Starting phenix.real_space_refine on Mon May 4 21:33:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s86_54651/05_2026/9s86_54651.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s86_54651/05_2026/9s86_54651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s86_54651/05_2026/9s86_54651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s86_54651/05_2026/9s86_54651.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s86_54651/05_2026/9s86_54651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s86_54651/05_2026/9s86_54651.map" } resolution = 2.97 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 75 5.16 5 C 15373 2.51 5 N 4266 2.21 5 O 4190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23908 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 6048 Classifications: {'peptide': 801} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 26, 'TRANS': 774} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 438 Unresolved non-hydrogen angles: 543 Unresolved non-hydrogen dihedrals: 348 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 3, 'ASP:plan': 25, 'GLU:plan': 37, 'GLN:plan1': 9, 'TYR:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'PHE:plan': 1, 'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 328 Chain: "B" Number of atoms: 5933 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 800, 5926 Classifications: {'peptide': 800} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PTRANS': 26, 'TRANS': 773} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 553 Unresolved non-hydrogen angles: 683 Unresolved non-hydrogen dihedrals: 442 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 45, 'HIS:plan': 3, 'ASP:plan': 29, 'GLN:plan1': 14, 'ASN:plan1': 8, 'ARG:plan': 6, 'TYR:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1, 'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 415 Conformer: "B" Number of residues, atoms: 800, 5926 Classifications: {'peptide': 800} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PTRANS': 26, 'TRANS': 773} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 553 Unresolved non-hydrogen angles: 683 Unresolved non-hydrogen dihedrals: 442 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 45, 'HIS:plan': 3, 'ASP:plan': 29, 'GLN:plan1': 14, 'ASN:plan1': 8, 'ARG:plan': 6, 'TYR:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1, 'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 415 bond proxies already assigned to first conformer: 6054 Chain: "C" Number of atoms: 5910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 800, 5903 Classifications: {'peptide': 800} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'PTRANS': 26, 'TRANS': 773} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 713 Unresolved non-hydrogen dihedrals: 457 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 48, 'HIS:plan': 3, 'ASP:plan': 32, 'GLN:plan1': 13, 'ASN:plan1': 10, 'ARG:plan': 6, 'TYR:plan': 3, 'PHE:plan': 1, 'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 443 Conformer: "B" Number of residues, atoms: 800, 5903 Classifications: {'peptide': 800} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'PTRANS': 26, 'TRANS': 773} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 713 Unresolved non-hydrogen dihedrals: 457 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 48, 'HIS:plan': 3, 'ASP:plan': 32, 'GLN:plan1': 13, 'ASN:plan1': 10, 'ARG:plan': 6, 'TYR:plan': 3, 'PHE:plan': 1, 'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 443 bond proxies already assigned to first conformer: 6031 Chain: "D" Number of atoms: 6017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 6017 Classifications: {'peptide': 800} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PTRANS': 26, 'TRANS': 773} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 456 Unresolved non-hydrogen angles: 559 Unresolved non-hydrogen dihedrals: 363 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 41, 'HIS:plan': 3, 'GLN:plan1': 7, 'ASP:plan': 27, 'ARG:plan': 5, 'ASN:plan1': 5, 'TYR:plan': 1, 'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 336 Time building chain proxies: 8.58, per 1000 atoms: 0.36 Number of scatterers: 23908 At special positions: 0 Unit cell: (136.095, 145.125, 112.23, 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) S 75 16.00 P 4 15.00 O 4190 8.00 N 4266 7.00 C 15373 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: 2.44 Conformation dependent library (CDL) restraints added in 1.5 seconds 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6022 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 24 sheets defined 59.6% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 13 through 27 removed outlier: 4.013A pdb=" N LEU A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 66 removed outlier: 3.953A pdb=" N ASN A 43 " --> pdb=" O HIS A 39 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 93 removed outlier: 3.729A pdb=" N LEU A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 108 through 116 removed outlier: 3.506A pdb=" N ASP A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 141 removed outlier: 3.631A pdb=" N ARG A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.892A pdb=" N VAL A 265 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A 266 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 306 removed outlier: 3.967A pdb=" N LEU A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 325 removed outlier: 3.847A pdb=" N VAL A 325 " --> pdb=" O THR A 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 325' Processing helix chain 'A' and resid 326 through 340 removed outlier: 3.505A pdb=" N MET A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 353 removed outlier: 3.569A pdb=" N GLN A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 378 through 400 Processing helix chain 'A' and resid 403 through 411 removed outlier: 3.663A pdb=" N GLY A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 431 Processing helix chain 'A' and resid 438 through 448 Processing helix chain 'A' and resid 450 through 457 removed outlier: 3.617A pdb=" N LYS A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.505A pdb=" N TRP A 473 " --> pdb=" O THR A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 490 removed outlier: 3.732A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.885A pdb=" N GLN A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 536 removed outlier: 3.646A pdb=" N TYR A 530 " --> pdb=" O ARG A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 558 through 575 Processing helix chain 'A' and resid 595 through 615 removed outlier: 3.596A pdb=" N VAL A 611 " --> pdb=" O ASP A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 642 Proline residue: A 640 - end of helix Processing helix chain 'A' and resid 658 through 666 Processing helix chain 'A' and resid 676 through 686 removed outlier: 3.977A pdb=" N GLU A 680 " --> pdb=" O GLY A 676 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 707 Processing helix chain 'A' and resid 709 through 717 removed outlier: 3.929A pdb=" N TYR A 713 " --> pdb=" O LYS A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 729 Processing helix chain 'A' and resid 740 through 750 removed outlier: 3.502A pdb=" N LEU A 747 " --> pdb=" O LEU A 743 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 776 removed outlier: 3.738A pdb=" N LEU A 776 " --> pdb=" O GLU A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 790 removed outlier: 3.674A pdb=" N ASN A 787 " --> pdb=" O LYS A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 794 Processing helix chain 'A' and resid 795 through 807 removed outlier: 3.888A pdb=" N ASP A 805 " --> pdb=" O LYS A 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 27 removed outlier: 3.525A pdb=" N LYS B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 68 removed outlier: 3.588A pdb=" N ASN B 43 " --> pdb=" O HIS B 39 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 45 " --> pdb=" O TRP B 41 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 108 through 114 removed outlier: 3.893A pdb=" N ASP B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 141 removed outlier: 3.715A pdb=" N ASP B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 257 removed outlier: 3.541A pdb=" N ALA B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU B 257 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 267 removed outlier: 4.144A pdb=" N SER B 262 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLU B 263 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL B 265 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER B 266 " --> pdb=" O GLU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 303 removed outlier: 4.119A pdb=" N LEU B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 313 Processing helix chain 'B' and resid 322 through 325 Processing helix chain 'B' and resid 326 through 339 Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 371 through 378 Processing helix chain 'B' and resid 378 through 400 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 423 through 431 removed outlier: 3.564A pdb=" N VAL B 429 " --> pdb=" O TRP B 425 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 Processing helix chain 'B' and resid 450 through 457 removed outlier: 3.741A pdb=" N LYS B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 474 Processing helix chain 'B' and resid 478 through 490 removed outlier: 3.614A pdb=" N HIS B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 495 Processing helix chain 'B' and resid 496 through 504 removed outlier: 3.583A pdb=" N LEU B 499 " --> pdb=" O ASP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 536 removed outlier: 3.530A pdb=" N HIS B 514 " --> pdb=" O PRO B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 558 through 575 removed outlier: 3.706A pdb=" N HIS B 564 " --> pdb=" O MET B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 613 removed outlier: 3.780A pdb=" N VAL B 611 " --> pdb=" O ASP B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 removed outlier: 4.148A pdb=" N LEU B 622 " --> pdb=" O GLY B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 642 removed outlier: 3.677A pdb=" N LEU B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) Proline residue: B 640 - end of helix Processing helix chain 'B' and resid 657 through 666 removed outlier: 3.923A pdb=" N MET B 661 " --> pdb=" O GLY B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 686 removed outlier: 4.271A pdb=" N GLU B 680 " --> pdb=" O GLY B 676 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS B 684 " --> pdb=" O GLU B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 690 Processing helix chain 'B' and resid 696 through 707 Processing helix chain 'B' and resid 710 through 717 Processing helix chain 'B' and resid 717 through 730 removed outlier: 3.754A pdb=" N HIS B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 749 removed outlier: 3.735A pdb=" N LEU B 747 " --> pdb=" O LEU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 775 removed outlier: 3.618A pdb=" N LYS B 769 " --> pdb=" O ASP B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 791 removed outlier: 3.502A pdb=" N ALA B 782 " --> pdb=" O GLU B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 794 No H-bonds generated for 'chain 'B' and resid 792 through 794' Processing helix chain 'B' and resid 795 through 807 Processing helix chain 'C' and resid 14 through 27 Processing helix chain 'C' and resid 37 through 68 removed outlier: 3.613A pdb=" N ASN C 43 " --> pdb=" O HIS C 39 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR C 45 " --> pdb=" O TRP C 41 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 93 removed outlier: 3.520A pdb=" N LEU C 90 " --> pdb=" O SER C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 108 through 114 removed outlier: 3.898A pdb=" N ASP C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 141 removed outlier: 3.522A pdb=" N ASP C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 246 removed outlier: 4.051A pdb=" N LYS C 246 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 257 removed outlier: 3.561A pdb=" N ALA C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU C 257 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 267 removed outlier: 4.088A pdb=" N SER C 262 " --> pdb=" O LYS C 259 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLU C 263 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL C 265 " --> pdb=" O SER C 262 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER C 266 " --> pdb=" O GLU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 278 through 303 removed outlier: 3.538A pdb=" N ARG C 282 " --> pdb=" O GLY C 278 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 313 Processing helix chain 'C' and resid 323 through 325 No H-bonds generated for 'chain 'C' and resid 323 through 325' Processing helix chain 'C' and resid 326 through 340 removed outlier: 3.916A pdb=" N GLN C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 371 through 378 Processing helix chain 'C' and resid 378 through 400 removed outlier: 3.508A pdb=" N PHE C 386 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 411 removed outlier: 3.583A pdb=" N LEU C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 418 removed outlier: 3.604A pdb=" N GLY C 418 " --> pdb=" O GLU C 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 415 through 418' Processing helix chain 'C' and resid 423 through 431 Processing helix chain 'C' and resid 438 through 448 Processing helix chain 'C' and resid 450 through 457 removed outlier: 3.861A pdb=" N LYS C 455 " --> pdb=" O ALA C 451 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 456 " --> pdb=" O ASP C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.581A pdb=" N TRP C 473 " --> pdb=" O THR C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 490 removed outlier: 3.519A pdb=" N HIS C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 495 Processing helix chain 'C' and resid 496 through 506 removed outlier: 4.275A pdb=" N GLN C 504 " --> pdb=" O ASN C 501 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS C 506 " --> pdb=" O LEU C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 536 Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 558 through 575 removed outlier: 3.716A pdb=" N HIS C 564 " --> pdb=" O MET C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 615 removed outlier: 3.974A pdb=" N VAL C 611 " --> pdb=" O ASP C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 620 No H-bonds generated for 'chain 'C' and resid 618 through 620' Processing helix chain 'C' and resid 631 through 642 removed outlier: 3.641A pdb=" N LEU C 637 " --> pdb=" O SER C 633 " (cutoff:3.500A) Proline residue: C 640 - end of helix Processing helix chain 'C' and resid 657 through 666 removed outlier: 4.260A pdb=" N MET C 661 " --> pdb=" O GLY C 657 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LLP C 662 " --> pdb=" O THR C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 686 removed outlier: 3.909A pdb=" N GLU C 680 " --> pdb=" O GLY C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 690 removed outlier: 3.779A pdb=" N ILE C 690 " --> pdb=" O ALA C 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 687 through 690' Processing helix chain 'C' and resid 696 through 707 Processing helix chain 'C' and resid 709 through 717 removed outlier: 3.961A pdb=" N TYR C 713 " --> pdb=" O LYS C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 729 Processing helix chain 'C' and resid 740 through 750 removed outlier: 3.741A pdb=" N LEU C 747 " --> pdb=" O LEU C 743 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 775 Processing helix chain 'C' and resid 776 through 790 removed outlier: 3.531A pdb=" N ALA C 782 " --> pdb=" O GLU C 778 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 790 " --> pdb=" O LEU C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 794 Processing helix chain 'C' and resid 795 through 807 removed outlier: 3.519A pdb=" N ASP C 805 " --> pdb=" O LYS C 801 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 27 Processing helix chain 'D' and resid 32 through 36 removed outlier: 3.563A pdb=" N ALA D 36 " --> pdb=" O PRO D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 42 Processing helix chain 'D' and resid 42 through 68 removed outlier: 3.971A pdb=" N ALA D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ARG D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 93 removed outlier: 3.585A pdb=" N LEU D 90 " --> pdb=" O SER D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 105 Processing helix chain 'D' and resid 108 through 116 removed outlier: 3.619A pdb=" N ASP D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 141 Processing helix chain 'D' and resid 251 through 257 removed outlier: 3.524A pdb=" N ALA D 255 " --> pdb=" O ASP D 251 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU D 257 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 267 removed outlier: 4.298A pdb=" N SER D 262 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLU D 263 " --> pdb=" O ASN D 260 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL D 265 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER D 266 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 306 removed outlier: 4.347A pdb=" N GLU D 280 " --> pdb=" O TYR D 276 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 304 " --> pdb=" O ARG D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 313 Processing helix chain 'D' and resid 323 through 325 No H-bonds generated for 'chain 'D' and resid 323 through 325' Processing helix chain 'D' and resid 326 through 338 Processing helix chain 'D' and resid 342 through 353 Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 371 through 376 Processing helix chain 'D' and resid 378 through 400 Processing helix chain 'D' and resid 403 through 411 Processing helix chain 'D' and resid 415 through 418 removed outlier: 4.218A pdb=" N GLY D 418 " --> pdb=" O GLU D 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 415 through 418' Processing helix chain 'D' and resid 423 through 431 Processing helix chain 'D' and resid 438 through 448 removed outlier: 3.551A pdb=" N LEU D 444 " --> pdb=" O LEU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 457 removed outlier: 3.635A pdb=" N LYS D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 474 Processing helix chain 'D' and resid 478 through 490 removed outlier: 3.579A pdb=" N VAL D 484 " --> pdb=" O SER D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 495 Processing helix chain 'D' and resid 496 through 504 Processing helix chain 'D' and resid 511 through 536 removed outlier: 3.621A pdb=" N TYR D 530 " --> pdb=" O ARG D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 556 Processing helix chain 'D' and resid 557 through 575 removed outlier: 3.875A pdb=" N ASN D 561 " --> pdb=" O ARG D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 615 removed outlier: 3.586A pdb=" N VAL D 611 " --> pdb=" O ASP D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 642 Proline residue: D 640 - end of helix Processing helix chain 'D' and resid 658 through 666 Processing helix chain 'D' and resid 676 through 686 removed outlier: 4.122A pdb=" N GLU D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 707 Processing helix chain 'D' and resid 709 through 717 removed outlier: 3.858A pdb=" N TYR D 713 " --> pdb=" O LYS D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 729 Processing helix chain 'D' and resid 740 through 750 removed outlier: 3.687A pdb=" N PHE D 750 " --> pdb=" O SER D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 775 removed outlier: 4.144A pdb=" N ASP D 759 " --> pdb=" O GLN D 755 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG D 761 " --> pdb=" O LEU D 757 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER D 762 " --> pdb=" O ALA D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 776 through 790 removed outlier: 3.706A pdb=" N ASN D 787 " --> pdb=" O LYS D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 794 Processing helix chain 'D' and resid 795 through 807 removed outlier: 3.617A pdb=" N THR D 799 " --> pdb=" O SER D 795 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP D 805 " --> pdb=" O LYS D 801 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 192 removed outlier: 10.306A pdb=" N HIS A 184 " --> pdb=" O ASP A 217 " (cutoff:3.500A) removed outlier: 11.053A pdb=" N ASP A 217 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A 186 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 220 " --> pdb=" O ASN A 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192 removed outlier: 10.306A pdb=" N HIS A 184 " --> pdb=" O ASP A 217 " (cutoff:3.500A) removed outlier: 11.053A pdb=" N ASP A 217 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A 186 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLY A 144 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N ARG A 232 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY A 146 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N TRP A 234 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLY A 148 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N ALA A 236 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLN A 71 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N HIS A 318 " --> pdb=" O GLN A 71 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR A 73 " --> pdb=" O HIS A 318 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N SER A 355 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 317 " --> pdb=" O SER A 355 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N THR A 357 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS A 433 " --> pdb=" O PHE A 354 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 157 through 161 Processing sheet with id=AA4, first strand: chain 'A' and resid 195 through 199 Processing sheet with id=AA5, first strand: chain 'A' and resid 368 through 370 Processing sheet with id=AA6, first strand: chain 'A' and resid 622 through 627 removed outlier: 6.566A pdb=" N LEU A 544 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE A 586 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASP A 546 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLY A 588 " --> pdb=" O ASP A 546 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLN A 548 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE A 549 " --> pdb=" O GLU A 646 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N SER A 645 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N THR A 673 " --> pdb=" O SER A 645 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLN A 647 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 691 " --> pdb=" O THR A 670 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 190 removed outlier: 12.256A pdb=" N LYS B 182 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 11.629A pdb=" N ILE B 219 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 10.352A pdb=" N HIS B 184 " --> pdb=" O ASP B 217 " (cutoff:3.500A) removed outlier: 11.140A pdb=" N ASP B 217 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR B 186 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR B 230 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP B 234 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 72 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N TYR B 147 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR B 74 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N ILE B 149 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLN B 71 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N HIS B 318 " --> pdb=" O GLN B 71 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR B 73 " --> pdb=" O HIS B 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 157 through 161 Processing sheet with id=AA9, first strand: chain 'B' and resid 195 through 199 Processing sheet with id=AB1, first strand: chain 'B' and resid 355 through 357 removed outlier: 6.654A pdb=" N TYR B 356 " --> pdb=" O ASN B 435 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL B 434 " --> pdb=" O THR B 462 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 368 through 370 Processing sheet with id=AB3, first strand: chain 'B' and resid 623 through 626 removed outlier: 6.804A pdb=" N PHE B 545 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLU B 646 " --> pdb=" O PHE B 545 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL B 547 " --> pdb=" O GLU B 646 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N SER B 645 " --> pdb=" O ILE B 671 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N THR B 673 " --> pdb=" O SER B 645 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLN B 647 " --> pdb=" O THR B 673 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR B 670 " --> pdb=" O PHE B 691 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE B 693 " --> pdb=" O THR B 670 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY B 672 " --> pdb=" O PHE B 693 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 229 through 238 removed outlier: 4.436A pdb=" N THR C 230 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL C 72 " --> pdb=" O ARG C 145 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N TYR C 147 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR C 74 " --> pdb=" O TYR C 147 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ILE C 149 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN C 71 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N HIS C 318 " --> pdb=" O GLN C 71 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR C 73 " --> pdb=" O HIS C 318 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 159 Processing sheet with id=AB6, first strand: chain 'C' and resid 181 through 192 removed outlier: 4.063A pdb=" N ALA C 215 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N ASN C 185 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N GLY C 213 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N ARG C 187 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 10.142A pdb=" N ILE C 211 " --> pdb=" O ARG C 187 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N LYS C 189 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N GLU C 209 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 195 through 198 Processing sheet with id=AB8, first strand: chain 'C' and resid 355 through 358 removed outlier: 3.591A pdb=" N ASN C 358 " --> pdb=" O ASN C 435 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL C 434 " --> pdb=" O THR C 462 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 368 through 370 Processing sheet with id=AC1, first strand: chain 'C' and resid 622 through 626 removed outlier: 5.800A pdb=" N LEU C 544 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE C 586 " --> pdb=" O LEU C 544 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP C 546 " --> pdb=" O ILE C 586 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE C 545 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N GLU C 646 " --> pdb=" O PHE C 545 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL C 547 " --> pdb=" O GLU C 646 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER C 645 " --> pdb=" O ILE C 671 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N THR C 673 " --> pdb=" O SER C 645 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLN C 647 " --> pdb=" O THR C 673 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR C 670 " --> pdb=" O PHE C 691 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N PHE C 693 " --> pdb=" O THR C 670 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLY C 672 " --> pdb=" O PHE C 693 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 183 through 192 removed outlier: 4.017A pdb=" N ALA D 215 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ASN D 185 " --> pdb=" O GLY D 213 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N GLY D 213 " --> pdb=" O ASN D 185 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N ARG D 187 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N ILE D 211 " --> pdb=" O ARG D 187 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N LYS D 189 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N GLU D 209 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU D 231 " --> pdb=" O GLN D 218 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 220 " --> pdb=" O ASN D 229 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLY D 144 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ARG D 232 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY D 146 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N TRP D 234 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLY D 148 " --> pdb=" O TRP D 234 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N ALA D 236 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL D 72 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N TYR D 147 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR D 74 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N ILE D 149 " --> pdb=" O TYR D 74 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN D 71 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N HIS D 318 " --> pdb=" O GLN D 71 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TYR D 73 " --> pdb=" O HIS D 318 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N SER D 355 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE D 317 " --> pdb=" O SER D 355 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N THR D 357 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS D 433 " --> pdb=" O PHE D 354 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL D 434 " --> pdb=" O THR D 462 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 157 through 161 Processing sheet with id=AC4, first strand: chain 'D' and resid 195 through 199 Processing sheet with id=AC5, first strand: chain 'D' and resid 368 through 370 Processing sheet with id=AC6, first strand: chain 'D' and resid 622 through 626 removed outlier: 6.338A pdb=" N LEU D 544 " --> pdb=" O VAL D 584 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILE D 586 " --> pdb=" O LEU D 544 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP D 546 " --> pdb=" O ILE D 586 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLY D 588 " --> pdb=" O ASP D 546 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLN D 548 " --> pdb=" O GLY D 588 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE D 549 " --> pdb=" O GLU D 646 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N SER D 645 " --> pdb=" O ILE D 671 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N THR D 673 " --> pdb=" O SER D 645 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLN D 647 " --> pdb=" O THR D 673 " (cutoff:3.500A) 1294 hydrogen bonds defined for protein. 3610 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: 5.14 Time building geometry restraints manager: 3.13 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: 7878 1.34 - 1.46: 5357 1.46 - 1.58: 11086 1.58 - 1.69: 4 1.69 - 1.81: 139 Bond restraints: 24464 Sorted by residual: bond pdb=" NZ LLP B 662 " pdb=" C4' LLP B 662 " ideal model delta sigma weight residual 1.273 1.431 -0.158 2.00e-02 2.50e+03 6.25e+01 bond pdb=" NZ LLP C 662 " pdb=" C4' LLP C 662 " ideal model delta sigma weight residual 1.273 1.430 -0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" NZ LLP A 662 " pdb=" C4' LLP A 662 " ideal model delta sigma weight residual 1.273 1.429 -0.156 2.00e-02 2.50e+03 6.12e+01 bond pdb=" NZ LLP D 662 " pdb=" C4' LLP D 662 " ideal model delta sigma weight residual 1.273 1.429 -0.156 2.00e-02 2.50e+03 6.09e+01 bond pdb=" OP4 LLP D 662 " pdb=" P LLP D 662 " ideal model delta sigma weight residual 1.726 1.608 0.118 2.00e-02 2.50e+03 3.49e+01 ... (remaining 24459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.75: 33399 5.75 - 11.51: 24 11.51 - 17.26: 1 17.26 - 23.02: 2 23.02 - 28.77: 1 Bond angle restraints: 33427 Sorted by residual: angle pdb=" CE LLP C 662 " pdb=" NZ LLP C 662 " pdb=" C4' LLP C 662 " ideal model delta sigma weight residual 119.26 90.49 28.77 3.00e+00 1.11e-01 9.20e+01 angle pdb=" NZ LLP B 662 " pdb=" C4' LLP B 662 " pdb=" C4 LLP B 662 " ideal model delta sigma weight residual 120.09 142.93 -22.84 3.00e+00 1.11e-01 5.80e+01 angle pdb=" C HIS C 806 " pdb=" CA AHIS C 806 " pdb=" CB AHIS C 806 " ideal model delta sigma weight residual 109.80 119.35 -9.55 1.61e+00 3.86e-01 3.52e+01 angle pdb=" C HIS B 806 " pdb=" CA AHIS B 806 " pdb=" CB AHIS B 806 " ideal model delta sigma weight residual 109.80 119.32 -9.52 1.61e+00 3.86e-01 3.50e+01 angle pdb=" CE LLP D 662 " pdb=" NZ LLP D 662 " pdb=" C4' LLP D 662 " ideal model delta sigma weight residual 119.26 101.65 17.61 3.00e+00 1.11e-01 3.45e+01 ... (remaining 33422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 13716 17.72 - 35.44: 453 35.44 - 53.16: 70 53.16 - 70.88: 14 70.88 - 88.60: 12 Dihedral angle restraints: 14265 sinusoidal: 4904 harmonic: 9361 Sorted by residual: dihedral pdb=" C HIS C 806 " pdb=" N HIS C 806 " pdb=" CA AHIS C 806 " pdb=" CB AHIS C 806 " ideal model delta harmonic sigma weight residual -122.60 -136.14 13.54 0 2.50e+00 1.60e-01 2.93e+01 dihedral pdb=" C HIS B 806 " pdb=" N HIS B 806 " pdb=" CA AHIS B 806 " pdb=" CB AHIS B 806 " ideal model delta harmonic sigma weight residual -122.60 -136.10 13.50 0 2.50e+00 1.60e-01 2.92e+01 dihedral pdb=" C HIS C 806 " pdb=" N HIS C 806 " pdb=" CA BHIS C 806 " pdb=" CB BHIS C 806 " ideal model delta harmonic sigma weight residual -122.60 -132.28 9.68 0 2.50e+00 1.60e-01 1.50e+01 ... (remaining 14262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3655 0.081 - 0.162: 205 0.162 - 0.243: 0 0.243 - 0.323: 2 0.323 - 0.404: 2 Chirality restraints: 3864 Sorted by residual: chirality pdb=" CA AHIS C 806 " pdb=" N HIS C 806 " pdb=" C HIS C 806 " pdb=" CB AHIS C 806 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA AHIS B 806 " pdb=" N HIS B 806 " pdb=" C HIS B 806 " pdb=" CB AHIS B 806 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA BHIS C 806 " pdb=" N HIS C 806 " pdb=" C HIS C 806 " pdb=" CB BHIS C 806 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 3861 not shown) Planarity restraints: 4272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP C 662 " 0.025 2.00e-02 2.50e+03 2.30e-01 5.30e+02 pdb=" NZ LLP C 662 " 0.170 2.00e-02 2.50e+03 pdb=" C4 LLP C 662 " 0.188 2.00e-02 2.50e+03 pdb=" C4' LLP C 662 " -0.383 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 LLP A 662 " -0.021 2.00e-02 2.50e+03 1.12e-01 3.14e+02 pdb=" C2' LLP A 662 " -0.060 2.00e-02 2.50e+03 pdb=" C3 LLP A 662 " 0.078 2.00e-02 2.50e+03 pdb=" C4 LLP A 662 " 0.119 2.00e-02 2.50e+03 pdb=" C4' LLP A 662 " -0.266 2.00e-02 2.50e+03 pdb=" C5 LLP A 662 " 0.049 2.00e-02 2.50e+03 pdb=" C5' LLP A 662 " 0.080 2.00e-02 2.50e+03 pdb=" C6 LLP A 662 " -0.033 2.00e-02 2.50e+03 pdb=" N1 LLP A 662 " -0.071 2.00e-02 2.50e+03 pdb=" O3 LLP A 662 " 0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 662 " 0.059 2.00e-02 2.50e+03 1.66e-01 2.75e+02 pdb=" NZ LLP B 662 " 0.065 2.00e-02 2.50e+03 pdb=" C4 LLP B 662 " 0.155 2.00e-02 2.50e+03 pdb=" C4' LLP B 662 " -0.279 2.00e-02 2.50e+03 ... (remaining 4269 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 175 2.49 - 3.09: 19209 3.09 - 3.69: 35962 3.69 - 4.30: 54739 4.30 - 4.90: 91905 Nonbonded interactions: 201990 Sorted by model distance: nonbonded pdb=" O LEU C 474 " pdb=" OG SER C 482 " model vdw 1.884 3.040 nonbonded pdb=" O ALA B 427 " pdb=" OG SER B 431 " model vdw 1.898 3.040 nonbonded pdb=" O LEU B 289 " pdb=" OG1 THR B 293 " model vdw 1.991 3.040 nonbonded pdb=" O LEU C 289 " pdb=" OG1 THR C 293 " model vdw 1.995 3.040 nonbonded pdb=" OG SER B 442 " pdb=" OD1 ASN B 463 " model vdw 2.034 3.040 ... (remaining 201985 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 'A' and ((resid 13 and (name N or name CA or name C or name O or name CB \ )) or resid 14 or (resid 15 through 16 and (name N or name CA or name C or name \ O or name CB )) or resid 17 or (resid 18 through 19 and (name N or name CA or na \ me C or name O or name CB )) or resid 20 through 37 or (resid 38 through 40 and \ (name N or name CA or name C or name O or name CB )) or resid 41 through 48 or ( \ resid 49 and (name N or name CA or name C or name O or name CB )) or resid 50 or \ (resid 51 and (name N or name CA or name C or name O or name CB )) or resid 52 \ through 77 or (resid 78 and (name N or name CA or name C or name O or name CB )) \ or resid 79 through 89 or (resid 90 and (name N or name CA or name C or name O \ or name CB )) or resid 91 through 96 or (resid 97 and (name N or name CA or name \ C or name O or name CB )) or resid 98 through 107 or (resid 108 and (name N or \ name CA or name C or name O or name CB )) or resid 109 through 134 or (resid 135 \ through 136 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 37 through 156 or (resid 157 and (name N or name CA or name C or name O or name \ CB )) or resid 158 or (resid 159 and (name N or name CA or name C or name O or n \ ame CB )) or resid 160 or (resid 161 and (name N or name CA or name C or name O \ or name CB )) or resid 162 through 165 or (resid 166 through 167 and (name N or \ name CA or name C or name O or name CB )) or resid 168 through 184 or (resid 185 \ and (name N or name CA or name C or name O or name CB )) or resid 186 through 1 \ 88 or (resid 189 and (name N or name CA or name C or name O or name CB )) or res \ id 190 through 196 or (resid 197 through 199 and (name N or name CA or name C or \ name O or name CB )) or resid 200 through 203 or (resid 204 and (name N or name \ CA or name C or name O or name CB )) or resid 205 through 206 or (resid 207 and \ (name N or name CA or name C or name O or name CB )) or resid 208 through 209 o \ r (resid 210 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 11 through 225 or (resid 226 through 227 and (name N or name CA or name C or nam \ e O or name CB )) or resid 228 through 261 or (resid 262 through 263 and (name N \ or name CA or name C or name O or name CB )) or resid 264 through 278 or (resid \ 279 through 280 and (name N or name CA or name C or name O or name CB )) or res \ id 281 through 285 or (resid 286 and (name N or name CA or name C or name O or n \ ame CB )) or resid 287 through 301 or (resid 302 through 303 and (name N or name \ CA or name C or name O or name CB )) or resid 304 through 320 or (resid 321 thr \ ough 322 and (name N or name CA or name C or name O or name CB )) or resid 323 t \ hrough 329 or (resid 330 and (name N or name CA or name C or name O or name CB ) \ ) or resid 331 through 350 or (resid 351 through 352 and (name N or name CA or n \ ame C or name O or name CB )) or resid 353 through 357 or (resid 358 and (name N \ or name CA or name C or name O or name CB )) or resid 359 through 361 or (resid \ 362 and (name N or name CA or name C or name O or name CB )) or resid 363 throu \ gh 389 or (resid 390 and (name N or name CA or name C or name O or name CB )) or \ resid 391 through 394 or (resid 395 and (name N or name CA or name C or name O \ or name CB )) or resid 396 through 398 or (resid 399 and (name N or name CA or n \ ame C or name O or name CB )) or resid 400 through 408 or (resid 409 through 410 \ and (name N or name CA or name C or name O or name CB )) or resid 411 through 4 \ 12 or (resid 413 through 415 and (name N or name CA or name C or name O or name \ CB )) or resid 416 or (resid 417 and (name N or name CA or name C or name O or n \ ame CB )) or resid 418 or (resid 419 and (name N or name CA or name C or name O \ or name CB )) or resid 420 through 430 or (resid 431 and (name N or name CA or n \ ame C or name O or name CB )) or resid 432 through 441 or (resid 442 and (name N \ or name CA or name C or name O or name CB )) or resid 443 or (resid 444 and (na \ me N or name CA or name C or name O or name CB )) or resid 445 through 446 or (r \ esid 447 and (name N or name CA or name C or name O or name CB )) or resid 448 o \ r (resid 449 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 50 through 462 or (resid 463 and (name N or name CA or name C or name O or name \ CB )) or resid 464 through 468 or (resid 469 and (name N or name CA or name C or \ name O or name CB )) or resid 470 through 480 or (resid 481 through 483 and (na \ me N or name CA or name C or name O or name CB )) or resid 484 through 493 or (r \ esid 494 and (name N or name CA or name C or name O or name CB )) or resid 495 t \ hrough 497 or (resid 498 and (name N or name CA or name C or name O or name CB ) \ ) or resid 499 through 503 or (resid 504 through 507 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 510 through 513 and (name N or name CA o \ r name C or name O or name CB )) or resid 514 through 517 or (resid 518 through \ 519 and (name N or name CA or name C or name O or name CB )) or resid 520 throug \ h 533 or (resid 534 and (name N or name CA or name C or name O or name CB )) or \ resid 535 through 572 or (resid 573 through 575 and (name N or name CA or name C \ or name O or name CB )) or resid 576 through 579 or (resid 580 and (name N or n \ ame CA or name C or name O or name CB )) or resid 581 through 595 or (resid 596 \ and (name N or name CA or name C or name O or name CB )) or resid 597 through 62 \ 0 or (resid 621 and (name N or name CA or name C or name O or name CB )) or resi \ d 622 through 653 or (resid 654 through 656 and (name N or name CA or name C or \ name O or name CB )) or resid 657 through 658 or (resid 659 and (name N or name \ CA or name C or name O or name CB )) or resid 660 through 664 or (resid 665 and \ (name N or name CA or name C or name O or name CB )) or resid 666 through 674 or \ (resid 675 and (name N or name CA or name C or name O or name CB )) or (resid 6 \ 76 through 678 and (name N or name CA or name C or name O or name CB )) or resid \ 679 or (resid 680 and (name N or name CA or name C or name O or name CB )) or r \ esid 681 through 682 or (resid 683 and (name N or name CA or name C or name O or \ name CB )) or resid 684 through 687 or (resid 688 through 689 and (name N or na \ me CA or name C or name O or name CB )) or resid 690 through 718 or (resid 719 a \ nd (name N or name CA or name C or name O or name CB )) or resid 720 through 723 \ or (resid 724 and (name N or name CA or name C or name O or name CB )) or resid \ 725 through 735 or (resid 736 and (name N or name CA or name C or name O or nam \ e CB )) or resid 737 through 740 or (resid 741 through 742 and (name N or name C \ A or name C or name O or name CB )) or resid 743 through 748 or (resid 749 and ( \ name N or name CA or name C or name O or name CB )) or resid 750 through 758 or \ (resid 759 and (name N or name CA or name C or name O or name CB )) or resid 760 \ through 764 or (resid 765 through 766 and (name N or name CA or name C or name \ O or name CB )) or resid 767 or (resid 768 through 769 and (name N or name CA or \ name C or name O or name CB )) or resid 770 through 782 or (resid 783 through 7 \ 86 and (name N or name CA or name C or name O or name CB )) or resid 787 through \ 795 or (resid 796 and (name N or name CA or name C or name O or name CB )) or r \ esid 797 or (resid 798 and (name N or name CA or name C or name O or name CB )) \ or resid 799 through 801 or (resid 802 and (name N or name CA or name C or name \ O or name CB )) or resid 803 through 805 or resid 807 through 813)) selection = (chain 'B' and (resid 13 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 or (resid 34 through 36 and (name N or nam \ e CA or name C or name O or name CB )) or resid 37 through 48 or (resid 49 and ( \ name N or name CA or name C or name O or name CB )) or resid 50 through 59 or (r \ esid 60 and (name N or name CA or name C or name O or name CB )) or resid 61 thr \ ough 64 or (resid 65 through 68 and (name N or name CA or name C or name O or na \ me CB )) or resid 69 through 77 or (resid 78 and (name N or name CA or name C or \ name O or name CB )) or resid 79 through 96 or (resid 97 and (name N or name CA \ or name C or name O or name CB )) or resid 98 through 174 or (resid 175 and (na \ me N or name CA or name C or name O or name CB )) or resid 176 through 196 or (r \ esid 197 through 199 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 209 or (resid 210 and (name N or name CA or name C or name O \ or name CB )) or resid 211 through 247 or (resid 248 through 249 and (name N or \ name CA or name C or name O or name CB )) or resid 250 through 257 or (resid 258 \ through 260 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 61 through 265 or (resid 266 and (name N or name CA or name C or name O or name \ CB )) or resid 267 through 278 or (resid 279 through 280 and (name N or name CA \ or name C or name O or name CB )) or resid 281 through 285 or (resid 286 and (na \ me N or name CA or name C or name O or name CB )) or resid 287 through 301 or (r \ esid 302 through 303 and (name N or name CA or name C or name O or name CB )) or \ resid 304 through 312 or (resid 313 through 314 and (name N or name CA or name \ C or name O or name CB )) or resid 315 through 350 or (resid 351 through 352 and \ (name N or name CA or name C or name O or name CB )) or resid 353 through 357 o \ r (resid 358 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 59 through 361 or (resid 362 and (name N or name CA or name C or name O or name \ CB )) or resid 363 through 371 or (resid 372 and (name N or name CA or name C or \ name O or name CB )) or resid 373 through 402 or (resid 403 through 405 and (na \ me N or name CA or name C or name O or name CB )) or resid 406 through 408 or (r \ esid 409 through 410 and (name N or name CA or name C or name O or name CB )) or \ resid 411 through 430 or (resid 431 and (name N or name CA or name C or name O \ or name CB )) or resid 432 through 439 or (resid 440 and (name N or name CA or n \ ame C or name O or name CB )) or resid 441 or (resid 442 and (name N or name CA \ or name C or name O or name CB )) or resid 443 or (resid 444 and (name N or name \ CA or name C or name O or name CB )) or resid 445 through 448 or (resid 449 and \ (name N or name CA or name C or name O or name CB )) or resid 450 through 462 o \ r (resid 463 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 64 through 480 or (resid 481 through 483 and (name N or name CA or name C or nam \ e O or name CB )) or resid 484 through 497 or (resid 498 and (name N or name CA \ or name C or name O or name CB )) or resid 499 through 507 or resid 510 through \ 595 or (resid 596 and (name N or name CA or name C or name O or name CB )) or re \ sid 597 through 606 or (resid 607 and (name N or name CA or name C or name O or \ name CB )) or resid 608 through 616 or (resid 617 and (name N or name CA or name \ C or name O or name CB )) or resid 618 through 620 or (resid 621 and (name N or \ name CA or name C or name O or name CB )) or resid 622 through 655 or (resid 65 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 657 through \ 658 or (resid 659 and (name N or name CA or name C or name O or name CB )) or re \ sid 660 through 677 or (resid 678 and (name N or name CA or name C or name O or \ name CB )) or resid 679 or (resid 680 and (name N or name CA or name C or name O \ or name CB )) or resid 681 through 682 or (resid 683 and (name N or name CA or \ name C or name O or name CB )) or resid 684 through 688 or (resid 689 and (name \ N or name CA or name C or name O or name CB )) or resid 690 through 723 or (resi \ d 724 and (name N or name CA or name C or name O or name CB )) or resid 725 thro \ ugh 740 or (resid 741 through 742 and (name N or name CA or name C or name O or \ name CB )) or resid 743 through 748 or (resid 749 and (name N or name CA or name \ C or name O or name CB )) or resid 750 through 765 or (resid 766 and (name N or \ name CA or name C or name O or name CB )) or resid 767 or (resid 768 through 76 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 770 through \ 772 or (resid 773 and (name N or name CA or name C or name O or name CB )) or re \ sid 774 through 782 or (resid 783 through 786 and (name N or name CA or name C o \ r name O or name CB )) or resid 787 through 795 or (resid 796 and (name N or nam \ e CA or name C or name O or name CB )) or resid 797 or (resid 798 and (name N or \ name CA or name C or name O or name CB )) or resid 799 or (resid 800 through 80 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 803 through \ 805 or resid 807 through 813)) selection = (chain 'C' and ((resid 13 and (name N or name CA or name C or name O or name CB \ )) or resid 14 through 31 or (resid 32 and (name N or name CA or name C or name \ O or name CB )) or resid 33 or (resid 34 through 36 and (name N or name CA or na \ me C or name O or name CB )) or resid 37 through 59 or (resid 60 and (name N or \ name CA or name C or name O or name CB )) or resid 61 through 65 or (resid 66 th \ rough 68 and (name N or name CA or name C or name O or name CB )) or resid 69 th \ rough 89 or (resid 90 and (name N or name CA or name C or name O or name CB )) o \ r resid 91 through 131 or (resid 132 and (name N or name CA or name C or name O \ or name CB )) or resid 133 through 134 or (resid 135 through 136 and (name N or \ name CA or name C or name O or name CB )) or resid 137 through 156 or (resid 157 \ and (name N or name CA or name C or name O or name CB )) or resid 158 or (resid \ 159 and (name N or name CA or name C or name O or name CB )) or resid 160 or (r \ esid 161 and (name N or name CA or name C or name O or name CB )) or resid 162 t \ hrough 165 or (resid 166 through 167 and (name N or name CA or name C or name O \ or name CB )) or resid 168 through 174 or (resid 175 and (name N or name CA or n \ ame C or name O or name CB )) or resid 176 through 245 or (resid 246 and (name N \ or name CA or name C or name O or name CB )) or resid 247 or (resid 248 through \ 249 and (name N or name CA or name C or name O or name CB )) or resid 250 throu \ gh 257 or (resid 258 through 260 and (name N or name CA or name C or name O or n \ ame CB )) or resid 261 through 265 or (resid 266 and (name N or name CA or name \ C or name O or name CB )) or resid 267 through 274 or (resid 275 through 277 and \ (name N or name CA or name C or name O or name CB )) or resid 278 or (resid 279 \ through 280 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 81 through 305 or (resid 306 and (name N or name CA or name C or name O or name \ CB )) or resid 307 through 312 or (resid 313 through 314 and (name N or name CA \ or name C or name O or name CB )) or resid 315 through 321 or (resid 322 and (na \ me N or name CA or name C or name O or name CB )) or resid 323 through 394 or (r \ esid 395 and (name N or name CA or name C or name O or name CB )) or resid 396 t \ hrough 398 or (resid 399 and (name N or name CA or name C or name O or name CB ) \ ) or resid 400 through 403 or (resid 404 through 405 and (name N or name CA or n \ ame C or name O or name CB )) or resid 406 through 412 or (resid 413 through 415 \ and (name N or name CA or name C or name O or name CB )) or resid 416 through 4 \ 18 or (resid 419 and (name N or name CA or name C or name O or name CB )) or res \ id 420 through 439 or (resid 440 and (name N or name CA or name C or name O or n \ ame CB )) or resid 441 through 462 or (resid 463 and (name N or name CA or name \ C or name O or name CB )) or resid 464 through 468 or (resid 469 and (name N or \ name CA or name C or name O or name CB )) or resid 470 through 480 or (resid 481 \ through 483 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 84 through 493 or (resid 494 and (name N or name CA or name C or name O or name \ CB )) or resid 495 through 503 or (resid 504 through 507 and (name N or name CA \ or name C or name O or name CB )) or (resid 510 through 513 and (name N or name \ CA or name C or name O or name CB )) or resid 514 through 533 or (resid 534 and \ (name N or name CA or name C or name O or name CB )) or resid 535 through 572 or \ (resid 573 through 575 and (name N or name CA or name C or name O or name CB )) \ or resid 576 through 579 or (resid 580 and (name N or name CA or name C or name \ O or name CB )) or resid 581 through 616 or (resid 617 and (name N or name CA o \ r name C or name O or name CB )) or resid 618 through 655 or (resid 656 and (nam \ e N or name CA or name C or name O or name CB )) or resid 657 through 658 or (re \ sid 659 and (name N or name CA or name C or name O or name CB )) or resid 660 th \ rough 674 or (resid 675 and (name N or name CA or name C or name O or name CB )) \ or resid 676 through 772 or (resid 773 and (name N or name CA or name C or name \ O or name CB )) or resid 774 through 797 or (resid 798 and (name N or name CA o \ r name C or name O or name CB )) or resid 799 or (resid 800 through 802 and (nam \ e N or name CA or name C or name O or name CB )) or resid 803 through 805 or res \ id 807 through 813)) selection = (chain 'D' and ((resid 13 and (name N or name CA or name C or name O or name CB \ )) or resid 14 through 31 or (resid 32 and (name N or name CA or name C or name \ O or name CB )) or resid 33 or (resid 34 through 36 and (name N or name CA or na \ me C or name O or name CB )) or resid 37 through 39 or (resid 40 and (name N or \ name CA or name C or name O or name CB )) or resid 41 through 48 or (resid 49 an \ d (name N or name CA or name C or name O or name CB )) or resid 50 or (resid 51 \ and (name N or name CA or name C or name O or name CB )) or resid 52 through 59 \ or (resid 60 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 1 through 65 or (resid 66 through 68 and (name N or name CA or name C or name O \ or name CB )) or resid 69 through 70 or (resid 71 and (name N or name CA or name \ C or name O or name CB )) or resid 72 through 77 or (resid 78 and (name N or na \ me CA or name C or name O or name CB )) or resid 79 through 96 or (resid 97 and \ (name N or name CA or name C or name O or name CB )) or resid 98 through 107 or \ (resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 113 or (resid 114 through 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 134 or (resid 135 through 136 and (name N o \ r name CA or name C or name O or name CB )) or resid 137 through 156 or (resid 1 \ 57 and (name N or name CA or name C or name O or name CB )) or resid 158 or (res \ id 159 and (name N or name CA or name C or name O or name CB )) or resid 160 or \ (resid 161 and (name N or name CA or name C or name O or name CB )) or resid 162 \ through 165 or (resid 166 through 167 and (name N or name CA or name C or name \ O or name CB )) or resid 168 through 174 or (resid 175 and (name N or name CA or \ name C or name O or name CB )) or resid 176 through 184 or (resid 185 and (name \ N or name CA or name C or name O or name CB )) or resid 186 through 196 or (res \ id 197 through 199 and (name N or name CA or name C or name O or name CB )) or r \ esid 200 through 203 or (resid 204 and (name N or name CA or name C or name O or \ name CB )) or resid 205 through 206 or (resid 207 and (name N or name CA or nam \ e C or name O or name CB )) or resid 208 through 209 or (resid 210 and (name N o \ r name CA or name C or name O or name CB )) or resid 211 through 225 or (resid 2 \ 26 through 227 and (name N or name CA or name C or name O or name CB )) or resid \ 228 through 261 or (resid 262 through 263 and (name N or name CA or name C or n \ ame O or name CB )) or resid 264 through 265 or (resid 266 and (name N or name C \ A or name C or name O or name CB )) or resid 267 through 274 or (resid 275 throu \ gh 277 and (name N or name CA or name C or name O or name CB )) or resid 278 thr \ ough 301 or (resid 302 through 303 and (name N or name CA or name C or name O or \ name CB )) or resid 304 through 313 or (resid 314 and (name N or name CA or nam \ e C or name O or name CB )) or resid 315 through 321 or (resid 322 and (name N o \ r name CA or name C or name O or name CB )) or resid 323 through 350 or (resid 3 \ 51 through 352 and (name N or name CA or name C or name O or name CB )) or resid \ 353 through 357 or (resid 358 and (name N or name CA or name C or name O or nam \ e CB )) or resid 359 through 366 or (resid 367 and (name N or name CA or name C \ or name O or name CB )) or resid 368 through 371 or (resid 372 and (name N or na \ me CA or name C or name O or name CB )) or resid 373 through 389 or (resid 390 a \ nd (name N or name CA or name C or name O or name CB )) or resid 391 through 394 \ or (resid 395 and (name N or name CA or name C or name O or name CB )) or resid \ 396 through 398 or (resid 399 and (name N or name CA or name C or name O or nam \ e CB )) or resid 400 through 408 or (resid 409 through 410 and (name N or name C \ A or name C or name O or name CB )) or resid 411 through 412 or (resid 413 throu \ gh 415 and (name N or name CA or name C or name O or name CB )) or resid 416 or \ (resid 417 and (name N or name CA or name C or name O or name CB )) or resid 418 \ or (resid 419 and (name N or name CA or name C or name O or name CB )) or resid \ 420 through 430 or (resid 431 and (name N or name CA or name C or name O or nam \ e CB )) or resid 432 through 441 or (resid 442 and (name N or name CA or name C \ or name O or name CB )) or resid 443 or (resid 444 and (name N or name CA or nam \ e C or name O or name CB )) or resid 445 through 446 or (resid 447 and (name N o \ r name CA or name C or name O or name CB )) or resid 448 or (resid 449 and (name \ N or name CA or name C or name O or name CB )) or resid 450 through 468 or (res \ id 469 and (name N or name CA or name C or name O or name CB )) or resid 470 thr \ ough 481 or (resid 482 through 483 and (name N or name CA or name C or name O or \ name CB )) or resid 484 through 485 or (resid 486 through 487 and (name N or na \ me CA or name C or name O or name CB )) or resid 488 through 491 or (resid 492 a \ nd (name N or name CA or name C or name O or name CB )) or resid 493 or (resid 4 \ 94 and (name N or name CA or name C or name O or name CB )) or resid 495 through \ 497 or (resid 498 and (name N or name CA or name C or name O or name CB )) or r \ esid 499 through 507 or resid 510 through 517 or (resid 518 through 519 and (nam \ e N or name CA or name C or name O or name CB )) or resid 520 through 532 or (re \ sid 533 through 534 and (name N or name CA or name C or name O or name CB )) or \ resid 535 or (resid 536 and (name N or name CA or name C or name O or name CB )) \ or resid 537 through 572 or (resid 573 through 575 and (name N or name CA or na \ me C or name O or name CB )) or resid 576 through 579 or (resid 580 and (name N \ or name CA or name C or name O or name CB )) or resid 581 through 595 or (resid \ 596 and (name N or name CA or name C or name O or name CB )) or resid 597 throug \ h 616 or (resid 617 and (name N or name CA or name C or name O or name CB )) or \ resid 618 through 653 or (resid 654 through 656 and (name N or name CA or name C \ or name O or name CB )) or resid 657 through 664 or (resid 665 and (name N or n \ ame CA or name C or name O or name CB )) or resid 666 through 677 or (resid 678 \ and (name N or name CA or name C or name O or name CB )) or resid 679 through 68 \ 8 or (resid 689 and (name N or name CA or name C or name O or name CB )) or resi \ d 690 through 723 or (resid 724 and (name N or name CA or name C or name O or na \ me CB )) or resid 725 through 740 or (resid 741 through 742 and (name N or name \ CA or name C or name O or name CB )) or resid 743 through 748 or (resid 749 and \ (name N or name CA or name C or name O or name CB )) or resid 750 through 758 or \ (resid 759 and (name N or name CA or name C or name O or name CB )) or resid 76 \ 0 through 764 or (resid 765 through 766 and (name N or name CA or name C or name \ O or name CB )) or resid 767 or (resid 768 through 769 and (name N or name CA o \ r name C or name O or name CB )) or resid 770 through 772 or (resid 773 and (nam \ e N or name CA or name C or name O or name CB )) or resid 774 through 782 or (re \ sid 783 through 786 and (name N or name CA or name C or name O or name CB )) or \ resid 787 through 799 or (resid 800 through 802 and (name N or name CA or name C \ or name O or name CB )) or resid 803 through 805 or resid 807 through 813)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.540 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 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:7.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 0.158 24464 Z= 0.262 Angle : 0.571 28.775 33427 Z= 0.290 Chirality : 0.039 0.404 3864 Planarity : 0.006 0.230 4272 Dihedral : 9.946 88.604 8243 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.89 % Favored : 94.05 % Rotamer: Outliers : 0.45 % Allowed : 2.61 % Favored : 96.94 % Cbeta Deviations : 0.10 % 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 are not related in a simple way. whole: -0.55 (0.15), residues: 3177 helix: 0.30 (0.13), residues: 1624 sheet: -0.68 (0.25), residues: 468 loop : -1.06 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 191 TYR 0.013 0.001 TYR C 356 PHE 0.010 0.001 PHE B 181 TRP 0.010 0.001 TRP C 473 HIS 0.005 0.001 HIS D 318 Details of bonding type rmsd covalent geometry : bond 0.00542 (24464) covalent geometry : angle 0.57106 (33427) hydrogen bonds : bond 0.26233 ( 1283) hydrogen bonds : angle 9.22137 ( 3610) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 118 ASP cc_start: 0.8387 (m-30) cc_final: 0.7988 (m-30) REVERT: B 332 MET cc_start: 0.8414 (mmt) cc_final: 0.7878 (mmt) REVERT: C 332 MET cc_start: 0.8367 (mmm) cc_final: 0.7978 (mmt) outliers start: 6 outliers final: 3 residues processed: 163 average time/residue: 0.4761 time to fit residues: 94.1059 Evaluate side-chains 124 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain D residue 51 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 4.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 HIS B 305 HIS ** B 806 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 ASN ** C 806 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN D 339 HIS D 359 HIS D 564 HIS D 749 ASN D 753 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.082376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.071254 restraints weight = 73333.055| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.29 r_work: 0.3090 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24464 Z= 0.148 Angle : 0.549 8.368 33427 Z= 0.294 Chirality : 0.041 0.206 3864 Planarity : 0.004 0.040 4272 Dihedral : 5.359 85.785 3531 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.72 % Rotamer: Outliers : 1.17 % Allowed : 5.67 % Favored : 93.16 % 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 are not related in a simple way. whole: 0.43 (0.15), residues: 3177 helix: 1.22 (0.13), residues: 1658 sheet: -0.35 (0.25), residues: 464 loop : -0.83 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 50 TYR 0.020 0.002 TYR B 595 PHE 0.017 0.002 PHE D 453 TRP 0.014 0.001 TRP B 473 HIS 0.004 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00321 (24464) covalent geometry : angle 0.54851 (33427) hydrogen bonds : bond 0.05376 ( 1283) hydrogen bonds : angle 5.35769 ( 3610) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.8894 (tp) cc_final: 0.8690 (tp) REVERT: A 89 MET cc_start: 0.8789 (mtm) cc_final: 0.8347 (mtm) REVERT: A 681 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8557 (mmt) REVERT: B 171 TYR cc_start: 0.8191 (m-80) cc_final: 0.7685 (m-80) REVERT: B 270 TYR cc_start: 0.8890 (m-80) cc_final: 0.8595 (m-80) REVERT: B 681 MET cc_start: 0.9039 (mtp) cc_final: 0.8839 (mtp) REVERT: C 332 MET cc_start: 0.8418 (mmm) cc_final: 0.7755 (mmt) REVERT: C 419 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.7029 (ttt90) REVERT: C 474 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8504 (tt) REVERT: D 85 LEU cc_start: 0.8940 (tp) cc_final: 0.8727 (tp) REVERT: D 89 MET cc_start: 0.8699 (mtm) cc_final: 0.8161 (mtm) REVERT: D 549 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8661 (pp) REVERT: D 681 MET cc_start: 0.9142 (tpp) cc_final: 0.8720 (mmt) REVERT: D 791 MET cc_start: 0.9160 (mmm) cc_final: 0.7898 (mmm) outliers start: 24 outliers final: 7 residues processed: 165 average time/residue: 0.4769 time to fit residues: 95.0920 Evaluate side-chains 136 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain D residue 549 ILE Chi-restraints excluded: chain D residue 785 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 62 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 289 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 359 HIS A 435 ASN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN C 237 GLN C 488 HIS ** C 806 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.079886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.068918 restraints weight = 73911.988| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.21 r_work: 0.3058 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 24464 Z= 0.241 Angle : 0.565 8.724 33427 Z= 0.299 Chirality : 0.042 0.174 3864 Planarity : 0.004 0.041 4272 Dihedral : 5.296 78.886 3527 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.12 % Rotamer: Outliers : 2.03 % Allowed : 6.98 % Favored : 91.00 % 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 are not related in a simple way. whole: 0.34 (0.15), residues: 3177 helix: 1.16 (0.13), residues: 1670 sheet: -0.48 (0.25), residues: 482 loop : -0.88 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 50 TYR 0.017 0.002 TYR A 287 PHE 0.018 0.002 PHE A 288 TRP 0.012 0.001 TRP C 473 HIS 0.005 0.001 HIS B 603 Details of bonding type rmsd covalent geometry : bond 0.00554 (24464) covalent geometry : angle 0.56470 (33427) hydrogen bonds : bond 0.04904 ( 1283) hydrogen bonds : angle 5.03734 ( 3610) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.8994 (tp) cc_final: 0.8561 (tp) REVERT: A 89 MET cc_start: 0.8782 (mtm) cc_final: 0.8415 (mtm) REVERT: A 681 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8430 (mmt) REVERT: B 229 ASN cc_start: 0.8742 (m-40) cc_final: 0.8416 (t0) REVERT: B 549 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9216 (pp) REVERT: C 332 MET cc_start: 0.8449 (mmm) cc_final: 0.7765 (mmt) REVERT: C 549 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9198 (pp) REVERT: D 26 MET cc_start: 0.7519 (mtm) cc_final: 0.7292 (mtp) REVERT: D 85 LEU cc_start: 0.9043 (tp) cc_final: 0.8735 (tp) REVERT: D 89 MET cc_start: 0.8762 (mtm) cc_final: 0.8436 (mtm) REVERT: D 549 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8718 (pp) REVERT: D 681 MET cc_start: 0.9146 (tpp) cc_final: 0.8569 (mmt) REVERT: D 791 MET cc_start: 0.9084 (mmm) cc_final: 0.8017 (mmm) outliers start: 43 outliers final: 12 residues processed: 152 average time/residue: 0.5199 time to fit residues: 94.2159 Evaluate side-chains 139 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 549 ILE Chi-restraints excluded: chain D residue 785 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 27 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 267 optimal weight: 0.8980 chunk 243 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 504 GLN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 806 HIS A ** 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 = 0.3474 r_free = 0.3474 target = 0.083364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.071858 restraints weight = 85523.388| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.61 r_work: 0.3096 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24464 Z= 0.116 Angle : 0.487 8.475 33427 Z= 0.257 Chirality : 0.039 0.176 3864 Planarity : 0.003 0.042 4272 Dihedral : 5.124 78.060 3527 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.84 % Rotamer: Outliers : 1.35 % Allowed : 8.55 % Favored : 90.09 % 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 are not related in a simple way. whole: 0.61 (0.15), residues: 3177 helix: 1.36 (0.13), residues: 1680 sheet: -0.17 (0.25), residues: 450 loop : -0.82 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 420 TYR 0.017 0.001 TYR D 287 PHE 0.014 0.001 PHE A 288 TRP 0.011 0.001 TRP C 473 HIS 0.004 0.001 HIS D 339 Details of bonding type rmsd covalent geometry : bond 0.00260 (24464) covalent geometry : angle 0.48686 (33427) hydrogen bonds : bond 0.03814 ( 1283) hydrogen bonds : angle 4.52937 ( 3610) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7684 (mtp) cc_final: 0.7466 (tpp) REVERT: A 85 LEU cc_start: 0.8973 (tp) cc_final: 0.8454 (tp) REVERT: A 89 MET cc_start: 0.8810 (mtm) cc_final: 0.8400 (mtm) REVERT: A 463 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8463 (t0) REVERT: A 549 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8679 (pp) REVERT: A 681 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8583 (mmt) REVERT: A 791 MET cc_start: 0.9055 (mmm) cc_final: 0.8794 (mmm) REVERT: B 78 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8285 (mm-30) REVERT: B 229 ASN cc_start: 0.8646 (m-40) cc_final: 0.8335 (t0) REVERT: B 549 ILE cc_start: 0.9424 (OUTLIER) cc_final: 0.9124 (pp) REVERT: C 171 TYR cc_start: 0.8249 (m-80) cc_final: 0.7891 (m-80) REVERT: C 229 ASN cc_start: 0.8928 (m-40) cc_final: 0.8621 (t0) REVERT: C 332 MET cc_start: 0.8433 (mmm) cc_final: 0.7716 (mmt) REVERT: C 549 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9120 (pp) REVERT: C 554 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8571 (mp0) REVERT: D 26 MET cc_start: 0.7414 (mtm) cc_final: 0.7147 (mtp) REVERT: D 85 LEU cc_start: 0.9004 (tp) cc_final: 0.8692 (tp) REVERT: D 89 MET cc_start: 0.8827 (mtm) cc_final: 0.8475 (mtm) REVERT: D 681 MET cc_start: 0.9124 (tpp) cc_final: 0.8590 (mmt) REVERT: D 791 MET cc_start: 0.9082 (mmm) cc_final: 0.7981 (mmm) outliers start: 30 outliers final: 9 residues processed: 157 average time/residue: 0.4584 time to fit residues: 86.8997 Evaluate side-chains 140 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 536 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 148 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 271 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 278 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 225 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 HIS A ** C 806 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.082000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.070179 restraints weight = 101448.419| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.92 r_work: 0.3052 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24464 Z= 0.175 Angle : 0.509 8.000 33427 Z= 0.268 Chirality : 0.040 0.180 3864 Planarity : 0.003 0.042 4272 Dihedral : 5.111 80.431 3527 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.47 % Favored : 95.50 % Rotamer: Outliers : 1.49 % Allowed : 9.28 % Favored : 89.24 % 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 are not related in a simple way. whole: 0.60 (0.15), residues: 3177 helix: 1.35 (0.13), residues: 1683 sheet: -0.23 (0.25), residues: 466 loop : -0.81 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 419 TYR 0.044 0.001 TYR A 287 PHE 0.016 0.001 PHE D 288 TRP 0.012 0.001 TRP C 473 HIS 0.004 0.001 HIS D 318 Details of bonding type rmsd covalent geometry : bond 0.00402 (24464) covalent geometry : angle 0.50917 (33427) hydrogen bonds : bond 0.03946 ( 1283) hydrogen bonds : angle 4.51431 ( 3610) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9037 (tp) cc_final: 0.8608 (tp) REVERT: A 89 MET cc_start: 0.8871 (mtm) cc_final: 0.8500 (mtm) REVERT: A 463 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8476 (t0) REVERT: A 549 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8702 (pp) REVERT: A 681 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8539 (mmt) REVERT: A 791 MET cc_start: 0.9083 (mmm) cc_final: 0.8693 (mmm) REVERT: B 229 ASN cc_start: 0.8714 (m-40) cc_final: 0.8285 (t0) REVERT: B 549 ILE cc_start: 0.9433 (OUTLIER) cc_final: 0.9151 (pp) REVERT: B 554 GLU cc_start: 0.8785 (mp0) cc_final: 0.8393 (mp0) REVERT: C 171 TYR cc_start: 0.8308 (m-80) cc_final: 0.8010 (m-80) REVERT: C 229 ASN cc_start: 0.8948 (m-40) cc_final: 0.8642 (t0) REVERT: C 332 MET cc_start: 0.8453 (mmm) cc_final: 0.7732 (mmt) REVERT: C 549 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9116 (pp) REVERT: D 26 MET cc_start: 0.7425 (mtm) cc_final: 0.7167 (mtp) REVERT: D 85 LEU cc_start: 0.9052 (tp) cc_final: 0.8726 (tp) REVERT: D 89 MET cc_start: 0.8843 (mtm) cc_final: 0.8484 (mtm) REVERT: D 155 MET cc_start: 0.7949 (ttm) cc_final: 0.7581 (ttm) REVERT: D 681 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8519 (mmt) REVERT: D 791 MET cc_start: 0.9070 (mmm) cc_final: 0.8050 (mmm) outliers start: 32 outliers final: 14 residues processed: 147 average time/residue: 0.4961 time to fit residues: 87.2720 Evaluate side-chains 142 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 785 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 171 optimal weight: 10.0000 chunk 293 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 237 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 chunk 247 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 203 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN C 523 ASN ** C 806 HIS A ** 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 = 0.3481 r_free = 0.3481 target = 0.084024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.072768 restraints weight = 72817.169| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.32 r_work: 0.3122 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24464 Z= 0.103 Angle : 0.471 7.866 33427 Z= 0.247 Chirality : 0.039 0.179 3864 Planarity : 0.003 0.038 4272 Dihedral : 5.012 80.067 3527 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.84 % Rotamer: Outliers : 1.53 % Allowed : 9.28 % Favored : 89.19 % 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 are not related in a simple way. whole: 0.75 (0.15), residues: 3177 helix: 1.48 (0.13), residues: 1685 sheet: -0.06 (0.25), residues: 450 loop : -0.80 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 419 TYR 0.047 0.001 TYR A 287 PHE 0.013 0.001 PHE D 288 TRP 0.010 0.001 TRP C 473 HIS 0.004 0.001 HIS D 339 Details of bonding type rmsd covalent geometry : bond 0.00222 (24464) covalent geometry : angle 0.47067 (33427) hydrogen bonds : bond 0.03402 ( 1283) hydrogen bonds : angle 4.29290 ( 3610) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9019 (tp) cc_final: 0.8440 (tp) REVERT: A 89 MET cc_start: 0.8814 (mtm) cc_final: 0.8385 (mtm) REVERT: A 287 TYR cc_start: 0.8661 (t80) cc_final: 0.8431 (t80) REVERT: A 463 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8430 (t0) REVERT: A 681 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8545 (mmt) REVERT: A 791 MET cc_start: 0.9038 (mmm) cc_final: 0.8811 (mmm) REVERT: B 229 ASN cc_start: 0.8627 (m-40) cc_final: 0.8280 (t0) REVERT: B 270 TYR cc_start: 0.8842 (m-80) cc_final: 0.8544 (m-80) REVERT: B 549 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9066 (pp) REVERT: B 554 GLU cc_start: 0.8760 (mp0) cc_final: 0.7853 (mp0) REVERT: C 171 TYR cc_start: 0.8222 (m-80) cc_final: 0.7865 (m-80) REVERT: C 229 ASN cc_start: 0.8893 (m-40) cc_final: 0.8576 (t0) REVERT: C 332 MET cc_start: 0.8435 (mmm) cc_final: 0.7693 (mmt) REVERT: C 549 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9038 (pp) REVERT: D 26 MET cc_start: 0.7366 (mtm) cc_final: 0.7102 (mtp) REVERT: D 85 LEU cc_start: 0.9015 (tp) cc_final: 0.8617 (tp) REVERT: D 89 MET cc_start: 0.8817 (mtm) cc_final: 0.8413 (mtm) REVERT: D 155 MET cc_start: 0.7842 (ttm) cc_final: 0.7466 (ttm) REVERT: D 332 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7862 (mmm) REVERT: D 533 GLN cc_start: 0.8977 (mt0) cc_final: 0.8730 (tm-30) REVERT: D 681 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8903 (mmm) outliers start: 33 outliers final: 14 residues processed: 157 average time/residue: 0.4748 time to fit residues: 89.8997 Evaluate side-chains 150 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 785 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 5 optimal weight: 9.9990 chunk 160 optimal weight: 0.4980 chunk 230 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 156 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 289 optimal weight: 20.0000 chunk 225 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 ASN C 806 HIS A Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.082672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.070975 restraints weight = 85729.588| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.62 r_work: 0.3064 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24464 Z= 0.177 Angle : 0.518 13.053 33427 Z= 0.268 Chirality : 0.040 0.195 3864 Planarity : 0.003 0.038 4272 Dihedral : 5.009 82.137 3527 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 1.44 % Allowed : 10.00 % Favored : 88.56 % 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 are not related in a simple way. whole: 0.71 (0.15), residues: 3177 helix: 1.46 (0.13), residues: 1686 sheet: -0.19 (0.25), residues: 468 loop : -0.80 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 419 TYR 0.051 0.002 TYR D 287 PHE 0.016 0.001 PHE D 288 TRP 0.011 0.001 TRP C 473 HIS 0.003 0.001 HIS B 603 Details of bonding type rmsd covalent geometry : bond 0.00409 (24464) covalent geometry : angle 0.51817 (33427) hydrogen bonds : bond 0.03724 ( 1283) hydrogen bonds : angle 4.37976 ( 3610) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9072 (tp) cc_final: 0.8470 (tp) REVERT: A 89 MET cc_start: 0.8853 (mtm) cc_final: 0.8391 (mtm) REVERT: A 463 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8438 (t0) REVERT: A 681 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8438 (mmt) REVERT: B 229 ASN cc_start: 0.8736 (m-40) cc_final: 0.8324 (t0) REVERT: B 270 TYR cc_start: 0.8876 (m-80) cc_final: 0.8554 (m-80) REVERT: B 549 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9108 (pp) REVERT: C 171 TYR cc_start: 0.8306 (m-80) cc_final: 0.7900 (m-80) REVERT: C 229 ASN cc_start: 0.8943 (m-40) cc_final: 0.8705 (t0) REVERT: C 549 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.9095 (pp) REVERT: C 554 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8543 (mp0) REVERT: D 26 MET cc_start: 0.7339 (mtm) cc_final: 0.7069 (mtp) REVERT: D 85 LEU cc_start: 0.9055 (tp) cc_final: 0.8638 (tp) REVERT: D 89 MET cc_start: 0.8859 (mtm) cc_final: 0.8447 (mtm) REVERT: D 155 MET cc_start: 0.7934 (ttm) cc_final: 0.7563 (ttm) REVERT: D 332 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7929 (mmm) REVERT: D 533 GLN cc_start: 0.8957 (mt0) cc_final: 0.8707 (tm-30) REVERT: D 681 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8916 (mmm) outliers start: 30 outliers final: 14 residues processed: 141 average time/residue: 0.5253 time to fit residues: 88.6086 Evaluate side-chains 148 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 558 GLN Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 785 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 36 optimal weight: 0.0980 chunk 91 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 317 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 286 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 287 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 ASN D 585 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.084347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.073196 restraints weight = 71794.443| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.29 r_work: 0.3129 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24464 Z= 0.101 Angle : 0.482 12.885 33427 Z= 0.248 Chirality : 0.039 0.170 3864 Planarity : 0.003 0.036 4272 Dihedral : 4.914 81.832 3527 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.87 % Rotamer: Outliers : 1.22 % Allowed : 10.27 % Favored : 88.52 % 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 are not related in a simple way. whole: 0.81 (0.15), residues: 3177 helix: 1.55 (0.13), residues: 1684 sheet: -0.15 (0.25), residues: 468 loop : -0.77 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 419 TYR 0.049 0.001 TYR D 287 PHE 0.017 0.001 PHE D 288 TRP 0.010 0.001 TRP C 473 HIS 0.004 0.001 HIS D 339 Details of bonding type rmsd covalent geometry : bond 0.00223 (24464) covalent geometry : angle 0.48230 (33427) hydrogen bonds : bond 0.03285 ( 1283) hydrogen bonds : angle 4.21204 ( 3610) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9027 (tp) cc_final: 0.8467 (tp) REVERT: A 89 MET cc_start: 0.8793 (mtm) cc_final: 0.8380 (mtm) REVERT: A 463 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8381 (t0) REVERT: A 681 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8531 (mmt) REVERT: A 791 MET cc_start: 0.9018 (mmm) cc_final: 0.8800 (mmm) REVERT: B 229 ASN cc_start: 0.8680 (m-40) cc_final: 0.8256 (t0) REVERT: B 270 TYR cc_start: 0.8857 (m-80) cc_final: 0.8530 (m-80) REVERT: B 549 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.9042 (pp) REVERT: B 554 GLU cc_start: 0.8810 (mp0) cc_final: 0.8367 (mp0) REVERT: C 171 TYR cc_start: 0.8218 (m-80) cc_final: 0.7812 (m-80) REVERT: C 229 ASN cc_start: 0.8918 (m-40) cc_final: 0.8616 (t0) REVERT: C 549 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9051 (pp) REVERT: C 554 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8550 (mp0) REVERT: D 26 MET cc_start: 0.7228 (mtm) cc_final: 0.6953 (mtp) REVERT: D 85 LEU cc_start: 0.9002 (tp) cc_final: 0.8625 (tp) REVERT: D 89 MET cc_start: 0.8842 (mtm) cc_final: 0.8445 (mtm) REVERT: D 155 MET cc_start: 0.7786 (ttm) cc_final: 0.7426 (ttm) REVERT: D 533 GLN cc_start: 0.8970 (mt0) cc_final: 0.8735 (tm-30) REVERT: D 681 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8577 (mmm) outliers start: 25 outliers final: 12 residues processed: 148 average time/residue: 0.5126 time to fit residues: 90.9076 Evaluate side-chains 149 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 558 GLN Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 785 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 277 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 61 optimal weight: 0.3980 chunk 71 optimal weight: 3.9990 chunk 302 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN D 558 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.084500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.072836 restraints weight = 88744.554| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.73 r_work: 0.3115 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24464 Z= 0.104 Angle : 0.483 12.683 33427 Z= 0.247 Chirality : 0.039 0.175 3864 Planarity : 0.003 0.034 4272 Dihedral : 4.858 82.687 3527 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.87 % Rotamer: Outliers : 1.08 % Allowed : 10.58 % Favored : 88.34 % 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 are not related in a simple way. whole: 0.79 (0.15), residues: 3177 helix: 1.55 (0.13), residues: 1702 sheet: -0.23 (0.24), residues: 480 loop : -0.81 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 419 TYR 0.049 0.001 TYR D 287 PHE 0.016 0.001 PHE D 288 TRP 0.010 0.001 TRP C 473 HIS 0.003 0.001 HIS D 339 Details of bonding type rmsd covalent geometry : bond 0.00235 (24464) covalent geometry : angle 0.48303 (33427) hydrogen bonds : bond 0.03229 ( 1283) hydrogen bonds : angle 4.15915 ( 3610) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9041 (tp) cc_final: 0.8482 (tp) REVERT: A 89 MET cc_start: 0.8808 (mtm) cc_final: 0.8429 (mtm) REVERT: A 463 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8355 (t0) REVERT: A 681 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8522 (mmt) REVERT: B 229 ASN cc_start: 0.8654 (m-40) cc_final: 0.8232 (t0) REVERT: B 270 TYR cc_start: 0.8840 (m-80) cc_final: 0.8514 (m-80) REVERT: B 549 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9045 (pp) REVERT: B 554 GLU cc_start: 0.8809 (mp0) cc_final: 0.8363 (mp0) REVERT: C 171 TYR cc_start: 0.8234 (m-80) cc_final: 0.7877 (m-80) REVERT: C 229 ASN cc_start: 0.8936 (m-40) cc_final: 0.8633 (t0) REVERT: C 549 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9048 (pp) REVERT: C 554 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8557 (mp0) REVERT: D 26 MET cc_start: 0.7206 (mtm) cc_final: 0.6955 (mtp) REVERT: D 85 LEU cc_start: 0.9026 (tp) cc_final: 0.8713 (tp) REVERT: D 89 MET cc_start: 0.8857 (mtm) cc_final: 0.8499 (mtm) REVERT: D 155 MET cc_start: 0.7778 (ttm) cc_final: 0.7426 (ttm) REVERT: D 332 MET cc_start: 0.8301 (tpt) cc_final: 0.8033 (mmm) REVERT: D 533 GLN cc_start: 0.8961 (mt0) cc_final: 0.8747 (tm-30) REVERT: D 681 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8801 (mmm) outliers start: 22 outliers final: 13 residues processed: 151 average time/residue: 0.4949 time to fit residues: 89.5841 Evaluate side-chains 153 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 785 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 24 optimal weight: 8.9990 chunk 242 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 238 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 16 optimal weight: 0.0470 chunk 289 optimal weight: 10.0000 overall best weight: 1.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 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 = 0.3484 r_free = 0.3484 target = 0.084181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.072654 restraints weight = 84862.019| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.62 r_work: 0.3110 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24464 Z= 0.120 Angle : 0.491 12.339 33427 Z= 0.252 Chirality : 0.039 0.177 3864 Planarity : 0.003 0.033 4272 Dihedral : 4.836 83.327 3527 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.28 % Favored : 95.69 % Rotamer: Outliers : 1.17 % Allowed : 10.81 % Favored : 88.02 % 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 are not related in a simple way. whole: 0.82 (0.15), residues: 3177 helix: 1.58 (0.13), residues: 1696 sheet: -0.26 (0.24), residues: 480 loop : -0.79 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 419 TYR 0.047 0.001 TYR D 287 PHE 0.017 0.001 PHE D 288 TRP 0.012 0.001 TRP C 369 HIS 0.003 0.001 HIS D 339 Details of bonding type rmsd covalent geometry : bond 0.00274 (24464) covalent geometry : angle 0.49069 (33427) hydrogen bonds : bond 0.03296 ( 1283) hydrogen bonds : angle 4.16127 ( 3610) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9039 (tp) cc_final: 0.8469 (tp) REVERT: A 89 MET cc_start: 0.8810 (mtm) cc_final: 0.8387 (mtm) REVERT: A 463 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8367 (t0) REVERT: A 681 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8489 (mmt) REVERT: B 229 ASN cc_start: 0.8649 (m-40) cc_final: 0.8228 (t0) REVERT: B 270 TYR cc_start: 0.8847 (m-80) cc_final: 0.8531 (m-80) REVERT: B 549 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.9039 (pp) REVERT: B 554 GLU cc_start: 0.8802 (mp0) cc_final: 0.8338 (mp0) REVERT: C 171 TYR cc_start: 0.8245 (m-80) cc_final: 0.7881 (m-80) REVERT: C 229 ASN cc_start: 0.8942 (m-40) cc_final: 0.8621 (t0) REVERT: C 423 MET cc_start: 0.8313 (mtm) cc_final: 0.8113 (mmm) REVERT: C 549 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9060 (pp) REVERT: C 554 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8544 (mp0) REVERT: D 85 LEU cc_start: 0.9026 (tp) cc_final: 0.8693 (tp) REVERT: D 89 MET cc_start: 0.8862 (mtm) cc_final: 0.8487 (mtm) REVERT: D 155 MET cc_start: 0.7783 (ttm) cc_final: 0.7432 (ttm) REVERT: D 332 MET cc_start: 0.8295 (tpt) cc_final: 0.8027 (mmm) REVERT: D 533 GLN cc_start: 0.8940 (mt0) cc_final: 0.8725 (tm-30) REVERT: D 681 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8811 (mmm) outliers start: 24 outliers final: 14 residues processed: 145 average time/residue: 0.5339 time to fit residues: 93.1419 Evaluate side-chains 152 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 558 GLN Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 785 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 272 optimal weight: 0.8980 chunk 175 optimal weight: 0.7980 chunk 189 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 274 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 chunk 308 optimal weight: 4.9990 chunk 201 optimal weight: 0.2980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.085298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.073634 restraints weight = 89345.073| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.73 r_work: 0.3134 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24464 Z= 0.097 Angle : 0.487 12.290 33427 Z= 0.247 Chirality : 0.039 0.179 3864 Planarity : 0.003 0.034 4272 Dihedral : 4.784 84.033 3527 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 1.13 % Allowed : 10.85 % Favored : 88.02 % 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 are not related in a simple way. whole: 0.90 (0.15), residues: 3177 helix: 1.66 (0.13), residues: 1687 sheet: -0.26 (0.24), residues: 483 loop : -0.71 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 419 TYR 0.045 0.001 TYR D 287 PHE 0.016 0.001 PHE D 288 TRP 0.011 0.001 TRP C 369 HIS 0.004 0.000 HIS D 339 Details of bonding type rmsd covalent geometry : bond 0.00215 (24464) covalent geometry : angle 0.48743 (33427) hydrogen bonds : bond 0.03098 ( 1283) hydrogen bonds : angle 4.08394 ( 3610) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6472.58 seconds wall clock time: 111 minutes 35.39 seconds (6695.39 seconds total)