Starting phenix.real_space_refine on Mon Apr 6 14:17:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j5k_61144/04_2026/9j5k_61144.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j5k_61144/04_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_61144/04_2026/9j5k_61144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j5k_61144/04_2026/9j5k_61144.map" model { file = "/net/cci-nas-00/data/ceres_data/9j5k_61144/04_2026/9j5k_61144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j5k_61144/04_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-2.1rc1-6017/lib/python3.9/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, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.32, 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: 1.68 Conformation dependent library (CDL) restraints added in 887.9 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: 0.64 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: 3.32 Time building geometry restraints manager: 2.24 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 2.400 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 2.320 nonbonded pdb=" NE2 HIS F 167 " pdb="MN MN F 401 " model vdw 2.143 2.400 ... (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: 3.430 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.940 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 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 covalent geometry : bond 0.00415 (19400) covalent geometry : angle 0.82062 (26576) hydrogen bonds : bond 0.14066 ( 1249) hydrogen bonds : angle 5.92485 ( 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 : 0.595 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: 0.1371 time to fit residues: 76.2117 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 : 0.733 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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** B 261 GLN B 462 ASN A 240 GLN A 485 ASN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN E 398 ASN D 240 GLN D 485 ASN D 533 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5086 r_free = 0.5086 target = 0.240576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.206315 restraints weight = 29142.751| |-----------------------------------------------------------------------------| r_work (start): 0.4765 rms_B_bonded: 3.30 r_work: 0.4354 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4372 r_free = 0.4372 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4370 r_free = 0.4370 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19400 Z= 0.164 Angle : 0.652 7.662 26576 Z= 0.332 Chirality : 0.043 0.235 3218 Planarity : 0.005 0.068 3474 Dihedral : 6.780 80.795 2909 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 4.91 % Allowed : 24.62 % Favored : 70.46 % 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: 0.13 (0.16), residues: 2670 helix: 0.82 (0.13), residues: 1790 sheet: -1.64 (0.55), residues: 100 loop : -1.28 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 239 TYR 0.020 0.002 TYR E 553 PHE 0.025 0.002 PHE D 532 TRP 0.032 0.002 TRP B 265 HIS 0.006 0.001 HIS F 118 Details of bonding type rmsd covalent geometry : bond 0.00357 (19400) covalent geometry : angle 0.65236 (26576) hydrogen bonds : bond 0.04246 ( 1249) hydrogen bonds : angle 4.82453 ( 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 316 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 231 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: C 66 MET cc_start: 0.7183 (mmm) cc_final: 0.6826 (mtt) REVERT: B 424 MET cc_start: 0.6543 (ttm) cc_final: 0.6086 (ttm) REVERT: B 524 SER cc_start: 0.8471 (m) cc_final: 0.8225 (t) REVERT: A 67 MET cc_start: 0.1481 (mpp) cc_final: -0.1177 (mmt) REVERT: A 218 VAL cc_start: 0.4852 (OUTLIER) cc_final: 0.4490 (t) REVERT: A 433 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.7225 (m-80) REVERT: A 435 ASP cc_start: 0.7863 (t0) cc_final: 0.7644 (t0) REVERT: A 542 ILE cc_start: 0.4782 (OUTLIER) cc_final: 0.4426 (mp) REVERT: F 66 MET cc_start: 0.7188 (mmm) cc_final: 0.6831 (mtt) REVERT: E 524 SER cc_start: 0.8511 (m) cc_final: 0.8268 (t) REVERT: D 67 MET cc_start: 0.1447 (mpp) cc_final: -0.1176 (mmt) REVERT: D 218 VAL cc_start: 0.4837 (OUTLIER) cc_final: 0.4455 (t) REVERT: D 402 ILE cc_start: 0.6962 (tt) cc_final: 0.6604 (pt) REVERT: D 433 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.7272 (m-80) REVERT: D 435 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7623 (t0) REVERT: D 460 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.8003 (tt) REVERT: D 542 ILE cc_start: 0.4798 (OUTLIER) cc_final: 0.4262 (mp) outliers start: 85 outliers final: 38 residues processed: 298 average time/residue: 0.1325 time to fit residues: 61.6786 Evaluate side-chains 245 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 480 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 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: 0.0970 chunk 178 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 233 optimal weight: 9.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN ** 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 ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN E 387 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 = 0.4983 r_free = 0.4983 target = 0.220832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.187986 restraints weight = 27748.214| |-----------------------------------------------------------------------------| r_work (start): 0.4646 rms_B_bonded: 3.38 r_work: 0.4176 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4192 r_free = 0.4192 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4192 r_free = 0.4192 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 19400 Z= 0.352 Angle : 0.834 10.546 26576 Z= 0.428 Chirality : 0.049 0.236 3218 Planarity : 0.006 0.061 3474 Dihedral : 6.542 59.540 2855 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.17 % Favored : 94.79 % Rotamer: Outliers : 7.80 % Allowed : 24.68 % Favored : 67.51 % 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: -0.63 (0.16), residues: 2670 helix: 0.23 (0.12), residues: 1808 sheet: -2.70 (0.47), residues: 116 loop : -1.39 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 412 TYR 0.060 0.003 TYR E 661 PHE 0.028 0.003 PHE C 220 TRP 0.027 0.002 TRP E 265 HIS 0.011 0.003 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00806 (19400) covalent geometry : angle 0.83363 (26576) hydrogen bonds : bond 0.05067 ( 1249) hydrogen bonds : angle 5.18973 ( 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 340 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 205 time to evaluate : 0.699 Fit side-chains REVERT: C 66 MET cc_start: 0.7534 (mmm) cc_final: 0.7166 (mtt) REVERT: C 86 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.8208 (m-80) REVERT: B 298 MET cc_start: 0.5916 (mmm) cc_final: 0.5358 (mmm) REVERT: B 524 SER cc_start: 0.8345 (m) cc_final: 0.8085 (t) REVERT: B 564 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.5930 (tt) REVERT: A 67 MET cc_start: 0.1813 (mpp) cc_final: -0.0769 (mmt) REVERT: A 218 VAL cc_start: 0.4829 (OUTLIER) cc_final: 0.4487 (t) REVERT: A 405 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7244 (tp) REVERT: A 490 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6333 (mt) REVERT: A 559 VAL cc_start: 0.6819 (m) cc_final: 0.6540 (p) REVERT: F 66 MET cc_start: 0.7682 (mmm) cc_final: 0.7252 (mtt) REVERT: F 86 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.8299 (m-80) REVERT: E 298 MET cc_start: 0.5882 (mmm) cc_final: 0.5283 (mmm) REVERT: E 379 LEU cc_start: 0.5054 (OUTLIER) cc_final: 0.4280 (mt) REVERT: E 524 SER cc_start: 0.8448 (m) cc_final: 0.8170 (t) REVERT: E 564 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.5925 (tt) REVERT: D 67 MET cc_start: 0.1732 (mpp) cc_final: -0.0801 (mmt) REVERT: D 218 VAL cc_start: 0.4789 (OUTLIER) cc_final: 0.4426 (t) REVERT: D 405 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7294 (tp) REVERT: D 433 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.7439 (m-80) REVERT: D 490 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6299 (mt) outliers start: 135 outliers final: 83 residues processed: 317 average time/residue: 0.1284 time to fit residues: 64.3952 Evaluate side-chains 277 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 182 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 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 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 506 MET 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 F residue 50 CYS Chi-restraints excluded: chain F residue 86 TYR 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 368 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 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: 3.9990 chunk 173 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 33 optimal weight: 40.0000 chunk 189 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 145 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** E 261 GLN E 387 ASN E 605 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.227360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.194770 restraints weight = 27808.645| |-----------------------------------------------------------------------------| r_work (start): 0.4704 rms_B_bonded: 3.79 r_work: 0.4261 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4261 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.4280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19400 Z= 0.153 Angle : 0.643 8.977 26576 Z= 0.326 Chirality : 0.042 0.149 3218 Planarity : 0.005 0.052 3474 Dihedral : 5.975 56.996 2853 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.12 % Favored : 95.84 % Rotamer: Outliers : 6.88 % Allowed : 26.47 % Favored : 66.65 % 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: -0.20 (0.16), residues: 2670 helix: 0.54 (0.12), residues: 1818 sheet: -2.20 (0.51), residues: 112 loop : -1.26 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 239 TYR 0.037 0.002 TYR E 661 PHE 0.027 0.002 PHE A 532 TRP 0.029 0.002 TRP D 444 HIS 0.006 0.001 HIS F 167 Details of bonding type rmsd covalent geometry : bond 0.00335 (19400) covalent geometry : angle 0.64299 (26576) hydrogen bonds : bond 0.03883 ( 1249) hydrogen bonds : angle 4.76427 ( 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 347 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 228 time to evaluate : 0.710 Fit side-chains REVERT: C 12 GLN cc_start: 0.8497 (tp40) cc_final: 0.8028 (tp40) REVERT: C 86 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.8139 (m-80) REVERT: C 103 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7248 (mt) REVERT: B 298 MET cc_start: 0.6074 (mmm) cc_final: 0.5647 (mmm) REVERT: B 424 MET cc_start: 0.6245 (ttm) cc_final: 0.5844 (ttm) REVERT: A 67 MET cc_start: 0.1595 (mpp) cc_final: -0.0516 (mmt) REVERT: A 218 VAL cc_start: 0.5198 (OUTLIER) cc_final: 0.4835 (t) REVERT: A 559 VAL cc_start: 0.6645 (m) cc_final: 0.6388 (p) REVERT: F 66 MET cc_start: 0.7505 (mmm) cc_final: 0.6989 (mtt) REVERT: F 86 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.8238 (m-80) REVERT: F 103 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7396 (mt) REVERT: E 298 MET cc_start: 0.5920 (mmm) cc_final: 0.5434 (mmm) REVERT: E 612 LYS cc_start: 0.7046 (ptpp) cc_final: 0.6779 (ptpp) REVERT: D 67 MET cc_start: 0.1713 (mpp) cc_final: -0.0406 (mmt) REVERT: D 218 VAL cc_start: 0.4972 (OUTLIER) cc_final: 0.4606 (t) REVERT: D 402 ILE cc_start: 0.6884 (tt) cc_final: 0.6543 (pt) REVERT: D 433 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: D 460 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8151 (tt) REVERT: D 559 VAL cc_start: 0.6577 (m) cc_final: 0.6317 (p) outliers start: 119 outliers final: 75 residues processed: 321 average time/residue: 0.1283 time to fit residues: 65.0203 Evaluate side-chains 298 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 215 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR 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 368 THR 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 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 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 506 MET Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain F residue 45 VAL 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 103 LEU 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 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 546 LEU 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 636 LYS 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 367 LEU 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 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: 0.9980 chunk 252 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 166 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 HIS B 261 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.5040 r_free = 0.5040 target = 0.227380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.196545 restraints weight = 27738.267| |-----------------------------------------------------------------------------| r_work (start): 0.4739 rms_B_bonded: 3.26 r_work: 0.4270 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4274 r_free = 0.4274 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4274 r_free = 0.4274 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19400 Z= 0.155 Angle : 0.629 8.902 26576 Z= 0.319 Chirality : 0.042 0.148 3218 Planarity : 0.005 0.049 3474 Dihedral : 5.708 58.053 2850 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.46 % Favored : 95.51 % Rotamer: Outliers : 7.28 % Allowed : 27.69 % Favored : 65.03 % 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: -0.02 (0.17), residues: 2670 helix: 0.65 (0.13), residues: 1832 sheet: -2.20 (0.52), residues: 112 loop : -1.16 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 239 TYR 0.062 0.002 TYR E 661 PHE 0.028 0.002 PHE F 220 TRP 0.025 0.001 TRP D 444 HIS 0.011 0.001 HIS F 167 Details of bonding type rmsd covalent geometry : bond 0.00346 (19400) covalent geometry : angle 0.62876 (26576) hydrogen bonds : bond 0.03726 ( 1249) hydrogen bonds : angle 4.63270 ( 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 356 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 230 time to evaluate : 0.807 Fit side-chains REVERT: C 12 GLN cc_start: 0.8523 (tp40) cc_final: 0.8028 (tp40) REVERT: C 86 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.8055 (m-80) REVERT: B 298 MET cc_start: 0.6212 (mmm) cc_final: 0.5727 (mmm) REVERT: B 414 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: A 218 VAL cc_start: 0.5007 (OUTLIER) cc_final: 0.4688 (t) REVERT: A 559 VAL cc_start: 0.6348 (m) cc_final: 0.6091 (p) REVERT: F 12 GLN cc_start: 0.8457 (tp40) cc_final: 0.8205 (tp40) REVERT: E 298 MET cc_start: 0.6155 (mmm) cc_final: 0.5609 (mmt) REVERT: E 378 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.6550 (t0) REVERT: E 379 LEU cc_start: 0.4563 (OUTLIER) cc_final: 0.3705 (mt) REVERT: E 389 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7055 (mt) REVERT: E 424 MET cc_start: 0.7008 (ttt) cc_final: 0.6755 (ttt) REVERT: D 218 VAL cc_start: 0.4958 (OUTLIER) cc_final: 0.4617 (t) REVERT: D 402 ILE cc_start: 0.7013 (tt) cc_final: 0.6711 (pt) REVERT: D 433 PHE cc_start: 0.7659 (m-80) cc_final: 0.7393 (m-80) REVERT: D 460 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8171 (tt) REVERT: D 559 VAL cc_start: 0.6395 (m) cc_final: 0.6126 (p) outliers start: 126 outliers final: 84 residues processed: 327 average time/residue: 0.1314 time to fit residues: 68.1635 Evaluate side-chains 304 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 212 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR 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 C residue 257 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 389 LEU Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 468 VAL 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 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 527 VAL Chi-restraints excluded: chain A residue 545 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 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 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 414 GLN 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 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 636 LYS 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 367 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 449 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 480 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 131 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 260 optimal weight: 0.8980 chunk 180 optimal weight: 9.9990 chunk 229 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 252 optimal weight: 0.3980 chunk 174 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN A 427 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5070 r_free = 0.5070 target = 0.236368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.205780 restraints weight = 29074.059| |-----------------------------------------------------------------------------| r_work (start): 0.4762 rms_B_bonded: 3.54 r_work: 0.4271 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4271 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.4280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19400 Z= 0.140 Angle : 0.626 9.168 26576 Z= 0.316 Chirality : 0.041 0.147 3218 Planarity : 0.005 0.051 3474 Dihedral : 5.605 58.887 2850 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.66 % Rotamer: Outliers : 7.05 % Allowed : 27.69 % Favored : 65.26 % 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: 0.13 (0.17), residues: 2670 helix: 0.73 (0.13), residues: 1838 sheet: -1.58 (0.61), residues: 92 loop : -1.17 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 239 TYR 0.054 0.002 TYR B 661 PHE 0.026 0.002 PHE C 220 TRP 0.025 0.001 TRP D 444 HIS 0.005 0.001 HIS F 167 Details of bonding type rmsd covalent geometry : bond 0.00308 (19400) covalent geometry : angle 0.62646 (26576) hydrogen bonds : bond 0.03612 ( 1249) hydrogen bonds : angle 4.54539 ( 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 353 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 231 time to evaluate : 0.759 Fit side-chains REVERT: C 12 GLN cc_start: 0.8498 (tp40) cc_final: 0.7979 (tp40) REVERT: C 86 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.8047 (m-80) REVERT: C 103 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7199 (mt) REVERT: B 298 MET cc_start: 0.6209 (mmm) cc_final: 0.5813 (mmm) REVERT: B 378 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7309 (t0) REVERT: B 411 PHE cc_start: 0.5823 (OUTLIER) cc_final: 0.5444 (t80) REVERT: B 414 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7184 (tm-30) REVERT: A 124 ASP cc_start: 0.4938 (OUTLIER) cc_final: 0.4150 (p0) REVERT: A 218 VAL cc_start: 0.5071 (OUTLIER) cc_final: 0.4756 (t) REVERT: A 559 VAL cc_start: 0.6397 (m) cc_final: 0.6185 (p) REVERT: F 103 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7289 (mt) REVERT: E 298 MET cc_start: 0.6260 (mmm) cc_final: 0.5771 (mmt) REVERT: E 378 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6366 (t0) REVERT: E 379 LEU cc_start: 0.4541 (OUTLIER) cc_final: 0.3747 (mt) REVERT: E 389 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6848 (mt) REVERT: D 124 ASP cc_start: 0.4776 (OUTLIER) cc_final: 0.4006 (p0) REVERT: D 218 VAL cc_start: 0.4987 (OUTLIER) cc_final: 0.4640 (t) REVERT: D 402 ILE cc_start: 0.6853 (tt) cc_final: 0.6584 (pt) REVERT: D 433 PHE cc_start: 0.7722 (m-80) cc_final: 0.7518 (m-80) REVERT: D 460 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8112 (tt) REVERT: D 559 VAL cc_start: 0.6299 (m) cc_final: 0.6063 (p) outliers start: 122 outliers final: 85 residues processed: 321 average time/residue: 0.1308 time to fit residues: 66.9538 Evaluate side-chains 312 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 213 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR 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 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 378 ASP 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 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 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 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 505 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 58 VAL Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 103 LEU 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 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 380 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 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 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 636 LYS 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 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: 0.6980 chunk 219 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 176 optimal weight: 20.0000 chunk 201 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN E 261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.234607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.200455 restraints weight = 29211.575| |-----------------------------------------------------------------------------| r_work (start): 0.4704 rms_B_bonded: 3.97 r_work: 0.4247 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4263 r_free = 0.4263 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4263 r_free = 0.4263 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19400 Z= 0.163 Angle : 0.648 8.838 26576 Z= 0.327 Chirality : 0.042 0.149 3218 Planarity : 0.005 0.054 3474 Dihedral : 5.689 59.626 2850 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.21 % Rotamer: Outliers : 7.05 % Allowed : 28.27 % Favored : 64.68 % 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: 0.15 (0.17), residues: 2670 helix: 0.75 (0.13), residues: 1836 sheet: -1.80 (0.60), residues: 92 loop : -1.12 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 268 TYR 0.050 0.002 TYR E 661 PHE 0.026 0.002 PHE C 220 TRP 0.024 0.001 TRP D 444 HIS 0.005 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00367 (19400) covalent geometry : angle 0.64809 (26576) hydrogen bonds : bond 0.03713 ( 1249) hydrogen bonds : angle 4.54037 ( 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 345 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 223 time to evaluate : 0.742 Fit side-chains REVERT: C 12 GLN cc_start: 0.8498 (tp40) cc_final: 0.7943 (tp40) REVERT: C 86 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.8153 (m-80) REVERT: C 103 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7213 (mt) REVERT: B 298 MET cc_start: 0.6319 (mmm) cc_final: 0.5941 (mmm) REVERT: B 411 PHE cc_start: 0.5837 (OUTLIER) cc_final: 0.5465 (t80) REVERT: B 414 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: A 124 ASP cc_start: 0.5032 (OUTLIER) cc_final: 0.4257 (p0) REVERT: A 218 VAL cc_start: 0.5020 (OUTLIER) cc_final: 0.4673 (t) REVERT: A 559 VAL cc_start: 0.6321 (m) cc_final: 0.6069 (p) REVERT: F 103 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7128 (mp) REVERT: E 298 MET cc_start: 0.6276 (mmm) cc_final: 0.5801 (mmt) REVERT: E 378 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6185 (t0) REVERT: E 379 LEU cc_start: 0.4477 (OUTLIER) cc_final: 0.3784 (mt) REVERT: E 389 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6831 (mt) REVERT: E 411 PHE cc_start: 0.5800 (OUTLIER) cc_final: 0.5426 (t80) REVERT: E 612 LYS cc_start: 0.7062 (ptpp) cc_final: 0.6800 (ptpp) REVERT: D 124 ASP cc_start: 0.4886 (OUTLIER) cc_final: 0.4128 (p0) REVERT: D 218 VAL cc_start: 0.4940 (OUTLIER) cc_final: 0.4579 (t) REVERT: D 402 ILE cc_start: 0.6841 (tt) cc_final: 0.6582 (pt) REVERT: D 460 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8076 (tt) REVERT: D 559 VAL cc_start: 0.6269 (m) cc_final: 0.6026 (p) outliers start: 122 outliers final: 84 residues processed: 312 average time/residue: 0.1289 time to fit residues: 63.8555 Evaluate side-chains 311 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 213 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR 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 156 THR 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 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 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 498 THR 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 603 VAL 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 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 71 ILE Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 103 LEU 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 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 411 PHE 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 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 546 LEU 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 378 ILE 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 527 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: 9.9990 chunk 217 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 chunk 169 optimal weight: 30.0000 chunk 111 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN A 450 HIS ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN D 450 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5059 r_free = 0.5059 target = 0.234957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.202081 restraints weight = 29266.281| |-----------------------------------------------------------------------------| r_work (start): 0.4729 rms_B_bonded: 3.73 r_work: 0.4268 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4277 r_free = 0.4277 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4277 r_free = 0.4277 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19400 Z= 0.160 Angle : 0.648 8.951 26576 Z= 0.326 Chirality : 0.042 0.154 3218 Planarity : 0.005 0.060 3474 Dihedral : 5.679 59.112 2850 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.79 % Favored : 95.17 % Rotamer: Outliers : 6.47 % Allowed : 28.61 % Favored : 64.91 % 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: 0.12 (0.17), residues: 2670 helix: 0.75 (0.12), residues: 1844 sheet: -1.91 (0.59), residues: 92 loop : -1.22 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 268 TYR 0.056 0.002 TYR B 661 PHE 0.025 0.002 PHE C 220 TRP 0.028 0.002 TRP D 444 HIS 0.005 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00360 (19400) covalent geometry : angle 0.64812 (26576) hydrogen bonds : bond 0.03689 ( 1249) hydrogen bonds : angle 4.51566 ( 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 337 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 225 time to evaluate : 0.725 Fit side-chains REVERT: C 12 GLN cc_start: 0.8459 (tp40) cc_final: 0.7919 (tp40) REVERT: C 86 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.8129 (m-80) REVERT: C 103 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7287 (mt) REVERT: B 298 MET cc_start: 0.6363 (mmm) cc_final: 0.5975 (mmm) REVERT: B 411 PHE cc_start: 0.5882 (OUTLIER) cc_final: 0.5460 (t80) REVERT: B 414 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7193 (tm-30) REVERT: A 124 ASP cc_start: 0.4948 (OUTLIER) cc_final: 0.4219 (p0) REVERT: A 218 VAL cc_start: 0.4984 (OUTLIER) cc_final: 0.4630 (t) REVERT: A 559 VAL cc_start: 0.6255 (m) cc_final: 0.6018 (p) REVERT: F 103 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7187 (mp) REVERT: E 298 MET cc_start: 0.6430 (mmm) cc_final: 0.5952 (mmt) REVERT: E 303 TYR cc_start: 0.8736 (m-80) cc_final: 0.8461 (m-80) REVERT: E 378 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6079 (t0) REVERT: E 379 LEU cc_start: 0.4535 (OUTLIER) cc_final: 0.3897 (mt) REVERT: E 389 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6958 (mt) REVERT: E 411 PHE cc_start: 0.5832 (OUTLIER) cc_final: 0.5428 (t80) REVERT: D 124 ASP cc_start: 0.4778 (OUTLIER) cc_final: 0.4076 (p0) REVERT: D 218 VAL cc_start: 0.4918 (OUTLIER) cc_final: 0.4545 (t) REVERT: D 402 ILE cc_start: 0.6803 (tt) cc_final: 0.6561 (pt) REVERT: D 460 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8133 (tt) REVERT: D 559 VAL cc_start: 0.6259 (m) cc_final: 0.6017 (p) outliers start: 112 outliers final: 87 residues processed: 305 average time/residue: 0.1334 time to fit residues: 64.3779 Evaluate side-chains 310 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 209 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR 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 156 THR 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 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 380 LEU 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 498 THR 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 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 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 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 71 ILE Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 103 LEU 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 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 380 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 415 TYR Chi-restraints excluded: chain E residue 431 VAL 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 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 603 VAL 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 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 367 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 449 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 480 VAL 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: 0.7980 chunk 222 optimal weight: 7.9990 chunk 240 optimal weight: 0.8980 chunk 192 optimal weight: 0.0170 chunk 27 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.220974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.190524 restraints weight = 28919.459| |-----------------------------------------------------------------------------| r_work (start): 0.4625 rms_B_bonded: 3.70 r_work: 0.4085 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4098 r_free = 0.4098 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4098 r_free = 0.4098 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19400 Z= 0.177 Angle : 0.669 10.490 26576 Z= 0.336 Chirality : 0.043 0.153 3218 Planarity : 0.005 0.065 3474 Dihedral : 5.757 58.582 2850 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.09 % Favored : 94.87 % Rotamer: Outliers : 6.65 % Allowed : 27.86 % Favored : 65.49 % 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: 0.05 (0.17), residues: 2670 helix: 0.73 (0.12), residues: 1830 sheet: -2.30 (0.56), residues: 94 loop : -1.24 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 268 TYR 0.042 0.002 TYR E 661 PHE 0.025 0.002 PHE A 532 TRP 0.024 0.002 TRP B 265 HIS 0.006 0.001 HIS F 167 Details of bonding type rmsd covalent geometry : bond 0.00401 (19400) covalent geometry : angle 0.66857 (26576) hydrogen bonds : bond 0.03795 ( 1249) hydrogen bonds : angle 4.53567 ( 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 334 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 219 time to evaluate : 0.709 Fit side-chains REVERT: C 12 GLN cc_start: 0.8464 (tp40) cc_final: 0.8195 (tp40) REVERT: C 86 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.8165 (m-80) REVERT: C 103 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7387 (mt) REVERT: B 411 PHE cc_start: 0.5953 (OUTLIER) cc_final: 0.5462 (t80) REVERT: B 414 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7206 (tm-30) REVERT: A 67 MET cc_start: 0.1710 (mpp) cc_final: -0.1129 (tpp) REVERT: A 124 ASP cc_start: 0.4800 (OUTLIER) cc_final: 0.4143 (p0) REVERT: A 218 VAL cc_start: 0.5052 (OUTLIER) cc_final: 0.4723 (t) REVERT: A 496 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7474 (mp) REVERT: A 559 VAL cc_start: 0.6225 (m) cc_final: 0.5976 (p) REVERT: F 103 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7262 (mp) REVERT: E 298 MET cc_start: 0.6552 (mmm) cc_final: 0.6186 (mmm) REVERT: E 365 GLU cc_start: 0.8844 (mp0) cc_final: 0.8498 (mp0) REVERT: E 378 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6304 (t0) REVERT: E 389 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7064 (mt) REVERT: E 411 PHE cc_start: 0.5885 (OUTLIER) cc_final: 0.5394 (t80) REVERT: D 67 MET cc_start: 0.1668 (mpp) cc_final: -0.1161 (tpp) REVERT: D 124 ASP cc_start: 0.4811 (OUTLIER) cc_final: 0.4131 (p0) REVERT: D 125 HIS cc_start: 0.4658 (t-90) cc_final: 0.3768 (p90) REVERT: D 218 VAL cc_start: 0.5036 (OUTLIER) cc_final: 0.4683 (t) REVERT: D 402 ILE cc_start: 0.6876 (tt) cc_final: 0.6630 (pt) REVERT: D 460 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8086 (tt) REVERT: D 559 VAL cc_start: 0.6210 (m) cc_final: 0.5963 (p) outliers start: 115 outliers final: 83 residues processed: 306 average time/residue: 0.1307 time to fit residues: 63.7295 Evaluate side-chains 312 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 215 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR 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 103 LEU Chi-restraints excluded: chain C residue 156 THR 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 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 380 LEU 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 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 603 VAL 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 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 505 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 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 71 ILE Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 103 LEU 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 378 ASP 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 411 PHE 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 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 546 LEU Chi-restraints excluded: chain E residue 548 ASP Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 619 VAL Chi-restraints excluded: chain E residue 627 LEU Chi-restraints excluded: chain E residue 633 LEU Chi-restraints excluded: chain E residue 653 VAL 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 527 VAL Chi-restraints excluded: chain D residue 545 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: 0.9980 chunk 85 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 199 optimal weight: 0.0980 chunk 59 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 128 optimal weight: 0.1980 chunk 38 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.223488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.190581 restraints weight = 29181.459| |-----------------------------------------------------------------------------| r_work (start): 0.4617 rms_B_bonded: 3.71 r_work: 0.4136 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4166 r_free = 0.4166 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4166 r_free = 0.4166 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3858 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= 0.143 Angle : 0.650 15.476 26576 Z= 0.323 Chirality : 0.042 0.317 3218 Planarity : 0.005 0.067 3474 Dihedral : 5.602 58.146 2850 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.42 % Favored : 95.54 % Rotamer: Outliers : 5.61 % Allowed : 28.61 % 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: 0.16 (0.17), residues: 2670 helix: 0.79 (0.12), residues: 1850 sheet: -1.99 (0.58), residues: 90 loop : -1.24 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 268 TYR 0.045 0.002 TYR E 661 PHE 0.039 0.002 PHE C 220 TRP 0.027 0.001 TRP A 444 HIS 0.006 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00318 (19400) covalent geometry : angle 0.64996 (26576) hydrogen bonds : bond 0.03551 ( 1249) hydrogen bonds : angle 4.44384 ( 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 325 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 228 time to evaluate : 0.661 Fit side-chains REVERT: C 11 ASP cc_start: 0.7737 (m-30) cc_final: 0.7452 (m-30) REVERT: C 12 GLN cc_start: 0.8400 (tp40) cc_final: 0.8147 (tp40) REVERT: C 86 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.8159 (m-80) REVERT: C 103 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7257 (mt) REVERT: C 228 PHE cc_start: 0.6484 (t80) cc_final: 0.6130 (t80) REVERT: B 298 MET cc_start: 0.6389 (mmm) cc_final: 0.6178 (mmt) REVERT: B 301 ILE cc_start: 0.7992 (tt) cc_final: 0.7781 (pt) REVERT: B 389 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6631 (mt) REVERT: B 414 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: A 124 ASP cc_start: 0.4866 (OUTLIER) cc_final: 0.4221 (p0) REVERT: A 218 VAL cc_start: 0.5091 (OUTLIER) cc_final: 0.4744 (t) REVERT: A 402 ILE cc_start: 0.6829 (tt) cc_final: 0.6593 (pt) REVERT: A 559 VAL cc_start: 0.6314 (m) cc_final: 0.6071 (p) REVERT: F 11 ASP cc_start: 0.7762 (m-30) cc_final: 0.7467 (m-30) REVERT: F 103 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7142 (mp) REVERT: E 298 MET cc_start: 0.6532 (mmm) cc_final: 0.6098 (mmt) REVERT: E 303 TYR cc_start: 0.8746 (m-80) cc_final: 0.8452 (m-80) REVERT: E 365 GLU cc_start: 0.8897 (mp0) cc_final: 0.8540 (mp0) REVERT: E 378 ASP cc_start: 0.6679 (OUTLIER) cc_final: 0.5752 (t0) REVERT: E 389 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6950 (mt) REVERT: D 67 MET cc_start: 0.1429 (mpp) cc_final: -0.1245 (tpp) REVERT: D 124 ASP cc_start: 0.4893 (OUTLIER) cc_final: 0.4281 (p0) REVERT: D 125 HIS cc_start: 0.4606 (t-90) cc_final: 0.3741 (p90) REVERT: D 218 VAL cc_start: 0.5023 (OUTLIER) cc_final: 0.4666 (t) REVERT: D 465 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8357 (tm-30) REVERT: D 559 VAL cc_start: 0.6314 (m) cc_final: 0.6075 (p) outliers start: 97 outliers final: 78 residues processed: 299 average time/residue: 0.1307 time to fit residues: 62.0351 Evaluate side-chains 307 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 218 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 50 CYS 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 156 THR 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 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 380 LEU Chi-restraints excluded: chain B residue 386 THR 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 498 THR 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 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 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 459 ASN Chi-restraints excluded: chain A residue 480 VAL 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 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 92 TYR Chi-restraints excluded: chain F residue 103 LEU 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 378 ASP 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 431 VAL 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 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 633 LEU Chi-restraints excluded: chain E residue 653 VAL 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 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: 6.9990 chunk 105 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 217 optimal weight: 0.0570 overall best weight: 2.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.221083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.189767 restraints weight = 27637.070| |-----------------------------------------------------------------------------| r_work (start): 0.4684 rms_B_bonded: 3.31 r_work: 0.4163 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4181 r_free = 0.4181 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 = 0.4182 r_free = 0.4182 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 19400 Z= 0.289 Angle : 0.773 16.036 26576 Z= 0.390 Chirality : 0.047 0.355 3218 Planarity : 0.006 0.071 3474 Dihedral : 5.909 58.391 2848 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.43 % Favored : 94.53 % Rotamer: Outliers : 5.66 % Allowed : 28.61 % Favored : 65.72 % 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: -0.32 (0.17), residues: 2670 helix: 0.48 (0.12), residues: 1838 sheet: -2.96 (0.51), residues: 96 loop : -1.39 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 268 TYR 0.049 0.003 TYR E 661 PHE 0.039 0.003 PHE C 220 TRP 0.024 0.002 TRP B 265 HIS 0.009 0.002 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00669 (19400) covalent geometry : angle 0.77311 (26576) hydrogen bonds : bond 0.04382 ( 1249) hydrogen bonds : angle 4.77842 ( 3675) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5340.06 seconds wall clock time: 91 minutes 55.55 seconds (5515.55 seconds total)