Starting phenix.real_space_refine on Thu Feb 15 02:59:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgz_31981/02_2024/7vgz_31981_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgz_31981/02_2024/7vgz_31981.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgz_31981/02_2024/7vgz_31981_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgz_31981/02_2024/7vgz_31981_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgz_31981/02_2024/7vgz_31981_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgz_31981/02_2024/7vgz_31981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgz_31981/02_2024/7vgz_31981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgz_31981/02_2024/7vgz_31981_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgz_31981/02_2024/7vgz_31981_neut_updated.pdb" } resolution = 3.3 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2159 atoms to isotropic. 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 61 5.16 5 C 5631 2.51 5 N 1476 2.21 5 O 1622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 171": "OD1" <-> "OD2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D ASP 246": "OD1" <-> "OD2" Residue "D ASP 254": "OD1" <-> "OD2" Residue "D ASP 258": "OD1" <-> "OD2" Residue "D ASP 322": "OD1" <-> "OD2" Residue "E ASP 36": "OD1" <-> "OD2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F ASP 62": "OD1" <-> "OD2" Residue "F PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8790 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2242 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1751 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 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: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2584 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {'CLR': 1, 'JEV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.64, per 1000 atoms: 0.53 Number of scatterers: 8790 At special positions: 0 Unit cell: (90.47, 116.2, 125.33, 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 61 16.00 O 1622 8.00 N 1476 7.00 C 5631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 177 " distance=2.03 Simple disulfide: pdb=" SG CYS D 121 " - pdb=" SG CYS D 149 " distance=2.04 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 229 " 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: 50.38 Conformation dependent library (CDL) restraints added in 13.5 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 15 sheets defined 35.2% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'B' and resid 24 through 54 Processing helix chain 'B' and resid 64 through 76 removed outlier: 4.466A pdb=" N VAL B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 90 Processing helix chain 'B' and resid 97 through 129 removed outlier: 3.754A pdb=" N SER B 103 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 138 No H-bonds generated for 'chain 'B' and resid 135 through 138' Processing helix chain 'B' and resid 141 through 165 removed outlier: 3.614A pdb=" N LEU B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Proline residue: B 161 - end of helix removed outlier: 4.637A pdb=" N ARG B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 195 Processing helix chain 'B' and resid 198 through 219 removed outlier: 4.089A pdb=" N VAL B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 250 removed outlier: 3.885A pdb=" N VAL B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N VAL B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N PHE B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 263 removed outlier: 3.833A pdb=" N LEU B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 removed outlier: 3.960A pdb=" N VAL B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) Proline residue: B 270 - end of helix No H-bonds generated for 'chain 'B' and resid 265 through 271' Processing helix chain 'B' and resid 274 through 294 removed outlier: 3.603A pdb=" N SER B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N CYS B 289 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 312 removed outlier: 3.933A pdb=" N GLU B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 32 removed outlier: 3.510A pdb=" N ALA C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ARG C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 208 through 211 No H-bonds generated for 'chain 'C' and resid 208 through 211' Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 242 through 254 Processing helix chain 'C' and resid 271 through 280 removed outlier: 3.770A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 296 through 309 removed outlier: 3.551A pdb=" N ASP C 309 " --> pdb=" O CYS C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'D' and resid 4 through 25 Processing helix chain 'D' and resid 30 through 36 removed outlier: 5.195A pdb=" N ASN D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 23 Processing helix chain 'E' and resid 30 through 43 Processing helix chain 'E' and resid 45 through 47 No H-bonds generated for 'chain 'E' and resid 45 through 47' Processing helix chain 'F' and resid 53 through 55 No H-bonds generated for 'chain 'F' and resid 53 through 55' Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 168 through 171 removed outlier: 3.506A pdb=" N GLN B 169 " --> pdb=" O THR B 178 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 319 through 323 removed outlier: 6.696A pdb=" N ILE C 264 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N HIS C 322 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU C 266 " --> pdb=" O HIS C 322 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS C 197 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N LEU C 38 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N PHE C 199 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 58 through 63 removed outlier: 6.730A pdb=" N ALA D 73 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N MET D 61 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL D 71 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TRP D 63 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU D 69 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP D 83 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LYS D 89 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.939A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 139 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG D 137 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 156 through 160 removed outlier: 3.756A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.576A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE D 199 " --> pdb=" O TRP D 211 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.726A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 273 through 276 removed outlier: 6.558A pdb=" N GLY D 288 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL D 276 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU D 286 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.834A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.703A pdb=" N LEU F 117 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA F 92 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 95 through 99 removed outlier: 5.730A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 140 through 142 Processing sheet with id= N, first strand: chain 'F' and resid 146 through 148 removed outlier: 6.558A pdb=" N LYS F 244 " --> pdb=" O VAL F 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'F' and resid 225 through 231 removed outlier: 3.659A pdb=" N ILE F 189 " --> pdb=" O TRP F 176 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU F 178 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU F 187 " --> pdb=" O LEU F 178 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1089 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1419 1.31 - 1.44: 2495 1.44 - 1.56: 4981 1.56 - 1.69: 0 1.69 - 1.82: 87 Bond restraints: 8982 Sorted by residual: bond pdb=" C12 JEV B 401 " pdb=" O1 JEV B 401 " ideal model delta sigma weight residual 1.488 1.319 0.169 2.00e-02 2.50e+03 7.13e+01 bond pdb=" CA TYR B 126 " pdb=" C TYR B 126 " ideal model delta sigma weight residual 1.523 1.437 0.087 1.30e-02 5.92e+03 4.45e+01 bond pdb=" CA TYR B 281 " pdb=" C TYR B 281 " ideal model delta sigma weight residual 1.522 1.464 0.058 1.38e-02 5.25e+03 1.79e+01 bond pdb=" N TYR B 282 " pdb=" CA TYR B 282 " ideal model delta sigma weight residual 1.457 1.404 0.053 1.27e-02 6.20e+03 1.74e+01 bond pdb=" C15 JEV B 401 " pdb=" O1 JEV B 401 " ideal model delta sigma weight residual 1.434 1.351 0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 8977 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.50: 130 105.50 - 112.65: 4748 112.65 - 119.79: 2949 119.79 - 126.94: 4260 126.94 - 134.09: 106 Bond angle restraints: 12193 Sorted by residual: angle pdb=" N TYR B 126 " pdb=" CA TYR B 126 " pdb=" C TYR B 126 " ideal model delta sigma weight residual 111.28 101.89 9.39 1.09e+00 8.42e-01 7.43e+01 angle pdb=" N PHE B 237 " pdb=" CA PHE B 237 " pdb=" C PHE B 237 " ideal model delta sigma weight residual 111.28 104.76 6.52 1.09e+00 8.42e-01 3.58e+01 angle pdb=" C TYR B 282 " pdb=" CA TYR B 282 " pdb=" CB TYR B 282 " ideal model delta sigma weight residual 109.24 118.49 -9.25 1.75e+00 3.27e-01 2.80e+01 angle pdb=" N ARG B 235 " pdb=" CA ARG B 235 " pdb=" C ARG B 235 " ideal model delta sigma weight residual 111.28 106.09 5.19 1.09e+00 8.42e-01 2.27e+01 angle pdb=" N TYR B 282 " pdb=" CA TYR B 282 " pdb=" C TYR B 282 " ideal model delta sigma weight residual 113.41 107.63 5.78 1.22e+00 6.72e-01 2.24e+01 ... (remaining 12188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.85: 5072 24.85 - 49.69: 248 49.69 - 74.54: 26 74.54 - 99.39: 4 99.39 - 124.23: 3 Dihedral angle restraints: 5353 sinusoidal: 2084 harmonic: 3269 Sorted by residual: dihedral pdb=" CB CYS D 121 " pdb=" SG CYS D 121 " pdb=" SG CYS D 149 " pdb=" CB CYS D 149 " ideal model delta sinusoidal sigma weight residual 93.00 167.31 -74.31 1 1.00e+01 1.00e-02 7.00e+01 dihedral pdb=" CB CYS B 100 " pdb=" SG CYS B 100 " pdb=" SG CYS B 177 " pdb=" CB CYS B 177 " ideal model delta sinusoidal sigma weight residual -86.00 -124.54 38.54 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" C1 CLR B 402 " pdb=" C2 CLR B 402 " pdb=" C3 CLR B 402 " pdb=" O1 CLR B 402 " ideal model delta sinusoidal sigma weight residual 180.04 55.81 124.23 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 5350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1255 0.076 - 0.152: 127 0.152 - 0.229: 3 0.229 - 0.305: 4 0.305 - 0.381: 2 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA CYS B 127 " pdb=" N CYS B 127 " pdb=" C CYS B 127 " pdb=" CB CYS B 127 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA TYR B 282 " pdb=" N TYR B 282 " pdb=" C TYR B 282 " pdb=" CB TYR B 282 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA TYR B 281 " pdb=" N TYR B 281 " pdb=" C TYR B 281 " pdb=" CB TYR B 281 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 1388 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 279 " 0.027 2.00e-02 2.50e+03 5.49e-02 3.02e+01 pdb=" C ALA B 279 " -0.095 2.00e-02 2.50e+03 pdb=" O ALA B 279 " 0.036 2.00e-02 2.50e+03 pdb=" N SER B 280 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 193 " -0.019 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C VAL B 193 " 0.062 2.00e-02 2.50e+03 pdb=" O VAL B 193 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE B 194 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 150 " -0.043 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO F 151 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO F 151 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 151 " -0.036 5.00e-02 4.00e+02 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 222 2.69 - 3.24: 8670 3.24 - 3.79: 14039 3.79 - 4.35: 18448 4.35 - 4.90: 31161 Nonbonded interactions: 72540 Sorted by model distance: nonbonded pdb=" OG SER D 331 " pdb=" OD1 ASP D 333 " model vdw 2.137 2.440 nonbonded pdb=" OG1 THR D 274 " pdb=" O VAL D 315 " model vdw 2.184 2.440 nonbonded pdb=" OG SER D 74 " pdb=" OD1 ASP D 76 " model vdw 2.193 2.440 nonbonded pdb=" OH TYR C 290 " pdb=" OE1 GLU C 298 " model vdw 2.251 2.440 nonbonded pdb=" O SER D 67 " pdb=" OG SER D 67 " model vdw 2.272 2.440 ... (remaining 72535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 6.930 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 23.280 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 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 : 0.005 0.169 8982 Z= 0.354 Angle : 0.683 9.393 12193 Z= 0.394 Chirality : 0.048 0.381 1391 Planarity : 0.005 0.066 1532 Dihedral : 14.134 124.233 3238 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.21 % Allowed : 0.96 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.10 (0.26), residues: 1107 helix: 1.03 (0.28), residues: 386 sheet: -0.23 (0.32), residues: 276 loop : -0.85 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 275 HIS 0.007 0.001 HIS B 195 PHE 0.014 0.001 PHE B 196 TYR 0.019 0.002 TYR B 126 ARG 0.007 0.001 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 1.031 Fit side-chains REVERT: B 169 GLN cc_start: 0.6863 (pp30) cc_final: 0.6415 (pp30) REVERT: B 287 ASN cc_start: 0.8591 (t0) cc_final: 0.8280 (t0) REVERT: C 26 ASP cc_start: 0.8306 (m-30) cc_final: 0.8041 (m-30) REVERT: D 226 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7732 (mt-10) REVERT: E 18 GLN cc_start: 0.8012 (tp40) cc_final: 0.7650 (tp40) outliers start: 2 outliers final: 1 residues processed: 131 average time/residue: 0.1998 time to fit residues: 35.7508 Evaluate side-chains 105 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 33 optimal weight: 0.0170 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8982 Z= 0.303 Angle : 0.607 9.654 12193 Z= 0.312 Chirality : 0.044 0.168 1391 Planarity : 0.004 0.056 1532 Dihedral : 7.313 81.560 1296 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.17 % Allowed : 9.66 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.11 (0.26), residues: 1107 helix: 1.16 (0.28), residues: 388 sheet: -0.33 (0.32), residues: 270 loop : -0.93 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 82 HIS 0.004 0.001 HIS F 35 PHE 0.015 0.002 PHE C 354 TYR 0.016 0.002 TYR B 282 ARG 0.004 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 1.048 Fit side-chains REVERT: B 169 GLN cc_start: 0.6857 (pp30) cc_final: 0.6471 (pp30) REVERT: B 171 ASP cc_start: 0.7510 (t70) cc_final: 0.7265 (t70) REVERT: C 26 ASP cc_start: 0.8288 (m-30) cc_final: 0.8030 (m-30) REVERT: D 226 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7744 (mt-10) outliers start: 11 outliers final: 6 residues processed: 122 average time/residue: 0.2489 time to fit residues: 40.9088 Evaluate side-chains 106 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain F residue 17 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 0.0470 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.2482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8982 Z= 0.227 Angle : 0.554 9.331 12193 Z= 0.285 Chirality : 0.042 0.147 1391 Planarity : 0.004 0.051 1532 Dihedral : 5.654 83.537 1296 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.38 % Allowed : 12.31 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.08 (0.26), residues: 1107 helix: 1.22 (0.28), residues: 388 sheet: -0.37 (0.32), residues: 274 loop : -0.91 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 82 HIS 0.003 0.001 HIS F 35 PHE 0.016 0.001 PHE C 354 TYR 0.015 0.001 TYR B 282 ARG 0.005 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 0.922 Fit side-chains REVERT: B 171 ASP cc_start: 0.7545 (t70) cc_final: 0.7027 (t70) REVERT: C 26 ASP cc_start: 0.8271 (m-30) cc_final: 0.8013 (m-30) REVERT: D 226 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7752 (mt-10) outliers start: 13 outliers final: 10 residues processed: 122 average time/residue: 0.2125 time to fit residues: 35.7343 Evaluate side-chains 111 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 89 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 47 optimal weight: 0.0570 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN B 169 GLN ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8982 Z= 0.380 Angle : 0.638 10.194 12193 Z= 0.328 Chirality : 0.045 0.155 1391 Planarity : 0.004 0.047 1532 Dihedral : 5.660 79.251 1296 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.55 % Allowed : 14.86 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.22 (0.25), residues: 1107 helix: 1.20 (0.27), residues: 385 sheet: -0.63 (0.31), residues: 280 loop : -0.93 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 82 HIS 0.004 0.001 HIS B 131 PHE 0.019 0.002 PHE C 354 TYR 0.018 0.002 TYR B 282 ARG 0.005 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 0.753 Fit side-chains REVERT: B 169 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6576 (pp30) REVERT: B 171 ASP cc_start: 0.7595 (t70) cc_final: 0.7136 (t70) REVERT: C 26 ASP cc_start: 0.8253 (m-30) cc_final: 0.7989 (m-30) REVERT: C 37 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8631 (tt) REVERT: D 226 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7729 (mt-10) outliers start: 24 outliers final: 14 residues processed: 129 average time/residue: 0.1894 time to fit residues: 33.1677 Evaluate side-chains 122 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 89 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.0060 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: