Starting phenix.real_space_refine on Thu Mar 5 17:43:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rr8_24655/03_2026/7rr8_24655.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rr8_24655/03_2026/7rr8_24655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rr8_24655/03_2026/7rr8_24655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rr8_24655/03_2026/7rr8_24655.map" model { file = "/net/cci-nas-00/data/ceres_data/7rr8_24655/03_2026/7rr8_24655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rr8_24655/03_2026/7rr8_24655.cif" } resolution = 3.51 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= 0.000 sd= 0.025 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 13 5.49 5 S 132 5.16 5 C 15482 2.51 5 N 3861 2.21 5 O 4441 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23929 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7779 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 978} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 7804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 7804 Classifications: {'peptide': 1027} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 981} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7780 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 978} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 218 Unusual residues: {'D12': 4, 'PTY': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 182 Unusual residues: {'D12': 4, 'PTY': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'PTY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 166 Unusual residues: {'D12': 5, 'PTY': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.20, per 1000 atoms: 0.22 Number of scatterers: 23929 At special positions: 0 Unit cell: (120.7, 115.6, 143.65, 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 132 16.00 P 13 15.00 O 4441 8.00 N 3861 7.00 C 15482 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 991.6 milliseconds 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5634 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 25 sheets defined 59.2% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 8 through 29 removed outlier: 4.107A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.511A pdb=" N ALA A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.589A pdb=" N ALA A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 329 through 359 removed outlier: 3.845A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 386 removed outlier: 3.840A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 424 removed outlier: 4.585A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 removed outlier: 4.152A pdb=" N MET A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 removed outlier: 3.853A pdb=" N VAL A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.506A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 453 through 458' Processing helix chain 'A' and resid 461 through 487 removed outlier: 3.712A pdb=" N ALA A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 477 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.750A pdb=" N ALA A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 537 removed outlier: 3.871A pdb=" N TRP A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 536 " --> pdb=" O GLY A 532 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 559 removed outlier: 3.594A pdb=" N TYR A 545 " --> pdb=" O TYR A 541 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 601 removed outlier: 3.514A pdb=" N THR A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 643 Processing helix chain 'A' and resid 649 through 657 removed outlier: 3.722A pdb=" N GLN A 657 " --> pdb=" O ARG A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 707 Processing helix chain 'A' and resid 732 through 740 removed outlier: 3.521A pdb=" N ALA A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.584A pdb=" N TRP A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 780 Processing helix chain 'A' and resid 782 through 788 Processing helix chain 'A' and resid 836 through 850 removed outlier: 4.060A pdb=" N ALA A 840 " --> pdb=" O SER A 836 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN A 846 " --> pdb=" O GLU A 842 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 850 " --> pdb=" O GLN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 866 removed outlier: 3.676A pdb=" N GLN A 865 " --> pdb=" O GLY A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 893 removed outlier: 3.822A pdb=" N ALA A 878 " --> pdb=" O PRO A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 903 removed outlier: 4.033A pdb=" N SER A 900 " --> pdb=" O SER A 896 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 919 removed outlier: 3.522A pdb=" N VAL A 909 " --> pdb=" O VAL A 905 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 919 " --> pdb=" O ALA A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 954 Processing helix chain 'A' and resid 959 through 991 removed outlier: 4.648A pdb=" N ARG A 973 " --> pdb=" O ARG A 969 " (cutoff:3.500A) Proline residue: A 974 - end of helix Proline residue: A 988 - end of helix Processing helix chain 'A' and resid 996 through 1032 removed outlier: 3.579A pdb=" N GLY A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A1009 " --> pdb=" O THR A1005 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE A1020 " --> pdb=" O VAL A1016 " (cutoff:3.500A) Proline residue: A1023 - end of helix Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 8 through 29 removed outlier: 3.532A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 67 removed outlier: 3.769A pdb=" N ASP C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR C 60 " --> pdb=" O THR C 56 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLN C 63 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL C 64 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.534A pdb=" N ALA C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 105 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 262 through 265 No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'C' and resid 298 through 313 Processing helix chain 'C' and resid 314 through 317 Processing helix chain 'C' and resid 329 through 359 Processing helix chain 'C' and resid 361 through 386 removed outlier: 3.736A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.938A pdb=" N ALA C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 391 through 423 removed outlier: 4.122A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 439 removed outlier: 3.911A pdb=" N GLN C 437 " --> pdb=" O LYS C 433 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 439 " --> pdb=" O MET C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 452 removed outlier: 5.154A pdb=" N SER C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 removed outlier: 3.992A pdb=" N PHE C 459 " --> pdb=" O MET C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 497 removed outlier: 3.883A pdb=" N GLN C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 511 through 537 removed outlier: 3.831A pdb=" N PHE C 516 " --> pdb=" O PHE C 512 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN C 517 " --> pdb=" O PHE C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 559 removed outlier: 3.673A pdb=" N VAL C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 601 Processing helix chain 'C' and resid 643 through 656 Processing helix chain 'C' and resid 691 through 696 Processing helix chain 'C' and resid 698 through 703 Processing helix chain 'C' and resid 705 through 709 Processing helix chain 'C' and resid 732 through 740 removed outlier: 3.646A pdb=" N LEU C 739 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 755 Processing helix chain 'C' and resid 777 through 780 removed outlier: 3.582A pdb=" N ARG C 780 " --> pdb=" O ALA C 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 777 through 780' Processing helix chain 'C' and resid 782 through 788 Processing helix chain 'C' and resid 802 through 805 removed outlier: 3.530A pdb=" N SER C 805 " --> pdb=" O SER C 802 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 802 through 805' Processing helix chain 'C' and resid 838 through 850 removed outlier: 4.013A pdb=" N LYS C 850 " --> pdb=" O GLN C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 893 removed outlier: 3.519A pdb=" N ALA C 873 " --> pdb=" O SER C 869 " (cutoff:3.500A) Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 895 through 902 Processing helix chain 'C' and resid 904 through 919 removed outlier: 3.590A pdb=" N GLY C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 955 removed outlier: 3.830A pdb=" N ILE C 945 " --> pdb=" O ASN C 941 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 992 removed outlier: 5.344A pdb=" N ARG C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Proline residue: C 974 - end of helix Proline residue: C 988 - end of helix Processing helix chain 'C' and resid 996 through 1033 removed outlier: 4.380A pdb=" N GLN C1000 " --> pdb=" O GLY C 996 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE C1019 " --> pdb=" O THR C1015 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE C1020 " --> pdb=" O VAL C1016 " (cutoff:3.500A) Proline residue: C1023 - end of helix Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 8 through 29 Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.574A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 112 removed outlier: 3.542A pdb=" N ALA B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 161 through 167 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 210 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 298 through 314 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 330 through 359 Processing helix chain 'B' and resid 361 through 366 removed outlier: 3.605A pdb=" N LEU B 366 " --> pdb=" O PHE B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 370 removed outlier: 3.674A pdb=" N ILE B 370 " --> pdb=" O ILE B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 370' Processing helix chain 'B' and resid 371 through 386 Processing helix chain 'B' and resid 391 through 424 removed outlier: 4.402A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 454 removed outlier: 4.822A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 460 through 497 removed outlier: 3.570A pdb=" N GLY B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix removed outlier: 3.618A pdb=" N LEU B 497 " --> pdb=" O CYS B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 535 Processing helix chain 'B' and resid 539 through 559 removed outlier: 3.525A pdb=" N VAL B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 602 removed outlier: 3.681A pdb=" N VAL B 590 " --> pdb=" O ARG B 586 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 602 " --> pdb=" O TYR B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 637 Processing helix chain 'B' and resid 639 through 642 Processing helix chain 'B' and resid 643 through 656 removed outlier: 3.601A pdb=" N MET B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG B 650 " --> pdb=" O ALA B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 708 Processing helix chain 'B' and resid 732 through 739 Processing helix chain 'B' and resid 742 through 755 removed outlier: 3.549A pdb=" N THR B 748 " --> pdb=" O ASN B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 780 Processing helix chain 'B' and resid 782 through 788 Processing helix chain 'B' and resid 801 through 804 No H-bonds generated for 'chain 'B' and resid 801 through 804' Processing helix chain 'B' and resid 837 through 849 removed outlier: 3.747A pdb=" N MET B 841 " --> pdb=" O THR B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 869 removed outlier: 3.788A pdb=" N GLN B 865 " --> pdb=" O GLY B 861 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 868 " --> pdb=" O TYR B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 893 removed outlier: 4.132A pdb=" N SER B 875 " --> pdb=" O ASN B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 903 removed outlier: 4.123A pdb=" N SER B 900 " --> pdb=" O SER B 896 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 919 removed outlier: 3.505A pdb=" N GLY B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 912 " --> pdb=" O GLY B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 955 Processing helix chain 'B' and resid 959 through 991 removed outlier: 3.655A pdb=" N VAL B 968 " --> pdb=" O THR B 964 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Proline residue: B 974 - end of helix Proline residue: B 988 - end of helix Processing helix chain 'B' and resid 996 through 1033 removed outlier: 3.991A pdb=" N GLN B1000 " --> pdb=" O GLY B 996 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE B1019 " --> pdb=" O THR B1015 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE B1020 " --> pdb=" O VAL B1016 " (cutoff:3.500A) Proline residue: B1023 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.054A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 12.287A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLU A 826 " --> pdb=" O PRO A 718 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU A 828 " --> pdb=" O VAL A 716 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL A 716 " --> pdb=" O LEU A 828 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.054A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 12.287A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.719A pdb=" N ASN A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.131A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER A 608 " --> pdb=" O SER A 630 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N THR A 624 " --> pdb=" O GLY A 614 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.573A pdb=" N TYR A 182 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N TYR A 772 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N MET A 184 " --> pdb=" O TYR A 772 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N MET A 774 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE A 186 " --> pdb=" O MET A 774 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN A 760 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 773 " --> pdb=" O TYR A 758 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TYR A 758 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 215 through 219 removed outlier: 4.160A pdb=" N GLY A 217 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER A 233 " --> pdb=" O PHE B 727 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ILE B 729 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A 235 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ILE B 731 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 253 removed outlier: 3.665A pdb=" N LYS A 252 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 805 through 812 removed outlier: 8.696A pdb=" N ILE C 235 " --> pdb=" O PRO A 725 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE A 727 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 790 through 792 Processing sheet with id=AB1, first strand: chain 'C' and resid 75 through 82 removed outlier: 4.362A pdb=" N ALA C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 172 through 177 removed outlier: 6.838A pdb=" N VAL C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.038A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 266 through 272 removed outlier: 7.564A pdb=" N TYR C 182 " --> pdb=" O LYS C 770 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N TYR C 772 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N MET C 184 " --> pdb=" O TYR C 772 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET C 774 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ILE C 186 " --> pdb=" O MET C 774 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN C 760 " --> pdb=" O VAL C 771 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL C 773 " --> pdb=" O TYR C 758 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N TYR C 758 " --> pdb=" O VAL C 773 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 250 through 253 removed outlier: 3.618A pdb=" N LYS C 252 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 717 through 718 Processing sheet with id=AB7, first strand: chain 'C' and resid 810 through 812 removed outlier: 4.431A pdb=" N SER B 233 " --> pdb=" O PRO C 725 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 790 through 792 Processing sheet with id=AB9, first strand: chain 'C' and resid 818 through 819 Processing sheet with id=AC1, first strand: chain 'B' and resid 127 through 131 removed outlier: 3.699A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.426A pdb=" N ARG B 815 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N GLU B 826 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU B 826 " --> pdb=" O PRO B 718 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU B 828 " --> pdb=" O VAL B 716 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL B 716 " --> pdb=" O LEU B 828 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 127 through 131 removed outlier: 3.699A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.426A pdb=" N ARG B 815 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N GLU B 826 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 175 through 178 removed outlier: 4.110A pdb=" N GLY B 288 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL B 139 " --> pdb=" O PRO B 326 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 175 through 178 removed outlier: 4.110A pdb=" N GLY B 288 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 286 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.434A pdb=" N TYR B 182 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N TYR B 772 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N MET B 184 " --> pdb=" O TYR B 772 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N MET B 774 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ILE B 186 " --> pdb=" O MET B 774 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN B 760 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL B 773 " --> pdb=" O TYR B 758 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TYR B 758 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 250 through 253 removed outlier: 7.271A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 790 through 792 1511 hydrogen bonds defined for protein. 4365 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: 5.43 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3902 1.29 - 1.43: 5744 1.43 - 1.56: 14415 1.56 - 1.69: 27 1.69 - 1.82: 258 Bond restraints: 24346 Sorted by residual: bond pdb=" C ASP B 407 " pdb=" O ASP B 407 " ideal model delta sigma weight residual 1.236 1.159 0.077 1.15e-02 7.56e+03 4.54e+01 bond pdb=" C PRO B 368 " pdb=" O PRO B 368 " ideal model delta sigma weight residual 1.237 1.167 0.070 1.28e-02 6.10e+03 3.01e+01 bond pdb=" C ILE C 474 " pdb=" O ILE C 474 " ideal model delta sigma weight residual 1.240 1.182 0.058 1.18e-02 7.18e+03 2.41e+01 bond pdb=" C ALA B 441 " pdb=" O ALA B 441 " ideal model delta sigma weight residual 1.237 1.181 0.055 1.19e-02 7.06e+03 2.15e+01 bond pdb=" N THR A 538 " pdb=" CA THR A 538 " ideal model delta sigma weight residual 1.454 1.499 -0.045 1.21e-02 6.83e+03 1.39e+01 ... (remaining 24341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 32493 3.21 - 6.42: 400 6.42 - 9.64: 21 9.64 - 12.85: 9 12.85 - 16.06: 1 Bond angle restraints: 32924 Sorted by residual: angle pdb=" C PRO C 800 " pdb=" CA PRO C 800 " pdb=" CB PRO C 800 " ideal model delta sigma weight residual 111.11 123.38 -12.27 1.17e+00 7.31e-01 1.10e+02 angle pdb=" CA PHE A 4 " pdb=" CB PHE A 4 " pdb=" CG PHE A 4 " ideal model delta sigma weight residual 113.80 106.15 7.65 1.00e+00 1.00e+00 5.86e+01 angle pdb=" CA GLY A 639 " pdb=" C GLY A 639 " pdb=" O GLY A 639 " ideal model delta sigma weight residual 122.23 117.72 4.51 6.90e-01 2.10e+00 4.27e+01 angle pdb=" C GLU B 866 " pdb=" CA GLU B 866 " pdb=" CB GLU B 866 " ideal model delta sigma weight residual 110.81 100.97 9.84 1.60e+00 3.91e-01 3.78e+01 angle pdb=" CA PHE B 801 " pdb=" C PHE B 801 " pdb=" O PHE B 801 " ideal model delta sigma weight residual 120.82 114.71 6.11 1.05e+00 9.07e-01 3.39e+01 ... (remaining 32919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.10: 14200 32.10 - 64.19: 411 64.19 - 96.29: 31 96.29 - 128.38: 1 128.38 - 160.48: 5 Dihedral angle restraints: 14648 sinusoidal: 5864 harmonic: 8784 Sorted by residual: dihedral pdb=" CA GLN A 34 " pdb=" C GLN A 34 " pdb=" N TYR A 35 " pdb=" CA TYR A 35 " ideal model delta harmonic sigma weight residual 180.00 153.20 26.80 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA THR B 329 " pdb=" C THR B 329 " pdb=" N THR B 330 " pdb=" CA THR B 330 " ideal model delta harmonic sigma weight residual 180.00 155.12 24.88 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" C PRO C 800 " pdb=" N PRO C 800 " pdb=" CA PRO C 800 " pdb=" CB PRO C 800 " ideal model delta harmonic sigma weight residual -120.70 -132.20 11.50 0 2.50e+00 1.60e-01 2.12e+01 ... (remaining 14645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3455 0.076 - 0.152: 352 0.152 - 0.229: 19 0.229 - 0.305: 4 0.305 - 0.381: 1 Chirality restraints: 3831 Sorted by residual: chirality pdb=" CA PRO C 800 " pdb=" N PRO C 800 " pdb=" C PRO C 800 " pdb=" CB PRO C 800 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C6 PTY B1202 " pdb=" C1 PTY B1202 " pdb=" C5 PTY B1202 " pdb=" O7 PTY B1202 " both_signs ideal model delta sigma weight residual False 2.49 2.22 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA VAL C 129 " pdb=" N VAL C 129 " pdb=" C VAL C 129 " pdb=" CB VAL C 129 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 3828 not shown) Planarity restraints: 4155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 4 " -0.028 2.00e-02 2.50e+03 2.50e-02 1.09e+01 pdb=" CG PHE A 4 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 4 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 4 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 4 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 4 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 4 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 682 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.07e+01 pdb=" C PHE C 682 " -0.056 2.00e-02 2.50e+03 pdb=" O PHE C 682 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU C 683 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 89 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C GLN A 89 " 0.047 2.00e-02 2.50e+03 pdb=" O GLN A 89 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE A 90 " -0.016 2.00e-02 2.50e+03 ... (remaining 4152 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2832 2.75 - 3.29: 23736 3.29 - 3.83: 40431 3.83 - 4.36: 48291 4.36 - 4.90: 84526 Nonbonded interactions: 199816 Sorted by model distance: nonbonded pdb=" O ALA A 430 " pdb=" OG SER A 434 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR B 44 " pdb=" OG SER B 132 " model vdw 2.228 3.040 nonbonded pdb=" O ILE A 647 " pdb=" OG1 THR A 648 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR A 892 " pdb=" O ILE A 943 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASP A 153 " pdb=" OH TYR A 182 " model vdw 2.246 3.040 ... (remaining 199811 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 1 through 499 or resid 511 through 658 or (resid 659 and ( \ name N or name CA or name C or name O or name CB )) or resid 660 through 702 or \ (resid 703 through 704 and (name N or name CA or name C or name O or name CB )) \ or resid 705 through 1034 or (resid 1101 and (name C1 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C1 \ 9 or name C2 or name C20 or name C21 or name C22 or name C3 or name C30 or name \ C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or n \ ame C38 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or n \ ame O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 )) \ or (resid 1102 and (name C1 or name C11 or name C12 or name C13 or name C14 or n \ ame C15 or name C16 or name C5 or name C6 or name C8 or name N1 or name O10 or n \ ame O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or \ name P1 )) or (resid 1103 and (name C1 or name O11 or name O12 or name O13 or n \ ame O14 or name O30 or name O4 or name P1 )) or (resid 1105 and (name C10 or nam \ e C11 or name C12 or name C4 or name C5 or name C6 or name C7 or name C8 or name \ C9 )) or (resid 1106 and (name C3 or name C4 or name C5 or name C6 or name C7 ) \ ) or (resid 1107 and (name C1 or name C10 or name C2 or name C3 or name C4 or na \ me C5 or name C6 or name C7 or name C8 or name C9 )))) selection = (chain 'B' and (resid 1 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or resid 7 through 407 or (resid 408 through 409 and (nam \ e N or name CA or name C or name O or name CB )) or resid 410 through 499 or res \ id 511 through 702 or (resid 703 through 704 and (name N or name CA or name C or \ name O or name CB )) or resid 705 through 1034 or (resid 1201 and (name C1 or n \ ame C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C \ 3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name C38 or name C5 or name C6 or name C8 or name N1 or nam \ e O10 or name O11 or name O12 or name O13 or name O14 or name O30 or name O4 or \ name O7 or name P1 )) or (resid 1202 and (name C1 or name C11 or name C12 or nam \ e C13 or name C14 or name C15 or name C16 or name C5 or name C6 or name C8 or na \ me N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or \ name O4 or name O7 or name P1 )) or (resid 1203 and (name C1 or name O11 or nam \ e O12 or name O13 or name O14 or name O30 or name O4 or name P1 )) or (resid 120 \ 5 and (name C10 or name C11 or name C12 or name C4 or name C5 or name C6 or name \ C7 or name C8 or name C9 )) or (resid 1206 and (name C3 or name C4 or name C5 o \ r name C6 or name C7 )) or resid 1207)) selection = (chain 'C' and (resid 1 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or resid 7 through 407 or (resid 408 through 409 and (nam \ e N or name CA or name C or name O or name CB )) or resid 410 through 499 or res \ id 511 through 658 or (resid 659 and (name N or name CA or name C or name O or n \ ame CB )) or resid 660 through 1034 or (resid 1101 and (name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C21 or name C22 or name C3 or name C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name C5 or name C6 or name C8 or name N1 or name O10 or nam \ e O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or n \ ame P1 )) or (resid 1102 and (name C1 or name C11 or name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C5 or name C6 or name C8 or name N1 or nam \ e O10 or name O11 or name O12 or name O13 or name O14 or name O30 or name O4 or \ name O7 or name P1 )) or (resid 1103 and (name C1 or name O11 or name O12 or nam \ e O13 or name O14 or name O30 or name O4 or name P1 )) or resid 1105 or (resid 1 \ 106 and (name C3 or name C4 or name C5 or name C6 or name C7 )) or (resid 1107 a \ nd (name C1 or name C10 or name C2 or name C3 or name C4 or name C5 or name C6 o \ r name C7 or name C8 or name C9 )))) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.020 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 0.077 24346 Z= 0.298 Angle : 0.793 16.059 32924 Z= 0.470 Chirality : 0.046 0.381 3831 Planarity : 0.004 0.036 4155 Dihedral : 14.589 160.476 9014 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.12 % Allowed : 0.72 % Favored : 99.16 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.22 % 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: 0.59 (0.16), residues: 3063 helix: 1.30 (0.13), residues: 1634 sheet: -0.52 (0.25), residues: 416 loop : -0.58 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 418 TYR 0.024 0.001 TYR A 35 PHE 0.058 0.001 PHE A 4 TRP 0.029 0.001 TRP B 859 HIS 0.002 0.000 HIS A 709 Details of bonding type rmsd covalent geometry : bond 0.00513 (24346) covalent geometry : angle 0.79314 (32924) hydrogen bonds : bond 0.13639 ( 1452) hydrogen bonds : angle 6.33883 ( 4365) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 372 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 410 ILE cc_start: 0.8522 (pt) cc_final: 0.8212 (pt) REVERT: A 414 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6465 (tm-30) REVERT: A 918 PHE cc_start: 0.7039 (t80) cc_final: 0.6822 (t80) REVERT: A 970 MET cc_start: 0.8019 (mtp) cc_final: 0.7718 (mtt) REVERT: C 438 ILE cc_start: 0.8706 (tp) cc_final: 0.8490 (tp) REVERT: C 948 PHE cc_start: 0.8303 (t80) cc_final: 0.8047 (t80) REVERT: B 664 PHE cc_start: 0.7509 (t80) cc_final: 0.7281 (t80) outliers start: 3 outliers final: 1 residues processed: 374 average time/residue: 0.1435 time to fit residues: 86.2047 Evaluate side-chains 303 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 302 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 862 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 737 GLN A1000 GLN C 360 GLN ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN C 517 ASN B 592 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.092442 restraints weight = 33355.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.093592 restraints weight = 22247.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.093773 restraints weight = 17033.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.094046 restraints weight = 16171.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.094142 restraints weight = 16593.278| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24346 Z= 0.180 Angle : 0.561 7.562 32924 Z= 0.291 Chirality : 0.043 0.172 3831 Planarity : 0.004 0.040 4155 Dihedral : 12.030 133.499 3686 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.16 % Allowed : 6.76 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.86 (0.16), residues: 3063 helix: 1.53 (0.13), residues: 1641 sheet: -0.50 (0.25), residues: 423 loop : -0.44 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 637 TYR 0.022 0.001 TYR A 49 PHE 0.025 0.001 PHE A 4 TRP 0.018 0.001 TRP C 515 HIS 0.002 0.001 HIS A 709 Details of bonding type rmsd covalent geometry : bond 0.00422 (24346) covalent geometry : angle 0.56107 (32924) hydrogen bonds : bond 0.04307 ( 1452) hydrogen bonds : angle 4.97682 ( 4365) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 323 time to evaluate : 0.750 Fit side-chains REVERT: A 414 GLU cc_start: 0.7390 (tm-30) cc_final: 0.6747 (tm-30) REVERT: A 918 PHE cc_start: 0.7224 (t80) cc_final: 0.6979 (t80) REVERT: A 970 MET cc_start: 0.8045 (mtp) cc_final: 0.7735 (mtt) REVERT: C 438 ILE cc_start: 0.8730 (tp) cc_final: 0.8504 (tp) REVERT: B 89 GLN cc_start: 0.7930 (tp-100) cc_final: 0.7704 (mm-40) REVERT: B 1032 ARG cc_start: 0.6961 (ttt180) cc_final: 0.6621 (ttm170) outliers start: 29 outliers final: 15 residues processed: 341 average time/residue: 0.1453 time to fit residues: 81.1992 Evaluate side-chains 317 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 302 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 795 ASP Chi-restraints excluded: chain C residue 934 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 937 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 294 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 296 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 237 GLN A 588 GLN ** C 415 ASN ** 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 = 0.3358 r_free = 0.3358 target = 0.119069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.091234 restraints weight = 33455.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.092505 restraints weight = 21823.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.093009 restraints weight = 17832.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.093521 restraints weight = 15263.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.093708 restraints weight = 15251.228| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24346 Z= 0.187 Angle : 0.557 7.906 32924 Z= 0.287 Chirality : 0.043 0.161 3831 Planarity : 0.004 0.053 4155 Dihedral : 11.311 118.524 3683 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.08 % Allowed : 9.12 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 3063 helix: 1.59 (0.13), residues: 1644 sheet: -0.54 (0.24), residues: 429 loop : -0.44 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 8 TYR 0.021 0.001 TYR A 49 PHE 0.021 0.001 PHE B 628 TRP 0.011 0.001 TRP C 515 HIS 0.002 0.001 HIS B 596 Details of bonding type rmsd covalent geometry : bond 0.00441 (24346) covalent geometry : angle 0.55734 (32924) hydrogen bonds : bond 0.04178 ( 1452) hydrogen bonds : angle 4.83050 ( 4365) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 319 time to evaluate : 0.952 Fit side-chains REVERT: A 414 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6793 (tm-30) REVERT: A 435 MET cc_start: 0.6241 (OUTLIER) cc_final: 0.5773 (mpp) REVERT: A 918 PHE cc_start: 0.7194 (t80) cc_final: 0.6962 (t80) REVERT: C 782 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8298 (mt) REVERT: B 89 GLN cc_start: 0.7971 (tp-100) cc_final: 0.7702 (mm-40) REVERT: B 918 PHE cc_start: 0.7952 (t80) cc_final: 0.7619 (t80) REVERT: B 919 ARG cc_start: 0.6151 (mpt180) cc_final: 0.5946 (mpt180) outliers start: 27 outliers final: 19 residues processed: 336 average time/residue: 0.1451 time to fit residues: 79.7424 Evaluate side-chains 325 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 304 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 795 ASP Chi-restraints excluded: chain C residue 934 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 835 LYS Chi-restraints excluded: chain B residue 937 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 255 optimal weight: 9.9990 chunk 264 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 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 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 GLN B 526 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.119871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.093344 restraints weight = 33329.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.093968 restraints weight = 22470.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.093910 restraints weight = 19047.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.093911 restraints weight = 18401.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.094012 restraints weight = 17737.998| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24346 Z= 0.148 Angle : 0.528 7.145 32924 Z= 0.270 Chirality : 0.042 0.151 3831 Planarity : 0.004 0.039 4155 Dihedral : 10.853 109.657 3683 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.28 % Allowed : 10.76 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.99 (0.15), residues: 3063 helix: 1.67 (0.13), residues: 1650 sheet: -0.58 (0.24), residues: 431 loop : -0.40 (0.21), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 8 TYR 0.013 0.001 TYR A 49 PHE 0.021 0.001 PHE B 628 TRP 0.010 0.001 TRP C 754 HIS 0.001 0.000 HIS B 596 Details of bonding type rmsd covalent geometry : bond 0.00342 (24346) covalent geometry : angle 0.52775 (32924) hydrogen bonds : bond 0.03865 ( 1452) hydrogen bonds : angle 4.70092 ( 4365) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 325 time to evaluate : 0.841 Fit side-chains REVERT: A 414 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6775 (tm-30) REVERT: A 435 MET cc_start: 0.6133 (mpp) cc_final: 0.5819 (pmm) REVERT: A 918 PHE cc_start: 0.7184 (t80) cc_final: 0.6976 (t80) REVERT: A 977 MET cc_start: 0.7982 (mmt) cc_final: 0.7464 (mmt) REVERT: C 782 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8281 (mt) REVERT: C 948 PHE cc_start: 0.8255 (t80) cc_final: 0.8042 (t80) REVERT: B 761 ASP cc_start: 0.8325 (m-30) cc_final: 0.8049 (m-30) REVERT: B 841 MET cc_start: 0.8328 (mtt) cc_final: 0.7936 (mtm) outliers start: 32 outliers final: 20 residues processed: 344 average time/residue: 0.1473 time to fit residues: 82.5692 Evaluate side-chains 327 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 306 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 795 ASP Chi-restraints excluded: chain C residue 801 PHE Chi-restraints excluded: chain C residue 934 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 830 GLN Chi-restraints excluded: chain B residue 835 LYS Chi-restraints excluded: chain B residue 937 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 44 optimal weight: 2.9990 chunk 280 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 242 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 279 optimal weight: 2.9990 chunk 274 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 HIS A 613 ASN A 737 GLN C 218 GLN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.094678 restraints weight = 33063.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.095264 restraints weight = 30387.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.096554 restraints weight = 26520.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.096710 restraints weight = 20680.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.097037 restraints weight = 19323.820| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24346 Z= 0.120 Angle : 0.503 7.842 32924 Z= 0.257 Chirality : 0.041 0.150 3831 Planarity : 0.003 0.038 4155 Dihedral : 10.300 95.481 3683 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.32 % Allowed : 11.88 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.12 (0.16), residues: 3063 helix: 1.78 (0.13), residues: 1640 sheet: -0.50 (0.24), residues: 427 loop : -0.36 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 8 TYR 0.010 0.001 TYR C 49 PHE 0.020 0.001 PHE B 628 TRP 0.010 0.001 TRP C 754 HIS 0.012 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00269 (24346) covalent geometry : angle 0.50266 (32924) hydrogen bonds : bond 0.03566 ( 1452) hydrogen bonds : angle 4.55357 ( 4365) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 321 time to evaluate : 0.744 Fit side-chains REVERT: A 414 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6414 (tm-30) REVERT: A 970 MET cc_start: 0.7844 (mtm) cc_final: 0.7595 (mtp) REVERT: C 744 ASN cc_start: 0.7937 (t0) cc_final: 0.7726 (m110) REVERT: C 782 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8243 (mt) REVERT: B 450 SER cc_start: 0.8902 (m) cc_final: 0.8454 (p) REVERT: B 918 PHE cc_start: 0.7696 (t80) cc_final: 0.7471 (t80) outliers start: 33 outliers final: 21 residues processed: 340 average time/residue: 0.1464 time to fit residues: 81.9208 Evaluate side-chains 329 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 307 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 795 ASP Chi-restraints excluded: chain C residue 801 PHE Chi-restraints excluded: chain C residue 934 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 830 GLN Chi-restraints excluded: chain B residue 937 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 121 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 235 optimal weight: 0.4980 chunk 298 optimal weight: 8.9990 chunk 272 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 285 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 HIS A 737 GLN A 928 GLN C 81 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.095113 restraints weight = 33138.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.095334 restraints weight = 27129.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.096057 restraints weight = 21951.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.096461 restraints weight = 19175.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.096666 restraints weight = 17649.485| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24346 Z= 0.115 Angle : 0.504 8.087 32924 Z= 0.256 Chirality : 0.041 0.148 3831 Planarity : 0.003 0.038 4155 Dihedral : 9.953 87.632 3683 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.32 % Allowed : 12.92 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.22 (0.16), residues: 3063 helix: 1.85 (0.13), residues: 1643 sheet: -0.41 (0.24), residues: 423 loop : -0.31 (0.21), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 8 TYR 0.009 0.001 TYR B 758 PHE 0.020 0.001 PHE B 628 TRP 0.009 0.001 TRP C 754 HIS 0.004 0.000 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00258 (24346) covalent geometry : angle 0.50374 (32924) hydrogen bonds : bond 0.03494 ( 1452) hydrogen bonds : angle 4.47764 ( 4365) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 316 time to evaluate : 0.906 Fit side-chains REVERT: A 182 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.8368 (m-10) REVERT: A 414 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6700 (tm-30) REVERT: A 970 MET cc_start: 0.7880 (mtm) cc_final: 0.7639 (mtp) REVERT: A 977 MET cc_start: 0.7831 (mmt) cc_final: 0.7430 (mmt) REVERT: C 712 MET cc_start: 0.8283 (tpt) cc_final: 0.8059 (tpt) REVERT: C 744 ASN cc_start: 0.7926 (t0) cc_final: 0.7701 (m110) REVERT: C 782 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8253 (mt) REVERT: B 435 MET cc_start: 0.8328 (mmm) cc_final: 0.8112 (mmm) REVERT: B 450 SER cc_start: 0.8865 (m) cc_final: 0.8400 (p) REVERT: B 761 ASP cc_start: 0.8312 (m-30) cc_final: 0.8088 (m-30) outliers start: 33 outliers final: 22 residues processed: 335 average time/residue: 0.1446 time to fit residues: 79.5908 Evaluate side-chains 323 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 299 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 801 PHE Chi-restraints excluded: chain C residue 934 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 830 GLN Chi-restraints excluded: chain B residue 835 LYS Chi-restraints excluded: chain B residue 937 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 211 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 chunk 226 optimal weight: 0.0670 chunk 201 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 94 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 HIS A 737 GLN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.096704 restraints weight = 33151.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.097460 restraints weight = 29180.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.098382 restraints weight = 26985.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.098816 restraints weight = 20564.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.098854 restraints weight = 19214.688| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24346 Z= 0.102 Angle : 0.493 8.659 32924 Z= 0.250 Chirality : 0.041 0.150 3831 Planarity : 0.003 0.038 4155 Dihedral : 9.569 83.502 3683 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.28 % Allowed : 13.36 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.28 (0.16), residues: 3063 helix: 1.88 (0.13), residues: 1653 sheet: -0.34 (0.24), residues: 417 loop : -0.29 (0.21), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 8 TYR 0.008 0.001 TYR B 758 PHE 0.020 0.001 PHE A 362 TRP 0.011 0.001 TRP C 754 HIS 0.005 0.000 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00219 (24346) covalent geometry : angle 0.49304 (32924) hydrogen bonds : bond 0.03297 ( 1452) hydrogen bonds : angle 4.37635 ( 4365) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 323 time to evaluate : 0.851 Fit side-chains REVERT: A 414 GLU cc_start: 0.6960 (tm-30) cc_final: 0.6368 (tm-30) REVERT: A 970 MET cc_start: 0.7710 (mtm) cc_final: 0.7483 (mtp) REVERT: A 977 MET cc_start: 0.7657 (mmt) cc_final: 0.7161 (mmt) REVERT: C 712 MET cc_start: 0.8267 (tpt) cc_final: 0.8039 (tpt) REVERT: B 450 SER cc_start: 0.8862 (m) cc_final: 0.8468 (p) REVERT: B 761 ASP cc_start: 0.8265 (m-30) cc_final: 0.8039 (m-30) outliers start: 32 outliers final: 22 residues processed: 343 average time/residue: 0.1430 time to fit residues: 81.2299 Evaluate side-chains 332 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 310 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 801 PHE Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 937 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 190 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 303 optimal weight: 7.9990 chunk 124 optimal weight: 0.3980 chunk 17 optimal weight: 0.3980 chunk 258 optimal weight: 4.9990 chunk 246 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 260 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 HIS A 737 GLN A1000 GLN ** C 360 GLN ** 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 = 0.3411 r_free = 0.3411 target = 0.123068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.097608 restraints weight = 32942.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.097257 restraints weight = 31091.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.098271 restraints weight = 29626.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.098740 restraints weight = 25066.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.099000 restraints weight = 21931.280| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24346 Z= 0.108 Angle : 0.502 9.165 32924 Z= 0.253 Chirality : 0.041 0.146 3831 Planarity : 0.003 0.038 4155 Dihedral : 9.416 81.476 3683 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.24 % Allowed : 14.08 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.32 (0.16), residues: 3063 helix: 1.90 (0.13), residues: 1653 sheet: -0.28 (0.25), residues: 417 loop : -0.27 (0.21), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 418 TYR 0.016 0.001 TYR A 182 PHE 0.019 0.001 PHE B 628 TRP 0.008 0.001 TRP C 754 HIS 0.003 0.000 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00238 (24346) covalent geometry : angle 0.50228 (32924) hydrogen bonds : bond 0.03331 ( 1452) hydrogen bonds : angle 4.36382 ( 4365) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 311 time to evaluate : 0.858 Fit side-chains REVERT: A 1 MET cc_start: 0.4747 (mpp) cc_final: 0.4462 (mpp) REVERT: A 414 GLU cc_start: 0.7012 (tm-30) cc_final: 0.6417 (tm-30) REVERT: A 483 LEU cc_start: 0.8394 (mp) cc_final: 0.8188 (mt) REVERT: A 970 MET cc_start: 0.7832 (mtm) cc_final: 0.7599 (mtp) REVERT: A 977 MET cc_start: 0.7718 (mmt) cc_final: 0.7199 (mmt) REVERT: C 712 MET cc_start: 0.8291 (tpt) cc_final: 0.8057 (tpt) REVERT: C 782 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8262 (mt) REVERT: B 89 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7512 (mm-40) REVERT: B 450 SER cc_start: 0.8835 (m) cc_final: 0.8442 (p) REVERT: B 761 ASP cc_start: 0.8276 (m-30) cc_final: 0.8020 (m-30) outliers start: 31 outliers final: 22 residues processed: 333 average time/residue: 0.1448 time to fit residues: 79.4297 Evaluate side-chains 326 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 302 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 801 PHE Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 830 GLN Chi-restraints excluded: chain B residue 937 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 273 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 274 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 188 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 228 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 HIS A 667 ASN A 928 GLN A1000 GLN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.096702 restraints weight = 33201.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.096702 restraints weight = 31908.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.098119 restraints weight = 28016.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.098334 restraints weight = 20758.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.098613 restraints weight = 18982.187| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24346 Z= 0.116 Angle : 0.509 10.517 32924 Z= 0.256 Chirality : 0.041 0.146 3831 Planarity : 0.003 0.039 4155 Dihedral : 9.285 80.647 3683 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.24 % Allowed : 14.28 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.32 (0.16), residues: 3063 helix: 1.89 (0.13), residues: 1653 sheet: -0.26 (0.24), residues: 423 loop : -0.26 (0.21), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 418 TYR 0.015 0.001 TYR A 182 PHE 0.020 0.001 PHE B 512 TRP 0.006 0.001 TRP C 789 HIS 0.007 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00264 (24346) covalent geometry : angle 0.50853 (32924) hydrogen bonds : bond 0.03390 ( 1452) hydrogen bonds : angle 4.37834 ( 4365) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 305 time to evaluate : 0.873 Fit side-chains REVERT: A 1 MET cc_start: 0.4685 (mpp) cc_final: 0.4424 (mpp) REVERT: A 414 GLU cc_start: 0.6954 (tm-30) cc_final: 0.6361 (tm-30) REVERT: A 918 PHE cc_start: 0.6948 (t80) cc_final: 0.6669 (t80) REVERT: A 970 MET cc_start: 0.7812 (mtm) cc_final: 0.7581 (mtp) REVERT: C 335 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8860 (mm) REVERT: C 712 MET cc_start: 0.8267 (tpt) cc_final: 0.8032 (tpt) REVERT: C 782 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8253 (mt) REVERT: B 89 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7536 (mm-40) REVERT: B 450 SER cc_start: 0.8850 (m) cc_final: 0.8478 (p) REVERT: B 761 ASP cc_start: 0.8248 (m-30) cc_final: 0.7974 (m-30) outliers start: 31 outliers final: 23 residues processed: 328 average time/residue: 0.1367 time to fit residues: 73.7978 Evaluate side-chains 326 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 300 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 801 PHE Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 830 GLN Chi-restraints excluded: chain B residue 937 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 98 optimal weight: 0.1980 chunk 283 optimal weight: 5.9990 chunk 270 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 288 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 195 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 234 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN A 526 HIS A1000 GLN ** C 360 GLN ** 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 = 0.3412 r_free = 0.3412 target = 0.123130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.097894 restraints weight = 32991.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.097893 restraints weight = 31170.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.098955 restraints weight = 28106.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.099330 restraints weight = 21644.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.100480 restraints weight = 20575.721| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24346 Z= 0.110 Angle : 0.509 11.466 32924 Z= 0.255 Chirality : 0.041 0.150 3831 Planarity : 0.003 0.038 4155 Dihedral : 9.170 78.937 3683 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.04 % Allowed : 14.64 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.36 (0.16), residues: 3063 helix: 1.92 (0.13), residues: 1653 sheet: -0.25 (0.24), residues: 423 loop : -0.24 (0.21), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 418 TYR 0.019 0.001 TYR A 35 PHE 0.019 0.001 PHE B 628 TRP 0.008 0.001 TRP A 634 HIS 0.003 0.000 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00245 (24346) covalent geometry : angle 0.50947 (32924) hydrogen bonds : bond 0.03330 ( 1452) hydrogen bonds : angle 4.34512 ( 4365) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 306 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4528 (mpp) cc_final: 0.4267 (mpp) REVERT: A 414 GLU cc_start: 0.6916 (tm-30) cc_final: 0.6312 (tm-30) REVERT: A 918 PHE cc_start: 0.6929 (t80) cc_final: 0.6655 (t80) REVERT: A 970 MET cc_start: 0.7767 (mtm) cc_final: 0.7540 (mtp) REVERT: C 335 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8849 (mm) REVERT: C 712 MET cc_start: 0.8258 (tpt) cc_final: 0.8021 (tpt) REVERT: C 782 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8242 (mt) REVERT: B 89 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7554 (mm-40) REVERT: B 450 SER cc_start: 0.8793 (m) cc_final: 0.8429 (p) REVERT: B 761 ASP cc_start: 0.8249 (m-30) cc_final: 0.7970 (m-30) outliers start: 26 outliers final: 23 residues processed: 326 average time/residue: 0.1479 time to fit residues: 79.7382 Evaluate side-chains 323 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 297 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 801 PHE Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 830 GLN Chi-restraints excluded: chain B residue 835 LYS Chi-restraints excluded: chain B residue 937 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 100 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.0770 chunk 238 optimal weight: 5.9990 chunk 136 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 overall best weight: 0.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 HIS A 928 GLN A1000 GLN ** C 360 GLN ** 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 = 0.3410 r_free = 0.3410 target = 0.122964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.097331 restraints weight = 32887.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.096980 restraints weight = 31586.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.098324 restraints weight = 28372.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.098528 restraints weight = 21482.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.098785 restraints weight = 19746.847| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24346 Z= 0.111 Angle : 0.508 11.383 32924 Z= 0.256 Chirality : 0.041 0.148 3831 Planarity : 0.003 0.038 4155 Dihedral : 9.103 77.762 3683 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.24 % Allowed : 14.28 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.36 (0.16), residues: 3063 helix: 1.92 (0.13), residues: 1654 sheet: -0.22 (0.24), residues: 423 loop : -0.25 (0.21), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 418 TYR 0.022 0.001 TYR A 35 PHE 0.022 0.001 PHE B 512 TRP 0.007 0.001 TRP A 634 HIS 0.001 0.000 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00249 (24346) covalent geometry : angle 0.50811 (32924) hydrogen bonds : bond 0.03337 ( 1452) hydrogen bonds : angle 4.34933 ( 4365) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3121.94 seconds wall clock time: 54 minutes 58.39 seconds (3298.39 seconds total)