.931A pdb=" N LEU E 264 " --> pdb=" O TRP E 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 56 through 59 removed outlier: 3.931A pdb=" N LEU F 264 " --> pdb=" O TRP F 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 56 through 59 removed outlier: 3.931A pdb=" N LEU G 264 " --> pdb=" O TRP G 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.930A pdb=" N LEU H 264 " --> pdb=" O TRP H 59 " (cutoff:3.500A) 1225 hydrogen bonds defined for protein. 3627 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.50 Time building geometry restraints manager: 10.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6756 1.35 - 1.49: 6983 1.49 - 1.62: 9045 1.62 - 1.76: 8 1.76 - 1.89: 128 Bond restraints: 22920 Sorted by residual: bond pdb=" CB CYS H 58 " pdb=" SG CYS H 58 " ideal model delta sigma weight residual 1.808 1.890 -0.082 3.30e-02 9.18e+02 6.15e+00 bond pdb=" CB CYS C 58 " pdb=" SG CYS C 58 " ideal model delta sigma weight residual 1.808 1.890 -0.082 3.30e-02 9.18e+02 6.13e+00 bond pdb=" CB CYS A 58 " pdb=" SG CYS A 58 " ideal model delta sigma weight residual 1.808 1.890 -0.082 3.30e-02 9.18e+02 6.10e+00 bond pdb=" CB CYS D 58 " pdb=" SG CYS D 58 " ideal model delta sigma weight residual 1.808 1.889 -0.081 3.30e-02 9.18e+02 6.10e+00 bond pdb=" CB CYS E 58 " pdb=" SG CYS E 58 " ideal model delta sigma weight residual 1.808 1.889 -0.081 3.30e-02 9.18e+02 6.07e+00 ... (remaining 22915 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.28: 668 107.28 - 113.98: 12826 113.98 - 120.69: 10372 120.69 - 127.39: 7038 127.39 - 134.09: 312 Bond angle restraints: 31216 Sorted by residual: angle pdb=" CA CYS G 265 " pdb=" CB CYS G 265 " pdb=" SG CYS G 265 " ideal model delta sigma weight residual 114.40 127.15 -12.75 2.30e+00 1.89e-01 3.07e+01 angle pdb=" CA CYS E 265 " pdb=" CB CYS E 265 " pdb=" SG CYS E 265 " ideal model delta sigma weight residual 114.40 127.11 -12.71 2.30e+00 1.89e-01 3.05e+01 angle pdb=" CA CYS C 265 " pdb=" CB CYS C 265 " pdb=" SG CYS C 265 " ideal model delta sigma weight residual 114.40 127.11 -12.71 2.30e+00 1.89e-01 3.05e+01 angle pdb=" CA CYS H 265 " pdb=" CB CYS H 265 " pdb=" SG CYS H 265 " ideal model delta sigma weight residual 114.40 127.10 -12.70 2.30e+00 1.89e-01 3.05e+01 angle pdb=" CA CYS F 265 " pdb=" CB CYS F 265 " pdb=" SG CYS F 265 " ideal model delta sigma weight residual 114.40 127.10 -12.70 2.30e+00 1.89e-01 3.05e+01 ... (remaining 31211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.58: 11402 15.58 - 31.17: 1407 31.17 - 46.75: 287 46.75 - 62.33: 72 62.33 - 77.91: 16 Dihedral angle restraints: 13184 sinusoidal: 5144 harmonic: 8040 Sorted by residual: dihedral pdb=" CB CYS E 58 " pdb=" SG CYS E 58 " pdb=" SG CYS E 265 " pdb=" CB CYS E 265 " ideal model delta sinusoidal sigma weight residual 93.00 39.42 53.58 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS G 58 " pdb=" SG CYS G 58 " pdb=" SG CYS G 265 " pdb=" CB CYS G 265 " ideal model delta sinusoidal sigma weight residual 93.00 39.42 53.58 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS F 58 " pdb=" SG CYS F 58 " pdb=" SG CYS F 265 " pdb=" CB CYS F 265 " ideal model delta sinusoidal sigma weight residual 93.00 39.43 53.57 1 1.00e+01 1.00e-02 3.90e+01 ... (remaining 13181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2102 0.038 - 0.076: 951 0.076 - 0.114: 331 0.114 - 0.152: 56 0.152 - 0.190: 8 Chirality restraints: 3448 Sorted by residual: chirality pdb=" CA CYS B 265 " pdb=" N CYS B 265 " pdb=" C CYS B 265 " pdb=" CB CYS B 265 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA CYS E 265 " pdb=" N CYS E 265 " pdb=" C CYS E 265 " pdb=" CB CYS E 265 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA CYS D 265 " pdb=" N CYS D 265 " pdb=" C CYS D 265 " pdb=" CB CYS D 265 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.81e-01 ... (remaining 3445 not shown) Planarity restraints: 3832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 242 " 0.014 2.00e-02 2.50e+03 1.11e-02 2.17e+00 pdb=" CG PHE B 242 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE B 242 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 242 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 242 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 242 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 242 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 242 " 0.014 2.00e-02 2.50e+03 1.10e-02 2.13e+00 pdb=" CG PHE C 242 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE C 242 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 242 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 242 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 242 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 242 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 242 " 0.014 2.00e-02 2.50e+03 1.10e-02 2.12e+00 pdb=" CG PHE A 242 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 242 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 242 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 242 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 242 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 242 " 0.003 2.00e-02 2.50e+03 ... (remaining 3829 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 604 2.70 - 3.25: 24596 3.25 - 3.80: 35506 3.80 - 4.35: 41354 4.35 - 4.90: 69124 Nonbonded interactions: 171184 Sorted by model distance: nonbonded pdb=" OE1 GLN G 115 " pdb=" NE2 GLN G 206 " model vdw 2.148 2.520 nonbonded pdb=" OE1 GLN C 115 " pdb=" NE2 GLN C 206 " model vdw 2.148 2.520 nonbonded pdb=" OE1 GLN B 115 " pdb=" NE2 GLN B 206 " model vdw 2.148 2.520 nonbonded pdb=" OE1 GLN F 115 " pdb=" NE2 GLN F 206 " model vdw 2.149 2.520 nonbonded pdb=" OE1 GLN D 115 " pdb=" NE2 GLN D 206 " model vdw 2.149 2.520 ... (remaining 171179 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' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 14704 2.51 5 N 3632 2.21 5 O 3832 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: 0.550 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: 0.040 Extract box with map and model: 3.830 Check model and map are aligned: 0.350 Convert atoms to be neutral: 0.210 Process input model: 56.790 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 0.007 0.082 22920 Z= 0.433 Angle : 0.770 12.750 31216 Z= 0.419 Chirality : 0.047 0.190 3448 Planarity : 0.003 0.029 3832 Dihedral : 14.038 77.914 7920 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.38 (0.13), residues: 2640 helix: -1.78 (0.11), residues: 1704 sheet: -3.36 (0.47), residues: 88 loop : -5.15 (0.13), residues: 848 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 934 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 950 average time/residue: 0.3440 time to fit residues: 491.2851 Evaluate side-chains 708 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 700 time to evaluate : 2.615 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1922 time to fit residues: 6.5207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.9990 chunk 200 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 chunk 68 optimal weight: 0.0670 chunk 134 optimal weight: 0.8980 chunk 106 optimal weight: 0.3980 chunk 206 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 GLN B 73 ASN B 212 GLN B 329 GLN C 73 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 GLN D 73 ASN D 212 GLN D 329 GLN E 73 ASN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN F 73 ASN F 212 GLN F 329 GLN G 73 ASN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN H 73 ASN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 212 GLN H 329 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 22920 Z= 0.201 Angle : 0.685 7.275 31216 Z= 0.354 Chirality : 0.042 0.170 3448 Planarity : 0.004 0.039 3832 Dihedral : 5.399 19.180 2952 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer Outliers : 5.43 % 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: -2.71 (0.15), residues: 2640 helix: -0.46 (0.12), residues: 1736 sheet: -2.32 (0.42), residues: 144 loop : -4.87 (0.16), residues: 760 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 733 time to evaluate : 2.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 130 outliers final: 80 residues processed: 767 average time/residue: 0.3114 time to fit residues: 371.8925 Evaluate side-chains 730 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 650 time to evaluate : 2.664 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 0 residues processed: 80 average time/residue: 0.1890 time to fit residues: 32.5038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 8.9990 chunk 74 optimal weight: 0.0980 chunk 199 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 chunk 240 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN B 294 ASN C 199 GLN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 GLN D 294 ASN E 199 GLN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 294 ASN G 73 ASN G 199 GLN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 ASN G 348 ASN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 22920 Z= 0.240 Angle : 0.676 12.636 31216 Z= 0.349 Chirality : 0.043 0.204 3448 Planarity : 0.004 0.039 3832 Dihedral : 5.288 20.036 2952 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer Outliers : 2.72 % 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: -1.91 (0.16), residues: 2640 helix: 0.14 (0.12), residues: 1744 sheet: -1.88 (0.44), residues: 144 loop : -4.58 (0.17), residues: 752 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 695 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 30 residues processed: 721 average time/residue: 0.2915 time to fit residues: 340.3040 Evaluate side-chains 663 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 633 time to evaluate : 2.605 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2091 time to fit residues: 14.7575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 255 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN C 199 GLN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN D 212 GLN D 294 ASN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN F 70 ASN F 79 HIS F 199 GLN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 22920 Z= 0.248 Angle : 0.657 10.767 31216 Z= 0.339 Chirality : 0.043 0.183 3448 Planarity : 0.003 0.036 3832 Dihedral : 5.168 19.805 2952 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer Outliers : 5.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.16), residues: 2640 helix: 0.49 (0.13), residues: 1752 sheet: None (None), residues: 0 loop : -3.96 (0.17), residues: 888 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 672 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 84 residues processed: 712 average time/residue: 0.2797 time to fit residues: 324.6097 Evaluate side-chains 703 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 619 time to evaluate : 2.589 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 0 residues processed: 84 average time/residue: 0.1910 time to fit residues: 33.9236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 3 optimal weight: 0.0050 chunk 190 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 217 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 130 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS D 212 GLN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 ASN F 79 HIS F 212 GLN G 73 ASN H 79 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.089 22920 Z= 0.307 Angle : 0.682 11.851 31216 Z= 0.351 Chirality : 0.044 0.188 3448 Planarity : 0.003 0.034 3832 Dihedral : 5.251 20.472 2952 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer Outliers : 3.68 % 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: -1.27 (0.17), residues: 2640 helix: 0.62 (0.13), residues: 1760 sheet: -1.59 (0.45), residues: 144 loop : -4.42 (0.18), residues: 736 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 642 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 57 residues processed: 687 average time/residue: 0.2832 time to fit residues: 318.8936 Evaluate side-chains 656 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 599 time to evaluate : 2.590 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.1868 time to fit residues: 23.7159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 8.9990 chunk 229 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 255 optimal weight: 0.7980 chunk 212 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 134 optimal weight: 8.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 73 ASN B 212 GLN D 70 ASN D 79 HIS D 212 GLN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 HIS F 294 ASN H 79 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 22920 Z= 0.208 Angle : 0.663 11.002 31216 Z= 0.338 Chirality : 0.043 0.171 3448 Planarity : 0.003 0.033 3832 Dihedral : 5.098 20.364 2952 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer Outliers : 3.39 % 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: -0.87 (0.17), residues: 2640 helix: 0.90 (0.13), residues: 1752 sheet: -1.31 (0.46), residues: 144 loop : -4.19 (0.18), residues: 744 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 657 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 61 residues processed: 683 average time/residue: 0.2862 time to fit residues: 317.5158 Evaluate side-chains 664 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 603 time to evaluate : 2.602 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.1955 time to fit residues: 26.0266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 186 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 142 optimal weight: 0.2980 chunk 254 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS D 294 ASN F 79 HIS F 212 GLN H 79 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 22920 Z= 0.204 Angle : 0.665 11.038 31216 Z= 0.338 Chirality : 0.042 0.183 3448 Planarity : 0.003 0.032 3832 Dihedral : 4.984 19.751 2952 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer Outliers : 1.42 % 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: -0.63 (0.17), residues: 2640 helix: 1.09 (0.13), residues: 1752 sheet: None (None), residues: 0 loop : -3.70 (0.17), residues: 888 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 650 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 661 average time/residue: 0.2903 time to fit residues: 310.3111 Evaluate side-chains 631 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 612 time to evaluate : 2.806 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2479 time to fit residues: 12.8341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 chunk 231 optimal weight: 10.0000 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN B 79 HIS B 212 GLN C 348 ASN D 212 GLN E 348 ASN F 79 HIS ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 348 ASN H 79 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 22920 Z= 0.221 Angle : 0.700 11.203 31216 Z= 0.348 Chirality : 0.043 0.201 3448 Planarity : 0.003 0.033 3832 Dihedral : 4.965 20.799 2952 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer Outliers : 1.80 % 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: -0.57 (0.17), residues: 2640 helix: 1.11 (0.13), residues: 1752 sheet: None (None), residues: 0 loop : -3.63 (0.17), residues: 888 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 642 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 39 residues processed: 652 average time/residue: 0.2971 time to fit residues: 310.4939 Evaluate side-chains 643 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 604 time to evaluate : 2.676 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.1865 time to fit residues: 17.1686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 237 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 186 optimal weight: 0.0980 chunk 72 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 chunk 236 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN B 212 GLN B 294 ASN D 212 GLN E 73 ASN F 79 HIS F 212 GLN H 79 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 22920 Z= 0.192 Angle : 0.704 11.104 31216 Z= 0.348 Chirality : 0.042 0.186 3448 Planarity : 0.003 0.035 3832 Dihedral : 4.837 21.621 2952 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer Outliers : 0.84 % 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: -0.45 (0.17), residues: 2640 helix: 1.18 (0.13), residues: 1768 sheet: None (None), residues: 0 loop : -3.61 (0.17), residues: 872 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 659 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 666 average time/residue: 0.2869 time to fit residues: 309.2030 Evaluate side-chains 652 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 639 time to evaluate : 2.477 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1918 time to fit residues: 8.2230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 263 optimal weight: 0.9990 chunk 242 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 21 optimal weight: 0.0770 chunk 161 optimal weight: 8.9990 chunk 128 optimal weight: 0.0040 chunk 166 optimal weight: 10.0000 overall best weight: 1.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS C 237 GLN D 79 HIS D 212 GLN F 79 HIS F 212 GLN H 212 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 22920 Z= 0.214 Angle : 0.711 11.132 31216 Z= 0.350 Chirality : 0.043 0.180 3448 Planarity : 0.003 0.037 3832 Dihedral : 4.831 20.861 2952 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer Outliers : 1.13 % 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: -0.38 (0.17), residues: 2640 helix: 1.23 (0.13), residues: 1768 sheet: None (None), residues: 0 loop : -3.56 (0.17), residues: 872 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 650 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 659 average time/residue: 0.2957 time to fit residues: 314.0797 Evaluate side-chains 641 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 626 time to evaluate : 2.723 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1949 time to fit residues: 9.2844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 193 optimal weight: 0.0870 chunk 30 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 209 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS B 348 ASN C 348 ASN D 70 ASN D 79 HIS D 212 GLN F 70 ASN F 79 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.142054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.117838 restraints weight = 30773.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.121762 restraints weight = 17179.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.124260 restraints weight = 11701.089| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 22920 Z= 0.269 Angle : 0.732 11.762 31216 Z= 0.361 Chirality : 0.044 0.179 3448 Planarity : 0.003 0.038 3832 Dihedral : 4.930 22.089 2952 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer Outliers : 1.00 % 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: -0.44 (0.17), residues: 2640 helix: 1.24 (0.13), residues: 1736 sheet: None (None), residues: 0 loop : -3.57 (0.17), residues: 904 =============================================================================== Job complete usr+sys time: 5447.18 seconds wall clock time: 98 minutes 37.64 seconds (5917.64 seconds total)