Starting phenix.real_space_refine (version: dev) on Mon Dec 12 06:13:55 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpw_21866/12_2022/6wpw_21866_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpw_21866/12_2022/6wpw_21866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpw_21866/12_2022/6wpw_21866.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpw_21866/12_2022/6wpw_21866.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpw_21866/12_2022/6wpw_21866_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpw_21866/12_2022/6wpw_21866_neut.pdb" } resolution = 3.1 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= 0.005 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 "C ARG 280": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 380": "NH1" <-> "NH2" Residue "C ARG 389": "NH1" <-> "NH2" Residue "D ARG 46": "NH1" <-> "NH2" Residue "D ARG 48": "NH1" <-> "NH2" Residue "D TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "P ARG 17": "NH1" <-> "NH2" Residue "R TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 261": "NH1" <-> "NH2" Residue "R ASP 299": "OD1" <-> "OD2" Residue "R ARG 336": "NH1" <-> "NH2" Residue "R TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 346": "NH1" <-> "NH2" Residue "R ARG 412": "NH1" <-> "NH2" Residue "R ARG 419": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 9262 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1835 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2601 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 449 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 244 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "R" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3162 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 14, 'TRANS': 383} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 5.69, per 1000 atoms: 0.61 Number of scatterers: 9262 At special positions: 0 Unit cell: (167.48, 108.12, 98.58, 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 56 16.00 O 1698 8.00 N 1627 7.00 C 5881 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.02 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.04 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.03 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " 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: 3.66 Conformation dependent library (CDL) restraints added in 1.5 seconds 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 40.7% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'C' and resid 11 through 39 removed outlier: 3.554A pdb=" N LYS C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN C 23 " --> pdb=" O GLN C 19 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS C 25 " --> pdb=" O GLU C 21 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS C 28 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN C 29 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 264 through 278 removed outlier: 3.876A pdb=" N GLU C 268 " --> pdb=" O ASN C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.854A pdb=" N ARG C 283 " --> pdb=" O ARG C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 304 removed outlier: 3.531A pdb=" N GLU C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 removed outlier: 4.215A pdb=" N ALA C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 353 removed outlier: 4.187A pdb=" N ILE C 341 " --> pdb=" O ALA C 337 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG C 342 " --> pdb=" O LYS C 338 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C 351 " --> pdb=" O ARG C 347 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER C 352 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY C 353 " --> pdb=" O SER C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 391 removed outlier: 3.852A pdb=" N ARG C 374 " --> pdb=" O GLU C 370 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 381 " --> pdb=" O ASN C 377 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 388 " --> pdb=" O GLN C 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 25 removed outlier: 3.552A pdb=" N GLU D 12 " --> pdb=" O ARG D 8 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN D 17 " --> pdb=" O GLN D 13 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 20 " --> pdb=" O ASN D 16 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA D 21 " --> pdb=" O GLN D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 35 removed outlier: 3.536A pdb=" N ILE D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 24 removed outlier: 3.665A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 44 removed outlier: 3.613A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.748A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 65 Processing helix chain 'P' and resid 2 through 29 Processing helix chain 'R' and resid 27 through 48 removed outlier: 3.503A pdb=" N PHE R 31 " --> pdb=" O GLN R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 166 removed outlier: 3.686A pdb=" N ILE R 128 " --> pdb=" O ASP R 124 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL R 143 " --> pdb=" O SER R 139 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY R 148 " --> pdb=" O MET R 144 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 170 removed outlier: 3.842A pdb=" N HIS R 170 " --> pdb=" O SER R 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 167 through 170' Processing helix chain 'R' and resid 172 through 197 removed outlier: 3.501A pdb=" N ILE R 194 " --> pdb=" O SER R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 202 removed outlier: 3.552A pdb=" N ARG R 201 " --> pdb=" O LEU R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 212 Processing helix chain 'R' and resid 221 through 252 removed outlier: 3.544A pdb=" N VAL R 226 " --> pdb=" O ALA R 222 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA R 227 " --> pdb=" O GLY R 223 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU R 245 " --> pdb=" O TRP R 241 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU R 249 " --> pdb=" O GLU R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 273 removed outlier: 3.683A pdb=" N GLY R 269 " --> pdb=" O SER R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 287 removed outlier: 3.632A pdb=" N VAL R 280 " --> pdb=" O MET R 276 " (cutoff:3.500A) Proline residue: R 281 - end of helix removed outlier: 4.027A pdb=" N VAL R 285 " --> pdb=" O PRO R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 330 removed outlier: 3.569A pdb=" N ARG R 308 " --> pdb=" O TRP R 304 " (cutoff:3.500A) Proline residue: R 310 - end of helix removed outlier: 3.768A pdb=" N ALA R 314 " --> pdb=" O PRO R 310 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE R 317 " --> pdb=" O LEU R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 330 through 335 removed outlier: 4.115A pdb=" N ALA R 335 " --> pdb=" O ALA R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 353 removed outlier: 3.596A pdb=" N LEU R 352 " --> pdb=" O ALA R 348 " (cutoff:3.500A) Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 360 through 366 removed outlier: 3.584A pdb=" N PHE R 365 " --> pdb=" O GLU R 362 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 389 removed outlier: 3.621A pdb=" N SER R 379 " --> pdb=" O GLY R 375 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE R 383 " --> pdb=" O SER R 379 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU R 386 " --> pdb=" O LEU R 382 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU R 388 " --> pdb=" O PHE R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 391 through 401 removed outlier: 3.648A pdb=" N ALA R 397 " --> pdb=" O GLY R 393 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 423 removed outlier: 3.502A pdb=" N HIS R 416 " --> pdb=" O ARG R 412 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG R 419 " --> pdb=" O TRP R 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 40 through 42 removed outlier: 3.955A pdb=" N PHE C 212 " --> pdb=" O PHE C 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.534A pdb=" N VAL C 247 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE C 244 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE C 290 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE C 246 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASN C 292 " --> pdb=" O PHE C 246 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL C 248 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.720A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY D 330 " --> pdb=" O CYS D 317 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS D 317 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.520A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D 70 " --> pdb=" O TRP D 82 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.912A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG D 137 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 146 through 151 removed outlier: 4.075A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 187 through 192 removed outlier: 7.105A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA D 208 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR D 221 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU D 210 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 233 through 234 removed outlier: 3.530A pdb=" N CYS D 250 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.640A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.957A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.105A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 77 through 80 removed outlier: 3.516A pdb=" N LYS R 98 " --> pdb=" O ALA R 77 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE R 79 " --> pdb=" O VAL R 96 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1098 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: 2.85 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2946 1.34 - 1.46: 2279 1.46 - 1.58: 4170 1.58 - 1.71: 0 1.71 - 1.83: 76 Bond restraints: 9471 Sorted by residual: bond pdb=" N VAL D 276 " pdb=" CA VAL D 276 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.14e+01 bond pdb=" N ILE D 273 " pdb=" CA ILE D 273 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.19e-02 7.06e+03 9.86e+00 bond pdb=" N VAL D 315 " pdb=" CA VAL D 315 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.79e+00 bond pdb=" N TYR D 289 " pdb=" CA TYR D 289 " ideal model delta sigma weight residual 1.453 1.491 -0.037 1.22e-02 6.72e+03 9.40e+00 bond pdb=" N VAL R 363 " pdb=" CA VAL R 363 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.26e-02 6.30e+03 8.73e+00 ... (remaining 9466 not shown) Histogram of bond angle deviations from ideal: 97.49 - 104.81: 117 104.81 - 112.14: 4471 112.14 - 119.47: 3404 119.47 - 126.79: 4696 126.79 - 134.12: 152 Bond angle restraints: 12840 Sorted by residual: angle pdb=" N PRO R 53 " pdb=" CA PRO R 53 " pdb=" C PRO R 53 " ideal model delta sigma weight residual 112.47 126.57 -14.10 2.06e+00 2.36e-01 4.68e+01 angle pdb=" N LEU R 242 " pdb=" CA LEU R 242 " pdb=" C LEU R 242 " ideal model delta sigma weight residual 111.69 104.42 7.27 1.23e+00 6.61e-01 3.50e+01 angle pdb=" C VAL R 57 " pdb=" N CYS R 58 " pdb=" CA CYS R 58 " ideal model delta sigma weight residual 122.09 112.83 9.26 1.79e+00 3.12e-01 2.67e+01 angle pdb=" C GLY C 353 " pdb=" N ASP C 354 " pdb=" CA ASP C 354 " ideal model delta sigma weight residual 121.54 131.14 -9.60 1.91e+00 2.74e-01 2.52e+01 angle pdb=" N PRO R 53 " pdb=" CA PRO R 53 " pdb=" CB PRO R 53 " ideal model delta sigma weight residual 103.25 98.01 5.24 1.05e+00 9.07e-01 2.49e+01 ... (remaining 12835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.82: 5235 14.82 - 29.65: 292 29.65 - 44.47: 58 44.47 - 59.29: 8 59.29 - 74.12: 4 Dihedral angle restraints: 5597 sinusoidal: 2190 harmonic: 3407 Sorted by residual: dihedral pdb=" CA ASN R 59 " pdb=" C ASN R 59 " pdb=" N ARG R 60 " pdb=" CA ARG R 60 " ideal model delta harmonic sigma weight residual 180.00 152.52 27.48 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA CYS R 58 " pdb=" C CYS R 58 " pdb=" N ASN R 59 " pdb=" CA ASN R 59 " ideal model delta harmonic sigma weight residual 180.00 154.59 25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -154.65 -25.35 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 5594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 998 0.054 - 0.108: 310 0.108 - 0.163: 92 0.163 - 0.217: 15 0.217 - 0.271: 5 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA ILE D 273 " pdb=" N ILE D 273 " pdb=" C ILE D 273 " pdb=" CB ILE D 273 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA PRO R 53 " pdb=" N PRO R 53 " pdb=" C PRO R 53 " pdb=" CB PRO R 53 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA LEU R 242 " pdb=" N LEU R 242 " pdb=" C LEU R 242 " pdb=" CB LEU R 242 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1417 not shown) Planarity restraints: 1644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 59 " -0.024 2.00e-02 2.50e+03 1.99e-02 7.95e+00 pdb=" CG TYR D 59 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR D 59 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR D 59 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 59 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR D 59 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR D 59 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 59 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 316 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.21e+00 pdb=" C LEU R 316 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU R 316 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE R 317 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 318 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C ASN R 318 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN R 318 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE R 319 " -0.016 2.00e-02 2.50e+03 ... (remaining 1641 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 13 2.37 - 3.00: 4432 3.00 - 3.63: 13402 3.63 - 4.27: 20910 4.27 - 4.90: 35167 Nonbonded interactions: 73924 Sorted by model distance: nonbonded pdb=" O ILE D 58 " pdb=" OG SER D 316 " model vdw 1.735 2.440 nonbonded pdb=" O GLY D 310 " pdb=" NZ LYS D 337 " model vdw 1.995 2.520 nonbonded pdb=" OG SER D 245 " pdb=" OD1 ASP D 247 " model vdw 2.204 2.440 nonbonded pdb=" O ASN D 313 " pdb=" OG SER D 331 " model vdw 2.226 2.440 nonbonded pdb=" OG SER D 161 " pdb=" OD1 ASP D 163 " model vdw 2.269 2.440 ... (remaining 73919 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5881 2.51 5 N 1627 2.21 5 O 1698 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 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.860 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 27.840 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 0.061 9471 Z= 0.434 Angle : 0.950 14.099 12840 Z= 0.553 Chirality : 0.059 0.271 1420 Planarity : 0.007 0.065 1644 Dihedral : 10.181 74.117 3377 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.20), residues: 1158 helix: -3.85 (0.14), residues: 441 sheet: -2.37 (0.32), residues: 228 loop : -2.40 (0.25), residues: 489 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.291 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2736 time to fit residues: 71.5735 Evaluate side-chains 147 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.969 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN C 23 ASN C 227 GLN C 357 HIS D 88 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 HIS D 311 HIS N 31 ASN N 82 GLN P 1 HIS ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 170 HIS R 177 HIS R 238 ASN R 250 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 9471 Z= 0.153 Angle : 0.560 6.371 12840 Z= 0.298 Chirality : 0.042 0.163 1420 Planarity : 0.004 0.042 1644 Dihedral : 5.387 40.234 1279 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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: -2.71 (0.23), residues: 1158 helix: -1.58 (0.22), residues: 438 sheet: -1.91 (0.32), residues: 234 loop : -1.75 (0.28), residues: 486 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 1.175 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 190 average time/residue: 0.2483 time to fit residues: 63.3310 Evaluate side-chains 163 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 158 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0862 time to fit residues: 2.4081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 GLN C 294 GLN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 ASN R 251 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9471 Z= 0.163 Angle : 0.518 6.506 12840 Z= 0.273 Chirality : 0.041 0.168 1420 Planarity : 0.003 0.035 1644 Dihedral : 4.828 31.831 1279 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.24), residues: 1158 helix: -0.17 (0.24), residues: 440 sheet: -1.57 (0.33), residues: 227 loop : -1.59 (0.28), residues: 491 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 169 time to evaluate : 1.247 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 175 average time/residue: 0.2606 time to fit residues: 61.8974 Evaluate side-chains 162 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1713 time to fit residues: 3.2870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 294 GLN ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 9471 Z= 0.143 Angle : 0.491 7.870 12840 Z= 0.258 Chirality : 0.040 0.169 1420 Planarity : 0.003 0.032 1644 Dihedral : 4.558 26.644 1279 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.71 % 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: -0.98 (0.25), residues: 1158 helix: 0.57 (0.25), residues: 445 sheet: -1.28 (0.34), residues: 227 loop : -1.42 (0.29), residues: 486 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 163 time to evaluate : 1.201 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 165 average time/residue: 0.2510 time to fit residues: 55.3466 Evaluate side-chains 158 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 152 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0920 time to fit residues: 2.5654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 0.0980 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 9471 Z= 0.159 Angle : 0.491 7.284 12840 Z= 0.257 Chirality : 0.040 0.176 1420 Planarity : 0.003 0.031 1644 Dihedral : 4.411 23.250 1279 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 1.02 % 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: -0.59 (0.26), residues: 1158 helix: 1.04 (0.25), residues: 445 sheet: -1.15 (0.34), residues: 229 loop : -1.31 (0.29), residues: 484 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 161 time to evaluate : 1.158 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 167 average time/residue: 0.2408 time to fit residues: 54.3437 Evaluate side-chains 155 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 152 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0971 time to fit residues: 2.0386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 9471 Z= 0.146 Angle : 0.478 7.049 12840 Z= 0.252 Chirality : 0.040 0.184 1420 Planarity : 0.003 0.031 1644 Dihedral : 4.304 20.592 1279 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 1.12 % 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: -0.37 (0.26), residues: 1158 helix: 1.28 (0.25), residues: 447 sheet: -0.98 (0.34), residues: 222 loop : -1.30 (0.29), residues: 489 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 1.204 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 156 average time/residue: 0.2409 time to fit residues: 51.1104 Evaluate side-chains 156 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 151 time to evaluate : 1.244 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1976 time to fit residues: 2.9840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 268 ASN ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9471 Z= 0.205 Angle : 0.504 6.243 12840 Z= 0.264 Chirality : 0.041 0.188 1420 Planarity : 0.003 0.032 1644 Dihedral : 4.390 21.207 1279 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 0.81 % 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: -0.23 (0.26), residues: 1158 helix: 1.47 (0.26), residues: 445 sheet: -0.95 (0.34), residues: 224 loop : -1.26 (0.29), residues: 489 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 161 time to evaluate : 1.068 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 164 average time/residue: 0.2466 time to fit residues: 54.8352 Evaluate side-chains 158 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1023 time to fit residues: 2.1857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 9471 Z= 0.155 Angle : 0.486 7.997 12840 Z= 0.256 Chirality : 0.040 0.192 1420 Planarity : 0.003 0.031 1644 Dihedral : 4.290 19.280 1279 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 0.41 % 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: -0.08 (0.26), residues: 1158 helix: 1.60 (0.26), residues: 447 sheet: -0.78 (0.34), residues: 222 loop : -1.25 (0.29), residues: 489 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 154 time to evaluate : 1.148 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 155 average time/residue: 0.2539 time to fit residues: 52.9312 Evaluate side-chains 148 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1116 time to fit residues: 1.7329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 31 optimal weight: 0.0870 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 0.0570 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 9471 Z= 0.135 Angle : 0.473 7.662 12840 Z= 0.248 Chirality : 0.040 0.202 1420 Planarity : 0.003 0.030 1644 Dihedral : 4.161 18.013 1279 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.51 % 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: 0.05 (0.26), residues: 1158 helix: 1.73 (0.26), residues: 446 sheet: -0.66 (0.34), residues: 242 loop : -1.24 (0.30), residues: 470 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 1.197 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 152 average time/residue: 0.2472 time to fit residues: 50.7489 Evaluate side-chains 145 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1088 time to fit residues: 1.9876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 9471 Z= 0.157 Angle : 0.487 7.519 12840 Z= 0.256 Chirality : 0.041 0.198 1420 Planarity : 0.003 0.038 1644 Dihedral : 4.150 18.059 1279 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 0.41 % 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: 0.08 (0.26), residues: 1158 helix: 1.73 (0.26), residues: 451 sheet: -0.59 (0.34), residues: 240 loop : -1.26 (0.30), residues: 467 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 151 time to evaluate : 1.138 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 153 average time/residue: 0.2480 time to fit residues: 50.8055 Evaluate side-chains 150 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1023 time to fit residues: 2.0156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 3.9990 chunk 13 optimal weight: 0.1980 chunk 25 optimal weight: 0.0170 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.130178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.104389 restraints weight = 14387.062| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.72 r_work: 0.3166 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 9471 Z= 0.129 Angle : 0.472 7.559 12840 Z= 0.249 Chirality : 0.040 0.205 1420 Planarity : 0.003 0.031 1644 Dihedral : 4.042 17.529 1279 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 0.41 % 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: 0.20 (0.26), residues: 1158 helix: 1.90 (0.26), residues: 447 sheet: -0.56 (0.34), residues: 241 loop : -1.23 (0.29), residues: 470 =============================================================================== Job complete usr+sys time: 2056.99 seconds wall clock time: 38 minutes 2.57 seconds (2282.57 seconds total)