Starting phenix.real_space_refine on Sun Jan 26 01:25:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8je1_36182/01_2025/8je1_36182.cif Found real_map, /net/cci-nas-00/data/ceres_data/8je1_36182/01_2025/8je1_36182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8je1_36182/01_2025/8je1_36182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8je1_36182/01_2025/8je1_36182.map" model { file = "/net/cci-nas-00/data/ceres_data/8je1_36182/01_2025/8je1_36182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8je1_36182/01_2025/8je1_36182.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8206 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 126 5.16 5 C 11119 2.51 5 N 3007 2.21 5 O 3254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 17507 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5570 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 16, 'TRANS': 658} Chain breaks: 12 Chain: "B" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 678 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 79} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 727 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain breaks: 1 Chain: "D" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3934 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 489} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "F" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3703 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 433} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 328 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 693 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 705 Chain: "I" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1767 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "R" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 106 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17171 SG CYS I 599 51.740 54.221 37.716 1.00146.96 S Time building chain proxies: 10.41, per 1000 atoms: 0.59 Number of scatterers: 17507 At special positions: 0 Unit cell: (110.94, 186.62, 204.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 126 16.00 O 3254 8.00 N 3007 7.00 C 11119 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: 4.11 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 701 " pdb="ZN ZN I 701 " - pdb=" NE2 HIS I 627 " pdb="ZN ZN I 701 " - pdb=" SG CYS I 599 " 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4184 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 65.2% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 9 through 23 removed outlier: 3.672A pdb=" N THR A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N THR A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 47 removed outlier: 3.710A pdb=" N ALA A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS A 46 " --> pdb=" O ILE A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 78 removed outlier: 3.597A pdb=" N HIS A 68 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 72 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 103 removed outlier: 3.648A pdb=" N MET A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR A 90 " --> pdb=" O MET A 86 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR A 100 " --> pdb=" O LYS A 96 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.536A pdb=" N MET A 151 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 152' Processing helix chain 'A' and resid 153 through 156 removed outlier: 3.628A pdb=" N GLN A 156 " --> pdb=" O GLU A 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 157 through 174 removed outlier: 4.144A pdb=" N LYS A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 191 removed outlier: 3.568A pdb=" N ILE A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 removed outlier: 3.525A pdb=" N GLN A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 228 removed outlier: 4.326A pdb=" N GLU A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU A 217 " --> pdb=" O THR A 213 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TYR A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 246 removed outlier: 3.842A pdb=" N LEU A 240 " --> pdb=" O MET A 236 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 272 removed outlier: 4.293A pdb=" N VAL A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET A 270 " --> pdb=" O CYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 280 Processing helix chain 'A' and resid 290 through 304 removed outlier: 4.250A pdb=" N MET A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 322 removed outlier: 3.627A pdb=" N ILE A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS A 320 " --> pdb=" O GLN A 316 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP A 321 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU A 322 " --> pdb=" O HIS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 3.858A pdb=" N LEU A 338 " --> pdb=" O ASN A 334 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 344 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU A 345 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 373 Processing helix chain 'A' and resid 387 through 400 removed outlier: 3.946A pdb=" N ALA A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 398 " --> pdb=" O TYR A 394 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 399 " --> pdb=" O CYS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 423 removed outlier: 3.838A pdb=" N SER A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 444 removed outlier: 3.868A pdb=" N TYR A 435 " --> pdb=" O PHE A 431 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA A 436 " --> pdb=" O GLN A 432 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N MET A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 470 removed outlier: 3.651A pdb=" N GLN A 463 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N TYR A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N GLU A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE A 469 " --> pdb=" O CYS A 465 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 492 removed outlier: 3.944A pdb=" N MET A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 478 " --> pdb=" O HIS A 474 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET A 480 " --> pdb=" O MET A 476 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER A 481 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN A 492 " --> pdb=" O ASN A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.838A pdb=" N TYR A 544 " --> pdb=" O PHE A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 589 removed outlier: 4.122A pdb=" N ALA A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'A' and resid 606 through 620 removed outlier: 3.677A pdb=" N LEU A 610 " --> pdb=" O ASN A 606 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 691 removed outlier: 4.150A pdb=" N SER A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP A 673 " --> pdb=" O ARG A 669 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 707 Processing helix chain 'A' and resid 714 through 720 removed outlier: 3.548A pdb=" N ILE A 718 " --> pdb=" O SER A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 728 removed outlier: 4.062A pdb=" N LEU A 725 " --> pdb=" O CYS A 721 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 728 " --> pdb=" O VAL A 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 36 removed outlier: 3.612A pdb=" N LEU B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.736A pdb=" N ASP B 48 " --> pdb=" O TYR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.501A pdb=" N GLY B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'C' and resid 34 through 37 removed outlier: 3.875A pdb=" N LEU C 37 " --> pdb=" O GLU C 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 34 through 37' Processing helix chain 'C' and resid 39 through 45 Processing helix chain 'C' and resid 66 through 83 removed outlier: 3.745A pdb=" N LEU C 70 " --> pdb=" O PRO C 66 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 72 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE C 77 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR C 78 " --> pdb=" O CYS C 74 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 79 " --> pdb=" O MET C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 111 removed outlier: 3.646A pdb=" N LEU C 103 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE C 109 " --> pdb=" O MET C 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 132 removed outlier: 3.767A pdb=" N ASP D 131 " --> pdb=" O ALA D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 140 removed outlier: 4.189A pdb=" N VAL D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 164 removed outlier: 3.539A pdb=" N ALA D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 176 Processing helix chain 'D' and resid 193 through 198 removed outlier: 3.719A pdb=" N ALA D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.570A pdb=" N TRP D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 229 removed outlier: 4.415A pdb=" N ALA D 226 " --> pdb=" O PRO D 222 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA D 227 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU D 228 " --> pdb=" O LYS D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 242 removed outlier: 4.106A pdb=" N GLU D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 252 removed outlier: 3.930A pdb=" N ARG D 249 " --> pdb=" O ASP D 245 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D 251 " --> pdb=" O ARG D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 262 removed outlier: 4.050A pdb=" N GLY D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 282 removed outlier: 3.892A pdb=" N THR D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR D 273 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 276 " --> pdb=" O THR D 272 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU D 278 " --> pdb=" O HIS D 274 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA D 279 " --> pdb=" O TYR D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 317 removed outlier: 3.755A pdb=" N ILE D 317 " --> pdb=" O GLU D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 337 removed outlier: 3.660A pdb=" N HIS D 325 " --> pdb=" O ARG D 321 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU D 329 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE D 330 " --> pdb=" O MET D 326 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG D 334 " --> pdb=" O ILE D 330 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE D 335 " --> pdb=" O VAL D 331 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY D 337 " --> pdb=" O GLU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 359 removed outlier: 4.826A pdb=" N ASN D 357 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU D 359 " --> pdb=" O ALA D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 375 removed outlier: 3.799A pdb=" N HIS D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 371 " --> pdb=" O TRP D 367 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU D 373 " --> pdb=" O HIS D 369 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN D 375 " --> pdb=" O LEU D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 398 removed outlier: 3.579A pdb=" N LEU D 386 " --> pdb=" O HIS D 382 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG D 387 " --> pdb=" O LYS D 383 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N PHE D 388 " --> pdb=" O ASP D 384 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN D 390 " --> pdb=" O LEU D 386 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL D 391 " --> pdb=" O ARG D 387 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE D 392 " --> pdb=" O PHE D 388 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE D 396 " --> pdb=" O PHE D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 429 removed outlier: 4.296A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN D 420 " --> pdb=" O LEU D 416 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N SER D 421 " --> pdb=" O GLU D 417 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N MET D 422 " --> pdb=" O ILE D 418 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN D 423 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG D 424 " --> pdb=" O GLN D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 457 removed outlier: 4.002A pdb=" N MET D 437 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 444 " --> pdb=" O TYR D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 476 removed outlier: 3.703A pdb=" N ASN D 473 " --> pdb=" O LYS D 469 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU D 474 " --> pdb=" O GLN D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 492 Processing helix chain 'D' and resid 511 through 522 Processing helix chain 'D' and resid 534 through 540 removed outlier: 3.649A pdb=" N ILE D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 561 Processing helix chain 'D' and resid 582 through 590 removed outlier: 4.148A pdb=" N LYS D 590 " --> pdb=" O GLU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 608 removed outlier: 3.511A pdb=" N ARG D 603 " --> pdb=" O CYS D 599 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL D 605 " --> pdb=" O ALA D 601 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG D 606 " --> pdb=" O ALA D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 627 removed outlier: 3.524A pdb=" N GLU D 621 " --> pdb=" O PRO D 617 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU D 622 " --> pdb=" O ARG D 618 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE D 623 " --> pdb=" O THR D 619 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY D 625 " --> pdb=" O GLU D 621 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE D 626 " --> pdb=" O GLU D 622 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS D 627 " --> pdb=" O PHE D 623 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 25 removed outlier: 3.905A pdb=" N ASN F 15 " --> pdb=" O ASP F 11 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS F 16 " --> pdb=" O GLU F 12 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR F 20 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA F 23 " --> pdb=" O THR F 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL F 25 " --> pdb=" O ILE F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 38 Processing helix chain 'F' and resid 38 through 47 removed outlier: 3.991A pdb=" N ILE F 42 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR F 43 " --> pdb=" O PHE F 39 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 60 Processing helix chain 'F' and resid 62 through 73 removed outlier: 4.217A pdb=" N VAL F 69 " --> pdb=" O LEU F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'F' and resid 82 through 105 removed outlier: 4.329A pdb=" N TYR F 87 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N HIS F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TRP F 91 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU F 92 " --> pdb=" O HIS F 88 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU F 93 " --> pdb=" O ARG F 89 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS F 96 " --> pdb=" O GLU F 92 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP F 99 " --> pdb=" O SER F 95 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TYR F 100 " --> pdb=" O LYS F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 112 Processing helix chain 'F' and resid 113 through 117 removed outlier: 3.548A pdb=" N ASN F 116 " --> pdb=" O ILE F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 151 Processing helix chain 'F' and resid 155 through 160 Processing helix chain 'F' and resid 162 through 168 removed outlier: 3.902A pdb=" N GLU F 166 " --> pdb=" O MET F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 192 removed outlier: 3.946A pdb=" N ILE F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL F 189 " --> pdb=" O ILE F 185 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL F 191 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU F 192 " --> pdb=" O PHE F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 207 Processing helix chain 'F' and resid 207 through 230 removed outlier: 3.535A pdb=" N THR F 215 " --> pdb=" O PHE F 211 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA F 223 " --> pdb=" O TYR F 219 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN F 225 " --> pdb=" O GLN F 221 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU F 226 " --> pdb=" O GLU F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 252 removed outlier: 3.956A pdb=" N GLU F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS F 252 " --> pdb=" O ILE F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 254 No H-bonds generated for 'chain 'F' and resid 253 through 254' Processing helix chain 'F' and resid 255 through 257 No H-bonds generated for 'chain 'F' and resid 255 through 257' Processing helix chain 'F' and resid 258 through 272 removed outlier: 4.293A pdb=" N VAL F 262 " --> pdb=" O SER F 258 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE F 263 " --> pdb=" O TYR F 259 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU F 265 " --> pdb=" O LYS F 261 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET F 270 " --> pdb=" O CYS F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 280 Processing helix chain 'F' and resid 290 through 304 removed outlier: 4.250A pdb=" N MET F 294 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL F 299 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU F 300 " --> pdb=" O ASN F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 322 removed outlier: 3.626A pdb=" N ILE F 312 " --> pdb=" O LEU F 308 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN F 313 " --> pdb=" O PRO F 309 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS F 320 " --> pdb=" O GLN F 316 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP F 321 " --> pdb=" O ASN F 317 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU F 322 " --> pdb=" O HIS F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 356 removed outlier: 3.858A pdb=" N LEU F 338 " --> pdb=" O ASN F 334 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU F 344 " --> pdb=" O VAL F 340 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU F 345 " --> pdb=" O GLU F 341 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL F 346 " --> pdb=" O SER F 342 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS F 347 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN F 352 " --> pdb=" O GLY F 348 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 373 Processing helix chain 'F' and resid 387 through 400 removed outlier: 3.946A pdb=" N ALA F 392 " --> pdb=" O PRO F 388 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU F 398 " --> pdb=" O TYR F 394 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU F 399 " --> pdb=" O CYS F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 423 removed outlier: 3.838A pdb=" N SER F 417 " --> pdb=" O ASP F 413 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE F 418 " --> pdb=" O ARG F 414 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE F 419 " --> pdb=" O LEU F 415 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR F 420 " --> pdb=" O THR F 416 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL F 421 " --> pdb=" O SER F 417 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 444 removed outlier: 3.868A pdb=" N TYR F 435 " --> pdb=" O PHE F 431 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA F 436 " --> pdb=" O GLN F 432 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG F 437 " --> pdb=" O LYS F 433 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N MET F 438 " --> pdb=" O PHE F 434 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS F 441 " --> pdb=" O ARG F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 470 removed outlier: 3.651A pdb=" N GLN F 463 " --> pdb=" O ASN F 459 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA F 464 " --> pdb=" O LYS F 460 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS F 465 " --> pdb=" O LEU F 461 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N TYR F 467 " --> pdb=" O GLN F 463 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N GLU F 468 " --> pdb=" O ALA F 464 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE F 469 " --> pdb=" O CYS F 465 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR F 470 " --> pdb=" O GLY F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 481 removed outlier: 3.944A pdb=" N MET F 476 " --> pdb=" O LYS F 472 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR F 477 " --> pdb=" O LEU F 473 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR F 478 " --> pdb=" O HIS F 474 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET F 480 " --> pdb=" O MET F 476 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER F 481 " --> pdb=" O TYR F 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 36 Processing helix chain 'H' and resid 33 through 38 removed outlier: 3.982A pdb=" N LEU H 37 " --> pdb=" O ARG H 33 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR H 38 " --> pdb=" O GLU H 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 33 through 38' Processing helix chain 'H' and resid 43 through 47 removed outlier: 3.644A pdb=" N LEU H 46 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER H 47 " --> pdb=" O ALA H 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 43 through 47' Processing helix chain 'H' and resid 66 through 83 removed outlier: 3.983A pdb=" N LEU H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER H 71 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS H 72 " --> pdb=" O HIS H 68 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL H 81 " --> pdb=" O PHE H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 108 removed outlier: 4.087A pdb=" N MET H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 383 through 399 Processing helix chain 'I' and resid 407 through 414 Processing helix chain 'I' and resid 417 through 429 Processing helix chain 'I' and resid 430 through 434 Processing helix chain 'I' and resid 436 through 455 removed outlier: 4.096A pdb=" N GLU I 441 " --> pdb=" O MET I 437 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE I 447 " --> pdb=" O ASN I 443 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL I 451 " --> pdb=" O PHE I 447 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS I 452 " --> pdb=" O LEU I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 461 through 472 Processing helix chain 'I' and resid 473 through 475 No H-bonds generated for 'chain 'I' and resid 473 through 475' Processing helix chain 'I' and resid 481 through 485 removed outlier: 3.594A pdb=" N PHE I 485 " --> pdb=" O ARG I 482 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 493 removed outlier: 3.650A pdb=" N ASN I 493 " --> pdb=" O HIS I 489 " (cutoff:3.500A) Processing helix chain 'I' and resid 512 through 522 removed outlier: 3.527A pdb=" N GLY I 522 " --> pdb=" O LEU I 518 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 533 removed outlier: 3.828A pdb=" N ASN I 533 " --> pdb=" O ASN I 530 " (cutoff:3.500A) Processing helix chain 'I' and resid 534 through 540 removed outlier: 3.509A pdb=" N ILE I 538 " --> pdb=" O SER I 534 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE I 539 " --> pdb=" O ALA I 535 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL I 540 " --> pdb=" O LEU I 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 534 through 540' Processing helix chain 'I' and resid 548 through 563 removed outlier: 4.416A pdb=" N LEU I 552 " --> pdb=" O ASP I 548 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS I 553 " --> pdb=" O PHE I 549 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER I 554 " --> pdb=" O LEU I 550 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU I 561 " --> pdb=" O ILE I 557 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA I 562 " --> pdb=" O SER I 558 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY I 563 " --> pdb=" O LEU I 559 " (cutoff:3.500A) Processing helix chain 'I' and resid 575 through 580 Processing helix chain 'I' and resid 586 through 591 Processing helix chain 'I' and resid 596 through 608 removed outlier: 4.013A pdb=" N ALA I 604 " --> pdb=" O LEU I 600 " (cutoff:3.500A) Processing helix chain 'I' and resid 617 through 624 removed outlier: 4.348A pdb=" N GLU I 622 " --> pdb=" O THR I 619 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE I 623 " --> pdb=" O LEU I 620 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 508 through 512 removed outlier: 4.228A pdb=" N GLN A 508 " --> pdb=" O TRP R 27 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA R 29 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A 561 " --> pdb=" O ASN R 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.567A pdb=" N LEU B 5 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 16 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE B 14 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR B 13 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N LYS C 32 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N PHE B 15 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 7 through 9 Processing sheet with id=AA4, first strand: chain 'H' and resid 29 through 31 removed outlier: 8.198A pdb=" N PHE H 62 " --> pdb=" O LYS H 20 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE H 22 " --> pdb=" O PHE H 62 " (cutoff:3.500A) 690 hydrogen bonds defined for protein. 2013 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: 4.31 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5511 1.34 - 1.46: 2645 1.46 - 1.58: 9457 1.58 - 1.70: 0 1.70 - 1.82: 208 Bond restraints: 17821 Sorted by residual: bond pdb=" N VAL F 375 " pdb=" CA VAL F 375 " ideal model delta sigma weight residual 1.459 1.491 -0.033 9.10e-03 1.21e+04 1.29e+01 bond pdb=" N VAL A 375 " pdb=" CA VAL A 375 " ideal model delta sigma weight residual 1.459 1.491 -0.032 9.10e-03 1.21e+04 1.24e+01 bond pdb=" N LEU I 450 " pdb=" CA LEU I 450 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.23e-02 6.61e+03 1.09e+01 bond pdb=" N ARG G 37 " pdb=" CA ARG G 37 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.11e-02 8.12e+03 1.05e+01 bond pdb=" N VAL G 3 " pdb=" CA VAL G 3 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.15e+00 ... (remaining 17816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 22839 1.96 - 3.91: 1029 3.91 - 5.87: 111 5.87 - 7.82: 34 7.82 - 9.78: 12 Bond angle restraints: 24025 Sorted by residual: angle pdb=" N PRO I 510 " pdb=" CA PRO I 510 " pdb=" CB PRO I 510 " ideal model delta sigma weight residual 103.25 111.64 -8.39 1.05e+00 9.07e-01 6.38e+01 angle pdb=" N PRO D 510 " pdb=" CA PRO D 510 " pdb=" CB PRO D 510 " ideal model delta sigma weight residual 103.25 111.21 -7.96 1.05e+00 9.07e-01 5.74e+01 angle pdb=" N LEU H 46 " pdb=" CA LEU H 46 " pdb=" C LEU H 46 " ideal model delta sigma weight residual 113.30 104.50 8.80 1.34e+00 5.57e-01 4.31e+01 angle pdb=" N ILE F 285 " pdb=" CA ILE F 285 " pdb=" C ILE F 285 " ideal model delta sigma weight residual 113.53 107.26 6.27 9.80e-01 1.04e+00 4.09e+01 angle pdb=" N ILE A 285 " pdb=" CA ILE A 285 " pdb=" C ILE A 285 " ideal model delta sigma weight residual 113.53 107.27 6.26 9.80e-01 1.04e+00 4.08e+01 ... (remaining 24020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 9426 17.42 - 34.83: 1110 34.83 - 52.25: 254 52.25 - 69.67: 70 69.67 - 87.08: 8 Dihedral angle restraints: 10868 sinusoidal: 4462 harmonic: 6406 Sorted by residual: dihedral pdb=" CA GLN I 592 " pdb=" C GLN I 592 " pdb=" N MET I 593 " pdb=" CA MET I 593 " ideal model delta harmonic sigma weight residual 180.00 150.67 29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA ASN F 169 " pdb=" C ASN F 169 " pdb=" N ASP F 170 " pdb=" CA ASP F 170 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA LYS F 62 " pdb=" C LYS F 62 " pdb=" N ILE F 63 " pdb=" CA ILE F 63 " ideal model delta harmonic sigma weight residual -180.00 -156.07 -23.93 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 10865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2109 0.055 - 0.109: 468 0.109 - 0.164: 99 0.164 - 0.218: 31 0.218 - 0.273: 4 Chirality restraints: 2711 Sorted by residual: chirality pdb=" CA PRO I 510 " pdb=" N PRO I 510 " pdb=" C PRO I 510 " pdb=" CB PRO I 510 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA LEU H 46 " pdb=" N LEU H 46 " pdb=" C LEU H 46 " pdb=" CB LEU H 46 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ILE H 30 " pdb=" N ILE H 30 " pdb=" C ILE H 30 " pdb=" CB ILE H 30 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 2708 not shown) Planarity restraints: 3058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET F 162 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.33e+00 pdb=" C MET F 162 " 0.050 2.00e-02 2.50e+03 pdb=" O MET F 162 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU F 163 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 8 " -0.234 9.50e-02 1.11e+02 1.05e-01 6.74e+00 pdb=" NE ARG G 8 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG G 8 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG G 8 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 8 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET H 45 " 0.012 2.00e-02 2.50e+03 2.45e-02 5.99e+00 pdb=" C MET H 45 " -0.042 2.00e-02 2.50e+03 pdb=" O MET H 45 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU H 46 " 0.014 2.00e-02 2.50e+03 ... (remaining 3055 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3060 2.76 - 3.30: 18229 3.30 - 3.83: 27559 3.83 - 4.37: 32621 4.37 - 4.90: 50269 Nonbonded interactions: 131738 Sorted by model distance: nonbonded pdb=" O THR A 613 " pdb=" OG SER A 616 " model vdw 2.228 3.040 nonbonded pdb=" O ASN A 624 " pdb=" OG SER A 639 " model vdw 2.238 3.040 nonbonded pdb=" OG SER A 233 " pdb=" OE1 GLN A 234 " model vdw 2.238 3.040 nonbonded pdb=" O LEU D 373 " pdb=" NZ LYS D 376 " model vdw 2.239 3.120 nonbonded pdb=" OD1 ASP I 567 " pdb="ZN ZN I 701 " model vdw 2.241 2.230 ... (remaining 131733 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 17 through 52 or resid 58 through 62 or (resid 63 and (nam \ e N or name CA or name C or name O or name CB )) or resid 64 through 86 or resid \ 89 through 110)) selection = (chain 'H' and (resid 17 through 87 or resid 89 through 110)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 39.420 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 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 : 0.005 0.041 17821 Z= 0.318 Angle : 0.897 9.779 24025 Z= 0.583 Chirality : 0.051 0.273 2711 Planarity : 0.006 0.105 3058 Dihedral : 15.830 87.084 6684 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.35 % Favored : 94.51 % Rotamer: Outliers : 0.88 % Allowed : 23.34 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.18), residues: 2096 helix: -0.52 (0.15), residues: 1117 sheet: -2.04 (1.46), residues: 12 loop : -1.49 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 33 HIS 0.008 0.001 HIS I 489 PHE 0.016 0.001 PHE D 626 TYR 0.021 0.001 TYR F 90 ARG 0.010 0.001 ARG F 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9345 (mmm) cc_final: 0.9037 (mmm) REVERT: D 403 LYS cc_start: 0.3909 (OUTLIER) cc_final: 0.3233 (mtmm) REVERT: F 476 MET cc_start: 0.5418 (mpp) cc_final: 0.4949 (mpp) REVERT: H 37 LEU cc_start: 0.9278 (mp) cc_final: 0.8992 (pp) REVERT: H 64 GLU cc_start: 0.6730 (mp0) cc_final: 0.6524 (mp0) REVERT: I 487 LEU cc_start: 0.8976 (pt) cc_final: 0.8751 (pt) outliers start: 17 outliers final: 4 residues processed: 146 average time/residue: 0.3209 time to fit residues: 71.0599 Evaluate side-chains 115 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain D residue 403 LYS Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 416 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 166 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 169 ASN A 193 GLN A 267 GLN A 283 HIS A 318 HIS A 474 HIS A 487 ASN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 ASN A 625 HIS A 643 ASN A 663 GLN C 58 ASN C 85 ASN D 115 ASN D 143 ASN D 262 ASN D 289 ASN D 319 GLN D 375 GLN D 394 GLN D 399 ASN D 468 ASN D 511 ASN D 530 ASN D 553 HIS F 178 GLN F 182 HIS F 267 GLN F 318 HIS F 347 HIS F 463 GLN G 10 HIS H 27 HIS H 35 HIS H 61 ASN ** I 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 439 ASN I 489 HIS I 511 ASN I 611 ASN R 28 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.048227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.035489 restraints weight = 223448.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.036304 restraints weight = 123622.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.036854 restraints weight = 85379.115| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17821 Z= 0.233 Angle : 0.662 9.100 24025 Z= 0.354 Chirality : 0.041 0.139 2711 Planarity : 0.005 0.069 3058 Dihedral : 5.525 41.105 2343 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.92 % Favored : 94.94 % Rotamer: Outliers : 3.21 % Allowed : 21.48 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.18), residues: 2096 helix: -0.20 (0.15), residues: 1205 sheet: -2.10 (1.58), residues: 12 loop : -1.59 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 14 HIS 0.008 0.001 HIS I 489 PHE 0.030 0.001 PHE I 388 TYR 0.022 0.001 TYR I 449 ARG 0.005 0.000 ARG F 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 118 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 678 MET cc_start: 0.9624 (mmp) cc_final: 0.9413 (mmm) REVERT: A 688 MET cc_start: 0.9244 (ppp) cc_final: 0.8956 (tmm) REVERT: C 105 MET cc_start: 0.8981 (mtm) cc_final: 0.8633 (mtm) REVERT: D 281 LEU cc_start: 0.9729 (OUTLIER) cc_final: 0.9518 (mp) REVERT: F 101 MET cc_start: 0.9118 (tpp) cc_final: 0.8781 (tpp) REVERT: F 278 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9152 (pp) REVERT: F 451 MET cc_start: 0.9656 (mmm) cc_final: 0.9257 (tpt) REVERT: H 37 LEU cc_start: 0.9265 (mp) cc_final: 0.8977 (pp) REVERT: H 105 MET cc_start: 0.9117 (mmm) cc_final: 0.8895 (mmm) REVERT: I 395 MET cc_start: 0.9286 (ppp) cc_final: 0.9027 (ppp) REVERT: I 541 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8453 (pm20) REVERT: I 593 MET cc_start: 0.8783 (pmm) cc_final: 0.8448 (pmm) outliers start: 62 outliers final: 21 residues processed: 174 average time/residue: 0.3002 time to fit residues: 80.0465 Evaluate side-chains 136 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 741 TYR Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 575 THR Chi-restraints excluded: chain F residue 39 PHE Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 541 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 102 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 173 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 196 optimal weight: 6.9990 chunk 166 optimal weight: 0.4980 chunk 30 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 GLN A 600 GLN D 155 ASN D 533 ASN F 67 ASN ** I 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 464 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.047964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.035331 restraints weight = 223345.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.036082 restraints weight = 125025.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.036648 restraints weight = 88286.627| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17821 Z= 0.196 Angle : 0.640 10.792 24025 Z= 0.332 Chirality : 0.040 0.150 2711 Planarity : 0.004 0.058 3058 Dihedral : 5.248 38.977 2335 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.44 % Favored : 95.42 % Rotamer: Outliers : 3.36 % Allowed : 20.91 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.19), residues: 2096 helix: 0.03 (0.15), residues: 1218 sheet: -2.31 (1.61), residues: 12 loop : -1.46 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 517 HIS 0.004 0.001 HIS A 318 PHE 0.022 0.001 PHE I 549 TYR 0.024 0.001 TYR I 449 ARG 0.007 0.000 ARG D 350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 117 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8224 (tmm) cc_final: 0.7455 (tpp) REVERT: A 237 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8497 (pm20) REVERT: A 297 MET cc_start: 0.9261 (tpp) cc_final: 0.9008 (tpp) REVERT: A 476 MET cc_start: 0.9695 (mpp) cc_final: 0.9395 (mpp) REVERT: A 678 MET cc_start: 0.9621 (mmp) cc_final: 0.9419 (mmm) REVERT: D 159 MET cc_start: 0.9179 (mmm) cc_final: 0.8713 (mpp) REVERT: D 281 LEU cc_start: 0.9711 (OUTLIER) cc_final: 0.9502 (mp) REVERT: D 422 MET cc_start: 0.8998 (mpp) cc_final: 0.8419 (mtm) REVERT: F 26 MET cc_start: 0.8526 (mtm) cc_final: 0.8300 (mpp) REVERT: F 60 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: F 278 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9149 (pp) REVERT: H 37 LEU cc_start: 0.9251 (mp) cc_final: 0.8969 (pp) REVERT: H 105 MET cc_start: 0.9097 (mmm) cc_final: 0.8888 (mmm) REVERT: I 541 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8427 (pm20) outliers start: 65 outliers final: 27 residues processed: 172 average time/residue: 0.2975 time to fit residues: 79.2848 Evaluate side-chains 142 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 741 TYR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain F residue 39 PHE Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 464 GLN Chi-restraints excluded: chain I residue 541 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 18 optimal weight: 0.1980 chunk 93 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 171 optimal weight: 30.0000 chunk 190 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 chunk 66 optimal weight: 40.0000 chunk 84 optimal weight: 20.0000 chunk 188 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 63 optimal weight: 20.0000 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 443 ASN D 572 GLN F 313 GLN ** I 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 464 GLN ** I 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.046548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.034771 restraints weight = 227782.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.035083 restraints weight = 149236.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.035184 restraints weight = 100130.683| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17821 Z= 0.395 Angle : 0.751 9.362 24025 Z= 0.397 Chirality : 0.043 0.167 2711 Planarity : 0.005 0.054 3058 Dihedral : 5.557 54.949 2335 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.78 % Favored : 94.08 % Rotamer: Outliers : 4.55 % Allowed : 22.57 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.18), residues: 2096 helix: -0.14 (0.15), residues: 1210 sheet: -3.75 (1.29), residues: 12 loop : -1.54 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 517 HIS 0.011 0.001 HIS A 182 PHE 0.019 0.002 PHE D 509 TYR 0.021 0.002 TYR I 449 ARG 0.008 0.001 ARG F 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 109 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9027 (mp) REVERT: A 101 MET cc_start: 0.8574 (tmm) cc_final: 0.8358 (tmm) REVERT: A 219 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.7840 (m-10) REVERT: A 297 MET cc_start: 0.9164 (tpp) cc_final: 0.8878 (tpp) REVERT: A 449 MET cc_start: 0.5535 (tpp) cc_final: 0.3907 (mmm) REVERT: A 476 MET cc_start: 0.9720 (mpp) cc_final: 0.9266 (mpp) REVERT: A 678 MET cc_start: 0.9597 (mmp) cc_final: 0.9329 (mmp) REVERT: A 688 MET cc_start: 0.9448 (tmm) cc_final: 0.9093 (ppp) REVERT: D 354 TYR cc_start: 0.9498 (OUTLIER) cc_final: 0.9207 (t80) REVERT: D 422 MET cc_start: 0.9042 (mpp) cc_final: 0.8550 (ttm) REVERT: D 627 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.6450 (t-90) REVERT: H 37 LEU cc_start: 0.9314 (mp) cc_final: 0.9013 (pp) REVERT: I 487 LEU cc_start: 0.9253 (pt) cc_final: 0.9045 (pt) REVERT: I 537 HIS cc_start: 0.8740 (OUTLIER) cc_final: 0.8265 (m170) REVERT: I 541 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8488 (pm20) REVERT: I 544 ARG cc_start: 0.8803 (mtm180) cc_final: 0.8558 (ptp90) REVERT: I 593 MET cc_start: 0.8995 (pmm) cc_final: 0.8794 (pmm) outliers start: 88 outliers final: 50 residues processed: 188 average time/residue: 0.2823 time to fit residues: 84.1170 Evaluate side-chains 162 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 106 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 354 TYR Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 441 GLU Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain D residue 575 THR Chi-restraints excluded: chain D residue 584 VAL Chi-restraints excluded: chain D residue 627 HIS Chi-restraints excluded: chain F residue 39 PHE Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 447 PHE Chi-restraints excluded: chain I residue 449 TYR Chi-restraints excluded: chain I residue 492 VAL Chi-restraints excluded: chain I residue 537 HIS Chi-restraints excluded: chain I residue 541 GLN Chi-restraints excluded: chain I residue 559 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 187 optimal weight: 0.0170 chunk 43 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 155 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 199 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 151 optimal weight: 0.0070 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.047301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.035606 restraints weight = 224085.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.036147 restraints weight = 124687.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.036003 restraints weight = 89331.725| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17821 Z= 0.156 Angle : 0.637 11.402 24025 Z= 0.323 Chirality : 0.040 0.234 2711 Planarity : 0.004 0.050 3058 Dihedral : 5.176 48.622 2335 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.92 % Favored : 94.99 % Rotamer: Outliers : 2.33 % Allowed : 23.50 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.19), residues: 2096 helix: 0.25 (0.15), residues: 1217 sheet: -4.04 (1.13), residues: 12 loop : -1.46 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 91 HIS 0.004 0.001 HIS A 696 PHE 0.015 0.001 PHE A 548 TYR 0.025 0.001 TYR I 449 ARG 0.005 0.000 ARG C 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 112 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8653 (mp) REVERT: A 237 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8479 (pm20) REVERT: A 297 MET cc_start: 0.9202 (tpp) cc_final: 0.8829 (tpp) REVERT: A 476 MET cc_start: 0.9651 (mpp) cc_final: 0.9418 (mpp) REVERT: A 576 MET cc_start: 0.6892 (mmt) cc_final: 0.6320 (mmt) REVERT: A 622 MET cc_start: 0.8891 (mpp) cc_final: 0.8541 (tpp) REVERT: A 688 MET cc_start: 0.9490 (tmm) cc_final: 0.9140 (ppp) REVERT: D 159 MET cc_start: 0.9265 (mmm) cc_final: 0.8799 (mpp) REVERT: D 422 MET cc_start: 0.9009 (mpp) cc_final: 0.8668 (mtm) REVERT: F 278 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9210 (pp) REVERT: F 369 ASP cc_start: 0.9793 (OUTLIER) cc_final: 0.9546 (m-30) REVERT: H 37 LEU cc_start: 0.9279 (mp) cc_final: 0.8972 (pp) REVERT: I 537 HIS cc_start: 0.8789 (OUTLIER) cc_final: 0.8286 (m170) REVERT: I 541 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8415 (pm20) REVERT: I 568 MET cc_start: 0.9023 (tpp) cc_final: 0.8821 (tpp) outliers start: 45 outliers final: 26 residues processed: 154 average time/residue: 0.2817 time to fit residues: 69.3326 Evaluate side-chains 141 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 442 CYS Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain D residue 584 VAL Chi-restraints excluded: chain D residue 610 ILE Chi-restraints excluded: chain F residue 39 PHE Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 481 THR Chi-restraints excluded: chain I residue 537 HIS Chi-restraints excluded: chain I residue 541 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.7363 > 50: distance: 35 - 38: 21.369 distance: 38 - 39: 26.792 distance: 39 - 40: 25.157 distance: 39 - 42: 6.229 distance: 40 - 41: 22.292 distance: 40 - 50: 36.118 distance: 42 - 43: 9.919 distance: 43 - 44: 5.823 distance: 43 - 45: 31.671 distance: 44 - 46: 7.942 distance: 45 - 47: 9.797 distance: 46 - 48: 19.563 distance: 47 - 48: 21.033 distance: 48 - 49: 20.088 distance: 50 - 51: 43.754 distance: 51 - 52: 25.638 distance: 52 - 53: 4.428 distance: 52 - 54: 26.050 distance: 54 - 55: 26.125 distance: 55 - 56: 13.254 distance: 56 - 59: 40.229 distance: 59 - 60: 18.605 distance: 60 - 61: 5.317 distance: 60 - 63: 21.804 distance: 61 - 62: 17.147 distance: 61 - 64: 34.378 distance: 64 - 65: 33.003 distance: 65 - 66: 9.786 distance: 65 - 68: 9.477 distance: 66 - 67: 23.927 distance: 66 - 71: 19.360 distance: 68 - 69: 8.374 distance: 68 - 70: 16.607 distance: 71 - 72: 3.412 distance: 72 - 75: 8.873 distance: 73 - 74: 3.742 distance: 73 - 80: 19.985 distance: 75 - 76: 12.693 distance: 76 - 77: 23.921 distance: 77 - 78: 6.097 distance: 77 - 79: 5.927 distance: 80 - 81: 23.929 distance: 81 - 82: 15.186 distance: 82 - 83: 35.537 distance: 82 - 86: 15.765 distance: 84 - 85: 16.286 distance: 86 - 87: 5.638 distance: 87 - 88: 17.872 distance: 87 - 90: 14.425 distance: 88 - 89: 28.329 distance: 88 - 93: 33.364 distance: 90 - 91: 14.164 distance: 91 - 92: 9.763 distance: 93 - 94: 13.434 distance: 94 - 95: 40.645 distance: 94 - 97: 11.068 distance: 95 - 96: 41.220 distance: 95 - 98: 27.855 distance: 98 - 99: 29.071 distance: 98 - 104: 22.533 distance: 99 - 100: 14.684 distance: 99 - 102: 39.864 distance: 100 - 101: 16.744 distance: 100 - 105: 28.879 distance: 103 - 104: 45.924