Starting phenix.real_space_refine on Thu Mar 5 17:19:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rr7_24654/03_2026/7rr7_24654.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rr7_24654/03_2026/7rr7_24654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rr7_24654/03_2026/7rr7_24654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rr7_24654/03_2026/7rr7_24654.map" model { file = "/net/cci-nas-00/data/ceres_data/7rr7_24654/03_2026/7rr7_24654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rr7_24654/03_2026/7rr7_24654.cif" } resolution = 3.05 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= 0.019 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 15 5.49 5 S 132 5.16 5 C 15333 2.51 5 N 3824 2.21 5 O 4430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23734 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 7732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7732 Classifications: {'peptide': 1018} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 972} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "C" Number of atoms: 7783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7783 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 979} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 7654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7654 Classifications: {'peptide': 1018} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 972} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 168 Unusual residues: {'D12': 4, 'PTY': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 129 Planarities with less than four sites: {'PTY:plan-2': 1, 'PTY:plan-1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 219 Unusual residues: {'D12': 2, 'PTY': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 105 Chain: "A" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 178 Unusual residues: {'D12': 6, 'PTY': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 92 Planarities with less than four sites: {'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 6.22, per 1000 atoms: 0.26 Number of scatterers: 23734 At special positions: 0 Unit cell: (115.6, 117.3, 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 15 15.00 O 4430 8.00 N 3824 7.00 C 15333 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: 1.97 Conformation dependent library (CDL) restraints added in 1.1 seconds 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5614 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 24 sheets defined 58.8% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'B' and resid 1 through 7 removed outlier: 3.582A pdb=" N PHE B 5 " --> pdb=" O MET B 1 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP B 7 " --> pdb=" O ASN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 29 removed outlier: 3.831A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.558A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 115 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 209 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 303 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 329 through 359 Processing helix chain 'B' and resid 361 through 386 removed outlier: 3.778A pdb=" N THR B 365 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 366 " --> pdb=" O PHE B 362 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 424 removed outlier: 4.189A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 438 Processing helix chain 'B' and resid 438 through 454 removed outlier: 3.679A pdb=" N LEU B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.923A pdb=" N PHE B 459 " --> pdb=" O MET B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 487 removed outlier: 4.091A pdb=" N ALA B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.811A pdb=" N ALA B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 537 removed outlier: 3.672A pdb=" N SER B 537 " --> pdb=" O GLY B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 558 removed outlier: 3.535A pdb=" N VAL B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 588 Processing helix chain 'B' and resid 590 through 601 Processing helix chain 'B' and resid 633 through 637 Processing helix chain 'B' and resid 639 through 642 removed outlier: 3.667A pdb=" N ASN B 642 " --> pdb=" O GLY B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 639 through 642' Processing helix chain 'B' and resid 643 through 655 removed outlier: 3.520A pdb=" N MET B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG B 650 " --> pdb=" O ALA B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 658 No H-bonds generated for 'chain 'B' and resid 656 through 658' Processing helix chain 'B' and resid 692 through 707 Processing helix chain 'B' and resid 732 through 740 Processing helix chain 'B' and resid 742 through 756 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 836 through 848 removed outlier: 3.503A pdb=" N GLU B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU B 843 " --> pdb=" O GLU B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 851 No H-bonds generated for 'chain 'B' and resid 849 through 851' Processing helix chain 'B' and resid 861 through 870 Processing helix chain 'B' and resid 871 through 892 removed outlier: 4.304A pdb=" N SER B 875 " --> pdb=" O ASN B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 903 removed outlier: 4.008A pdb=" N SER B 900 " --> pdb=" O SER B 896 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 920 removed outlier: 4.116A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B 912 " --> pdb=" O GLY B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 957 Processing helix chain 'B' and resid 961 through 991 removed outlier: 4.596A 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 998 through 1017 removed outlier: 3.922A pdb=" N GLY B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL B1007 " --> pdb=" O VAL B1003 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR B1013 " --> pdb=" O GLY B1009 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B1015 " --> pdb=" O MET B1011 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B1017 " --> pdb=" O THR B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1020 No H-bonds generated for 'chain 'B' and resid 1018 through 1020' Processing helix chain 'B' and resid 1021 through 1031 Processing helix chain 'C' and resid 2 through 7 removed outlier: 4.263A pdb=" N ASP C 7 " --> pdb=" O ASN C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 25 removed outlier: 3.601A pdb=" N ILE C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY C 23 " --> pdb=" O ILE C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.627A pdb=" N LYS C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 removed outlier: 3.603A pdb=" N ASP C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 119 through 126 removed outlier: 3.883A pdb=" N GLN C 123 " --> pdb=" O PRO C 119 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN C 124 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 168 removed outlier: 4.440A pdb=" N LYS C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ASP C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) 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 298 through 314 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 329 through 359 removed outlier: 3.614A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 366 Processing helix chain 'C' and resid 366 through 386 removed outlier: 3.784A pdb=" N ALA C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.738A 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 406 removed outlier: 4.298A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 423 Processing helix chain 'C' and resid 426 through 434 Processing helix chain 'C' and resid 439 through 452 removed outlier: 3.865A pdb=" N VAL C 443 " --> pdb=" O GLN C 439 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 Processing helix chain 'C' and resid 461 through 487 removed outlier: 3.858A pdb=" N ALA C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE C 474 " --> pdb=" O PHE C 470 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA C 477 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.596A pdb=" N ALA C 491 " --> pdb=" O ILE C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 537 removed outlier: 3.562A pdb=" N MET C 519 " --> pdb=" O TRP C 515 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 559 removed outlier: 3.622A 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 633 through 637 Processing helix chain 'C' and resid 639 through 642 Processing helix chain 'C' and resid 643 through 656 removed outlier: 3.512A pdb=" N ARG C 650 " --> pdb=" O ALA C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 707 removed outlier: 3.580A pdb=" N GLN C 697 " --> pdb=" O GLU C 693 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' and resid 742 through 754 removed outlier: 4.046A pdb=" N THR C 748 " --> pdb=" O ASN C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 780 Processing helix chain 'C' and resid 782 through 787 removed outlier: 3.754A pdb=" N ILE C 786 " --> pdb=" O PRO C 783 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY C 787 " --> pdb=" O ASP C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 850 removed outlier: 3.797A pdb=" N GLU C 842 " --> pdb=" O GLY C 838 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 850 " --> pdb=" O GLN C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 893 removed outlier: 3.707A pdb=" N GLN C 865 " --> pdb=" O GLY C 861 " (cutoff:3.500A) Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 896 through 901 removed outlier: 3.539A pdb=" N VAL C 901 " --> pdb=" O ILE C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 917 removed outlier: 3.610A pdb=" N GLY C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA C 912 " --> pdb=" O GLY C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 954 removed outlier: 3.839A pdb=" N ILE C 945 " --> pdb=" O ASN C 941 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 971 Processing helix chain 'C' and resid 972 through 992 Proline residue: C 988 - end of helix Processing helix chain 'C' and resid 998 through 1017 removed outlier: 3.926A pdb=" N ALA C1002 " --> pdb=" O GLY C 998 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1034 Proline residue: C1023 - end of helix Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.546A pdb=" N LYS A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.803A pdb=" N LEU A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 3.859A 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 162 through 167 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 removed outlier: 3.586A pdb=" N LYS A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) 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 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 360 removed outlier: 3.868A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 387 Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 424 removed outlier: 4.553A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.460A 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) removed outlier: 3.921A pdb=" N ASN A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 450 removed outlier: 5.314A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.953A pdb=" N PHE A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 496 removed outlier: 4.289A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 516 through 536 removed outlier: 3.597A pdb=" N ARG A 536 " --> pdb=" O GLY A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 559 removed outlier: 3.570A pdb=" N TYR A 545 " --> pdb=" O TYR A 541 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG A 558 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 602 removed outlier: 3.593A pdb=" N GLU A 602 " --> pdb=" O TYR A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 606 removed outlier: 3.596A pdb=" N VAL A 606 " --> pdb=" O LYS A 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 603 through 606' Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 639 through 642 removed outlier: 3.624A pdb=" N ASN A 642 " --> pdb=" O GLY A 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 639 through 642' Processing helix chain 'A' and resid 643 through 657 removed outlier: 4.029A pdb=" N ARG A 650 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN A 657 " --> pdb=" O ARG A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 708 removed outlier: 4.271A pdb=" N LYS A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 695 " --> pdb=" O GLY A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 744 through 756 removed outlier: 3.670A 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 removed outlier: 3.716A pdb=" N ILE A 786 " --> pdb=" O PRO A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 842 through 849 Processing helix chain 'A' and resid 860 through 867 removed outlier: 4.107A pdb=" N GLN A 865 " --> pdb=" O GLY A 861 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 867 " --> pdb=" O SER A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 893 Processing helix chain 'A' and resid 896 through 901 Processing helix chain 'A' and resid 904 through 920 removed outlier: 4.159A pdb=" N GLY A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 955 removed outlier: 3.840A pdb=" N ILE A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 952 " --> pdb=" O PHE A 948 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 955 " --> pdb=" O ASP A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 970 No H-bonds generated for 'chain 'A' and resid 968 through 970' Processing helix chain 'A' and resid 971 through 986 removed outlier: 4.435A pdb=" N ILE A 975 " --> pdb=" O ARG A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 991 Processing helix chain 'A' and resid 996 through 1017 removed outlier: 3.611A pdb=" N GLY A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A1013 " --> pdb=" O GLY A1009 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A1016 " --> pdb=" O VAL A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1020 No H-bonds generated for 'chain 'A' and resid 1018 through 1020' Processing helix chain 'A' and resid 1021 through 1032 removed outlier: 4.671A pdb=" N VAL A1027 " --> pdb=" O PRO A1023 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 128 through 132 removed outlier: 3.587A pdb=" N GLU B 130 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ALA B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.283A pdb=" N ARG B 815 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N GLU B 826 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN B 830 " --> pdb=" O SER B 715 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N SER B 715 " --> pdb=" O GLN B 830 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 679 through 680 removed outlier: 3.793A pdb=" N GLY B 829 " --> pdb=" O PHE B 680 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.542A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR B 327 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY B 141 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR B 325 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B 143 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ILE B 323 " --> pdb=" O ILE B 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.542A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN B 144 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B 284 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ALA B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE B 278 " --> pdb=" O ASN B 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.845A pdb=" N TYR B 182 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS B 770 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 760 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL B 773 " --> pdb=" O TYR B 758 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TYR B 758 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 217 through 218 removed outlier: 4.266A pdb=" N GLY B 217 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N SER B 233 " --> pdb=" O PHE C 727 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE C 729 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE B 235 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE C 731 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 250 through 252 removed outlier: 7.243A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 805 through 812 removed outlier: 4.731A pdb=" N SER A 233 " --> pdb=" O PRO B 725 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLN A 237 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N ILE B 731 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLY A 217 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA A 236 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ALA A 215 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 790 through 792 Processing sheet with id=AB1, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.471A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 12.159A pdb=" N ARG C 815 " --> pdb=" O GLU C 826 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N GLU C 826 " --> pdb=" O ARG C 815 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU C 817 " --> pdb=" O SER C 824 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 684 " --> pdb=" O MET C 825 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 172 through 174 removed outlier: 3.528A pdb=" N ASP C 174 " --> pdb=" O LYS C 292 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 608 " --> pdb=" O SER C 630 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY C 614 " --> pdb=" O THR C 624 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N THR C 624 " --> pdb=" O GLY C 614 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 322 through 328 removed outlier: 6.851A pdb=" N VAL C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 608 " --> pdb=" O SER C 630 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY C 614 " --> pdb=" O THR C 624 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N THR C 624 " --> pdb=" O GLY C 614 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 266 through 272 removed outlier: 3.541A pdb=" N TRP C 187 " --> pdb=" O LYS C 267 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N TYR C 182 " --> pdb=" O LYS C 770 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N TYR C 772 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N MET C 184 " --> pdb=" O TYR C 772 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N MET C 774 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE C 186 " --> pdb=" O MET C 774 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN C 760 " --> pdb=" O VAL C 771 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL C 773 " --> pdb=" O TYR C 758 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR C 758 " --> pdb=" O VAL C 773 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 217 through 219 removed outlier: 4.406A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 232 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER C 233 " --> pdb=" O PHE A 727 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE A 729 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE C 235 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE A 731 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 250 through 253 removed outlier: 3.735A pdb=" N LYS C 252 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 713 through 714 Processing sheet with id=AB8, first strand: chain 'C' and resid 790 through 792 Processing sheet with id=AB9, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.755A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.621A pdb=" N ASN A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.023A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.048A pdb=" N TYR A 182 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS A 770 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN A 760 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 773 " --> pdb=" O TYR A 758 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TYR A 758 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 250 through 253 removed outlier: 3.712A pdb=" N LYS A 252 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 713 through 718 removed outlier: 5.021A pdb=" N SER A 715 " --> pdb=" O GLN A 830 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN A 830 " --> pdb=" O SER A 715 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 790 through 792 1423 hydrogen bonds defined for protein. 4104 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: 6.44 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3883 1.30 - 1.43: 5655 1.43 - 1.56: 14312 1.56 - 1.69: 32 1.69 - 1.82: 258 Bond restraints: 24140 Sorted by residual: bond pdb=" C PRO A 31 " pdb=" O PRO A 31 " ideal model delta sigma weight residual 1.233 1.170 0.063 9.60e-03 1.09e+04 4.29e+01 bond pdb=" CA PRO A 31 " pdb=" C PRO A 31 " ideal model delta sigma weight residual 1.522 1.568 -0.046 9.40e-03 1.13e+04 2.35e+01 bond pdb=" C PRO A 368 " pdb=" O PRO A 368 " ideal model delta sigma weight residual 1.238 1.180 0.058 1.24e-02 6.50e+03 2.17e+01 bond pdb=" C THR C 93 " pdb=" O THR C 93 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.21e-02 6.83e+03 2.17e+01 bond pdb=" C PRO B 31 " pdb=" O PRO B 31 " ideal model delta sigma weight residual 1.235 1.176 0.059 1.30e-02 5.92e+03 2.09e+01 ... (remaining 24135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 32279 3.21 - 6.41: 360 6.41 - 9.62: 21 9.62 - 12.82: 12 12.82 - 16.03: 1 Bond angle restraints: 32673 Sorted by residual: angle pdb=" CA ALA C 491 " pdb=" C ALA C 491 " pdb=" O ALA C 491 " ideal model delta sigma weight residual 120.70 114.15 6.55 1.03e+00 9.43e-01 4.04e+01 angle pdb=" N THR A 934 " pdb=" CA THR A 934 " pdb=" C THR A 934 " ideal model delta sigma weight residual 112.23 104.77 7.46 1.26e+00 6.30e-01 3.51e+01 angle pdb=" CA MET A 395 " pdb=" C MET A 395 " pdb=" O MET A 395 " ideal model delta sigma weight residual 120.55 114.29 6.26 1.06e+00 8.90e-01 3.48e+01 angle pdb=" CA ILE C 685 " pdb=" C ILE C 685 " pdb=" O ILE C 685 " ideal model delta sigma weight residual 121.72 116.33 5.39 9.60e-01 1.09e+00 3.15e+01 angle pdb=" O11 PTY C1104 " pdb=" P1 PTY C1104 " pdb=" O14 PTY C1104 " ideal model delta sigma weight residual 92.90 108.93 -16.03 3.00e+00 1.11e-01 2.85e+01 ... (remaining 32668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 14191 34.22 - 68.43: 300 68.43 - 102.65: 28 102.65 - 136.86: 3 136.86 - 171.08: 7 Dihedral angle restraints: 14529 sinusoidal: 5780 harmonic: 8749 Sorted by residual: dihedral pdb=" C THR B 489 " pdb=" N THR B 489 " pdb=" CA THR B 489 " pdb=" CB THR B 489 " ideal model delta harmonic sigma weight residual -122.00 -135.26 13.26 0 2.50e+00 1.60e-01 2.81e+01 dihedral pdb=" N1 PTY C1104 " pdb=" C2 PTY C1104 " pdb=" C3 PTY C1104 " pdb=" O11 PTY C1104 " ideal model delta sinusoidal sigma weight residual 65.33 -123.59 -171.08 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" N1 PTY C1106 " pdb=" C2 PTY C1106 " pdb=" C3 PTY C1106 " pdb=" O11 PTY C1106 " ideal model delta sinusoidal sigma weight residual 65.33 -132.77 -161.90 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 14526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3588 0.093 - 0.185: 224 0.185 - 0.278: 11 0.278 - 0.370: 0 0.370 - 0.463: 3 Chirality restraints: 3826 Sorted by residual: chirality pdb=" C6 PTY B1102 " pdb=" C1 PTY B1102 " pdb=" C5 PTY B1102 " pdb=" O7 PTY B1102 " both_signs ideal model delta sigma weight residual False 2.49 2.03 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" C6 PTY C1102 " pdb=" C1 PTY C1102 " pdb=" C5 PTY C1102 " pdb=" O7 PTY C1102 " both_signs ideal model delta sigma weight residual False 2.49 2.06 0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" CA THR B 489 " pdb=" N THR B 489 " pdb=" C THR B 489 " pdb=" CB THR B 489 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.41 2.00e-01 2.50e+01 4.25e+00 ... (remaining 3823 not shown) Planarity restraints: 4124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 929 " 0.027 2.00e-02 2.50e+03 5.35e-02 2.86e+01 pdb=" C VAL A 929 " -0.093 2.00e-02 2.50e+03 pdb=" O VAL A 929 " 0.035 2.00e-02 2.50e+03 pdb=" N GLY A 930 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 361 " 0.017 2.00e-02 2.50e+03 3.57e-02 1.28e+01 pdb=" C ASN A 361 " -0.062 2.00e-02 2.50e+03 pdb=" O ASN A 361 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE A 362 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 184 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" C MET B 184 " -0.054 2.00e-02 2.50e+03 pdb=" O MET B 184 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG B 185 " 0.019 2.00e-02 2.50e+03 ... (remaining 4121 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2079 2.74 - 3.28: 24046 3.28 - 3.82: 39490 3.82 - 4.36: 47140 4.36 - 4.90: 83383 Nonbonded interactions: 196138 Sorted by model distance: nonbonded pdb=" OH TYR C 467 " pdb=" OE1 GLN C 928 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR C 758 " pdb=" OD1 ASP C 761 " model vdw 2.234 3.040 nonbonded pdb=" OD2 ASP B 408 " pdb=" OG SER B 481 " model vdw 2.235 3.040 nonbonded pdb=" O HIS B 596 " pdb=" OG1 THR B 600 " model vdw 2.242 3.040 nonbonded pdb=" O GLY A 994 " pdb=" OG SER A 997 " model vdw 2.242 3.040 ... (remaining 196133 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 385 or (resid 386 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 387 through 478 or (resid 479 and (name N or name CA or name C o \ r name CB )) or resid 480 through 500 or resid 516 through 1032 or (resid 1103 a \ nd (name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name \ C16 or name C5 or name C6 or name C8 or name O10 or name O11 or name O12 or name \ O13 or name O14 or name O7 or name P1 )) or (resid 1104 and (name C1 or name C5 \ or name C6 or name N1 or name O11 or name O12 or name O13 or name O14 or name O \ 4 or name O7 or name P1 )) or resid 1110)) selection = (chain 'B' and (resid 1 through 421 or (resid 422 through 423 and (name N or nam \ e CA or name C or name O or name CB )) or resid 424 through 449 or (resid 450 an \ d (name N or name CA or name C or name CB or name OG )) or resid 451 through 500 \ or (resid 516 and (name N or name CA or name C or name O or name CB )) or resid \ 517 through 521 or (resid 522 and (name N or name CA or name C or name O or nam \ e CB )) or resid 523 through 526 or (resid 527 and (name N or name CA or name C \ or name O or name CB )) or resid 528 through 539 or (resid 540 and (name N or na \ me CA or name C or name O or name CB )) or resid 541 through 619 or (resid 620 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD or na \ me NE or name CZ )) or resid 621 through 682 or (resid 683 and (name N or name C \ A or name C or name O or name CB or name CG or name CD or name OE1)) or resid 68 \ 4 through 849 or (resid 850 and (name N or name CA or name C or name O or name C \ B )) or resid 851 through 949 or (resid 950 and (name N or name CA or name C or \ name O or name CB )) or resid 951 through 954 or (resid 955 and (name N or name \ CA or name C or name O or name CB )) or resid 956 through 961 or (resid 962 thro \ ugh 963 and (name N or name CA or name C or name O or name CB )) or resid 964 th \ rough 968 or (resid 969 and (name N or name CA or name C or name O or name CB )) \ or resid 970 through 1020 or (resid 1021 and (name N or name CA or name C or na \ me O or name CB )) or resid 1022 through 1028 or (resid 1029 through 1032 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 1102 and (name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C \ 5 or name C6 or name C8 or name O10 or name O11 or name O12 or name O13 or name \ O14 or name O7 or name P1 )) or (resid 1103 and (name C1 or name C5 or name C6 o \ r name N1 or name O11 or name O12 or name O13 or name O14 or name O4 or name O7 \ or name P1 )) or resid 1109)) selection = (chain 'C' and (resid 1 through 385 or (resid 386 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 387 through 421 or (resid 422 through 423 and (name N or name CA \ or name C or name O or name CB )) or resid 424 through 449 or (resid 450 and (n \ ame N or name CA or name C or name CB or name OG )) or resid 451 through 478 or \ (resid 479 and (name N or name CA or name C or name CB )) or resid 480 through 5 \ 00 or (resid 516 and (name N or name CA or name C or name O or name CB )) or res \ id 517 through 526 or (resid 527 and (name N or name CA or name C or name O or n \ ame CB )) or resid 528 through 539 or (resid 540 and (name N or name CA or name \ C or name O or name CB )) or resid 541 through 619 or (resid 620 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ )) or resid 621 through 682 or (resid 683 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1)) or resid 684 through 849 \ or (resid 850 and (name N or name CA or name C or name O or name CB )) or resid \ 851 through 949 or (resid 950 and (name N or name CA or name C or name O or name \ CB )) or resid 951 through 954 or (resid 955 and (name N or name CA or name C o \ r name O or name CB )) or resid 956 through 961 or (resid 962 through 963 and (n \ ame N or name CA or name C or name O or name CB )) or resid 964 through 968 or ( \ resid 969 and (name N or name CA or name C or name O or name CB )) or resid 970 \ through 1020 or (resid 1021 and (name N or name CA or name C or name O or name C \ B )) or resid 1022 through 1028 or (resid 1029 through 1032 and (name N or name \ CA or name C or name O or name CB )) 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 C5 or name C6 o \ r name C8 or name O10 or name O11 or name O12 or name O13 or name O14 or name O7 \ or name P1 )) or (resid 1102 and (name C1 or name C5 or name C6 or name N1 or n \ ame O11 or name O12 or name O13 or name O14 or name O4 or name O7 or name P1 )) \ or resid 1108)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.820 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.050 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 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 0.085 24140 Z= 0.282 Angle : 0.766 16.029 32673 Z= 0.433 Chirality : 0.047 0.463 3826 Planarity : 0.004 0.054 4124 Dihedral : 14.437 171.077 8915 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.28 % Allowed : 0.93 % Favored : 98.79 % Cbeta Deviations : 0.07 % 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: 0.40 (0.16), residues: 3049 helix: 1.11 (0.14), residues: 1588 sheet: -0.86 (0.26), residues: 411 loop : -0.41 (0.21), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 586 TYR 0.021 0.001 TYR A 49 PHE 0.021 0.001 PHE A 362 TRP 0.033 0.002 TRP B 895 HIS 0.005 0.001 HIS C 525 Details of bonding type rmsd covalent geometry : bond 0.00482 (24140) covalent geometry : angle 0.76561 (32673) hydrogen bonds : bond 0.15561 ( 1399) hydrogen bonds : angle 6.91230 ( 4104) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 316 time to evaluate : 0.853 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 496 MET cc_start: 0.8012 (ttm) cc_final: 0.7799 (ttm) REVERT: B 519 MET cc_start: 0.3844 (mtm) cc_final: 0.3572 (mtt) REVERT: A 496 MET cc_start: 0.8353 (ptp) cc_final: 0.8131 (ptp) REVERT: A 541 TYR cc_start: 0.6358 (m-10) cc_final: 0.6070 (m-80) REVERT: A 909 VAL cc_start: 0.8239 (t) cc_final: 0.7974 (t) outliers start: 7 outliers final: 1 residues processed: 321 average time/residue: 0.1401 time to fit residues: 73.8977 Evaluate side-chains 258 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 355 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 526 HIS ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN C 415 ASN A 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.117124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.093607 restraints weight = 40763.587| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.20 r_work: 0.3236 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24140 Z= 0.127 Angle : 0.540 10.191 32673 Z= 0.273 Chirality : 0.041 0.151 3826 Planarity : 0.004 0.042 4124 Dihedral : 12.789 175.930 3655 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.65 % Allowed : 6.42 % Favored : 92.94 % 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: 0.59 (0.16), residues: 3049 helix: 1.29 (0.13), residues: 1618 sheet: -0.82 (0.25), residues: 425 loop : -0.39 (0.21), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 468 TYR 0.017 0.001 TYR B 49 PHE 0.022 0.001 PHE A 362 TRP 0.014 0.001 TRP C 515 HIS 0.007 0.001 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00277 (24140) covalent geometry : angle 0.53972 (32673) hydrogen bonds : bond 0.03904 ( 1399) hydrogen bonds : angle 4.96349 ( 4104) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 288 time to evaluate : 0.773 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 408 ASP cc_start: 0.8828 (t0) cc_final: 0.8300 (t0) REVERT: B 496 MET cc_start: 0.8473 (ttm) cc_final: 0.8271 (ttm) REVERT: B 662 MET cc_start: 0.8621 (ttp) cc_final: 0.8359 (tmm) REVERT: B 825 MET cc_start: 0.8771 (mmt) cc_final: 0.8386 (mmm) REVERT: C 892 TYR cc_start: 0.8087 (m-80) cc_final: 0.7749 (m-80) REVERT: A 130 GLU cc_start: 0.8157 (pm20) cc_final: 0.7904 (pm20) REVERT: A 541 TYR cc_start: 0.5893 (m-10) cc_final: 0.5597 (m-80) outliers start: 16 outliers final: 6 residues processed: 293 average time/residue: 0.1308 time to fit residues: 64.3726 Evaluate side-chains 269 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 263 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 9 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 263 optimal weight: 7.9990 chunk 276 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 HIS C 744 ASN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 GLN A 231 ASN A 928 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.112595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.089175 restraints weight = 41468.828| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.21 r_work: 0.3165 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24140 Z= 0.210 Angle : 0.576 7.479 32673 Z= 0.292 Chirality : 0.043 0.141 3826 Planarity : 0.004 0.044 4124 Dihedral : 12.162 179.630 3655 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.41 % Allowed : 9.41 % Favored : 89.18 % 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: 0.46 (0.16), residues: 3049 helix: 1.22 (0.13), residues: 1622 sheet: -0.93 (0.26), residues: 407 loop : -0.52 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 468 TYR 0.032 0.002 TYR B 49 PHE 0.025 0.001 PHE A 682 TRP 0.011 0.001 TRP A 789 HIS 0.008 0.001 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00499 (24140) covalent geometry : angle 0.57632 (32673) hydrogen bonds : bond 0.04056 ( 1399) hydrogen bonds : angle 4.78513 ( 4104) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 277 time to evaluate : 0.880 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 408 ASP cc_start: 0.8872 (t0) cc_final: 0.8572 (t0) REVERT: B 496 MET cc_start: 0.8610 (ttm) cc_final: 0.8406 (ttm) REVERT: B 662 MET cc_start: 0.8638 (ttp) cc_final: 0.8378 (tmm) REVERT: C 892 TYR cc_start: 0.8196 (m-80) cc_final: 0.7239 (m-10) REVERT: A 130 GLU cc_start: 0.8275 (pm20) cc_final: 0.7957 (pm20) REVERT: A 541 TYR cc_start: 0.5868 (m-10) cc_final: 0.5470 (m-80) outliers start: 35 outliers final: 22 residues processed: 291 average time/residue: 0.1296 time to fit residues: 63.5433 Evaluate side-chains 280 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 258 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 649 MET Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 977 MET Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 44 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 chunk 217 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 253 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 297 optimal weight: 20.0000 chunk 117 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 HIS C 74 ASN ** C 747 ASN ** 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 = 0.3674 r_free = 0.3674 target = 0.113066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.089772 restraints weight = 41572.954| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.20 r_work: 0.3180 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24140 Z= 0.173 Angle : 0.541 8.569 32673 Z= 0.273 Chirality : 0.042 0.142 3826 Planarity : 0.004 0.045 4124 Dihedral : 11.790 178.291 3655 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.45 % Allowed : 11.18 % Favored : 87.36 % 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: 0.48 (0.16), residues: 3049 helix: 1.26 (0.13), residues: 1626 sheet: -0.99 (0.25), residues: 414 loop : -0.53 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 780 TYR 0.024 0.001 TYR B 49 PHE 0.019 0.001 PHE A 682 TRP 0.013 0.001 TRP A 789 HIS 0.007 0.001 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00410 (24140) covalent geometry : angle 0.54059 (32673) hydrogen bonds : bond 0.03705 ( 1399) hydrogen bonds : angle 4.65859 ( 4104) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 267 time to evaluate : 0.772 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 408 ASP cc_start: 0.9004 (t0) cc_final: 0.8572 (t0) REVERT: B 496 MET cc_start: 0.8594 (ttm) cc_final: 0.8328 (ttm) REVERT: B 662 MET cc_start: 0.8626 (ttp) cc_final: 0.8314 (tmm) REVERT: B 825 MET cc_start: 0.8986 (mmt) cc_final: 0.8546 (mmt) REVERT: C 947 GLU cc_start: 0.7903 (tp30) cc_final: 0.7496 (mm-30) REVERT: A 130 GLU cc_start: 0.8300 (pm20) cc_final: 0.7924 (pm20) REVERT: A 541 TYR cc_start: 0.5851 (m-10) cc_final: 0.5496 (m-80) outliers start: 36 outliers final: 22 residues processed: 285 average time/residue: 0.1294 time to fit residues: 62.3832 Evaluate side-chains 276 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 254 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 649 MET Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 977 MET Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 987 MET Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 931 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 37 optimal weight: 0.5980 chunk 202 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 256 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 267 optimal weight: 0.6980 chunk 301 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 865 GLN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.114396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.090809 restraints weight = 41147.528| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.23 r_work: 0.3200 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24140 Z= 0.130 Angle : 0.515 9.514 32673 Z= 0.259 Chirality : 0.041 0.151 3826 Planarity : 0.004 0.045 4124 Dihedral : 11.307 178.173 3655 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.70 % Allowed : 11.95 % Favored : 86.35 % 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: 0.61 (0.16), residues: 3049 helix: 1.42 (0.13), residues: 1618 sheet: -0.98 (0.25), residues: 412 loop : -0.52 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.019 0.001 TYR B 49 PHE 0.015 0.001 PHE A 682 TRP 0.032 0.001 TRP C 515 HIS 0.004 0.001 HIS C 525 Details of bonding type rmsd covalent geometry : bond 0.00301 (24140) covalent geometry : angle 0.51467 (32673) hydrogen bonds : bond 0.03408 ( 1399) hydrogen bonds : angle 4.51172 ( 4104) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 282 time to evaluate : 0.818 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 408 ASP cc_start: 0.8872 (t0) cc_final: 0.8535 (t0) REVERT: B 496 MET cc_start: 0.8576 (ttm) cc_final: 0.8296 (ttm) REVERT: B 519 MET cc_start: 0.4445 (mtm) cc_final: 0.4211 (mtt) REVERT: B 662 MET cc_start: 0.8569 (ttp) cc_final: 0.8335 (tmm) REVERT: B 825 MET cc_start: 0.8932 (mmt) cc_final: 0.8543 (mmt) REVERT: C 947 GLU cc_start: 0.8019 (tp30) cc_final: 0.7599 (mm-30) REVERT: A 130 GLU cc_start: 0.8259 (pm20) cc_final: 0.7958 (pm20) REVERT: A 184 MET cc_start: 0.9147 (tpp) cc_final: 0.8921 (tpt) REVERT: A 541 TYR cc_start: 0.5871 (m-10) cc_final: 0.5484 (m-80) outliers start: 42 outliers final: 27 residues processed: 305 average time/residue: 0.1318 time to fit residues: 68.1069 Evaluate side-chains 285 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 258 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 649 MET Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 977 MET Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 987 MET Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 952 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 205 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 865 GLN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.115599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.091688 restraints weight = 41073.423| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.27 r_work: 0.3200 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24140 Z= 0.112 Angle : 0.504 10.176 32673 Z= 0.252 Chirality : 0.041 0.158 3826 Planarity : 0.003 0.045 4124 Dihedral : 10.796 176.596 3652 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.33 % Allowed : 12.92 % Favored : 85.75 % 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: 0.75 (0.16), residues: 3049 helix: 1.53 (0.13), residues: 1616 sheet: -0.91 (0.24), residues: 418 loop : -0.47 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 780 TYR 0.013 0.001 TYR B 49 PHE 0.023 0.001 PHE C 885 TRP 0.023 0.001 TRP C 515 HIS 0.004 0.001 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00252 (24140) covalent geometry : angle 0.50436 (32673) hydrogen bonds : bond 0.03213 ( 1399) hydrogen bonds : angle 4.40033 ( 4104) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 279 time to evaluate : 0.741 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 408 ASP cc_start: 0.8906 (t0) cc_final: 0.8551 (t0) REVERT: B 496 MET cc_start: 0.8563 (ttm) cc_final: 0.8342 (ttm) REVERT: B 825 MET cc_start: 0.8945 (mmt) cc_final: 0.8555 (mmt) REVERT: C 781 MET cc_start: 0.8981 (mmt) cc_final: 0.8563 (mmt) REVERT: C 947 GLU cc_start: 0.8010 (tp30) cc_final: 0.7660 (tp30) REVERT: C 951 ASP cc_start: 0.8240 (m-30) cc_final: 0.7988 (m-30) REVERT: A 130 GLU cc_start: 0.8284 (pm20) cc_final: 0.7958 (pm20) REVERT: A 184 MET cc_start: 0.9180 (tpp) cc_final: 0.8953 (tpt) REVERT: A 541 TYR cc_start: 0.5993 (m-10) cc_final: 0.5570 (m-80) outliers start: 33 outliers final: 28 residues processed: 300 average time/residue: 0.1237 time to fit residues: 63.0820 Evaluate side-chains 292 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 649 MET Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 977 MET Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 987 MET Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 811 TYR Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 952 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 131 optimal weight: 2.9990 chunk 22 optimal weight: 0.0020 chunk 18 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 290 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 296 optimal weight: 8.9990 chunk 182 optimal weight: 0.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 HIS ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.115407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.091574 restraints weight = 40959.799| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.27 r_work: 0.3197 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24140 Z= 0.118 Angle : 0.515 10.287 32673 Z= 0.255 Chirality : 0.041 0.166 3826 Planarity : 0.003 0.045 4124 Dihedral : 10.483 174.518 3652 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.74 % Allowed : 13.08 % Favored : 85.18 % 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: 0.81 (0.16), residues: 3049 helix: 1.57 (0.13), residues: 1617 sheet: -0.83 (0.25), residues: 409 loop : -0.45 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 780 TYR 0.013 0.001 TYR B 49 PHE 0.019 0.001 PHE C 885 TRP 0.020 0.001 TRP C 515 HIS 0.008 0.001 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00271 (24140) covalent geometry : angle 0.51500 (32673) hydrogen bonds : bond 0.03214 ( 1399) hydrogen bonds : angle 4.37900 ( 4104) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 269 time to evaluate : 0.572 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 408 ASP cc_start: 0.8919 (t0) cc_final: 0.8552 (t0) REVERT: B 496 MET cc_start: 0.8558 (ttm) cc_final: 0.8341 (ttm) REVERT: B 662 MET cc_start: 0.8583 (ttp) cc_final: 0.8310 (tmm) REVERT: B 825 MET cc_start: 0.8948 (mmt) cc_final: 0.8543 (mmt) REVERT: C 781 MET cc_start: 0.8972 (mmt) cc_final: 0.8608 (mmt) REVERT: A 130 GLU cc_start: 0.8289 (pm20) cc_final: 0.7959 (pm20) REVERT: A 184 MET cc_start: 0.9188 (tpp) cc_final: 0.8963 (tpt) REVERT: A 541 TYR cc_start: 0.6005 (m-10) cc_final: 0.5606 (m-80) outliers start: 43 outliers final: 30 residues processed: 298 average time/residue: 0.1252 time to fit residues: 63.6175 Evaluate side-chains 300 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 270 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 649 MET Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 977 MET Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 811 TYR Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 982 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 297 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 301 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 165 optimal weight: 7.9990 chunk 223 optimal weight: 0.6980 chunk 219 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 HIS ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.114698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.090828 restraints weight = 41216.897| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.27 r_work: 0.3206 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24140 Z= 0.136 Angle : 0.529 10.860 32673 Z= 0.261 Chirality : 0.041 0.166 3826 Planarity : 0.003 0.044 4124 Dihedral : 10.247 171.646 3652 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.53 % Allowed : 13.52 % Favored : 84.94 % 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: 0.81 (0.16), residues: 3049 helix: 1.56 (0.13), residues: 1618 sheet: -0.81 (0.25), residues: 408 loop : -0.44 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.013 0.001 TYR B 49 PHE 0.018 0.001 PHE C 885 TRP 0.018 0.001 TRP C 515 HIS 0.008 0.001 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00318 (24140) covalent geometry : angle 0.52876 (32673) hydrogen bonds : bond 0.03304 ( 1399) hydrogen bonds : angle 4.39136 ( 4104) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 268 time to evaluate : 0.641 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 408 ASP cc_start: 0.8942 (t0) cc_final: 0.8554 (t0) REVERT: B 478 MET cc_start: 0.7770 (mmm) cc_final: 0.7565 (mmp) REVERT: B 496 MET cc_start: 0.8568 (ttm) cc_final: 0.8307 (ttm) REVERT: B 662 MET cc_start: 0.8593 (ttp) cc_final: 0.8378 (tmm) REVERT: B 825 MET cc_start: 0.8987 (mmt) cc_final: 0.8547 (mmt) REVERT: C 781 MET cc_start: 0.8966 (mmt) cc_final: 0.8592 (mmt) REVERT: C 951 ASP cc_start: 0.8380 (m-30) cc_final: 0.8157 (m-30) REVERT: A 130 GLU cc_start: 0.8309 (pm20) cc_final: 0.7949 (pm20) REVERT: A 496 MET cc_start: 0.8539 (ptp) cc_final: 0.8162 (pmm) REVERT: A 541 TYR cc_start: 0.6059 (m-10) cc_final: 0.5664 (m-80) outliers start: 38 outliers final: 32 residues processed: 292 average time/residue: 0.1253 time to fit residues: 62.4240 Evaluate side-chains 296 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 264 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 649 MET Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 977 MET Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 811 TYR Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 982 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 38 optimal weight: 4.9990 chunk 193 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 268 optimal weight: 7.9990 chunk 98 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 chunk 266 optimal weight: 0.0970 chunk 262 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.1378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN B 526 HIS ** C 747 ASN ** 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 = 0.3696 r_free = 0.3696 target = 0.115287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.091361 restraints weight = 41189.818| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.28 r_work: 0.3194 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24140 Z= 0.126 Angle : 0.526 11.580 32673 Z= 0.259 Chirality : 0.041 0.197 3826 Planarity : 0.003 0.045 4124 Dihedral : 10.017 168.822 3652 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.45 % Allowed : 13.73 % Favored : 84.82 % 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: 0.85 (0.16), residues: 3049 helix: 1.59 (0.13), residues: 1615 sheet: -0.78 (0.25), residues: 407 loop : -0.41 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.012 0.001 TYR B 327 PHE 0.018 0.001 PHE C 885 TRP 0.017 0.001 TRP C 515 HIS 0.007 0.001 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00294 (24140) covalent geometry : angle 0.52611 (32673) hydrogen bonds : bond 0.03253 ( 1399) hydrogen bonds : angle 4.37646 ( 4104) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 272 time to evaluate : 0.688 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 108 GLN cc_start: 0.8294 (tp-100) cc_final: 0.7955 (tp-100) REVERT: B 408 ASP cc_start: 0.8951 (t0) cc_final: 0.8551 (t0) REVERT: B 496 MET cc_start: 0.8539 (ttm) cc_final: 0.8280 (ttm) REVERT: B 825 MET cc_start: 0.8964 (mmt) cc_final: 0.8512 (mmt) REVERT: C 781 MET cc_start: 0.8969 (mmt) cc_final: 0.8638 (mmt) REVERT: C 951 ASP cc_start: 0.8382 (m-30) cc_final: 0.8155 (m-30) REVERT: A 130 GLU cc_start: 0.8284 (pm20) cc_final: 0.7925 (pm20) REVERT: A 541 TYR cc_start: 0.6042 (m-10) cc_final: 0.5673 (m-80) outliers start: 36 outliers final: 30 residues processed: 294 average time/residue: 0.1232 time to fit residues: 61.7779 Evaluate side-chains 293 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 263 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 649 MET Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 977 MET Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 811 TYR Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 982 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 152 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 137 optimal weight: 0.0030 chunk 266 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 526 HIS ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.115214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.091345 restraints weight = 41148.371| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.28 r_work: 0.3191 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24140 Z= 0.129 Angle : 0.532 11.582 32673 Z= 0.261 Chirality : 0.041 0.171 3826 Planarity : 0.003 0.045 4124 Dihedral : 9.842 165.380 3652 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.41 % Allowed : 13.77 % Favored : 84.82 % 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: 3049 helix: 1.60 (0.13), residues: 1615 sheet: -0.76 (0.25), residues: 409 loop : -0.41 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 780 TYR 0.013 0.001 TYR C 182 PHE 0.018 0.001 PHE C 885 TRP 0.017 0.001 TRP C 515 HIS 0.008 0.001 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00300 (24140) covalent geometry : angle 0.53198 (32673) hydrogen bonds : bond 0.03261 ( 1399) hydrogen bonds : angle 4.37864 ( 4104) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 266 time to evaluate : 0.852 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 408 ASP cc_start: 0.8957 (t0) cc_final: 0.8561 (t0) REVERT: B 496 MET cc_start: 0.8556 (ttm) cc_final: 0.8287 (ttm) REVERT: B 825 MET cc_start: 0.8957 (mmt) cc_final: 0.8500 (mmt) REVERT: B 1008 MET cc_start: 0.8243 (ttp) cc_final: 0.7815 (ttt) REVERT: C 781 MET cc_start: 0.8974 (mmt) cc_final: 0.8642 (mmt) REVERT: C 951 ASP cc_start: 0.8429 (m-30) cc_final: 0.8228 (m-30) REVERT: A 130 GLU cc_start: 0.8280 (pm20) cc_final: 0.7935 (pm20) REVERT: A 496 MET cc_start: 0.8591 (ptp) cc_final: 0.8215 (pmm) REVERT: A 541 TYR cc_start: 0.6062 (m-10) cc_final: 0.5691 (m-80) REVERT: A 712 MET cc_start: 0.8014 (tpp) cc_final: 0.7541 (tpp) outliers start: 35 outliers final: 31 residues processed: 288 average time/residue: 0.1323 time to fit residues: 65.0177 Evaluate side-chains 290 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 259 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 649 MET Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 977 MET Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 811 TYR Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 982 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 63 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 151 optimal weight: 0.3980 chunk 206 optimal weight: 8.9990 chunk 128 optimal weight: 0.0980 chunk 154 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 282 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN B 526 HIS ** C 747 ASN ** 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 = 0.3709 r_free = 0.3709 target = 0.116174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.092204 restraints weight = 40925.293| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.28 r_work: 0.3207 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24140 Z= 0.112 Angle : 0.527 12.006 32673 Z= 0.258 Chirality : 0.041 0.175 3826 Planarity : 0.003 0.045 4124 Dihedral : 9.605 161.098 3652 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.29 % Allowed : 14.01 % Favored : 84.70 % 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: 0.94 (0.16), residues: 3049 helix: 1.65 (0.13), residues: 1615 sheet: -0.72 (0.25), residues: 410 loop : -0.36 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 780 TYR 0.014 0.001 TYR C 182 PHE 0.018 0.001 PHE C 885 TRP 0.016 0.001 TRP C 515 HIS 0.008 0.001 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00257 (24140) covalent geometry : angle 0.52738 (32673) hydrogen bonds : bond 0.03157 ( 1399) hydrogen bonds : angle 4.33568 ( 4104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5915.64 seconds wall clock time: 101 minutes 46.24 seconds (6106.24 seconds total)