Starting phenix.real_space_refine on Sat Jul 4 08:34:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j5k_61144/07_2026/9j5k_61144.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j5k_61144/07_2026/9j5k_61144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j5k_61144/07_2026/9j5k_61144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j5k_61144/07_2026/9j5k_61144.map" model { file = "/net/cci-nas-00/data/ceres_data/9j5k_61144/07_2026/9j5k_61144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j5k_61144/07_2026/9j5k_61144.cif" } resolution = 3.39 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 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= 0.003 sd= 0.130 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: 6 Type Number sf(0) Gaussians Mn 4 7.51 5 P 2 5.49 5 S 70 5.16 5 C 12066 2.51 5 N 3278 2.21 5 O 3636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19056 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2320 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 278} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3425 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 419 Unresolved non-hydrogen angles: 520 Unresolved non-hydrogen dihedrals: 351 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'ASP:plan': 15, 'PHE:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 2, 'TYR:plan': 3, 'GLU:plan': 9, 'GLN:plan1': 4, 'HIS:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 209 Chain: "A" Number of atoms: 3742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 3742 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PTRANS': 28, 'TRANS': 540} Chain breaks: 1 Unresolved non-hydrogen bonds: 736 Unresolved non-hydrogen angles: 930 Unresolved non-hydrogen dihedrals: 595 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 30, 'ASN:plan1': 7, 'ASP:plan': 17, 'GLN:plan1': 11, 'ARG:plan': 21, 'PHE:plan': 6, 'TYR:plan': 5, 'HIS:plan': 6, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 460 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 39 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2320 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 278} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3425 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 419 Unresolved non-hydrogen angles: 520 Unresolved non-hydrogen dihedrals: 351 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'ASP:plan': 15, 'PHE:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 2, 'TYR:plan': 3, 'GLU:plan': 9, 'GLN:plan1': 4, 'HIS:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 209 Chain: "D" Number of atoms: 3742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 3742 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PTRANS': 28, 'TRANS': 540} Chain breaks: 1 Unresolved non-hydrogen bonds: 736 Unresolved non-hydrogen angles: 930 Unresolved non-hydrogen dihedrals: 595 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 30, 'ASN:plan1': 7, 'ASP:plan': 17, 'GLN:plan1': 11, 'ARG:plan': 21, 'PHE:plan': 6, 'TYR:plan': 5, 'HIS:plan': 6, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 460 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 39 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Time building chain proxies: 4.39, per 1000 atoms: 0.23 Number of scatterers: 19056 At special positions: 0 Unit cell: (161.2, 217.36, 130, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 4 24.99 S 70 16.00 P 2 15.00 O 3636 8.00 N 3278 7.00 C 12066 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: 1.77 Conformation dependent library (CDL) restraints added in 886.9 milliseconds 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5152 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 6 sheets defined 74.6% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'C' and resid 5 through 19 removed outlier: 3.879A pdb=" N GLU C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 61 through 73 removed outlier: 3.546A pdb=" N GLU C 67 " --> pdb=" O HIS C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 107 removed outlier: 3.850A pdb=" N THR C 96 " --> pdb=" O TYR C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 140 through 151 removed outlier: 3.640A pdb=" N ASP C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 183 removed outlier: 3.589A pdb=" N ILE C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.762A pdb=" N LEU C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 removed outlier: 3.604A pdb=" N SER C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU C 226 " --> pdb=" O GLN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 221 removed outlier: 3.573A pdb=" N GLN B 221 " --> pdb=" O PRO B 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 218 through 221' Processing helix chain 'B' and resid 223 through 245 removed outlier: 8.319A pdb=" N ASP B 234 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N SER B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 269 removed outlier: 4.438A pdb=" N SER B 252 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 279 removed outlier: 3.840A pdb=" N THR B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 288 removed outlier: 6.744A pdb=" N ASP B 286 " --> pdb=" O ARG B 283 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 288 " --> pdb=" O GLY B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 308 removed outlier: 3.895A pdb=" N ASN B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 323 Processing helix chain 'B' and resid 327 through 338 removed outlier: 3.582A pdb=" N ILE B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 359 Processing helix chain 'B' and resid 362 through 370 Processing helix chain 'B' and resid 382 through 396 removed outlier: 4.009A pdb=" N THR B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 396 " --> pdb=" O THR B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 408 through 415 Processing helix chain 'B' and resid 417 through 431 removed outlier: 3.891A pdb=" N ILE B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 453 removed outlier: 3.597A pdb=" N ALA B 438 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 461 Processing helix chain 'B' and resid 471 through 474 removed outlier: 3.535A pdb=" N GLU B 474 " --> pdb=" O ASN B 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 471 through 474' Processing helix chain 'B' and resid 475 through 490 removed outlier: 4.074A pdb=" N SER B 479 " --> pdb=" O SER B 475 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 505 removed outlier: 4.244A pdb=" N LEU B 503 " --> pdb=" O MET B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 525 through 542 Processing helix chain 'B' and resid 546 through 554 Processing helix chain 'B' and resid 566 through 583 removed outlier: 3.698A pdb=" N TRP B 572 " --> pdb=" O VAL B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 599 removed outlier: 4.035A pdb=" N THR B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 612 removed outlier: 3.758A pdb=" N LYS B 612 " --> pdb=" O PHE B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 634 removed outlier: 3.705A pdb=" N THR B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 646 Processing helix chain 'B' and resid 651 through 670 Processing helix chain 'A' and resid 13 through 19 removed outlier: 3.755A pdb=" N LYS A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 32 removed outlier: 3.631A pdb=" N ASN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 41 removed outlier: 3.679A pdb=" N ILE A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 56 removed outlier: 4.666A pdb=" N ILE A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Proline residue: A 51 - end of helix Processing helix chain 'A' and resid 61 through 80 removed outlier: 3.619A pdb=" N VAL A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Proline residue: A 76 - end of helix removed outlier: 4.278A pdb=" N GLY A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 96 removed outlier: 3.530A pdb=" N LEU A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 121 Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 140 through 152 removed outlier: 4.478A pdb=" N SER A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 173 removed outlier: 3.612A pdb=" N LYS A 161 " --> pdb=" O PRO A 157 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.808A pdb=" N ARG A 180 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 212 Processing helix chain 'A' and resid 217 through 230 Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 241 through 252 Processing helix chain 'A' and resid 256 through 272 removed outlier: 4.168A pdb=" N TYR A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU A 267 " --> pdb=" O ASN A 263 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 290 removed outlier: 4.038A pdb=" N THR A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Proline residue: A 283 - end of helix removed outlier: 3.984A pdb=" N LEU A 289 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 311 removed outlier: 3.695A pdb=" N ARG A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 330 removed outlier: 3.557A pdb=" N GLN A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Proline residue: A 322 - end of helix removed outlier: 4.041A pdb=" N ASP A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 351 removed outlier: 4.447A pdb=" N SER A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Proline residue: A 348 - end of helix removed outlier: 3.599A pdb=" N GLY A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 367 Proline residue: A 361 - end of helix Processing helix chain 'A' and resid 371 through 389 removed outlier: 3.607A pdb=" N ASN A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLN A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 407 removed outlier: 3.868A pdb=" N SER A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Proline residue: A 400 - end of helix removed outlier: 3.576A pdb=" N GLU A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 420 removed outlier: 3.765A pdb=" N ARG A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 429 removed outlier: 4.289A pdb=" N LEU A 424 " --> pdb=" O TYR A 420 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 445 removed outlier: 3.991A pdb=" N MET A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 467 through 485 removed outlier: 4.189A pdb=" N TRP A 471 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Proline residue: A 478 - end of helix removed outlier: 4.063A pdb=" N LEU A 481 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU A 482 " --> pdb=" O PRO A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 503 removed outlier: 3.609A pdb=" N ARG A 497 " --> pdb=" O MET A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 523 Proline residue: A 517 - end of helix Processing helix chain 'A' and resid 527 through 542 Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 549 through 563 Proline residue: A 556 - end of helix Processing helix chain 'A' and resid 567 through 582 removed outlier: 3.571A pdb=" N ASN A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 19 removed outlier: 3.862A pdb=" N GLU F 19 " --> pdb=" O GLU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 40 Processing helix chain 'F' and resid 61 through 73 removed outlier: 3.553A pdb=" N GLU F 67 " --> pdb=" O HIS F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 107 removed outlier: 3.794A pdb=" N THR F 96 " --> pdb=" O TYR F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 125 Processing helix chain 'F' and resid 128 through 138 Processing helix chain 'F' and resid 140 through 151 removed outlier: 3.636A pdb=" N ASP F 151 " --> pdb=" O THR F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 183 removed outlier: 3.642A pdb=" N ILE F 180 " --> pdb=" O THR F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 201 removed outlier: 3.765A pdb=" N LEU F 199 " --> pdb=" O MET F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 233 removed outlier: 3.581A pdb=" N SER F 225 " --> pdb=" O GLY F 221 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU F 226 " --> pdb=" O GLN F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 268 Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'E' and resid 193 through 197 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 218 through 221 removed outlier: 3.572A pdb=" N GLN E 221 " --> pdb=" O PRO E 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 218 through 221' Processing helix chain 'E' and resid 223 through 245 removed outlier: 8.318A pdb=" N ASP E 234 " --> pdb=" O LYS E 230 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N SER E 235 " --> pdb=" O HIS E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 269 removed outlier: 4.431A pdb=" N SER E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N THR E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 279 removed outlier: 3.849A pdb=" N THR E 275 " --> pdb=" O THR E 271 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR E 277 " --> pdb=" O ASP E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 288 removed outlier: 6.722A pdb=" N ASP E 286 " --> pdb=" O ARG E 283 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU E 288 " --> pdb=" O GLY E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 308 removed outlier: 3.924A pdb=" N ASN E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 323 Processing helix chain 'E' and resid 327 through 338 removed outlier: 3.572A pdb=" N ILE E 331 " --> pdb=" O GLU E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 359 Processing helix chain 'E' and resid 362 through 370 Processing helix chain 'E' and resid 382 through 396 removed outlier: 4.028A pdb=" N THR E 386 " --> pdb=" O ASN E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 404 Processing helix chain 'E' and resid 408 through 415 Processing helix chain 'E' and resid 417 through 431 removed outlier: 3.881A pdb=" N ILE E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 453 removed outlier: 3.583A pdb=" N ALA E 438 " --> pdb=" O THR E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 463 Processing helix chain 'E' and resid 471 through 474 removed outlier: 3.543A pdb=" N GLU E 474 " --> pdb=" O ASN E 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 471 through 474' Processing helix chain 'E' and resid 475 through 490 removed outlier: 4.087A pdb=" N SER E 479 " --> pdb=" O SER E 475 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE E 480 " --> pdb=" O PRO E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 505 removed outlier: 4.296A pdb=" N LEU E 503 " --> pdb=" O MET E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 519 Processing helix chain 'E' and resid 525 through 542 Processing helix chain 'E' and resid 546 through 554 Processing helix chain 'E' and resid 566 through 583 removed outlier: 3.699A pdb=" N TRP E 572 " --> pdb=" O VAL E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 599 removed outlier: 4.038A pdb=" N THR E 593 " --> pdb=" O LEU E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 612 removed outlier: 3.737A pdb=" N LYS E 612 " --> pdb=" O PHE E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 616 through 634 removed outlier: 3.707A pdb=" N THR E 625 " --> pdb=" O ALA E 621 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 646 Processing helix chain 'E' and resid 651 through 670 Processing helix chain 'D' and resid 13 through 19 removed outlier: 3.754A pdb=" N LYS D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 32 removed outlier: 3.628A pdb=" N ASN D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 41 removed outlier: 3.678A pdb=" N ILE D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 56 removed outlier: 4.663A pdb=" N ILE D 50 " --> pdb=" O ARG D 46 " (cutoff:3.500A) Proline residue: D 51 - end of helix Processing helix chain 'D' and resid 61 through 80 removed outlier: 3.615A pdb=" N VAL D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Proline residue: D 76 - end of helix removed outlier: 4.276A pdb=" N GLY D 80 " --> pdb=" O PRO D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 96 removed outlier: 3.531A pdb=" N LEU D 91 " --> pdb=" O LEU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 121 Processing helix chain 'D' and resid 124 through 134 Processing helix chain 'D' and resid 140 through 152 removed outlier: 4.479A pdb=" N SER D 144 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 173 removed outlier: 3.611A pdb=" N LYS D 161 " --> pdb=" O PRO D 157 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN D 173 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.808A pdb=" N ARG D 180 " --> pdb=" O MET D 176 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR D 185 " --> pdb=" O ARG D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 212 Processing helix chain 'D' and resid 217 through 230 Processing helix chain 'D' and resid 236 through 241 Processing helix chain 'D' and resid 241 through 252 Processing helix chain 'D' and resid 256 through 272 removed outlier: 4.169A pdb=" N TYR D 266 " --> pdb=" O ALA D 262 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLU D 267 " --> pdb=" O ASN D 263 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 290 removed outlier: 4.038A pdb=" N THR D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Proline residue: D 283 - end of helix removed outlier: 3.986A pdb=" N LEU D 289 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG D 290 " --> pdb=" O VAL D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 311 removed outlier: 3.691A pdb=" N ARG D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY D 302 " --> pdb=" O ILE D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 330 removed outlier: 3.557A pdb=" N GLN D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) Proline residue: D 322 - end of helix removed outlier: 4.043A pdb=" N ASP D 330 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 351 removed outlier: 4.457A pdb=" N SER D 341 " --> pdb=" O SER D 337 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) Proline residue: D 348 - end of helix removed outlier: 3.624A pdb=" N GLY D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 367 Proline residue: D 361 - end of helix Processing helix chain 'D' and resid 371 through 389 removed outlier: 3.564A pdb=" N ASN D 377 " --> pdb=" O ASP D 373 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLN D 384 " --> pdb=" O SER D 380 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 388 " --> pdb=" O GLN D 384 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE D 389 " --> pdb=" O VAL D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 407 removed outlier: 3.861A pdb=" N SER D 395 " --> pdb=" O ILE D 391 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN D 396 " --> pdb=" O ASP D 392 " (cutoff:3.500A) Proline residue: D 400 - end of helix removed outlier: 3.552A pdb=" N GLU D 407 " --> pdb=" O VAL D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 420 removed outlier: 3.743A pdb=" N ARG D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 429 removed outlier: 4.117A pdb=" N LEU D 424 " --> pdb=" O TYR D 420 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 425 " --> pdb=" O ILE D 421 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN D 427 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 445 removed outlier: 4.077A pdb=" N MET D 442 " --> pdb=" O GLY D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 467 through 485 removed outlier: 4.160A pdb=" N TRP D 471 " --> pdb=" O PHE D 467 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL D 477 " --> pdb=" O MET D 473 " (cutoff:3.500A) Proline residue: D 478 - end of helix removed outlier: 3.994A pdb=" N LEU D 481 " --> pdb=" O VAL D 477 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU D 482 " --> pdb=" O PRO D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 503 removed outlier: 3.589A pdb=" N ARG D 497 " --> pdb=" O MET D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 523 Proline residue: D 517 - end of helix Processing helix chain 'D' and resid 527 through 542 Processing helix chain 'D' and resid 543 through 545 No H-bonds generated for 'chain 'D' and resid 543 through 545' Processing helix chain 'D' and resid 549 through 563 Proline residue: D 556 - end of helix Processing helix chain 'D' and resid 567 through 582 removed outlier: 3.571A pdb=" N ASN D 582 " --> pdb=" O GLN D 578 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.204A pdb=" N PHE C 164 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 111 through 113 removed outlier: 3.626A pdb=" N ALA C 273 " --> pdb=" O PHE C 289 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE C 289 " --> pdb=" O ALA C 273 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.408A pdb=" N ASP C 202 " --> pdb=" O PHE C 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.057A pdb=" N PHE F 164 " --> pdb=" O SER F 238 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL F 237 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE F 259 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG F 239 " --> pdb=" O ILE F 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 111 through 113 removed outlier: 3.619A pdb=" N ALA F 273 " --> pdb=" O PHE F 289 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE F 289 " --> pdb=" O ALA F 273 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.412A pdb=" N ASP F 202 " --> pdb=" O PHE F 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 1249 hydrogen bonds defined for protein. 3675 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: 3.45 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3306 1.30 - 1.43: 4583 1.43 - 1.56: 11403 1.56 - 1.69: 0 1.69 - 1.82: 108 Bond restraints: 19400 Sorted by residual: bond pdb=" OG1 TPO Y 4 " pdb=" P TPO Y 4 " ideal model delta sigma weight residual 1.717 1.555 0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" OG1 TPO X 4 " pdb=" P TPO X 4 " ideal model delta sigma weight residual 1.717 1.555 0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" C VAL F 87 " pdb=" O VAL F 87 " ideal model delta sigma weight residual 1.237 1.171 0.066 1.09e-02 8.42e+03 3.68e+01 bond pdb=" C VAL C 87 " pdb=" O VAL C 87 " ideal model delta sigma weight residual 1.237 1.172 0.065 1.09e-02 8.42e+03 3.53e+01 bond pdb=" C ASN C 117 " pdb=" O ASN C 117 " ideal model delta sigma weight residual 1.236 1.168 0.068 1.29e-02 6.01e+03 2.78e+01 ... (remaining 19395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.07: 26480 5.07 - 10.14: 90 10.14 - 15.21: 1 15.21 - 20.28: 2 20.28 - 25.35: 3 Bond angle restraints: 26576 Sorted by residual: angle pdb=" C ASN C 117 " pdb=" CA ASN C 117 " pdb=" CB ASN C 117 " ideal model delta sigma weight residual 110.38 85.04 25.34 2.04e+00 2.40e-01 1.54e+02 angle pdb=" CB TPO Y 4 " pdb=" OG1 TPO Y 4 " pdb=" P TPO Y 4 " ideal model delta sigma weight residual 119.31 93.96 25.35 3.00e+00 1.11e-01 7.14e+01 angle pdb=" N VAL C 87 " pdb=" CA VAL C 87 " pdb=" CB VAL C 87 " ideal model delta sigma weight residual 111.82 100.81 11.01 1.36e+00 5.41e-01 6.56e+01 angle pdb=" C TPO Y 4 " pdb=" CA TPO Y 4 " pdb=" CB TPO Y 4 " ideal model delta sigma weight residual 109.10 126.36 -17.26 2.20e+00 2.07e-01 6.16e+01 angle pdb=" C TPO X 4 " pdb=" CA TPO X 4 " pdb=" CB TPO X 4 " ideal model delta sigma weight residual 109.10 125.73 -16.63 2.20e+00 2.07e-01 5.71e+01 ... (remaining 26571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10313 17.96 - 35.93: 951 35.93 - 53.89: 286 53.89 - 71.85: 48 71.85 - 89.81: 30 Dihedral angle restraints: 11628 sinusoidal: 3726 harmonic: 7902 Sorted by residual: dihedral pdb=" C ASN C 117 " pdb=" N ASN C 117 " pdb=" CA ASN C 117 " pdb=" CB ASN C 117 " ideal model delta harmonic sigma weight residual -122.60 -91.66 -30.94 0 2.50e+00 1.60e-01 1.53e+02 dihedral pdb=" C TPO Y 4 " pdb=" N TPO Y 4 " pdb=" CA TPO Y 4 " pdb=" CB TPO Y 4 " ideal model delta harmonic sigma weight residual -122.60 -138.61 16.01 0 2.50e+00 1.60e-01 4.10e+01 dihedral pdb=" N VAL C 87 " pdb=" C VAL C 87 " pdb=" CA VAL C 87 " pdb=" CB VAL C 87 " ideal model delta harmonic sigma weight residual 123.40 107.70 15.70 0 2.50e+00 1.60e-01 3.94e+01 ... (remaining 11625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3063 0.093 - 0.185: 145 0.185 - 0.278: 6 0.278 - 0.371: 3 0.371 - 0.463: 1 Chirality restraints: 3218 Sorted by residual: chirality pdb=" CA TPO Y 4 " pdb=" N TPO Y 4 " pdb=" C TPO Y 4 " pdb=" CB TPO Y 4 " both_signs ideal model delta sigma weight residual False 2.53 2.06 0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CB VAL X 5 " pdb=" CA VAL X 5 " pdb=" CG1 VAL X 5 " pdb=" CG2 VAL X 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA VAL F 87 " pdb=" N VAL F 87 " pdb=" C VAL F 87 " pdb=" CB VAL F 87 " both_signs ideal model delta sigma weight residual False 2.44 2.77 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 3215 not shown) Planarity restraints: 3474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG X 2 " 0.881 9.50e-02 1.11e+02 3.95e-01 9.46e+01 pdb=" NE ARG X 2 " -0.053 2.00e-02 2.50e+03 pdb=" CZ ARG X 2 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG X 2 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG X 2 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Y 2 " 0.857 9.50e-02 1.11e+02 3.84e-01 8.96e+01 pdb=" NE ARG Y 2 " -0.051 2.00e-02 2.50e+03 pdb=" CZ ARG Y 2 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG Y 2 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG Y 2 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 449 " -0.015 2.00e-02 2.50e+03 2.12e-02 1.13e+01 pdb=" CG TRP E 449 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP E 449 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP E 449 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP E 449 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP E 449 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP E 449 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 449 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 449 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP E 449 " -0.001 2.00e-02 2.50e+03 ... (remaining 3471 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 116 2.45 - 3.06: 13177 3.06 - 3.67: 31060 3.67 - 4.29: 41732 4.29 - 4.90: 68234 Nonbonded interactions: 154319 Sorted by model distance: nonbonded pdb=" ND1 HIS F 241 " pdb="MN MN F 401 " model vdw 1.832 3.140 nonbonded pdb=" OG SER C 93 " pdb=" OE1 GLU C 132 " model vdw 2.033 3.040 nonbonded pdb=" OH TYR F 86 " pdb=" O LEU F 114 " model vdw 2.125 3.040 nonbonded pdb=" OD2 ASP F 85 " pdb="MN MN F 401 " model vdw 2.138 3.060 nonbonded pdb=" NE2 HIS F 167 " pdb="MN MN F 401 " model vdw 2.143 3.140 ... (remaining 154314 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'X' selection = chain 'Y' } 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=0.33 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.220 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.340 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 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 : 0.004 0.162 19400 Z= 0.235 Angle : 0.821 25.355 26576 Z= 0.460 Chirality : 0.045 0.463 3218 Planarity : 0.011 0.395 3474 Dihedral : 16.791 89.815 6476 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.01 % Favored : 95.77 % Rotamer: Outliers : 4.68 % Allowed : 25.49 % Favored : 69.83 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.17), residues: 2670 helix: 0.81 (0.13), residues: 1798 sheet: -2.09 (0.62), residues: 68 loop : -1.12 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 239 TYR 0.020 0.002 TYR E 661 PHE 0.019 0.001 PHE C 228 TRP 0.048 0.002 TRP E 449 HIS 0.015 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.23 (19400) covalent geometry : angle 0.82062 / 0.46 (26576) hydrogen bonds : bond 0.14066 / 9.09 ( 1249) hydrogen bonds : angle 5.92485 / 4.20 ( 3675) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 294 time to evaluate : 0.719 Fit side-chains REVERT: C 11 ASP cc_start: 0.7267 (m-30) cc_final: 0.7043 (m-30) REVERT: C 12 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7851 (tp40) REVERT: B 524 SER cc_start: 0.8778 (m) cc_final: 0.8381 (t) REVERT: A 493 MET cc_start: 0.7610 (tmm) cc_final: 0.7384 (tmm) REVERT: X 2 ARG cc_start: 0.4232 (OUTLIER) cc_final: 0.3347 (tpm170) REVERT: F 11 ASP cc_start: 0.7310 (m-30) cc_final: 0.7086 (m-30) REVERT: F 57 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7884 (m-30) REVERT: F 276 MET cc_start: 0.6931 (tpp) cc_final: 0.6690 (tpt) REVERT: E 524 SER cc_start: 0.8774 (m) cc_final: 0.8384 (t) REVERT: E 608 PHE cc_start: 0.6053 (m-80) cc_final: 0.5809 (m-80) REVERT: E 661 TYR cc_start: 0.6819 (t80) cc_final: 0.6565 (t80) REVERT: D 399 LEU cc_start: 0.7624 (mm) cc_final: 0.7323 (pp) REVERT: D 454 ASP cc_start: 0.7982 (t70) cc_final: 0.7479 (m-30) REVERT: Y 2 ARG cc_start: 0.4602 (OUTLIER) cc_final: 0.3908 (tpm170) outliers start: 81 outliers final: 44 residues processed: 363 average time/residue: 0.1455 time to fit residues: 81.5491 Evaluate side-chains 256 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 89 ARG Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain X residue 2 ARG Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 89 ARG Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 531 LYS Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 513 SER Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain Y residue 2 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 HIS B 261 GLN B 462 ASN A 240 GLN A 485 ASN E 261 GLN E 398 ASN D 240 GLN D 485 ASN D 533 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5085 r_free = 0.5085 target = 0.240417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.206257 restraints weight = 29136.710| |-----------------------------------------------------------------------------| r_work (start): 0.4762 rms_B_bonded: 3.63 r_work: 0.4336 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4359 r_free = 0.4359 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4358 r_free = 0.4358 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.4358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19400 Z= 0.161 Angle : 0.653 7.570 26576 Z= 0.333 Chirality : 0.043 0.232 3218 Planarity : 0.005 0.070 3474 Dihedral : 6.769 80.630 2909 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.97 % Favored : 95.99 % Rotamer: Outliers : 5.14 % Allowed : 24.22 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.16), residues: 2670 helix: 0.81 (0.13), residues: 1790 sheet: -1.67 (0.55), residues: 100 loop : -1.30 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 239 TYR 0.021 0.002 TYR E 553 PHE 0.026 0.002 PHE A 532 TRP 0.032 0.002 TRP B 265 HIS 0.008 0.001 HIS F 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (19400) covalent geometry : angle 0.65298 / 0.33 (26576) hydrogen bonds : bond 0.04158 / 2.72 ( 1249) hydrogen bonds : angle 4.80757 / 3.42 ( 3675) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 231 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: C 66 MET cc_start: 0.7241 (mmm) cc_final: 0.6863 (mtt) REVERT: C 268 ARG cc_start: 0.7764 (mtm110) cc_final: 0.6995 (ttm-80) REVERT: B 424 MET cc_start: 0.6581 (ttm) cc_final: 0.6126 (ttm) REVERT: B 524 SER cc_start: 0.8480 (m) cc_final: 0.8227 (t) REVERT: A 67 MET cc_start: 0.1706 (mpp) cc_final: -0.1213 (mmt) REVERT: A 218 VAL cc_start: 0.4839 (OUTLIER) cc_final: 0.4484 (t) REVERT: A 433 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7260 (m-80) REVERT: A 542 ILE cc_start: 0.4838 (OUTLIER) cc_final: 0.4486 (mp) REVERT: F 66 MET cc_start: 0.7295 (mmm) cc_final: 0.6879 (mtt) REVERT: F 85 ASP cc_start: 0.7781 (m-30) cc_final: 0.7538 (m-30) REVERT: F 228 PHE cc_start: 0.6499 (t80) cc_final: 0.6292 (t80) REVERT: F 268 ARG cc_start: 0.7727 (mtm110) cc_final: 0.7008 (ttm-80) REVERT: E 524 SER cc_start: 0.8513 (m) cc_final: 0.8269 (t) REVERT: E 536 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7735 (tm) REVERT: D 67 MET cc_start: 0.1454 (mpp) cc_final: -0.1197 (mmt) REVERT: D 218 VAL cc_start: 0.4804 (OUTLIER) cc_final: 0.4432 (t) REVERT: D 402 ILE cc_start: 0.6986 (tt) cc_final: 0.6631 (pt) REVERT: D 433 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7298 (m-80) REVERT: D 435 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7662 (t0) REVERT: D 460 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7997 (tt) REVERT: D 542 ILE cc_start: 0.4848 (OUTLIER) cc_final: 0.4280 (mp) outliers start: 89 outliers final: 37 residues processed: 302 average time/residue: 0.1377 time to fit residues: 65.0895 Evaluate side-chains 248 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 531 LYS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 435 ASP Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 542 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 223 optimal weight: 50.0000 chunk 51 optimal weight: 8.9990 chunk 190 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 185 optimal weight: 6.9990 chunk 197 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 233 optimal weight: 9.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 302 ASN B 387 ASN B 423 ASN A 377 ASN ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 ASN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN E 387 ASN E 398 ASN E 423 ASN E 462 ASN D 377 ASN D 485 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5009 r_free = 0.5009 target = 0.229164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.195074 restraints weight = 29095.395| |-----------------------------------------------------------------------------| r_work (start): 0.4647 rms_B_bonded: 3.76 r_work: 0.4171 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4179 r_free = 0.4179 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4179 r_free = 0.4179 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 19400 Z= 0.326 Angle : 0.813 10.024 26576 Z= 0.417 Chirality : 0.048 0.226 3218 Planarity : 0.006 0.058 3474 Dihedral : 6.341 55.688 2854 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.98 % Favored : 94.98 % Rotamer: Outliers : 7.80 % Allowed : 24.16 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.16), residues: 2670 helix: 0.27 (0.12), residues: 1810 sheet: -2.62 (0.48), residues: 116 loop : -1.35 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 181 TYR 0.021 0.003 TYR E 391 PHE 0.030 0.003 PHE C 220 TRP 0.027 0.002 TRP D 444 HIS 0.010 0.002 HIS F 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.33 (19400) covalent geometry : angle 0.81283 / 0.42 (26576) hydrogen bonds : bond 0.04912 / 3.23 ( 1249) hydrogen bonds : angle 5.13361 / 3.65 ( 3675) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 204 time to evaluate : 0.767 Fit side-chains REVERT: C 66 MET cc_start: 0.7599 (mmm) cc_final: 0.7171 (mtt) REVERT: C 86 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.8269 (m-80) REVERT: C 132 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7200 (pt0) REVERT: C 236 LEU cc_start: 0.5063 (tt) cc_final: 0.3996 (tp) REVERT: B 298 MET cc_start: 0.5994 (mmm) cc_final: 0.5453 (mmm) REVERT: B 424 MET cc_start: 0.6785 (ttm) cc_final: 0.6418 (ttm) REVERT: B 485 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8076 (tt) REVERT: B 524 SER cc_start: 0.8365 (m) cc_final: 0.8103 (t) REVERT: B 564 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.5917 (tt) REVERT: A 67 MET cc_start: 0.1571 (mpp) cc_final: -0.0930 (mmt) REVERT: A 218 VAL cc_start: 0.4856 (OUTLIER) cc_final: 0.4506 (t) REVERT: A 405 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7199 (tp) REVERT: A 490 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6359 (mt) REVERT: A 542 ILE cc_start: 0.4831 (OUTLIER) cc_final: 0.4247 (mp) REVERT: A 559 VAL cc_start: 0.6860 (m) cc_final: 0.6568 (p) REVERT: F 66 MET cc_start: 0.7691 (mmm) cc_final: 0.7253 (mtt) REVERT: E 298 MET cc_start: 0.5893 (mmm) cc_final: 0.5332 (mmm) REVERT: E 379 LEU cc_start: 0.4887 (OUTLIER) cc_final: 0.4097 (mt) REVERT: E 524 SER cc_start: 0.8469 (m) cc_final: 0.8181 (t) REVERT: E 536 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8029 (tm) REVERT: E 564 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.5885 (tt) REVERT: D 67 MET cc_start: 0.1707 (mpp) cc_final: -0.0784 (mmt) REVERT: D 218 VAL cc_start: 0.4856 (OUTLIER) cc_final: 0.4478 (t) REVERT: D 405 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7350 (tp) REVERT: D 433 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: D 490 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6273 (mt) outliers start: 135 outliers final: 81 residues processed: 318 average time/residue: 0.1241 time to fit residues: 62.9628 Evaluate side-chains 279 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 183 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 531 LYS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 619 VAL Chi-restraints excluded: chain E residue 633 LEU Chi-restraints excluded: chain E residue 644 ILE Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 458 ASN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 542 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 237 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 0.0030 chunk 3 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 33 optimal weight: 40.0000 chunk 189 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 145 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 387 ASN B 605 ASN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN F 241 HIS E 261 GLN E 387 ASN E 398 ASN E 423 ASN E 605 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5068 r_free = 0.5068 target = 0.236190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.201809 restraints weight = 29161.016| |-----------------------------------------------------------------------------| r_work (start): 0.4709 rms_B_bonded: 3.83 r_work: 0.4267 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4280 r_free = 0.4280 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4280 r_free = 0.4280 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19400 Z= 0.143 Angle : 0.628 8.091 26576 Z= 0.320 Chirality : 0.041 0.154 3218 Planarity : 0.005 0.051 3474 Dihedral : 5.819 57.326 2852 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.96 % Rotamer: Outliers : 6.47 % Allowed : 27.11 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.16), residues: 2670 helix: 0.56 (0.12), residues: 1820 sheet: -1.54 (0.74), residues: 60 loop : -1.24 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 239 TYR 0.020 0.002 TYR E 661 PHE 0.027 0.002 PHE A 532 TRP 0.029 0.002 TRP D 444 HIS 0.007 0.001 HIS F 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (19400) covalent geometry : angle 0.62801 / 0.32 (26576) hydrogen bonds : bond 0.03752 / 2.46 ( 1249) hydrogen bonds : angle 4.69699 / 3.34 ( 3675) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 228 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: C 12 GLN cc_start: 0.8516 (tp40) cc_final: 0.8059 (tp40) REVERT: C 86 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: C 103 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7295 (mt) REVERT: B 298 MET cc_start: 0.6100 (mmm) cc_final: 0.5674 (mmm) REVERT: B 424 MET cc_start: 0.6416 (ttm) cc_final: 0.6085 (ttm) REVERT: B 485 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7803 (tt) REVERT: B 536 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7544 (tp) REVERT: B 612 LYS cc_start: 0.6845 (ptpp) cc_final: 0.6539 (ptpp) REVERT: A 67 MET cc_start: 0.1543 (mpp) cc_final: -0.0523 (mmt) REVERT: A 218 VAL cc_start: 0.5175 (OUTLIER) cc_final: 0.4788 (t) REVERT: A 559 VAL cc_start: 0.6620 (m) cc_final: 0.6364 (p) REVERT: E 298 MET cc_start: 0.5952 (mmm) cc_final: 0.5481 (mmm) REVERT: E 303 TYR cc_start: 0.8705 (m-80) cc_final: 0.8461 (m-80) REVERT: E 536 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7990 (tm) REVERT: E 612 LYS cc_start: 0.6896 (ptpp) cc_final: 0.6590 (ptpp) REVERT: D 67 MET cc_start: 0.1497 (mpp) cc_final: -0.0537 (mmt) REVERT: D 218 VAL cc_start: 0.5018 (OUTLIER) cc_final: 0.4671 (t) REVERT: D 402 ILE cc_start: 0.6855 (tt) cc_final: 0.6539 (pt) REVERT: D 433 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.7356 (m-80) REVERT: D 460 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8057 (tt) REVERT: D 490 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.6011 (mt) REVERT: D 559 VAL cc_start: 0.6548 (m) cc_final: 0.6295 (p) outliers start: 112 outliers final: 69 residues processed: 314 average time/residue: 0.1281 time to fit residues: 63.5294 Evaluate side-chains 295 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 216 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 531 LYS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 633 LEU Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 545 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 53 optimal weight: 0.7980 chunk 252 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN E 261 GLN D 427 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5048 r_free = 0.5048 target = 0.228158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.196245 restraints weight = 27765.917| |-----------------------------------------------------------------------------| r_work (start): 0.4730 rms_B_bonded: 3.43 r_work: 0.4304 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4318 r_free = 0.4318 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4318 r_free = 0.4318 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19400 Z= 0.150 Angle : 0.622 9.053 26576 Z= 0.316 Chirality : 0.042 0.160 3218 Planarity : 0.005 0.050 3474 Dihedral : 5.642 58.260 2850 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.38 % Favored : 95.58 % Rotamer: Outliers : 7.57 % Allowed : 26.76 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.17), residues: 2670 helix: 0.69 (0.13), residues: 1838 sheet: -1.37 (0.60), residues: 92 loop : -1.21 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 239 TYR 0.029 0.002 TYR E 661 PHE 0.026 0.002 PHE F 220 TRP 0.025 0.001 TRP D 444 HIS 0.006 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (19400) covalent geometry : angle 0.62246 / 0.32 (26576) hydrogen bonds : bond 0.03650 / 2.38 ( 1249) hydrogen bonds : angle 4.57587 / 3.25 ( 3675) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 231 time to evaluate : 0.773 Fit side-chains REVERT: C 12 GLN cc_start: 0.8456 (tp40) cc_final: 0.7941 (tp40) REVERT: C 86 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: B 298 MET cc_start: 0.6228 (mmm) cc_final: 0.5742 (mmm) REVERT: B 414 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: B 424 MET cc_start: 0.6480 (ttm) cc_final: 0.6139 (ttm) REVERT: B 485 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7883 (tt) REVERT: B 612 LYS cc_start: 0.7075 (ptpp) cc_final: 0.6774 (ptpp) REVERT: A 218 VAL cc_start: 0.4903 (OUTLIER) cc_final: 0.4549 (t) REVERT: A 496 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7650 (mp) REVERT: A 559 VAL cc_start: 0.6415 (m) cc_final: 0.6193 (p) REVERT: F 12 GLN cc_start: 0.8439 (tp40) cc_final: 0.8175 (tp40) REVERT: E 298 MET cc_start: 0.6204 (mmm) cc_final: 0.5647 (mmt) REVERT: E 378 ASP cc_start: 0.7295 (OUTLIER) cc_final: 0.6451 (t0) REVERT: E 379 LEU cc_start: 0.4593 (OUTLIER) cc_final: 0.3827 (mt) REVERT: E 389 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6824 (mt) REVERT: E 536 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7969 (tm) REVERT: E 612 LYS cc_start: 0.7031 (ptpp) cc_final: 0.6730 (ptpp) REVERT: D 218 VAL cc_start: 0.4935 (OUTLIER) cc_final: 0.4610 (t) REVERT: D 402 ILE cc_start: 0.6984 (tt) cc_final: 0.6690 (pt) REVERT: D 433 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7334 (m-80) REVERT: D 460 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8091 (tt) REVERT: D 490 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.5777 (mt) REVERT: D 559 VAL cc_start: 0.6376 (m) cc_final: 0.6136 (p) outliers start: 131 outliers final: 81 residues processed: 334 average time/residue: 0.1302 time to fit residues: 69.0824 Evaluate side-chains 309 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 215 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 531 LYS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 619 VAL Chi-restraints excluded: chain E residue 633 LEU Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 569 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 131 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 260 optimal weight: 0.0970 chunk 180 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 252 optimal weight: 4.9990 chunk 174 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.235567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.199357 restraints weight = 28938.518| |-----------------------------------------------------------------------------| r_work (start): 0.4676 rms_B_bonded: 4.07 r_work: 0.4272 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4294 r_free = 0.4294 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4294 r_free = 0.4294 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19400 Z= 0.151 Angle : 0.631 8.831 26576 Z= 0.318 Chirality : 0.042 0.153 3218 Planarity : 0.005 0.051 3474 Dihedral : 5.601 59.257 2850 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.47 % Rotamer: Outliers : 6.76 % Allowed : 27.51 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.17), residues: 2670 helix: 0.76 (0.13), residues: 1838 sheet: -1.48 (0.59), residues: 92 loop : -1.18 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 239 TYR 0.054 0.002 TYR B 661 PHE 0.027 0.002 PHE C 220 TRP 0.024 0.001 TRP D 444 HIS 0.005 0.001 HIS F 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (19400) covalent geometry : angle 0.63089 / 0.32 (26576) hydrogen bonds : bond 0.03618 / 2.36 ( 1249) hydrogen bonds : angle 4.52477 / 3.21 ( 3675) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 227 time to evaluate : 0.729 Fit side-chains REVERT: C 12 GLN cc_start: 0.8425 (tp40) cc_final: 0.7888 (tp40) REVERT: C 86 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.7903 (m-80) REVERT: C 103 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.6891 (mp) REVERT: B 298 MET cc_start: 0.6242 (mmm) cc_final: 0.5860 (mmm) REVERT: B 411 PHE cc_start: 0.5818 (OUTLIER) cc_final: 0.5470 (t80) REVERT: B 414 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7139 (tm-30) REVERT: B 424 MET cc_start: 0.6433 (ttm) cc_final: 0.6067 (ttm) REVERT: B 485 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7888 (tt) REVERT: A 124 ASP cc_start: 0.5027 (OUTLIER) cc_final: 0.4215 (p0) REVERT: A 218 VAL cc_start: 0.4993 (OUTLIER) cc_final: 0.4683 (t) REVERT: A 559 VAL cc_start: 0.6331 (m) cc_final: 0.6084 (p) REVERT: E 298 MET cc_start: 0.6274 (mmm) cc_final: 0.5772 (mmt) REVERT: E 378 ASP cc_start: 0.6971 (OUTLIER) cc_final: 0.6165 (t0) REVERT: E 379 LEU cc_start: 0.4571 (OUTLIER) cc_final: 0.3760 (mt) REVERT: E 389 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6824 (mt) REVERT: E 536 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7937 (tm) REVERT: E 612 LYS cc_start: 0.7011 (ptpp) cc_final: 0.6765 (mttp) REVERT: D 124 ASP cc_start: 0.5019 (OUTLIER) cc_final: 0.4216 (p0) REVERT: D 218 VAL cc_start: 0.5045 (OUTLIER) cc_final: 0.4666 (t) REVERT: D 402 ILE cc_start: 0.6781 (tt) cc_final: 0.6520 (pt) REVERT: D 433 PHE cc_start: 0.7558 (m-80) cc_final: 0.7331 (m-80) REVERT: D 460 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8040 (tt) REVERT: D 490 LEU cc_start: 0.6280 (OUTLIER) cc_final: 0.5840 (mt) REVERT: D 559 VAL cc_start: 0.6381 (m) cc_final: 0.6139 (p) outliers start: 117 outliers final: 81 residues processed: 315 average time/residue: 0.1229 time to fit residues: 61.6608 Evaluate side-chains 304 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 208 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 411 PHE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 531 LYS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 548 ASP Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 619 VAL Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 633 LEU Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 569 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 16 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 84 optimal weight: 30.0000 chunk 176 optimal weight: 8.9990 chunk 201 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN B 261 GLN B 352 GLN ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN E 352 GLN E 423 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4998 r_free = 0.4998 target = 0.227961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 127)---------------| | r_work = 0.4591 r_free = 0.4591 target = 0.178992 restraints weight = 29009.680| |-----------------------------------------------------------------------------| r_work (start): 0.4472 rms_B_bonded: 2.54 r_work: 0.4195 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4209 r_free = 0.4209 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4209 r_free = 0.4209 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 19400 Z= 0.301 Angle : 0.783 11.164 26576 Z= 0.398 Chirality : 0.047 0.203 3218 Planarity : 0.006 0.058 3474 Dihedral : 6.187 58.961 2850 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.66 % Favored : 94.31 % Rotamer: Outliers : 7.05 % Allowed : 27.34 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.17), residues: 2670 helix: 0.43 (0.12), residues: 1830 sheet: -2.72 (0.50), residues: 96 loop : -1.36 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 239 TYR 0.066 0.003 TYR E 661 PHE 0.033 0.003 PHE E 484 TRP 0.030 0.002 TRP D 444 HIS 0.008 0.002 HIS F 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.30 (19400) covalent geometry : angle 0.78323 / 0.40 (26576) hydrogen bonds : bond 0.04545 / 2.97 ( 1249) hydrogen bonds : angle 4.91327 / 3.50 ( 3675) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 207 time to evaluate : 0.666 Fit side-chains REVERT: C 12 GLN cc_start: 0.8488 (tp40) cc_final: 0.8216 (tp40) REVERT: C 86 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.8187 (m-80) REVERT: C 236 LEU cc_start: 0.5146 (tt) cc_final: 0.4914 (tt) REVERT: B 298 MET cc_start: 0.6348 (mmm) cc_final: 0.5968 (mmm) REVERT: B 402 ASN cc_start: 0.4577 (OUTLIER) cc_final: 0.4135 (m110) REVERT: B 411 PHE cc_start: 0.6211 (OUTLIER) cc_final: 0.5574 (t80) REVERT: B 485 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7887 (tp) REVERT: A 218 VAL cc_start: 0.5063 (OUTLIER) cc_final: 0.4691 (t) REVERT: A 496 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7393 (mp) REVERT: A 559 VAL cc_start: 0.6582 (m) cc_final: 0.6296 (p) REVERT: F 236 LEU cc_start: 0.4827 (tt) cc_final: 0.4042 (tp) REVERT: E 298 MET cc_start: 0.6487 (mmm) cc_final: 0.6114 (mmm) REVERT: E 378 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.6564 (t0) REVERT: E 379 LEU cc_start: 0.5223 (OUTLIER) cc_final: 0.4357 (mt) REVERT: E 411 PHE cc_start: 0.6274 (OUTLIER) cc_final: 0.5626 (t80) REVERT: E 536 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8023 (tm) REVERT: D 218 VAL cc_start: 0.5111 (OUTLIER) cc_final: 0.4761 (t) REVERT: D 402 ILE cc_start: 0.7013 (tt) cc_final: 0.6693 (pt) REVERT: D 405 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7195 (tp) REVERT: D 460 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8079 (tt) REVERT: D 490 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.6058 (mt) REVERT: D 559 VAL cc_start: 0.6715 (m) cc_final: 0.6409 (p) outliers start: 122 outliers final: 86 residues processed: 300 average time/residue: 0.1216 time to fit residues: 58.2314 Evaluate side-chains 300 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 200 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 411 PHE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 411 PHE Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 531 LYS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 548 ASP Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 619 VAL Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 633 LEU Chi-restraints excluded: chain E residue 644 ILE Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 569 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 66 optimal weight: 0.0670 chunk 142 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 chunk 217 optimal weight: 0.0170 chunk 156 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 chunk 169 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 chunk 112 optimal weight: 0.0970 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN E 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5070 r_free = 0.5070 target = 0.236242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.203994 restraints weight = 29205.075| |-----------------------------------------------------------------------------| r_work (start): 0.4756 rms_B_bonded: 3.56 r_work: 0.4276 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4301 r_free = 0.4301 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4301 r_free = 0.4301 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.4301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19400 Z= 0.134 Angle : 0.649 9.233 26576 Z= 0.324 Chirality : 0.042 0.429 3218 Planarity : 0.005 0.053 3474 Dihedral : 5.727 58.034 2850 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.96 % Rotamer: Outliers : 5.61 % Allowed : 29.02 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.17), residues: 2670 helix: 0.70 (0.12), residues: 1846 sheet: -2.30 (0.54), residues: 98 loop : -1.25 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 239 TYR 0.045 0.002 TYR E 661 PHE 0.036 0.002 PHE C 220 TRP 0.031 0.002 TRP D 444 HIS 0.009 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (19400) covalent geometry : angle 0.64864 / 0.32 (26576) hydrogen bonds : bond 0.03598 / 2.32 ( 1249) hydrogen bonds : angle 4.53479 / 3.22 ( 3675) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 229 time to evaluate : 0.635 Fit side-chains REVERT: C 12 GLN cc_start: 0.8334 (tp40) cc_final: 0.7905 (tp40) REVERT: C 228 PHE cc_start: 0.6633 (t80) cc_final: 0.6429 (t80) REVERT: B 298 MET cc_start: 0.6487 (mmm) cc_final: 0.6005 (mmm) REVERT: B 411 PHE cc_start: 0.5941 (OUTLIER) cc_final: 0.5460 (t80) REVERT: B 414 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7121 (tm-30) REVERT: B 424 MET cc_start: 0.6490 (ttm) cc_final: 0.6283 (ttm) REVERT: A 67 MET cc_start: 0.1967 (mpp) cc_final: -0.1141 (tpp) REVERT: A 124 ASP cc_start: 0.4861 (OUTLIER) cc_final: 0.4197 (p0) REVERT: A 218 VAL cc_start: 0.4851 (OUTLIER) cc_final: 0.4495 (t) REVERT: A 559 VAL cc_start: 0.6199 (m) cc_final: 0.5962 (p) REVERT: E 298 MET cc_start: 0.6440 (mmm) cc_final: 0.6053 (mmm) REVERT: E 303 TYR cc_start: 0.8738 (m-80) cc_final: 0.8471 (m-80) REVERT: E 378 ASP cc_start: 0.6917 (OUTLIER) cc_final: 0.6147 (t0) REVERT: E 389 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7226 (mt) REVERT: E 411 PHE cc_start: 0.6077 (OUTLIER) cc_final: 0.5512 (t80) REVERT: D 124 ASP cc_start: 0.4905 (OUTLIER) cc_final: 0.4204 (p0) REVERT: D 218 VAL cc_start: 0.4907 (OUTLIER) cc_final: 0.4543 (t) REVERT: D 402 ILE cc_start: 0.6803 (tt) cc_final: 0.6558 (pt) REVERT: D 460 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8149 (tt) REVERT: D 490 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.5956 (mt) REVERT: D 559 VAL cc_start: 0.6201 (m) cc_final: 0.5967 (p) outliers start: 97 outliers final: 78 residues processed: 299 average time/residue: 0.1183 time to fit residues: 56.8963 Evaluate side-chains 303 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 214 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 411 PHE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 411 PHE Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 531 LYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 548 ASP Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 619 VAL Chi-restraints excluded: chain E residue 627 LEU Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 633 LEU Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 569 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 265 optimal weight: 0.8980 chunk 222 optimal weight: 6.9990 chunk 240 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 57 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 169 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 387 ASN ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5043 r_free = 0.5043 target = 0.227633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.199590 restraints weight = 27619.177| |-----------------------------------------------------------------------------| r_work (start): 0.4784 rms_B_bonded: 3.12 r_work: 0.4293 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4322 r_free = 0.4322 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4322 r_free = 0.4322 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19400 Z= 0.145 Angle : 0.643 8.895 26576 Z= 0.322 Chirality : 0.042 0.261 3218 Planarity : 0.005 0.065 3474 Dihedral : 5.625 57.402 2850 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.42 % Favored : 95.54 % Rotamer: Outliers : 5.32 % Allowed : 28.90 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2670 helix: 0.78 (0.12), residues: 1846 sheet: -2.27 (0.54), residues: 98 loop : -1.25 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 268 TYR 0.044 0.002 TYR B 661 PHE 0.029 0.002 PHE C 220 TRP 0.027 0.002 TRP B 265 HIS 0.005 0.001 HIS F 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (19400) covalent geometry : angle 0.64327 / 0.32 (26576) hydrogen bonds : bond 0.03609 / 2.34 ( 1249) hydrogen bonds : angle 4.45252 / 3.16 ( 3675) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 223 time to evaluate : 0.731 Fit side-chains REVERT: C 12 GLN cc_start: 0.8322 (tp40) cc_final: 0.8064 (tp40) REVERT: B 298 MET cc_start: 0.6516 (mmm) cc_final: 0.6019 (mmm) REVERT: B 336 ARG cc_start: 0.4087 (tpt-90) cc_final: 0.3706 (ttm170) REVERT: B 414 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: A 124 ASP cc_start: 0.4753 (OUTLIER) cc_final: 0.4165 (p0) REVERT: A 218 VAL cc_start: 0.4821 (OUTLIER) cc_final: 0.4490 (t) REVERT: A 496 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7535 (mp) REVERT: A 559 VAL cc_start: 0.6254 (m) cc_final: 0.6042 (p) REVERT: E 298 MET cc_start: 0.6482 (mmm) cc_final: 0.5977 (mmt) REVERT: E 303 TYR cc_start: 0.8731 (m-80) cc_final: 0.8472 (m-80) REVERT: E 365 GLU cc_start: 0.8762 (mp0) cc_final: 0.8452 (mp0) REVERT: E 378 ASP cc_start: 0.6949 (OUTLIER) cc_final: 0.6104 (t0) REVERT: E 379 LEU cc_start: 0.4714 (OUTLIER) cc_final: 0.3891 (mt) REVERT: E 389 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7166 (mt) REVERT: D 67 MET cc_start: 0.1800 (mpp) cc_final: -0.1155 (tpp) REVERT: D 124 ASP cc_start: 0.4786 (OUTLIER) cc_final: 0.4222 (p0) REVERT: D 218 VAL cc_start: 0.4923 (OUTLIER) cc_final: 0.4571 (t) REVERT: D 402 ILE cc_start: 0.6801 (tt) cc_final: 0.6569 (pt) REVERT: D 460 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8135 (tt) REVERT: D 490 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5698 (mt) REVERT: D 559 VAL cc_start: 0.6257 (m) cc_final: 0.6042 (p) outliers start: 92 outliers final: 76 residues processed: 293 average time/residue: 0.1255 time to fit residues: 59.0576 Evaluate side-chains 301 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 214 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 531 LYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 548 ASP Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 619 VAL Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 633 LEU Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 569 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 103 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 20 optimal weight: 0.0870 chunk 199 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 193 optimal weight: 0.0170 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 387 ASN ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5077 r_free = 0.5077 target = 0.237257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.204217 restraints weight = 29283.657| |-----------------------------------------------------------------------------| r_work (start): 0.4785 rms_B_bonded: 3.40 r_work: 0.4378 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4345 r_free = 0.4345 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4345 r_free = 0.4345 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19400 Z= 0.129 Angle : 0.634 12.711 26576 Z= 0.316 Chirality : 0.041 0.226 3218 Planarity : 0.005 0.053 3474 Dihedral : 5.368 59.239 2850 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.66 % Rotamer: Outliers : 5.20 % Allowed : 29.19 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.17), residues: 2670 helix: 0.83 (0.13), residues: 1848 sheet: -2.15 (0.54), residues: 98 loop : -1.26 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 268 TYR 0.035 0.002 TYR B 661 PHE 0.028 0.002 PHE A 532 TRP 0.027 0.002 TRP A 444 HIS 0.005 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (19400) covalent geometry : angle 0.63362 / 0.32 (26576) hydrogen bonds : bond 0.03423 / 2.20 ( 1249) hydrogen bonds : angle 4.37740 / 3.10 ( 3675) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 238 time to evaluate : 0.734 Fit side-chains REVERT: C 11 ASP cc_start: 0.7568 (m-30) cc_final: 0.7235 (m-30) REVERT: C 103 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.6893 (mp) REVERT: B 298 MET cc_start: 0.6505 (mmm) cc_final: 0.6071 (mmm) REVERT: B 336 ARG cc_start: 0.3814 (tpt-90) cc_final: 0.3465 (ttm170) REVERT: B 365 GLU cc_start: 0.8775 (mp0) cc_final: 0.8184 (mp0) REVERT: B 389 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6676 (mt) REVERT: B 414 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6918 (tm-30) REVERT: A 67 MET cc_start: 0.1742 (mpp) cc_final: -0.1230 (tpp) REVERT: A 124 ASP cc_start: 0.5114 (OUTLIER) cc_final: 0.4530 (p0) REVERT: A 218 VAL cc_start: 0.4838 (OUTLIER) cc_final: 0.4506 (t) REVERT: A 454 ASP cc_start: 0.8205 (t0) cc_final: 0.7979 (m-30) REVERT: A 465 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8419 (tm-30) REVERT: F 11 ASP cc_start: 0.7656 (m-30) cc_final: 0.7356 (m-30) REVERT: F 192 GLU cc_start: 0.7683 (pm20) cc_final: 0.7371 (pm20) REVERT: E 298 MET cc_start: 0.6488 (mmm) cc_final: 0.6046 (mmt) REVERT: E 303 TYR cc_start: 0.8772 (m-80) cc_final: 0.8505 (m-80) REVERT: E 336 ARG cc_start: 0.3825 (tpt-90) cc_final: 0.3400 (ttm170) REVERT: E 365 GLU cc_start: 0.8815 (mp0) cc_final: 0.8194 (mp0) REVERT: E 379 LEU cc_start: 0.4435 (OUTLIER) cc_final: 0.3798 (mt) REVERT: E 389 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6982 (mt) REVERT: E 589 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7656 (mp) REVERT: D 67 MET cc_start: 0.1495 (mpp) cc_final: -0.1273 (tpp) REVERT: D 124 ASP cc_start: 0.4938 (OUTLIER) cc_final: 0.4361 (p0) REVERT: D 125 HIS cc_start: 0.4609 (t-90) cc_final: 0.3682 (p90) REVERT: D 218 VAL cc_start: 0.4961 (OUTLIER) cc_final: 0.4608 (t) REVERT: D 465 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8331 (tm-30) REVERT: D 490 LEU cc_start: 0.6053 (OUTLIER) cc_final: 0.5568 (mt) REVERT: D 559 VAL cc_start: 0.6244 (m) cc_final: 0.6037 (p) outliers start: 90 outliers final: 64 residues processed: 309 average time/residue: 0.1152 time to fit residues: 57.2705 Evaluate side-chains 295 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 220 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 531 LYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 548 ASP Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 619 VAL Chi-restraints excluded: chain E residue 633 LEU Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 569 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 203 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 105 optimal weight: 30.0000 chunk 33 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 217 optimal weight: 0.4980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.227482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.195601 restraints weight = 29023.284| |-----------------------------------------------------------------------------| r_work (start): 0.4670 rms_B_bonded: 3.88 r_work: 0.4126 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 19400 Z= 0.322 Angle : 0.809 16.004 26576 Z= 0.409 Chirality : 0.049 0.263 3218 Planarity : 0.006 0.052 3474 Dihedral : 5.907 57.783 2846 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.24 % Favored : 94.72 % Rotamer: Outliers : 4.86 % Allowed : 29.83 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.17), residues: 2670 helix: 0.46 (0.12), residues: 1836 sheet: -3.12 (0.48), residues: 94 loop : -1.40 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 268 TYR 0.042 0.003 TYR E 661 PHE 0.033 0.003 PHE C 220 TRP 0.025 0.002 TRP B 265 HIS 0.008 0.002 HIS F 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00748 / 0.32 (19400) covalent geometry : angle 0.80924 / 0.41 (26576) hydrogen bonds : bond 0.04548 / 2.97 ( 1249) hydrogen bonds : angle 4.85125 / 3.46 ( 3675) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5167.39 seconds wall clock time: 89 minutes 1.33 seconds (5341.33 seconds total)