Starting phenix.real_space_refine on Mon May 19 20:04:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7luv_23527/05_2025/7luv_23527.cif Found real_map, /net/cci-nas-00/data/ceres_data/7luv_23527/05_2025/7luv_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/cci-nas-00/data/ceres_data/7luv_23527/05_2025/7luv_23527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7luv_23527/05_2025/7luv_23527.map" model { file = "/net/cci-nas-00/data/ceres_data/7luv_23527/05_2025/7luv_23527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7luv_23527/05_2025/7luv_23527.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 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. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18773 Number of models: 1 Model: "" Number of chains: 8 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: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 240 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 32} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 5783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5783 Classifications: {'peptide': 717} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 28} Link IDs: {'PTRANS': 22, 'TRANS': 694} Chain breaks: 8 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 805 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'TRANS': 160} Chain breaks: 9 Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 483 Unresolved non-hydrogen dihedrals: 161 Planarities with less than four sites: {'UNK:plan-1': 161} Unresolved non-hydrogen planarities: 161 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: 12.23, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.21 Conformation dependent library (CDL) restraints added in 2.3 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: 2.16 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: 6.29 Time building geometry restraints manager: 6.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 0.00 - 2.52: 25449 2.52 - 5.04: 346 5.04 - 7.56: 43 7.56 - 10.08: 2 10.08 - 12.61: 2 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 3.040 nonbonded pdb=" O PRO A 215 " pdb=" ND2 ASN A 221 " model vdw 2.090 3.120 nonbonded pdb=" O ILE C 807 " pdb=" NH2 ARG M 75 " model vdw 2.133 3.120 nonbonded pdb=" O ASP B 32 " pdb=" OG SER B 35 " model vdw 2.136 3.040 nonbonded pdb=" O VAL D 34 " pdb=" OG1 THR D 38 " model vdw 2.146 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 9.290 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: 0.990 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 44.490 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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= 0.312 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 : 10.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.61 % Favored : 90.10 % Rotamer: Outliers : 0.05 % Allowed : 1.05 % Favored : 98.90 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 280 HIS 0.007 0.002 HIS A 341 PHE 0.030 0.003 PHE C 694 TYR 0.028 0.002 TYR C 680 ARG 0.008 0.001 ARG C 578 Details of bonding type rmsd hydrogen bonds : bond 0.15288 ( 923) hydrogen bonds : angle 9.46347 ( 2667) covalent geometry : bond 0.00712 (19115) covalent geometry : angle 0.79600 (25842) *********************** 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 to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7932 (mmtt) REVERT: B 183 MET cc_start: 0.8638 (tpt) cc_final: 0.8424 (tpp) REVERT: C 320 LYS cc_start: 0.9168 (tptt) cc_final: 0.8954 (tppp) REVERT: E 83 MET cc_start: 0.7944 (mmm) cc_final: 0.6608 (mpp) REVERT: E 242 MET cc_start: 0.8179 (mpp) cc_final: 0.7869 (mpp) REVERT: E 282 LEU cc_start: 0.9448 (tt) cc_final: 0.9216 (tt) REVERT: M 150 TYR cc_start: 0.6405 (m-80) cc_final: 0.5780 (m-10) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.3538 time to fit residues: 98.3631 Evaluate side-chains 120 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 6.9990 chunk 175 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 210 optimal weight: 9.9990 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 199 HIS A 265 HIS A 357 GLN A 378 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 ASN B 58 HIS B 227 HIS E 72 HIS E 202 ASN E 305 HIS M 122 GLN ** M 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 392 HIS M 423 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.085776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.065971 restraints weight = 78203.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.066823 restraints weight = 44616.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.067603 restraints weight = 30084.372| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19115 Z= 0.143 Angle : 0.630 8.699 25842 Z= 0.327 Chirality : 0.042 0.174 2968 Planarity : 0.004 0.038 3259 Dihedral : 5.132 31.067 2530 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.60 % Allowed : 5.09 % Favored : 94.31 % 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: -2.15 (0.17), residues: 2112 helix: -0.69 (0.14), residues: 1180 sheet: -1.21 (0.34), residues: 211 loop : -2.59 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 280 HIS 0.006 0.001 HIS B 109 PHE 0.023 0.001 PHE C 607 TYR 0.019 0.001 TYR M 390 ARG 0.006 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.05393 ( 923) hydrogen bonds : angle 5.26270 ( 2667) covalent geometry : bond 0.00282 (19115) covalent geometry : angle 0.63003 (25842) *********************** 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 167 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.8460 (tpp) cc_final: 0.8030 (tpp) REVERT: A 445 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7840 (mmtt) REVERT: A 457 ASP cc_start: 0.8996 (t0) cc_final: 0.8788 (t0) REVERT: B 183 MET cc_start: 0.8609 (tpt) cc_final: 0.8378 (tpp) REVERT: C 320 LYS cc_start: 0.9179 (tptt) cc_final: 0.8749 (tmtt) REVERT: C 323 MET cc_start: 0.8047 (tpt) cc_final: 0.7843 (tpt) REVERT: C 654 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: E 83 MET cc_start: 0.7841 (mmm) cc_final: 0.6556 (mpp) REVERT: M 150 TYR cc_start: 0.5904 (m-80) cc_final: 0.5266 (m-80) REVERT: M 245 MET cc_start: 0.8350 (pmm) cc_final: 0.7974 (tmm) outliers start: 12 outliers final: 7 residues processed: 163 average time/residue: 0.3220 time to fit residues: 80.8752 Evaluate side-chains 115 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 741 ASN Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain M residue 239 ARG Chi-restraints excluded: chain M residue 246 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.9144 > 50: distance: 38 - 42: 6.067 distance: 42 - 43: 9.397 distance: 43 - 44: 14.977 distance: 43 - 46: 11.765 distance: 44 - 45: 22.990 distance: 44 - 51: 19.583 distance: 46 - 47: 17.046 distance: 47 - 48: 3.827 distance: 48 - 49: 5.664 distance: 48 - 50: 6.985 distance: 51 - 52: 15.551 distance: 52 - 53: 18.734 distance: 52 - 55: 16.042 distance: 53 - 54: 9.751 distance: 53 - 57: 7.545 distance: 54 - 82: 32.945 distance: 55 - 56: 44.094 distance: 57 - 58: 8.248 distance: 58 - 59: 7.338 distance: 58 - 61: 9.519 distance: 59 - 60: 20.772 distance: 59 - 65: 10.247 distance: 61 - 62: 17.154 distance: 62 - 63: 12.295 distance: 62 - 64: 16.682 distance: 65 - 66: 14.587 distance: 66 - 67: 18.803 distance: 66 - 69: 19.971 distance: 67 - 68: 14.360 distance: 67 - 75: 19.873 distance: 68 - 97: 12.859 distance: 69 - 70: 19.719 distance: 70 - 71: 24.742 distance: 70 - 72: 9.437 distance: 71 - 73: 13.081 distance: 72 - 74: 19.730 distance: 73 - 74: 18.265 distance: 75 - 76: 10.451 distance: 76 - 77: 20.267 distance: 76 - 79: 3.872 distance: 77 - 78: 10.299 distance: 77 - 82: 15.322 distance: 78 - 105: 12.193 distance: 79 - 80: 24.373 distance: 79 - 81: 30.886 distance: 82 - 83: 14.434 distance: 83 - 84: 15.187 distance: 83 - 86: 14.222 distance: 84 - 85: 13.068 distance: 84 - 89: 6.380 distance: 86 - 87: 16.155 distance: 86 - 88: 26.542 distance: 89 - 90: 34.417 distance: 90 - 91: 44.185 distance: 90 - 93: 31.533 distance: 91 - 92: 42.610 distance: 91 - 97: 28.866 distance: 93 - 95: 12.168 distance: 94 - 96: 10.550 distance: 97 - 98: 8.633 distance: 98 - 99: 7.388 distance: 98 - 101: 11.001 distance: 99 - 100: 14.358 distance: 99 - 105: 5.710 distance: 101 - 102: 10.905 distance: 102 - 103: 5.988 distance: 102 - 104: 11.325 distance: 105 - 106: 10.595 distance: 106 - 107: 10.574 distance: 106 - 109: 7.588 distance: 107 - 108: 13.871 distance: 107 - 114: 17.312 distance: 109 - 110: 12.033 distance: 110 - 111: 11.017 distance: 111 - 112: 23.396 distance: 112 - 113: 14.338 distance: 114 - 115: 4.732 distance: 115 - 116: 10.378 distance: 115 - 118: 5.123 distance: 116 - 117: 17.952 distance: 116 - 128: 10.890 distance: 117 - 152: 20.179 distance: 118 - 119: 12.683 distance: 119 - 120: 9.350 distance: 119 - 121: 7.402 distance: 120 - 122: 6.061 distance: 121 - 123: 4.080 distance: 121 - 124: 3.319 distance: 122 - 123: 3.264 distance: 123 - 125: 4.776 distance: 124 - 126: 4.417 distance: 126 - 127: 4.046