Starting phenix.real_space_refine (version: dev) on Wed Feb 22 23:20:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7luv_23527/02_2023/7luv_23527.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7luv_23527/02_2023/7luv_23527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7luv_23527/02_2023/7luv_23527.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7luv_23527/02_2023/7luv_23527.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7luv_23527/02_2023/7luv_23527.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7luv_23527/02_2023/7luv_23527.pdb" } resolution = 3.7 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= 0.001 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 Process input model Symmetric amino acids flipped Residue "A ARG 30": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 110": "NH1" <-> "NH2" Residue "A ARG 311": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 578": "NH1" <-> "NH2" Residue "C PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 610": "NH1" <-> "NH2" Residue "C TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 714": "NH1" <-> "NH2" Residue "C ARG 730": "NH1" <-> "NH2" Residue "C ARG 820": "NH1" <-> "NH2" Residue "C ARG 908": "NH1" <-> "NH2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 358": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 18773 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 4026 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 21, 'TRANS': 461} Chain breaks: 4 Chain: "B" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1576 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain breaks: 3 Chain: "C" Number of atoms: 6828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 911, 6828 Classifications: {'peptide': 911} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 204} Link IDs: {'PTRANS': 22, 'TRANS': 888} Chain breaks: 20 Unresolved non-hydrogen bonds: 411 Unresolved non-hydrogen angles: 617 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 205} Unresolved non-hydrogen planarities: 205 Chain: "D" Number of atoms: 1212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1212 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 3, 'TRANS': 146} Chain breaks: 2 Chain: "E" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2121 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 264} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3010 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain breaks: 1 Time building chain proxies: 10.53, per 1000 atoms: 0.56 Number of scatterers: 18773 At special positions: 0 Unit cell: (98.7595, 190.708, 156.653, 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 71 16.00 O 3516 8.00 N 3146 7.00 C 12040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 8.34 Conformation dependent library (CDL) restraints added in 2.8 seconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4614 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 11 sheets defined 69.0% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 Processing helix chain 'A' and resid 26 through 31 removed outlier: 3.797A pdb=" N HIS A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 61 through 77 Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 116 through 131 removed outlier: 3.514A pdb=" N LEU A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 147 removed outlier: 3.629A pdb=" N PHE A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Proline residue: A 142 - end of helix removed outlier: 3.565A pdb=" N ARG A 147 " --> pdb=" O TYR A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.756A pdb=" N PHE A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 191 removed outlier: 4.305A pdb=" N LYS A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ARG A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 185 " --> pdb=" O TRP A 181 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASN A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 214 removed outlier: 3.712A pdb=" N TYR A 204 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS A 205 " --> pdb=" O ASN A 201 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 266 removed outlier: 3.743A pdb=" N ASP A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 279 through 321 removed outlier: 3.776A pdb=" N ASP A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Proline residue: A 290 - end of helix removed outlier: 3.892A pdb=" N ILE A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A 307 " --> pdb=" O TYR A 303 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ARG A 313 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 343 through 362 removed outlier: 3.804A pdb=" N ARG A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASN A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 removed outlier: 3.737A pdb=" N LYS A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 415 removed outlier: 4.124A pdb=" N GLN A 397 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE A 398 " --> pdb=" O TYR A 394 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN A 407 " --> pdb=" O CYS A 403 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 430 removed outlier: 3.950A pdb=" N ARG A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 454 Processing helix chain 'A' and resid 460 through 468 removed outlier: 4.695A pdb=" N ILE A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 491 removed outlier: 4.610A pdb=" N VAL A 474 " --> pdb=" O ASP A 470 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 475 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG A 476 " --> pdb=" O TYR A 472 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A 483 " --> pdb=" O MET A 479 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.802A pdb=" N VAL A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP A 532 " --> pdb=" O ILE A 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 38 removed outlier: 4.054A pdb=" N THR B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N HIS B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 33 " --> pdb=" O ASN B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 83 removed outlier: 3.972A pdb=" N TYR B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN B 74 " --> pdb=" O TYR B 70 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR B 75 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP B 83 " --> pdb=" O GLN B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 122 removed outlier: 4.196A pdb=" N THR B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 107 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN B 111 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU B 115 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 122 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 159 removed outlier: 3.944A pdb=" N GLY B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 195 removed outlier: 3.736A pdb=" N ASP B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 186 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.632A pdb=" N ARG B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 212 through 225 removed outlier: 4.695A pdb=" N MET B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 50 removed outlier: 3.793A pdb=" N UNK C 48 " --> pdb=" O UNK C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 73 removed outlier: 4.389A pdb=" N PHE C 71 " --> pdb=" O GLU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 96 removed outlier: 3.607A pdb=" N UNK C 91 " --> pdb=" O UNK C 87 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N UNK C 92 " --> pdb=" O UNK C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 116 Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 135 through 143 removed outlier: 3.555A pdb=" N LEU C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 150 removed outlier: 3.932A pdb=" N LEU C 150 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 167 removed outlier: 3.666A pdb=" N THR C 155 " --> pdb=" O ASN C 151 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS C 160 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS C 163 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 194 removed outlier: 3.728A pdb=" N ALA C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 200 removed outlier: 3.748A pdb=" N SER C 200 " --> pdb=" O ASP C 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 201 through 216 removed outlier: 3.895A pdb=" N TYR C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 232 removed outlier: 3.720A pdb=" N ASP C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 removed outlier: 3.903A pdb=" N TYR C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 249 removed outlier: 4.135A pdb=" N LYS C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'C' and resid 271 through 283 Processing helix chain 'C' and resid 294 through 307 Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 322 through 340 removed outlier: 4.143A pdb=" N GLN C 331 " --> pdb=" O GLN C 327 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR C 335 " --> pdb=" O GLN C 331 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 403 removed outlier: 3.783A pdb=" N GLY C 403 " --> pdb=" O ILE C 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 399 through 403' Processing helix chain 'C' and resid 404 through 414 removed outlier: 3.740A pdb=" N LEU C 408 " --> pdb=" O LYS C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 427 removed outlier: 3.797A pdb=" N GLN C 426 " --> pdb=" O HIS C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 433 removed outlier: 3.964A pdb=" N LEU C 431 " --> pdb=" O PRO C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 456 removed outlier: 3.575A pdb=" N ARG C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR C 447 " --> pdb=" O ARG C 443 " (cutoff:3.500A) Proline residue: C 451 - end of helix Processing helix chain 'C' and resid 521 through 527 Processing helix chain 'C' and resid 536 through 541 Processing helix chain 'C' and resid 542 through 560 removed outlier: 3.703A pdb=" N LEU C 546 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS C 548 " --> pdb=" O THR C 544 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG C 551 " --> pdb=" O SER C 547 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 552 " --> pdb=" O LYS C 548 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 572 removed outlier: 4.303A pdb=" N VAL C 568 " --> pdb=" O GLU C 564 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 580 removed outlier: 3.660A pdb=" N TYR C 576 " --> pdb=" O LYS C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 588 removed outlier: 3.684A pdb=" N SER C 586 " --> pdb=" O PRO C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 597 removed outlier: 3.955A pdb=" N THR C 595 " --> pdb=" O ASN C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 603 Processing helix chain 'C' and resid 609 through 620 Processing helix chain 'C' and resid 625 through 643 Processing helix chain 'C' and resid 650 through 663 removed outlier: 5.853A pdb=" N ARG C 656 " --> pdb=" O ALA C 652 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG C 657 " --> pdb=" O LYS C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 670 removed outlier: 3.716A pdb=" N SER C 669 " --> pdb=" O ASN C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 681 removed outlier: 4.332A pdb=" N ASN C 679 " --> pdb=" O LYS C 675 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR C 680 " --> pdb=" O GLN C 676 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP C 681 " --> pdb=" O ILE C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 691 removed outlier: 4.203A pdb=" N LEU C 686 " --> pdb=" O LYS C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 694 No H-bonds generated for 'chain 'C' and resid 692 through 694' Processing helix chain 'C' and resid 695 through 710 removed outlier: 4.011A pdb=" N TYR C 699 " --> pdb=" O ASN C 695 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP C 700 " --> pdb=" O ASP C 696 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 701 " --> pdb=" O PHE C 697 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 704 " --> pdb=" O ASP C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 742 Processing helix chain 'C' and resid 750 through 759 removed outlier: 3.816A pdb=" N LYS C 756 " --> pdb=" O THR C 752 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR C 757 " --> pdb=" O TYR C 753 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N HIS C 759 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 778 removed outlier: 3.943A pdb=" N VAL C 766 " --> pdb=" O ASN C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 786 through 794 removed outlier: 3.865A pdb=" N MET C 792 " --> pdb=" O LYS C 788 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 793 " --> pdb=" O GLN C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 808 removed outlier: 3.662A pdb=" N ARG C 804 " --> pdb=" O LYS C 800 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS C 805 " --> pdb=" O GLN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 827 removed outlier: 3.779A pdb=" N PHE C 824 " --> pdb=" O ARG C 820 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 841 Processing helix chain 'C' and resid 856 through 877 removed outlier: 4.192A pdb=" N THR C 864 " --> pdb=" O ASP C 860 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C 866 " --> pdb=" O MET C 862 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS C 875 " --> pdb=" O GLU C 871 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS C 876 " --> pdb=" O LEU C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 886 removed outlier: 4.067A pdb=" N GLU C 884 " --> pdb=" O LYS C 880 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN C 885 " --> pdb=" O ALA C 881 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C 886 " --> pdb=" O PHE C 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 880 through 886' Processing helix chain 'C' and resid 901 through 908 removed outlier: 3.706A pdb=" N TRP C 907 " --> pdb=" O THR C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 6942 through 6949 Processing helix chain 'C' and resid 6992 through 7012 removed outlier: 3.843A pdb=" N UNK C6996 " --> pdb=" O UNK C6992 " (cutoff:3.500A) Processing helix chain 'C' and resid 7029 through 7034 Processing helix chain 'C' and resid 7050 through 7058 removed outlier: 4.625A pdb=" N UNK C7056 " --> pdb=" O UNK C7052 " (cutoff:3.500A) Processing helix chain 'C' and resid 7132 through 7141 removed outlier: 4.106A pdb=" N UNK C7137 " --> pdb=" O UNK C7133 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N UNK C7141 " --> pdb=" O UNK C7137 " (cutoff:3.500A) Processing helix chain 'C' and resid 7142 through 7149 removed outlier: 3.965A pdb=" N UNK C7146 " --> pdb=" O UNK C7142 " (cutoff:3.500A) Processing helix chain 'C' and resid 7160 through 7175 removed outlier: 3.930A pdb=" N UNK C7173 " --> pdb=" O UNK C7169 " (cutoff:3.500A) Processing helix chain 'C' and resid 7181 through 7200 Processing helix chain 'C' and resid 7212 through 7223 removed outlier: 3.846A pdb=" N UNK C7217 " --> pdb=" O UNK C7213 " (cutoff:3.500A) Processing helix chain 'C' and resid 7235 through 7246 removed outlier: 4.634A pdb=" N UNK C7242 " --> pdb=" O UNK C7238 " (cutoff:3.500A) Processing helix chain 'C' and resid 7257 through 7266 Processing helix chain 'D' and resid 6 through 17 removed outlier: 4.250A pdb=" N LYS D 14 " --> pdb=" O GLN D 10 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR D 17 " --> pdb=" O THR D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 39 removed outlier: 3.616A pdb=" N ASN D 25 " --> pdb=" O ASP D 21 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE D 30 " --> pdb=" O LYS D 26 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL D 34 " --> pdb=" O ILE D 30 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 102 removed outlier: 3.624A pdb=" N GLU D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR D 96 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN D 102 " --> pdb=" O ALA D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 139 removed outlier: 3.788A pdb=" N ILE D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 227 removed outlier: 3.699A pdb=" N ASN D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE D 213 " --> pdb=" O MET D 209 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU D 214 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 190 through 193 removed outlier: 3.520A pdb=" N HIS E 193 " --> pdb=" O LYS E 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 190 through 193' Processing helix chain 'M' and resid 63 through 68 removed outlier: 4.066A pdb=" N ASP M 66 " --> pdb=" O GLY M 63 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU M 68 " --> pdb=" O LYS M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 80 Processing helix chain 'M' and resid 86 through 97 Proline residue: M 94 - end of helix Processing helix chain 'M' and resid 112 through 124 removed outlier: 3.767A pdb=" N PHE M 116 " --> pdb=" O LYS M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 154 Processing helix chain 'M' and resid 170 through 180 removed outlier: 3.749A pdb=" N ASP M 174 " --> pdb=" O PRO M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 200 removed outlier: 4.130A pdb=" N ALA M 197 " --> pdb=" O GLY M 193 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU M 198 " --> pdb=" O ARG M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 223 removed outlier: 3.760A pdb=" N GLU M 223 " --> pdb=" O LYS M 219 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 237 Processing helix chain 'M' and resid 253 through 259 removed outlier: 4.045A pdb=" N ILE M 257 " --> pdb=" O GLU M 253 " (cutoff:3.500A) Processing helix chain 'M' and resid 291 through 296 Processing helix chain 'M' and resid 297 through 300 Processing helix chain 'M' and resid 315 through 327 removed outlier: 3.523A pdb=" N ASN M 320 " --> pdb=" O THR M 316 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU M 325 " --> pdb=" O GLU M 321 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU M 326 " --> pdb=" O LEU M 322 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN M 327 " --> pdb=" O THR M 323 " (cutoff:3.500A) Processing helix chain 'M' and resid 341 through 354 removed outlier: 4.007A pdb=" N TYR M 349 " --> pdb=" O ARG M 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 363 through 367 Processing helix chain 'M' and resid 386 through 397 removed outlier: 3.586A pdb=" N ALA M 397 " --> pdb=" O ARG M 393 " (cutoff:3.500A) Processing helix chain 'M' and resid 413 through 427 removed outlier: 4.334A pdb=" N GLN M 423 " --> pdb=" O LEU M 419 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLU M 424 " --> pdb=" O ALA M 420 " (cutoff:3.500A) Processing helix chain 'M' and resid 439 through 443 Processing sheet with id=AA1, first strand: chain 'C' and resid 471 through 474 Processing sheet with id=AA2, first strand: chain 'C' and resid 488 through 491 removed outlier: 3.854A pdb=" N SER C 497 " --> pdb=" O TYR C 504 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 69 through 71 Processing sheet with id=AA4, first strand: chain 'E' and resid 117 through 120 Processing sheet with id=AA5, first strand: chain 'E' and resid 165 through 168 removed outlier: 4.055A pdb=" N LEU E 186 " --> pdb=" O HIS E 197 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N HIS E 197 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASN E 188 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU E 195 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 212 through 217 Processing sheet with id=AA7, first strand: chain 'E' and resid 258 through 261 removed outlier: 3.691A pdb=" N THR E 270 " --> pdb=" O TYR E 278 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR E 278 " --> pdb=" O THR E 270 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N CYS E 277 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ILE E 290 " --> pdb=" O CYS E 277 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE E 279 " --> pdb=" O GLU E 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 301 through 303 removed outlier: 6.376A pdb=" N VAL E 319 " --> pdb=" O SER E 332 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER E 332 " --> pdb=" O VAL E 319 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE E 321 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 344 through 346 removed outlier: 3.655A pdb=" N LYS E 345 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE E 354 " --> pdb=" O LYS E 345 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 162 through 165 removed outlier: 5.542A pdb=" N ALA M 163 " --> pdb=" O VAL M 189 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL M 133 " --> pdb=" O VAL M 188 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ALA M 190 " --> pdb=" O VAL M 133 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL M 135 " --> pdb=" O ALA M 190 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP M 215 " --> pdb=" O ILE M 136 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE M 212 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N PHE M 246 " --> pdb=" O PHE M 212 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE M 214 " --> pdb=" O PHE M 246 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL M 102 " --> pdb=" O MET M 245 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N SER M 247 " --> pdb=" O VAL M 102 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N CYS M 104 " --> pdb=" O SER M 247 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU M 103 " --> pdb=" O ILE M 268 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 333 through 335 removed outlier: 3.684A pdb=" N CYS M 360 " --> pdb=" O VAL M 309 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE M 310 " --> pdb=" O ILE M 379 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TYR M 284 " --> pdb=" O SER M 408 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL M 410 " --> pdb=" O TYR M 284 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE M 286 " --> pdb=" O VAL M 410 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA M 431 " --> pdb=" O GLN M 283 " (cutoff:3.500A) 923 hydrogen bonds defined for protein. 2667 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: 5.96 Time building geometry restraints manager: 8.81 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: 6026 1.34 - 1.46: 3869 1.46 - 1.58: 9107 1.58 - 1.69: 0 1.69 - 1.81: 113 Bond restraints: 19115 Sorted by residual: bond pdb=" CA PHE A 496 " pdb=" C PHE A 496 " ideal model delta sigma weight residual 1.523 1.471 0.052 1.80e-02 3.09e+03 8.46e+00 bond pdb=" C LEU A 213 " pdb=" N LEU A 214 " ideal model delta sigma weight residual 1.333 1.262 0.070 2.74e-02 1.33e+03 6.55e+00 bond pdb=" C PHE A 140 " pdb=" N TRP A 141 " ideal model delta sigma weight residual 1.332 1.311 0.021 1.33e-02 5.65e+03 2.54e+00 bond pdb=" CB TRP A 141 " pdb=" CG TRP A 141 " ideal model delta sigma weight residual 1.498 1.455 0.043 3.10e-02 1.04e+03 1.91e+00 bond pdb=" CB LYS C 404 " pdb=" CG LYS C 404 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.76e+00 ... (remaining 19110 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.15: 321 106.15 - 113.11: 10701 113.11 - 120.07: 6911 120.07 - 127.03: 7736 127.03 - 134.00: 173 Bond angle restraints: 25842 Sorted by residual: angle pdb=" C LYS B 53 " pdb=" N LEU B 54 " pdb=" CA LEU B 54 " ideal model delta sigma weight residual 119.78 125.14 -5.36 1.24e+00 6.50e-01 1.87e+01 angle pdb=" N VAL C 310 " pdb=" CA VAL C 310 " pdb=" C VAL C 310 " ideal model delta sigma weight residual 109.34 117.80 -8.46 2.08e+00 2.31e-01 1.66e+01 angle pdb=" N LYS B 98 " pdb=" CA LYS B 98 " pdb=" C LYS B 98 " ideal model delta sigma weight residual 114.56 109.85 4.71 1.27e+00 6.20e-01 1.37e+01 angle pdb=" N PHE C 312 " pdb=" CA PHE C 312 " pdb=" C PHE C 312 " ideal model delta sigma weight residual 110.80 117.92 -7.12 2.13e+00 2.20e-01 1.12e+01 angle pdb=" N VAL C 417 " pdb=" CA VAL C 417 " pdb=" C VAL C 417 " ideal model delta sigma weight residual 113.71 110.61 3.10 9.50e-01 1.11e+00 1.07e+01 ... (remaining 25837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.56: 10945 15.56 - 31.13: 523 31.13 - 46.69: 88 46.69 - 62.26: 1 62.26 - 77.82: 11 Dihedral angle restraints: 11568 sinusoidal: 4518 harmonic: 7050 Sorted by residual: dihedral pdb=" CA LEU A 130 " pdb=" C LEU A 130 " pdb=" N LEU A 131 " pdb=" CA LEU A 131 " ideal model delta harmonic sigma weight residual 180.00 146.43 33.57 0 5.00e+00 4.00e-02 4.51e+01 dihedral pdb=" CA PRO B 149 " pdb=" C PRO B 149 " pdb=" N SER B 150 " pdb=" CA SER B 150 " ideal model delta harmonic sigma weight residual 180.00 149.39 30.61 0 5.00e+00 4.00e-02 3.75e+01 dihedral pdb=" CA SER E 254 " pdb=" C SER E 254 " pdb=" N SER E 255 " pdb=" CA SER E 255 " ideal model delta harmonic sigma weight residual 180.00 151.53 28.47 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 11565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1524 0.033 - 0.066: 970 0.066 - 0.099: 349 0.099 - 0.132: 110 0.132 - 0.165: 15 Chirality restraints: 2968 Sorted by residual: chirality pdb=" CA ILE M 372 " pdb=" N ILE M 372 " pdb=" C ILE M 372 " pdb=" CB ILE M 372 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CA ILE E 290 " pdb=" N ILE E 290 " pdb=" C ILE E 290 " pdb=" CB ILE E 290 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CA VAL M 189 " pdb=" N VAL M 189 " pdb=" C VAL M 189 " pdb=" CB VAL M 189 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 2965 not shown) Planarity restraints: 3259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 887 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO C 888 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 888 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 888 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 694 " -0.011 2.00e-02 2.50e+03 1.31e-02 3.00e+00 pdb=" CG PHE C 694 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE C 694 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 694 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 694 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 694 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 694 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 214 " -0.009 2.00e-02 2.50e+03 1.09e-02 2.98e+00 pdb=" CG TRP B 214 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP B 214 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 214 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 214 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 214 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 214 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 214 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 214 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 214 " -0.002 2.00e-02 2.50e+03 ... (remaining 3256 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 222 2.62 - 3.19: 18950 3.19 - 3.76: 26280 3.76 - 4.33: 37482 4.33 - 4.90: 59115 Nonbonded interactions: 142049 Sorted by model distance: nonbonded pdb=" O LEU B 121 " pdb=" OG SER B 125 " model vdw 2.050 2.440 nonbonded pdb=" O PRO A 215 " pdb=" ND2 ASN A 221 " model vdw 2.090 2.520 nonbonded pdb=" O ILE C 807 " pdb=" NH2 ARG M 75 " model vdw 2.133 2.520 nonbonded pdb=" O ASP B 32 " pdb=" OG SER B 35 " model vdw 2.136 2.440 nonbonded pdb=" O VAL D 34 " pdb=" OG1 THR D 38 " model vdw 2.146 2.440 ... (remaining 142044 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 71 5.16 5 C 12040 2.51 5 N 3146 2.21 5 O 3516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.400 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: 28.110 Check model and map are aligned: 0.290 Process input model: 48.780 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.180 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 0.070 19115 Z= 0.451 Angle : 0.796 12.606 25842 Z= 0.428 Chirality : 0.048 0.165 2968 Planarity : 0.004 0.050 3259 Dihedral : 9.840 77.819 6954 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.61 % Favored : 90.10 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -4.47 (0.15), residues: 2112 helix: -2.92 (0.11), residues: 1179 sheet: -1.60 (0.33), residues: 209 loop : -3.14 (0.21), residues: 724 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.3587 time to fit residues: 99.7871 Evaluate side-chains 117 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.404 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 166 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS A 265 HIS A 350 ASN A 357 GLN A 378 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 ASN A 530 ASN B 58 HIS B 227 HIS C 211 HIS C 487 HIS C 741 ASN C 789 GLN D 59 GLN E 72 HIS E 202 ASN E 305 HIS M 122 GLN M 380 ASN M 392 HIS M 423 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 19115 Z= 0.171 Angle : 0.617 9.423 25842 Z= 0.318 Chirality : 0.041 0.165 2968 Planarity : 0.004 0.037 3259 Dihedral : 5.099 30.448 2530 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.97 % Favored : 93.99 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.10 (0.17), residues: 2112 helix: -0.64 (0.14), residues: 1179 sheet: -1.11 (0.34), residues: 211 loop : -2.61 (0.22), residues: 722 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 151 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 160 average time/residue: 0.3241 time to fit residues: 80.9042 Evaluate side-chains 118 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 2.348 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2604 time to fit residues: 5.6492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 0.0030 chunk 40 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 117 optimal weight: 0.0050 chunk 130 optimal weight: 6.9990 chunk 44 optimal weight: 0.0770 chunk 105 optimal weight: 9.9990 overall best weight: 0.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 19115 Z= 0.145 Angle : 0.557 8.164 25842 Z= 0.286 Chirality : 0.039 0.150 2968 Planarity : 0.003 0.035 3259 Dihedral : 4.665 29.146 2530 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.73 % Favored : 94.22 % Rotamer Outliers : 0.85 % 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: -1.10 (0.18), residues: 2112 helix: 0.32 (0.15), residues: 1179 sheet: -0.76 (0.35), residues: 210 loop : -2.45 (0.22), residues: 723 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 153 average time/residue: 0.2976 time to fit residues: 72.9771 Evaluate side-chains 123 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 2.399 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1888 time to fit residues: 5.5647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 69 optimal weight: 0.4980 chunk 125 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN M 148 ASN M 380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 19115 Z= 0.164 Angle : 0.553 8.676 25842 Z= 0.283 Chirality : 0.039 0.151 2968 Planarity : 0.003 0.042 3259 Dihedral : 4.492 28.386 2530 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.44 % Favored : 93.51 % Rotamer Outliers : 1.05 % 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: -0.60 (0.19), residues: 2112 helix: 0.75 (0.16), residues: 1175 sheet: -0.71 (0.36), residues: 200 loop : -2.22 (0.22), residues: 737 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 143 average time/residue: 0.2862 time to fit residues: 67.1193 Evaluate side-chains 115 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 2.277 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1851 time to fit residues: 5.5728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 397 GLN A 497 GLN C 476 ASN C 676 GLN ** C 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 ASN M 252 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 19115 Z= 0.355 Angle : 0.681 10.643 25842 Z= 0.348 Chirality : 0.043 0.154 2968 Planarity : 0.004 0.035 3259 Dihedral : 4.905 29.557 2530 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.20 % Favored : 92.71 % Rotamer Outliers : 0.85 % 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: -0.66 (0.19), residues: 2112 helix: 0.71 (0.16), residues: 1167 sheet: -0.68 (0.35), residues: 217 loop : -2.27 (0.23), residues: 728 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 124 average time/residue: 0.2901 time to fit residues: 59.6404 Evaluate side-chains 112 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 2.472 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1769 time to fit residues: 6.5473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN A 397 GLN A 497 GLN ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 ASN M 339 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 19115 Z= 0.171 Angle : 0.569 9.313 25842 Z= 0.289 Chirality : 0.040 0.151 2968 Planarity : 0.003 0.037 3259 Dihedral : 4.616 28.511 2530 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.16 % Favored : 93.80 % Rotamer Outliers : 0.70 % 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: -0.24 (0.19), residues: 2112 helix: 1.04 (0.16), residues: 1174 sheet: -0.40 (0.36), residues: 210 loop : -2.10 (0.23), residues: 728 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 129 average time/residue: 0.2960 time to fit residues: 62.7192 Evaluate side-chains 110 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 2.080 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1834 time to fit residues: 4.7177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 0.0670 chunk 15 optimal weight: 0.0370 chunk 79 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 118 optimal weight: 0.3980 chunk 78 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 87 optimal weight: 0.0170 chunk 85 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 HIS M 148 ASN M 231 GLN M 339 HIS M 423 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 19115 Z= 0.129 Angle : 0.530 7.883 25842 Z= 0.271 Chirality : 0.038 0.149 2968 Planarity : 0.003 0.039 3259 Dihedral : 4.218 26.478 2530 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.02 % Favored : 94.93 % Rotamer Outliers : 0.70 % 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: 0.12 (0.19), residues: 2112 helix: 1.37 (0.16), residues: 1168 sheet: -0.34 (0.37), residues: 200 loop : -1.94 (0.23), residues: 744 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 2.334 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 147 average time/residue: 0.2858 time to fit residues: 69.1578 Evaluate side-chains 115 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 2.742 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1867 time to fit residues: 4.2236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 109 optimal weight: 30.0000 chunk 127 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 422 HIS ** C 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 339 HIS M 423 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 19115 Z= 0.284 Angle : 0.619 9.338 25842 Z= 0.316 Chirality : 0.042 0.154 2968 Planarity : 0.004 0.037 3259 Dihedral : 4.484 27.343 2530 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.44 % Favored : 93.51 % Rotamer Outliers : 0.55 % 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: -0.01 (0.19), residues: 2112 helix: 1.27 (0.16), residues: 1178 sheet: -0.60 (0.36), residues: 213 loop : -2.00 (0.23), residues: 721 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 117 average time/residue: 0.2813 time to fit residues: 54.7398 Evaluate side-chains 109 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 2.316 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1982 time to fit residues: 5.2813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 339 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 19115 Z= 0.220 Angle : 0.591 12.392 25842 Z= 0.300 Chirality : 0.040 0.193 2968 Planarity : 0.003 0.038 3259 Dihedral : 4.482 27.150 2530 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.58 % Favored : 93.37 % Rotamer Outliers : 0.55 % 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: 0.06 (0.19), residues: 2112 helix: 1.30 (0.16), residues: 1180 sheet: -0.34 (0.35), residues: 221 loop : -2.03 (0.23), residues: 711 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 120 average time/residue: 0.2932 time to fit residues: 57.8102 Evaluate side-chains 110 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 2.121 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1913 time to fit residues: 5.4872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 65 optimal weight: 0.0980 chunk 95 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 19115 Z= 0.142 Angle : 0.559 11.731 25842 Z= 0.282 Chirality : 0.039 0.148 2968 Planarity : 0.003 0.038 3259 Dihedral : 4.266 26.218 2530 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.73 % Favored : 94.22 % Rotamer Outliers : 0.05 % 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: 0.30 (0.19), residues: 2112 helix: 1.53 (0.16), residues: 1172 sheet: -0.47 (0.36), residues: 214 loop : -1.87 (0.23), residues: 726 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.2904 time to fit residues: 58.3485 Evaluate side-chains 110 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 2.273 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 0.0030 chunk 16 optimal weight: 0.4980 chunk 31 optimal weight: 8.9990 chunk 115 optimal weight: 0.0170 chunk 48 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.4630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 875 HIS M 339 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.087969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.067857 restraints weight = 78176.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.068589 restraints weight = 46143.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.069207 restraints weight = 31242.525| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 19115 Z= 0.134 Angle : 0.553 9.752 25842 Z= 0.277 Chirality : 0.039 0.147 2968 Planarity : 0.003 0.037 3259 Dihedral : 4.066 25.319 2530 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 0.35 % 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: 0.42 (0.19), residues: 2112 helix: 1.61 (0.16), residues: 1183 sheet: -0.30 (0.36), residues: 212 loop : -1.87 (0.23), residues: 717 =============================================================================== Job complete usr+sys time: 3039.78 seconds wall clock time: 56 minutes 58.59 seconds (3418.59 seconds total)