Starting phenix.real_space_refine on Mon Aug 25 00:54:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8je1_36182/08_2025/8je1_36182.cif Found real_map, /net/cci-nas-00/data/ceres_data/8je1_36182/08_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_36182/08_2025/8je1_36182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8je1_36182/08_2025/8je1_36182.map" model { file = "/net/cci-nas-00/data/ceres_data/8je1_36182/08_2025/8je1_36182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8je1_36182/08_2025/8je1_36182.cif" } resolution = 3.95 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= -0.001 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASN:plan1': 4, 'ARG:plan': 3, 'GLU:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} 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: 4.51, per 1000 atoms: 0.26 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: 1.58 Conformation dependent library (CDL) restraints added in 794.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.57 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: 2.63 Time building geometry restraints manager: 2.04 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: 8.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.680 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.630 ------------------------------------------------------------------------------- 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 17823 Z= 0.344 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 : 17.30 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG F 56 TYR 0.021 0.001 TYR F 90 PHE 0.016 0.001 PHE D 626 TRP 0.014 0.002 TRP R 33 HIS 0.008 0.001 HIS I 489 Details of bonding type rmsd covalent geometry : bond 0.00487 (17821) covalent geometry : angle 0.89672 (24025) hydrogen bonds : bond 0.22898 ( 690) hydrogen bonds : angle 7.36108 ( 2013) metal coordination : bond 0.00025 ( 2) *********************** 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 : 0.779 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: 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: 0.6523 (mp0) REVERT: I 487 LEU cc_start: 0.8976 (pt) cc_final: 0.8751 (pt) outliers start: 17 outliers final: 5 residues processed: 146 average time/residue: 0.1428 time to fit residues: 31.7154 Evaluate side-chains 116 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 675 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 98 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 533 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.048270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.035618 restraints weight = 222900.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.036410 restraints weight = 122955.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.036954 restraints weight = 85572.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.037328 restraints weight = 67034.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.037569 restraints weight = 56479.172| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17823 Z= 0.183 Angle : 0.667 9.084 24025 Z= 0.357 Chirality : 0.041 0.137 2711 Planarity : 0.005 0.071 3058 Dihedral : 5.559 42.003 2345 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.92 % Favored : 94.94 % Rotamer: Outliers : 2.90 % Allowed : 21.69 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -1.27 (0.18), residues: 2096 helix: -0.23 (0.15), residues: 1208 sheet: -2.11 (1.59), residues: 12 loop : -1.62 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 56 TYR 0.022 0.001 TYR I 449 PHE 0.030 0.001 PHE I 388 TRP 0.010 0.001 TRP F 14 HIS 0.008 0.001 HIS I 489 Details of bonding type rmsd covalent geometry : bond 0.00374 (17821) covalent geometry : angle 0.66692 (24025) hydrogen bonds : bond 0.06477 ( 690) hydrogen bonds : angle 5.92801 ( 2013) metal coordination : bond 0.00225 ( 2) *********************** 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 170 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 114 time to evaluate : 0.693 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: 0.9005 (mmm) cc_final: 0.8778 (mmm) REVERT: A 283 HIS cc_start: 0.9372 (OUTLIER) cc_final: 0.9165 (m-70) REVERT: A 678 MET cc_start: 0.9610 (mmp) cc_final: 0.9385 (mmm) REVERT: A 688 MET cc_start: 0.9149 (ppp) cc_final: 0.8891 (tmm) REVERT: C 105 MET cc_start: 0.8974 (mtm) cc_final: 0.8630 (mtm) REVERT: F 101 MET cc_start: 0.9106 (tpp) cc_final: 0.8765 (tpp) REVERT: F 136 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7367 (pp) REVERT: F 451 MET cc_start: 0.9550 (mmm) cc_final: 0.9169 (tpt) REVERT: F 457 MET cc_start: 0.8346 (ptt) cc_final: 0.8102 (ptp) REVERT: H 37 LEU cc_start: 0.9276 (mp) cc_final: 0.8998 (pp) REVERT: H 105 MET cc_start: 0.9124 (mmm) cc_final: 0.8882 (mmm) REVERT: I 395 MET cc_start: 0.9286 (ppp) cc_final: 0.9018 (ppp) REVERT: I 541 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8462 (pm20) REVERT: I 593 MET cc_start: 0.8781 (pmm) cc_final: 0.8451 (pmm) outliers start: 56 outliers final: 19 residues processed: 165 average time/residue: 0.1313 time to fit residues: 33.7913 Evaluate side-chains 135 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 283 HIS 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 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 136 LEU 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 61 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 200 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 146 optimal weight: 0.9980 chunk 152 optimal weight: 0.0170 chunk 95 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 13 optimal weight: 0.0970 chunk 60 optimal weight: 8.9990 overall best weight: 1.8220 ------------------------------------------------------------------------------- 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 600 GLN D 155 ASN F 67 ASN ** I 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 464 GLN R 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.047957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.035423 restraints weight = 224716.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.036532 restraints weight = 136813.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.036665 restraints weight = 79756.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.036723 restraints weight = 72146.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.036820 restraints weight = 72184.515| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- 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: 0.8171 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17823 Z= 0.144 Angle : 0.639 10.451 24025 Z= 0.333 Chirality : 0.040 0.143 2711 Planarity : 0.004 0.063 3058 Dihedral : 5.305 38.932 2335 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.58 % Favored : 95.27 % Rotamer: Outliers : 3.11 % Allowed : 21.48 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -1.01 (0.18), residues: 2096 helix: -0.01 (0.15), residues: 1219 sheet: -2.32 (1.60), residues: 12 loop : -1.55 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 63 TYR 0.018 0.001 TYR I 449 PHE 0.021 0.001 PHE I 549 TRP 0.013 0.001 TRP A 517 HIS 0.010 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00300 (17821) covalent geometry : angle 0.63890 (24025) hydrogen bonds : bond 0.05085 ( 690) hydrogen bonds : angle 5.52668 ( 2013) metal coordination : bond 0.00219 ( 2) *********************** 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 178 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 118 time to evaluate : 0.627 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 1 MET cc_start: 0.8153 (tmm) cc_final: 0.7365 (tpp) REVERT: A 283 HIS cc_start: 0.9334 (OUTLIER) cc_final: 0.9105 (m90) REVERT: A 297 MET cc_start: 0.9237 (tpp) cc_final: 0.9010 (tpp) REVERT: A 476 MET cc_start: 0.9701 (mpp) cc_final: 0.9461 (mpp) REVERT: D 159 MET cc_start: 0.9177 (mmm) cc_final: 0.8707 (mpp) REVERT: D 422 MET cc_start: 0.9039 (mpp) cc_final: 0.8437 (mtm) REVERT: F 278 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9165 (pp) REVERT: G 35 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9094 (mp) REVERT: H 37 LEU cc_start: 0.9261 (mp) cc_final: 0.8983 (pp) REVERT: I 541 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8429 (pm20) outliers start: 60 outliers final: 29 residues processed: 171 average time/residue: 0.1298 time to fit residues: 34.2572 Evaluate side-chains 142 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 283 HIS 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 741 TYR 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 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 358 MET Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain D residue 593 MET 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 181 ILE Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain G residue 35 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 111 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 187 optimal weight: 20.0000 chunk 176 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 ** I 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 464 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.047942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.036101 restraints weight = 224584.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.036767 restraints weight = 123951.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.036586 restraints weight = 85958.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.036727 restraints weight = 89519.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.036803 restraints weight = 76888.140| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 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 = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17823 Z= 0.130 Angle : 0.620 11.845 24025 Z= 0.320 Chirality : 0.039 0.146 2711 Planarity : 0.004 0.054 3058 Dihedral : 5.118 38.063 2335 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.58 % Favored : 95.27 % Rotamer: Outliers : 3.26 % Allowed : 22.05 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -0.83 (0.19), residues: 2096 helix: 0.16 (0.15), residues: 1222 sheet: -3.70 (1.16), residues: 12 loop : -1.49 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 161 TYR 0.023 0.001 TYR I 449 PHE 0.013 0.001 PHE I 447 TRP 0.012 0.001 TRP A 517 HIS 0.003 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00276 (17821) covalent geometry : angle 0.61966 (24025) hydrogen bonds : bond 0.04395 ( 690) hydrogen bonds : angle 5.27941 ( 2013) metal coordination : bond 0.00184 ( 2) *********************** 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 176 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 113 time to evaluate : 0.454 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 86 MET cc_start: 0.9046 (mmm) cc_final: 0.8731 (mmm) REVERT: A 101 MET cc_start: 0.8466 (tmm) cc_final: 0.8202 (tmm) REVERT: A 283 HIS cc_start: 0.9319 (OUTLIER) cc_final: 0.9091 (m90) REVERT: A 297 MET cc_start: 0.9226 (tpp) cc_final: 0.8923 (tpp) REVERT: A 335 MET cc_start: 0.8976 (ppp) cc_final: 0.8764 (ppp) REVERT: A 476 MET cc_start: 0.9681 (mpp) cc_final: 0.9356 (mpp) REVERT: A 688 MET cc_start: 0.9467 (tmm) cc_final: 0.9070 (ppp) REVERT: D 159 MET cc_start: 0.9207 (mmm) cc_final: 0.8721 (mpp) REVERT: D 220 MET cc_start: 0.8274 (mmm) cc_final: 0.7980 (mmm) REVERT: D 422 MET cc_start: 0.8979 (mpp) cc_final: 0.8489 (mtm) REVERT: F 60 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8576 (tt0) REVERT: F 278 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9183 (pp) REVERT: F 449 MET cc_start: 0.3984 (ptp) cc_final: 0.2971 (pmm) REVERT: F 457 MET cc_start: 0.8338 (ptt) cc_final: 0.8067 (ptp) REVERT: H 37 LEU cc_start: 0.9272 (mp) cc_final: 0.8987 (pp) REVERT: I 537 HIS cc_start: 0.8746 (OUTLIER) cc_final: 0.8258 (m170) REVERT: I 541 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8418 (pm20) outliers start: 63 outliers final: 35 residues processed: 171 average time/residue: 0.1117 time to fit residues: 29.9295 Evaluate side-chains 151 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 283 HIS 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 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 88 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 398 LEU 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 593 MET 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 191 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 420 THR 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 Chi-restraints excluded: chain I residue 542 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 155 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 19 optimal weight: 0.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN ** I 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.047563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.035296 restraints weight = 223791.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.036346 restraints weight = 133241.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.036371 restraints weight = 77396.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.036465 restraints weight = 80162.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.036576 restraints weight = 74032.837| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- 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: 0.8178 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17823 Z= 0.143 Angle : 0.624 11.081 24025 Z= 0.319 Chirality : 0.039 0.147 2711 Planarity : 0.004 0.050 3058 Dihedral : 5.011 38.726 2335 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 3.11 % Allowed : 22.83 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -0.60 (0.19), residues: 2096 helix: 0.38 (0.15), residues: 1211 sheet: -1.68 (0.99), residues: 22 loop : -1.46 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.023 0.001 TYR I 449 PHE 0.027 0.001 PHE A 548 TRP 0.012 0.001 TRP A 517 HIS 0.013 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00308 (17821) covalent geometry : angle 0.62397 (24025) hydrogen bonds : bond 0.04062 ( 690) hydrogen bonds : angle 5.18560 ( 2013) metal coordination : bond 0.00250 ( 2) *********************** 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 171 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 111 time to evaluate : 0.732 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 86 MET cc_start: 0.9104 (mmm) cc_final: 0.8772 (mmm) REVERT: A 101 MET cc_start: 0.8573 (tmm) cc_final: 0.8296 (tmm) REVERT: A 163 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8700 (mp) REVERT: A 283 HIS cc_start: 0.9309 (OUTLIER) cc_final: 0.9077 (m90) REVERT: A 297 MET cc_start: 0.9287 (tpp) cc_final: 0.8937 (tpp) REVERT: A 476 MET cc_start: 0.9704 (mpp) cc_final: 0.9360 (mpp) REVERT: A 576 MET cc_start: 0.6889 (mmt) cc_final: 0.6421 (mmt) REVERT: A 688 MET cc_start: 0.9441 (tmm) cc_final: 0.9109 (ppp) REVERT: D 159 MET cc_start: 0.9223 (mmm) cc_final: 0.8754 (mpp) REVERT: D 220 MET cc_start: 0.8282 (mmm) cc_final: 0.8039 (mmm) REVERT: D 422 MET cc_start: 0.8973 (mpp) cc_final: 0.8700 (mtm) REVERT: F 60 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8569 (tt0) REVERT: F 278 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9173 (pp) REVERT: F 449 MET cc_start: 0.3735 (ptp) cc_final: 0.2524 (pmm) REVERT: H 37 LEU cc_start: 0.9266 (mp) cc_final: 0.8972 (pp) REVERT: I 537 HIS cc_start: 0.8755 (OUTLIER) cc_final: 0.8260 (m170) REVERT: I 541 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8444 (pm20) REVERT: I 593 MET cc_start: 0.8881 (pmm) cc_final: 0.8619 (pmm) outliers start: 60 outliers final: 44 residues processed: 166 average time/residue: 0.1132 time to fit residues: 30.3189 Evaluate side-chains 158 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 108 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 163 LEU 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 283 HIS 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 556 LEU Chi-restraints excluded: chain A residue 635 GLU 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 D residue 136 ILE 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 398 LEU 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 593 MET Chi-restraints excluded: chain D residue 610 ILE Chi-restraints excluded: chain F residue 39 PHE 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 191 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 420 THR 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 536 LEU 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 ************** Weight determination summary: number of chunks: 212 random chunks: chunk 158 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.0970 chunk 156 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.047583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.035870 restraints weight = 222304.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.036506 restraints weight = 121617.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.036373 restraints weight = 83850.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.036459 restraints weight = 87594.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.036566 restraints weight = 73745.037| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 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 = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17823 Z= 0.121 Angle : 0.614 11.830 24025 Z= 0.311 Chirality : 0.039 0.169 2711 Planarity : 0.004 0.049 3058 Dihedral : 4.895 37.842 2335 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.87 % Favored : 95.04 % Rotamer: Outliers : 3.11 % Allowed : 23.24 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -0.50 (0.19), residues: 2096 helix: 0.45 (0.15), residues: 1211 sheet: -1.14 (1.07), residues: 20 loop : -1.41 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 63 TYR 0.025 0.001 TYR I 449 PHE 0.016 0.001 PHE A 548 TRP 0.009 0.001 TRP F 14 HIS 0.008 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00258 (17821) covalent geometry : angle 0.61386 (24025) hydrogen bonds : bond 0.03765 ( 690) hydrogen bonds : angle 5.03098 ( 2013) metal coordination : bond 0.00181 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 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 171 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 111 time to evaluate : 0.717 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 101 MET cc_start: 0.8617 (tmm) cc_final: 0.8338 (tmm) REVERT: A 297 MET cc_start: 0.9262 (tpp) cc_final: 0.8862 (tpp) REVERT: A 476 MET cc_start: 0.9694 (mpp) cc_final: 0.9435 (mpp) REVERT: A 688 MET cc_start: 0.9496 (tmm) cc_final: 0.9196 (ppp) REVERT: C 105 MET cc_start: 0.8974 (mtm) cc_final: 0.8248 (mtm) REVERT: D 159 MET cc_start: 0.9255 (mmm) cc_final: 0.8795 (mpp) REVERT: D 220 MET cc_start: 0.8364 (mmm) cc_final: 0.8145 (mmm) REVERT: D 354 TYR cc_start: 0.9420 (OUTLIER) cc_final: 0.9172 (t80) REVERT: F 60 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8658 (tt0) REVERT: F 278 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9167 (pp) REVERT: H 37 LEU cc_start: 0.9283 (mp) cc_final: 0.8977 (pp) REVERT: I 537 HIS cc_start: 0.8766 (OUTLIER) cc_final: 0.8243 (m170) REVERT: I 541 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8419 (pm20) outliers start: 60 outliers final: 42 residues processed: 166 average time/residue: 0.1160 time to fit residues: 30.8798 Evaluate side-chains 154 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 107 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU 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 283 HIS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 556 LEU 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 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 354 TYR Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 398 LEU 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 593 MET Chi-restraints excluded: chain D residue 610 ILE 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 191 VAL 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 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 536 LEU Chi-restraints excluded: chain I residue 537 HIS Chi-restraints excluded: chain I residue 541 GLN Chi-restraints excluded: chain I residue 542 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 51 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 177 optimal weight: 20.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS ** A 508 GLN ** 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 = 0.3486 r_free = 0.3486 target = 0.047563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.035036 restraints weight = 223578.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035832 restraints weight = 124276.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.036355 restraints weight = 85953.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.036718 restraints weight = 68034.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.036939 restraints weight = 57261.841| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17823 Z= 0.115 Angle : 0.620 12.489 24025 Z= 0.312 Chirality : 0.039 0.210 2711 Planarity : 0.004 0.048 3058 Dihedral : 4.826 37.397 2335 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.01 % Favored : 94.89 % Rotamer: Outliers : 3.42 % Allowed : 23.29 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -0.43 (0.19), residues: 2096 helix: 0.53 (0.15), residues: 1226 sheet: -3.76 (1.23), residues: 10 loop : -1.41 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 63 TYR 0.015 0.001 TYR I 440 PHE 0.012 0.001 PHE I 447 TRP 0.009 0.001 TRP F 14 HIS 0.005 0.001 HIS I 434 Details of bonding type rmsd covalent geometry : bond 0.00247 (17821) covalent geometry : angle 0.61967 (24025) hydrogen bonds : bond 0.03555 ( 690) hydrogen bonds : angle 4.93727 ( 2013) metal coordination : bond 0.00163 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 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 176 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 110 time to evaluate : 0.746 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 86 MET cc_start: 0.8943 (mmm) cc_final: 0.8702 (mmm) REVERT: A 163 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8684 (mp) REVERT: A 297 MET cc_start: 0.9280 (tpp) cc_final: 0.8865 (tpp) REVERT: A 449 MET cc_start: 0.5127 (tpp) cc_final: 0.4030 (mmm) REVERT: A 476 MET cc_start: 0.9704 (mpp) cc_final: 0.9440 (mpp) REVERT: A 576 MET cc_start: 0.6709 (mmt) cc_final: 0.6077 (mmm) REVERT: A 665 MET cc_start: 0.9145 (pmm) cc_final: 0.8911 (pmm) REVERT: A 688 MET cc_start: 0.9488 (tmm) cc_final: 0.9175 (ppp) REVERT: D 159 MET cc_start: 0.9213 (mmm) cc_final: 0.8808 (mpp) REVERT: D 220 MET cc_start: 0.8281 (mmm) cc_final: 0.8077 (mmm) REVERT: F 86 MET cc_start: 0.8196 (mmp) cc_final: 0.7989 (mmm) REVERT: F 278 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9118 (pp) REVERT: F 369 ASP cc_start: 0.9749 (OUTLIER) cc_final: 0.9515 (m-30) REVERT: I 537 HIS cc_start: 0.8773 (OUTLIER) cc_final: 0.8265 (m170) REVERT: I 541 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8393 (pm20) REVERT: I 568 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8601 (tpp) outliers start: 66 outliers final: 42 residues processed: 171 average time/residue: 0.1237 time to fit residues: 33.9497 Evaluate side-chains 156 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 108 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 163 LEU 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 283 HIS 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 556 LEU Chi-restraints excluded: chain B residue 12 THR 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 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 398 LEU 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 593 MET Chi-restraints excluded: chain D residue 610 ILE 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 191 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 299 VAL 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 46 LEU Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 481 THR Chi-restraints excluded: chain I residue 536 LEU Chi-restraints excluded: chain I residue 537 HIS Chi-restraints excluded: chain I residue 541 GLN Chi-restraints excluded: chain I residue 542 TYR Chi-restraints excluded: chain I residue 568 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 6 optimal weight: 0.7980 chunk 167 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 147 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 17 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** 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 = 0.3488 r_free = 0.3488 target = 0.047633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.035931 restraints weight = 223490.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.036455 restraints weight = 123483.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.036339 restraints weight = 88616.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.036446 restraints weight = 89898.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.036576 restraints weight = 76625.089| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 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 = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17823 Z= 0.118 Angle : 0.636 12.723 24025 Z= 0.317 Chirality : 0.039 0.220 2711 Planarity : 0.004 0.047 3058 Dihedral : 4.780 37.492 2335 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.82 % Favored : 95.08 % Rotamer: Outliers : 2.85 % Allowed : 23.81 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -0.38 (0.19), residues: 2096 helix: 0.57 (0.15), residues: 1215 sheet: -0.69 (1.13), residues: 20 loop : -1.40 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 424 TYR 0.024 0.001 TYR D 354 PHE 0.013 0.001 PHE I 447 TRP 0.009 0.001 TRP A 14 HIS 0.004 0.001 HIS A 547 Details of bonding type rmsd covalent geometry : bond 0.00260 (17821) covalent geometry : angle 0.63585 (24025) hydrogen bonds : bond 0.03494 ( 690) hydrogen bonds : angle 4.88520 ( 2013) metal coordination : bond 0.00172 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 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 163 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 108 time to evaluate : 0.711 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 86 MET cc_start: 0.9016 (mmm) cc_final: 0.8691 (mmm) REVERT: A 163 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8698 (mp) REVERT: A 283 HIS cc_start: 0.9147 (OUTLIER) cc_final: 0.8872 (m90) REVERT: A 297 MET cc_start: 0.9276 (tpp) cc_final: 0.8842 (tpp) REVERT: A 449 MET cc_start: 0.5178 (tpp) cc_final: 0.4016 (mmm) REVERT: A 476 MET cc_start: 0.9703 (mpp) cc_final: 0.9453 (mpp) REVERT: A 576 MET cc_start: 0.6724 (mmt) cc_final: 0.6109 (mmm) REVERT: A 688 MET cc_start: 0.9532 (tmm) cc_final: 0.9232 (ppp) REVERT: B 6 MET cc_start: 0.8422 (ptp) cc_final: 0.7490 (pmm) REVERT: C 105 MET cc_start: 0.8932 (mtm) cc_final: 0.8227 (mtm) REVERT: D 159 MET cc_start: 0.9241 (mmm) cc_final: 0.8808 (mpp) REVERT: D 220 MET cc_start: 0.8363 (mmm) cc_final: 0.8151 (mmm) REVERT: D 326 MET cc_start: 0.9320 (tpp) cc_final: 0.9042 (tmm) REVERT: D 358 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7669 (ttp) REVERT: F 86 MET cc_start: 0.8234 (mmp) cc_final: 0.8007 (mmm) REVERT: F 278 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9170 (pp) REVERT: F 369 ASP cc_start: 0.9790 (OUTLIER) cc_final: 0.9547 (m-30) REVERT: I 537 HIS cc_start: 0.8755 (OUTLIER) cc_final: 0.8254 (m170) REVERT: I 541 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8383 (pm20) REVERT: I 568 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8571 (tpp) outliers start: 55 outliers final: 42 residues processed: 158 average time/residue: 0.1185 time to fit residues: 30.1468 Evaluate side-chains 157 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 107 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 163 LEU 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 283 HIS 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 375 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 35 LEU 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 189 THR Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 398 LEU 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 593 MET Chi-restraints excluded: chain D residue 610 ILE 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 278 LEU Chi-restraints excluded: chain F residue 299 VAL 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 536 LEU Chi-restraints excluded: chain I residue 537 HIS Chi-restraints excluded: chain I residue 541 GLN Chi-restraints excluded: chain I residue 542 TYR Chi-restraints excluded: chain I residue 568 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 145 optimal weight: 0.3980 chunk 200 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 148 optimal weight: 0.0010 chunk 175 optimal weight: 5.9990 chunk 152 optimal weight: 0.3980 chunk 125 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN F 283 HIS I 464 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.047931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.036397 restraints weight = 222605.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.036770 restraints weight = 115265.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.036762 restraints weight = 78046.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.036888 restraints weight = 79939.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.036999 restraints weight = 68423.075| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 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 = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 17823 Z= 0.106 Angle : 0.642 13.122 24025 Z= 0.315 Chirality : 0.039 0.214 2711 Planarity : 0.004 0.047 3058 Dihedral : 4.662 37.187 2335 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.87 % Favored : 95.04 % Rotamer: Outliers : 2.54 % Allowed : 24.02 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -0.37 (0.19), residues: 2096 helix: 0.58 (0.15), residues: 1227 sheet: -3.63 (1.32), residues: 10 loop : -1.40 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 56 TYR 0.017 0.001 TYR I 440 PHE 0.015 0.001 PHE I 447 TRP 0.009 0.001 TRP A 14 HIS 0.006 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00222 (17821) covalent geometry : angle 0.64157 (24025) hydrogen bonds : bond 0.03227 ( 690) hydrogen bonds : angle 4.78110 ( 2013) metal coordination : bond 0.00041 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 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 161 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 112 time to evaluate : 0.824 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 86 MET cc_start: 0.9052 (mmm) cc_final: 0.8793 (mmm) REVERT: A 163 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8669 (mp) REVERT: A 297 MET cc_start: 0.9272 (tpp) cc_final: 0.8847 (tpp) REVERT: A 449 MET cc_start: 0.5089 (tpp) cc_final: 0.3946 (mmm) REVERT: A 476 MET cc_start: 0.9693 (mpp) cc_final: 0.9490 (mpp) REVERT: A 576 MET cc_start: 0.6637 (mmt) cc_final: 0.6196 (mmt) REVERT: A 688 MET cc_start: 0.9505 (tmm) cc_final: 0.9198 (ppp) REVERT: B 1 MET cc_start: 0.4893 (tpt) cc_final: 0.4054 (ttt) REVERT: B 6 MET cc_start: 0.8382 (ptp) cc_final: 0.7453 (pmm) REVERT: C 105 MET cc_start: 0.9023 (mtm) cc_final: 0.8765 (mtm) REVERT: D 159 MET cc_start: 0.9189 (mmm) cc_final: 0.8795 (mpp) REVERT: D 326 MET cc_start: 0.9306 (tpp) cc_final: 0.8994 (tmm) REVERT: D 358 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7512 (ttp) REVERT: F 86 MET cc_start: 0.8357 (mmp) cc_final: 0.8082 (mmm) REVERT: F 101 MET cc_start: 0.8982 (tmm) cc_final: 0.8157 (tmm) REVERT: F 278 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9172 (pp) REVERT: F 335 MET cc_start: 0.6731 (tpt) cc_final: 0.6468 (mmm) REVERT: F 369 ASP cc_start: 0.9782 (OUTLIER) cc_final: 0.9535 (m-30) REVERT: I 537 HIS cc_start: 0.8750 (OUTLIER) cc_final: 0.8259 (m170) REVERT: I 541 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8366 (pm20) REVERT: I 568 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8523 (tpp) outliers start: 49 outliers final: 33 residues processed: 158 average time/residue: 0.1248 time to fit residues: 31.1590 Evaluate side-chains 147 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 237 GLU 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 620 VAL Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 38 THR 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 398 LEU Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain D residue 584 VAL Chi-restraints excluded: chain D residue 593 MET Chi-restraints excluded: chain D residue 610 ILE Chi-restraints excluded: chain D residue 624 VAL 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 278 LEU Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 437 ARG Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 464 GLN Chi-restraints excluded: chain I residue 481 THR Chi-restraints excluded: chain I residue 536 LEU Chi-restraints excluded: chain I residue 537 HIS Chi-restraints excluded: chain I residue 541 GLN Chi-restraints excluded: chain I residue 542 TYR Chi-restraints excluded: chain I residue 568 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 104 optimal weight: 1.9990 chunk 150 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 chunk 140 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 133 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 209 optimal weight: 7.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.047904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.036421 restraints weight = 221206.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.036628 restraints weight = 123705.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.036639 restraints weight = 94503.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.036748 restraints weight = 88443.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.036852 restraints weight = 75569.704| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 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 = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 17823 Z= 0.106 Angle : 0.665 16.839 24025 Z= 0.324 Chirality : 0.039 0.214 2711 Planarity : 0.004 0.047 3058 Dihedral : 4.533 30.054 2333 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.77 % Favored : 95.13 % Rotamer: Outliers : 1.97 % Allowed : 24.59 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -0.28 (0.19), residues: 2096 helix: 0.64 (0.15), residues: 1223 sheet: -3.54 (1.37), residues: 10 loop : -1.32 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 56 TYR 0.022 0.001 TYR I 440 PHE 0.016 0.001 PHE I 447 TRP 0.009 0.001 TRP A 14 HIS 0.004 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.00231 (17821) covalent geometry : angle 0.66542 (24025) hydrogen bonds : bond 0.03209 ( 690) hydrogen bonds : angle 4.78040 ( 2013) metal coordination : bond 0.00084 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 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 146 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.583 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: A 1 MET cc_start: 0.8175 (tmm) cc_final: 0.7475 (tpp) REVERT: A 86 MET cc_start: 0.9043 (mmm) cc_final: 0.8750 (mmm) REVERT: A 163 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8632 (mp) REVERT: A 297 MET cc_start: 0.9271 (tpp) cc_final: 0.8839 (tpp) REVERT: A 449 MET cc_start: 0.5168 (tpp) cc_final: 0.3917 (mmm) REVERT: A 476 MET cc_start: 0.9697 (mpp) cc_final: 0.9496 (mpp) REVERT: A 576 MET cc_start: 0.6533 (mmt) cc_final: 0.6093 (mmt) REVERT: A 688 MET cc_start: 0.9519 (tmm) cc_final: 0.9211 (ppp) REVERT: B 1 MET cc_start: 0.4784 (tpt) cc_final: 0.3998 (ttt) REVERT: B 6 MET cc_start: 0.8392 (ptp) cc_final: 0.7507 (pmm) REVERT: C 105 MET cc_start: 0.8892 (mtm) cc_final: 0.8193 (mtm) REVERT: D 159 MET cc_start: 0.9198 (mmm) cc_final: 0.8782 (mpp) REVERT: D 326 MET cc_start: 0.9334 (tpp) cc_final: 0.8987 (tmm) REVERT: F 86 MET cc_start: 0.8333 (mmp) cc_final: 0.8051 (mmm) REVERT: F 101 MET cc_start: 0.9000 (mmm) cc_final: 0.8213 (tmm) REVERT: F 278 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9191 (pp) REVERT: F 335 MET cc_start: 0.6764 (tpt) cc_final: 0.6504 (mmm) REVERT: I 537 HIS cc_start: 0.8733 (OUTLIER) cc_final: 0.8220 (m170) REVERT: I 541 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8371 (pm20) outliers start: 38 outliers final: 32 residues processed: 144 average time/residue: 0.1167 time to fit residues: 26.8606 Evaluate side-chains 142 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 237 GLU 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 B residue 12 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain D residue 584 VAL Chi-restraints excluded: chain D residue 593 MET Chi-restraints excluded: chain D residue 610 ILE Chi-restraints excluded: chain D residue 624 VAL 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 181 ILE Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 437 ARG Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 481 THR Chi-restraints excluded: chain I residue 536 LEU Chi-restraints excluded: chain I residue 537 HIS Chi-restraints excluded: chain I residue 541 GLN Chi-restraints excluded: chain I residue 542 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 53 optimal weight: 5.9990 chunk 160 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 19 optimal weight: 0.5980 chunk 166 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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** ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.046976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.034488 restraints weight = 226600.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.035245 restraints weight = 128564.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.035764 restraints weight = 90024.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.036121 restraints weight = 71211.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.036319 restraints weight = 60380.066| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 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 = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17823 Z= 0.157 Angle : 0.676 14.952 24025 Z= 0.336 Chirality : 0.040 0.205 2711 Planarity : 0.004 0.046 3058 Dihedral : 4.609 34.550 2333 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.11 % Favored : 94.80 % Rotamer: Outliers : 2.23 % Allowed : 24.38 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -0.14 (0.19), residues: 2096 helix: 0.75 (0.15), residues: 1212 sheet: -0.45 (1.18), residues: 20 loop : -1.27 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 424 TYR 0.016 0.001 TYR I 440 PHE 0.015 0.001 PHE A 548 TRP 0.009 0.001 TRP F 14 HIS 0.004 0.001 HIS A 547 Details of bonding type rmsd covalent geometry : bond 0.00340 (17821) covalent geometry : angle 0.67591 (24025) hydrogen bonds : bond 0.03603 ( 690) hydrogen bonds : angle 4.93529 ( 2013) metal coordination : bond 0.00290 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3925.56 seconds wall clock time: 68 minutes 15.80 seconds (4095.80 seconds total)