Starting phenix.real_space_refine on Tue Mar 19 09:34:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr7_24654/03_2024/7rr7_24654_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr7_24654/03_2024/7rr7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr7_24654/03_2024/7rr7_24654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr7_24654/03_2024/7rr7_24654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr7_24654/03_2024/7rr7_24654_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr7_24654/03_2024/7rr7_24654_updated.pdb" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: {'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'TYR:plan': 1} 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-1': 1, 'PTY:plan-2': 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: 12.31, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 8.77 Conformation dependent library (CDL) restraints added in 3.9 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... running ksdssp... Secondary structure from input PDB file: 126 helices and 27 sheets defined 52.5% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.84 Creating SS restraints... Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 29 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 54 through 60 Processing helix chain 'B' and resid 62 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 100 through 117 Proline residue: B 116 - end of helix Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 161 Processing helix chain 'B' and resid 163 through 166 No H-bonds generated for 'chain 'B' and resid 163 through 166' Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 243 through 247 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 304 through 316 Proline residue: B 315 - end of helix Processing helix chain 'B' and resid 330 through 358 Processing helix chain 'B' and resid 362 through 385 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 392 through 423 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 427 through 437 Processing helix chain 'B' and resid 439 through 458 removed outlier: 4.285A pdb=" N VAL B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) Proline residue: B 455 - end of helix removed outlier: 4.070A pdb=" N PHE B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 486 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 488 through 495 Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'B' and resid 539 through 557 removed outlier: 3.535A pdb=" N VAL B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 587 No H-bonds generated for 'chain 'B' and resid 584 through 587' Processing helix chain 'B' and resid 591 through 600 Processing helix chain 'B' and resid 634 through 636 No H-bonds generated for 'chain 'B' and resid 634 through 636' Processing helix chain 'B' and resid 640 through 642 No H-bonds generated for 'chain 'B' and resid 640 through 642' Processing helix chain 'B' and resid 644 through 657 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) removed outlier: 3.538A pdb=" N SER B 656 " --> pdb=" O THR B 652 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLN B 657 " --> pdb=" O ARG B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 708 removed outlier: 3.535A pdb=" N LYS B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 743 through 755 Processing helix chain 'B' and resid 777 through 779 No H-bonds generated for 'chain 'B' and resid 777 through 779' Processing helix chain 'B' and resid 783 through 788 Processing helix chain 'B' and resid 837 through 850 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) removed outlier: 4.135A pdb=" N LYS B 850 " --> pdb=" O GLN B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 869 Processing helix chain 'B' and resid 872 through 891 Processing helix chain 'B' and resid 897 through 919 removed outlier: 3.813A pdb=" N VAL B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL B 904 " --> pdb=" O SER B 900 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL B 905 " --> pdb=" O VAL B 901 " (cutoff:3.500A) Proline residue: B 906 - end of helix 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 925 through 956 Processing helix chain 'B' and resid 962 through 990 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 999 through 1016 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) 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 1022 through 1032 removed outlier: 3.664A pdb=" N ARG B1032 " --> pdb=" O VAL B1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 9 through 24 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 26 through 29 No H-bonds generated for 'chain 'C' and resid 26 through 29' Processing helix chain 'C' and resid 54 through 60 removed outlier: 3.603A pdb=" N ASP C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.955A pdb=" N LEU C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 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) No H-bonds generated for 'chain 'C' and resid 120 through 125' Processing helix chain 'C' and resid 151 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 190 through 195 Processing helix chain 'C' and resid 200 through 210 Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 299 through 316 Proline residue: C 315 - end of helix Processing helix chain 'C' and resid 330 through 358 removed outlier: 3.653A pdb=" N PHE C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 365 No H-bonds generated for 'chain 'C' and resid 362 through 365' Processing helix chain 'C' and resid 367 through 385 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 392 through 402 Processing helix chain 'C' and resid 405 through 422 removed outlier: 4.487A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 433 Processing helix chain 'C' and resid 440 through 458 removed outlier: 3.544A pdb=" N VAL C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N PHE C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Proline residue: C 455 - end of helix removed outlier: 4.060A pdb=" N PHE C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 486 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 488 through 495 Processing helix chain 'C' and resid 514 through 536 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 539 through 558 removed outlier: 3.622A pdb=" N VAL C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 600 Processing helix chain 'C' and resid 634 through 636 No H-bonds generated for 'chain 'C' and resid 634 through 636' Processing helix chain 'C' and resid 640 through 642 No H-bonds generated for 'chain 'C' and resid 640 through 642' Processing helix chain 'C' and resid 644 through 657 removed outlier: 3.512A pdb=" N ARG C 650 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN C 657 " --> pdb=" O ARG C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 708 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) removed outlier: 3.512A pdb=" N LYS C 708 " --> pdb=" O ALA C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 743 through 753 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 779 No H-bonds generated for 'chain 'C' and resid 777 through 779' Processing helix chain 'C' and resid 783 through 786 removed outlier: 3.754A pdb=" N ILE C 786 " --> pdb=" O PRO C 783 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 783 through 786' Processing helix chain 'C' and resid 801 through 804 Processing helix chain 'C' and resid 837 through 849 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) Processing helix chain 'C' and resid 862 through 892 Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 897 through 900 No H-bonds generated for 'chain 'C' and resid 897 through 900' Processing helix chain 'C' and resid 905 through 916 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 925 through 953 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 960 through 970 Processing helix chain 'C' and resid 973 through 991 Proline residue: C 988 - end of helix Processing helix chain 'C' and resid 999 through 1016 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 1018 through 1033 Proline residue: C1023 - end of helix Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.546A pdb=" N LYS A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 100 through 117 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) Proline residue: A 116 - end of helix Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 151 through 161 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.672A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 243 through 247 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 299 through 316 Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 330 through 359 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 367 through 386 Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 392 through 423 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 427 through 449 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 454 through 457 No H-bonds generated for 'chain 'A' and resid 454 through 457' Processing helix chain 'A' and resid 461 through 495 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 558 removed outlier: 3.888A pdb=" N LEU A 544 " --> pdb=" O TYR A 541 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY A 551 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 601 Processing helix chain 'A' and resid 603 through 605 No H-bonds generated for 'chain 'A' and resid 603 through 605' Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 644 through 656 removed outlier: 4.029A pdb=" N ARG A 650 " --> pdb=" O ALA A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 707 removed outlier: 3.651A pdb=" N LEU A 695 " --> pdb=" O GLY A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 745 through 755 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 779 No H-bonds generated for 'chain 'A' and resid 777 through 779' Processing helix chain 'A' and resid 783 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 801 through 803 No H-bonds generated for 'chain 'A' and resid 801 through 803' Processing helix chain 'A' and resid 837 through 840 No H-bonds generated for 'chain 'A' and resid 837 through 840' Processing helix chain 'A' and resid 843 through 848 Processing helix chain 'A' and resid 861 through 868 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) removed outlier: 4.075A pdb=" N LEU A 868 " --> pdb=" O TYR A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 892 Processing helix chain 'A' and resid 897 through 900 Processing helix chain 'A' and resid 905 through 919 removed outlier: 4.159A pdb=" N GLY A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 953 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) Processing helix chain 'A' and resid 969 through 985 removed outlier: 3.993A pdb=" N ARG A 973 " --> pdb=" O MET A 970 " (cutoff:3.500A) Proline residue: A 974 - end of helix Processing helix chain 'A' and resid 987 through 990 No H-bonds generated for 'chain 'A' and resid 987 through 990' Processing helix chain 'A' and resid 997 through 1016 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 1022 through 1031 removed outlier: 4.671A pdb=" N VAL A1027 " --> pdb=" O PRO A1023 " (cutoff:3.500A) Processing sheet with id= A, 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) Processing sheet with id= B, first strand: chain 'B' and resid 141 through 144 Processing sheet with id= C, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.164A pdb=" N VAL B 768 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N MET B 184 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LYS B 770 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ILE B 186 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR B 772 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N MET B 188 " --> pdb=" O TYR B 772 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N MET B 774 " --> pdb=" O MET B 188 " (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= D, first strand: chain 'B' and resid 278 through 281 removed outlier: 3.679A pdb=" N ILE B 278 " --> pdb=" O ASN B 613 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER B 630 " --> pdb=" O GLU B 607 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL B 609 " --> pdb=" O PHE B 628 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE B 628 " --> pdb=" O VAL B 609 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA B 611 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE B 626 " --> pdb=" O ALA B 611 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ASN B 613 " --> pdb=" O THR B 624 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N THR B 624 " --> pdb=" O ASN B 613 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 855 through 859 Processing sheet with id= F, first strand: chain 'B' and resid 724 through 731 Processing sheet with id= G, first strand: chain 'B' and resid 790 through 792 Processing sheet with id= H, first strand: chain 'B' and resid 172 through 177 removed outlier: 6.990A pdb=" N LYS B 292 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL B 175 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLY B 290 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing sheet with id= I, 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) Processing sheet with id= J, first strand: chain 'C' and resid 141 through 143 Processing sheet with id= K, 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) Processing sheet with id= L, 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) Processing sheet with id= M, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.036A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N SER C 630 " --> pdb=" O GLU C 607 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL C 609 " --> pdb=" O PHE C 628 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE C 628 " --> pdb=" O VAL C 609 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA C 611 " --> pdb=" O ILE C 626 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE C 626 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 824 through 827 removed outlier: 3.519A pdb=" N LEU C 684 " --> pdb=" O MET C 825 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 726 through 731 Processing sheet with id= P, first strand: chain 'C' and resid 761 through 764 Processing sheet with id= Q, first strand: chain 'C' and resid 790 through 792 Processing sheet with id= R, first strand: chain 'C' and resid 136 through 139 removed outlier: 7.250A pdb=" N ILE C 291 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL C 139 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU C 289 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP C 174 " --> pdb=" O LYS C 292 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 250 through 253 removed outlier: 6.998A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing sheet with id= T, 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= U, first strand: chain 'A' and resid 321 through 324 removed outlier: 4.621A pdb=" N ASN A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing sheet with id= V, 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= W, first strand: chain 'A' and resid 681 through 683 Processing sheet with id= X, first strand: chain 'A' and resid 723 through 731 Processing sheet with id= Y, first strand: chain 'A' and resid 790 through 792 Processing sheet with id= Z, first strand: chain 'A' and resid 172 through 177 removed outlier: 6.719A pdb=" N LYS A 292 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL A 175 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLY A 290 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 250 through 253 removed outlier: 7.102A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) 1180 hydrogen bonds defined for protein. 3390 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: 9.06 Time building geometry restraints manager: 9.60 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: 99.18 - 106.21: 699 106.21 - 113.24: 13141 113.24 - 120.27: 8884 120.27 - 127.30: 9752 127.30 - 134.34: 197 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: 2098 2.74 - 3.28: 24219 3.28 - 3.82: 39701 3.82 - 4.36: 47551 4.36 - 4.90: 83445 Nonbonded interactions: 197014 Sorted by model distance: nonbonded pdb=" OH TYR C 467 " pdb=" OE1 GLN C 928 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR C 758 " pdb=" OD1 ASP C 761 " model vdw 2.234 2.440 nonbonded pdb=" OD2 ASP B 408 " pdb=" OG SER B 481 " model vdw 2.235 2.440 nonbonded pdb=" O HIS B 596 " pdb=" OG1 THR B 600 " model vdw 2.242 2.440 nonbonded pdb=" O GLY A 994 " pdb=" OG SER A 997 " model vdw 2.242 2.440 ... (remaining 197009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.980 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 60.940 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.790 ------------------------------------------------------------------------------- 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= 0.321 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (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 TRP 0.033 0.002 TRP B 895 HIS 0.005 0.001 HIS C 525 PHE 0.021 0.001 PHE A 362 TYR 0.021 0.001 TYR A 49 ARG 0.006 0.000 ARG B 586 *********************** 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 fitting. rotamer outliers: 7 poor density : 316 time to evaluate : 2.469 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: 0.3200 time to fit residues: 167.5322 Evaluate side-chains 258 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 2.575 ------------------------------------------------------------------------------- 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 256 optimal weight: 10.0000 chunk 230 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 238 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 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** B 865 GLN C 74 ASN C 89 GLN A 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0654 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= 0.171 Angle : 0.505 9.482 32673 Z= 0.250 Chirality : 0.040 0.136 3826 Planarity : 0.004 0.041 4124 Dihedral : 12.700 171.734 3655 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.97 % Allowed : 6.58 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.16), residues: 3049 helix: 1.27 (0.14), residues: 1598 sheet: -0.88 (0.26), residues: 421 loop : -0.38 (0.21), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 515 HIS 0.006 0.001 HIS B 526 PHE 0.020 0.001 PHE A 362 TYR 0.015 0.001 TYR A 49 ARG 0.006 0.000 ARG A 518 *********************** 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 308 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 284 time to evaluate : 2.680 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 496 MET cc_start: 0.7992 (ttm) cc_final: 0.7738 (ttm) REVERT: B 825 MET cc_start: 0.8379 (mmt) cc_final: 0.7985 (mmm) REVERT: C 892 TYR cc_start: 0.7851 (m-80) cc_final: 0.7602 (m-80) REVERT: A 29 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8510 (pttp) REVERT: A 541 TYR cc_start: 0.6391 (m-10) cc_final: 0.6160 (m-80) outliers start: 24 outliers final: 11 residues processed: 294 average time/residue: 0.3059 time to fit residues: 149.6424 Evaluate side-chains 273 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 261 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 844 MET 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 153 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 0.0980 chunk 187 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 276 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 chunk 246 optimal weight: 8.9990 chunk 274 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 89 GLN C 744 ASN A 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24140 Z= 0.171 Angle : 0.484 6.819 32673 Z= 0.240 Chirality : 0.040 0.136 3826 Planarity : 0.003 0.041 4124 Dihedral : 11.924 176.961 3655 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.33 % Allowed : 8.52 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.16), residues: 3049 helix: 1.34 (0.14), residues: 1608 sheet: -0.79 (0.26), residues: 417 loop : -0.36 (0.21), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 515 HIS 0.008 0.001 HIS B 526 PHE 0.015 0.001 PHE A 362 TYR 0.016 0.001 TYR A 49 ARG 0.004 0.000 ARG A 518 *********************** 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 323 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 290 time to evaluate : 2.608 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 519 MET cc_start: 0.4161 (mtm) cc_final: 0.3914 (mtt) REVERT: C 892 TYR cc_start: 0.7950 (m-80) cc_final: 0.7471 (m-80) REVERT: A 164 ASP cc_start: 0.7129 (p0) cc_final: 0.6898 (p0) REVERT: A 541 TYR cc_start: 0.6514 (m-10) cc_final: 0.6276 (m-80) REVERT: A 546 LEU cc_start: 0.8300 (mp) cc_final: 0.7721 (tt) outliers start: 33 outliers final: 21 residues processed: 303 average time/residue: 0.3445 time to fit residues: 176.2170 Evaluate side-chains 284 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 263 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP 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 B residue 1016 VAL Chi-restraints excluded: chain C residue 21 LEU 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 180 SER Chi-restraints excluded: chain C residue 355 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 101 ASP Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 931 LEU 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 273 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 143 optimal weight: 0.0010 chunk 30 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 293 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 263 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- 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** A 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24140 Z= 0.172 Angle : 0.483 6.765 32673 Z= 0.239 Chirality : 0.040 0.146 3826 Planarity : 0.003 0.040 4124 Dihedral : 11.359 177.318 3655 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.57 % Allowed : 10.01 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.16), residues: 3049 helix: 1.38 (0.14), residues: 1606 sheet: -0.76 (0.26), residues: 410 loop : -0.32 (0.21), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 515 HIS 0.007 0.001 HIS B 526 PHE 0.014 0.001 PHE A 682 TYR 0.015 0.001 TYR B 49 ARG 0.003 0.000 ARG A 518 *********************** 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 316 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 277 time to evaluate : 2.789 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: C 355 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.8070 (mtm) REVERT: A 164 ASP cc_start: 0.7140 (p0) cc_final: 0.6902 (p0) REVERT: A 541 TYR cc_start: 0.6574 (m-10) cc_final: 0.6256 (m-80) outliers start: 39 outliers final: 25 residues processed: 294 average time/residue: 0.3118 time to fit residues: 152.3391 Evaluate side-chains 289 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 263 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 SER 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 C residue 986 VAL Chi-restraints excluded: chain C residue 987 MET Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 730 ASP 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 244 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 218 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 250 optimal weight: 0.9980 chunk 203 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 263 optimal weight: 0.0670 chunk 74 optimal weight: 1.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- 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** C 74 ASN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24140 Z= 0.153 Angle : 0.478 6.960 32673 Z= 0.235 Chirality : 0.040 0.154 3826 Planarity : 0.003 0.040 4124 Dihedral : 10.752 172.893 3655 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.78 % Allowed : 10.70 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.16), residues: 3049 helix: 1.47 (0.14), residues: 1602 sheet: -0.71 (0.26), residues: 410 loop : -0.26 (0.21), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 515 HIS 0.003 0.001 HIS B 526 PHE 0.011 0.001 PHE A 682 TYR 0.015 0.001 TYR B 49 ARG 0.005 0.000 ARG B 971 *********************** 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 330 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 286 time to evaluate : 2.834 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: C 892 TYR cc_start: 0.7941 (m-80) cc_final: 0.7696 (m-80) REVERT: A 164 ASP cc_start: 0.7131 (p0) cc_final: 0.6931 (p0) REVERT: A 541 TYR cc_start: 0.6557 (m-10) cc_final: 0.6211 (m-80) outliers start: 44 outliers final: 30 residues processed: 311 average time/residue: 0.3025 time to fit residues: 156.6930 Evaluate side-chains 292 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 262 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 405 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 29 LYS Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 357 LEU 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 847 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 982 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 294 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN C 74 ASN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24140 Z= 0.235 Angle : 0.512 7.622 32673 Z= 0.252 Chirality : 0.041 0.155 3826 Planarity : 0.003 0.042 4124 Dihedral : 10.346 165.287 3652 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.70 % Allowed : 11.51 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.16), residues: 3049 helix: 1.43 (0.14), residues: 1602 sheet: -0.75 (0.26), residues: 400 loop : -0.35 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 515 HIS 0.004 0.001 HIS B 526 PHE 0.023 0.001 PHE C 885 TYR 0.019 0.001 TYR B 49 ARG 0.003 0.000 ARG B 780 *********************** 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 316 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 274 time to evaluate : 2.648 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 108 GLN cc_start: 0.7614 (tp-100) cc_final: 0.7293 (tp-100) REVERT: C 892 TYR cc_start: 0.8000 (m-80) cc_final: 0.7724 (m-80) REVERT: A 184 MET cc_start: 0.8804 (tpp) cc_final: 0.8525 (tpt) REVERT: A 541 TYR cc_start: 0.6504 (m-10) cc_final: 0.6179 (m-80) REVERT: A 546 LEU cc_start: 0.8234 (mp) cc_final: 0.7614 (tt) outliers start: 42 outliers final: 29 residues processed: 302 average time/residue: 0.2952 time to fit residues: 147.8758 Evaluate side-chains 287 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 258 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 21 LEU 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 180 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 649 MET Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 101 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 982 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 167 optimal weight: 7.9990 chunk 214 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 247 optimal weight: 0.8980 chunk 164 optimal weight: 0.1980 chunk 293 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 178 optimal weight: 0.0070 chunk 135 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 GLN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24140 Z= 0.142 Angle : 0.489 7.189 32673 Z= 0.238 Chirality : 0.040 0.160 3826 Planarity : 0.003 0.041 4124 Dihedral : 9.987 162.866 3652 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.49 % Allowed : 11.99 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.16), residues: 3049 helix: 1.51 (0.14), residues: 1608 sheet: -0.69 (0.26), residues: 412 loop : -0.27 (0.21), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 515 HIS 0.004 0.000 HIS B 526 PHE 0.019 0.001 PHE C 885 TYR 0.013 0.001 TYR C 857 ARG 0.004 0.000 ARG B 971 *********************** 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 313 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 276 time to evaluate : 2.709 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: C 892 TYR cc_start: 0.7915 (m-80) cc_final: 0.7700 (m-80) REVERT: A 541 TYR cc_start: 0.6540 (m-10) cc_final: 0.6200 (m-80) REVERT: A 546 LEU cc_start: 0.8276 (mp) cc_final: 0.7750 (tt) outliers start: 37 outliers final: 28 residues processed: 297 average time/residue: 0.3069 time to fit residues: 151.7108 Evaluate side-chains 292 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 264 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 21 LEU 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 180 SER Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 649 MET Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 987 MET Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 626 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 982 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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** A 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1378 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= 0.223 Angle : 0.516 7.726 32673 Z= 0.252 Chirality : 0.041 0.167 3826 Planarity : 0.003 0.041 4124 Dihedral : 9.799 155.588 3652 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.53 % Allowed : 12.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.16), residues: 3049 helix: 1.52 (0.14), residues: 1595 sheet: -0.68 (0.26), residues: 400 loop : -0.31 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 515 HIS 0.004 0.001 HIS B 526 PHE 0.018 0.001 PHE C 885 TYR 0.017 0.001 TYR B 49 ARG 0.004 0.000 ARG A 971 *********************** 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 303 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 265 time to evaluate : 2.684 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 390 ILE cc_start: 0.8690 (mm) cc_final: 0.8438 (mt) REVERT: B 1008 MET cc_start: 0.7796 (ttp) cc_final: 0.7441 (ttt) REVERT: C 892 TYR cc_start: 0.7990 (m-80) cc_final: 0.7750 (m-80) REVERT: A 184 MET cc_start: 0.8786 (tpp) cc_final: 0.8507 (tpt) REVERT: A 541 TYR cc_start: 0.6553 (m-10) cc_final: 0.6205 (m-80) REVERT: A 546 LEU cc_start: 0.8268 (mp) cc_final: 0.7752 (tt) outliers start: 38 outliers final: 30 residues processed: 288 average time/residue: 0.3081 time to fit residues: 147.6581 Evaluate side-chains 288 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 258 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 21 LEU 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 180 SER Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 649 MET Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 407 ASP 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 982 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 8.9990 chunk 280 optimal weight: 4.9990 chunk 256 optimal weight: 6.9990 chunk 273 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 258 optimal weight: 2.9990 chunk 272 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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** A 120 GLN A 469 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24140 Z= 0.324 Angle : 0.566 8.240 32673 Z= 0.279 Chirality : 0.043 0.161 3826 Planarity : 0.004 0.042 4124 Dihedral : 9.775 147.108 3652 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.53 % Allowed : 12.80 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 3049 helix: 1.38 (0.13), residues: 1597 sheet: -0.80 (0.26), residues: 405 loop : -0.40 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 515 HIS 0.004 0.001 HIS B 526 PHE 0.018 0.001 PHE A 682 TYR 0.021 0.001 TYR B 49 ARG 0.003 0.000 ARG C 971 *********************** 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 296 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 258 time to evaluate : 2.804 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 108 GLN cc_start: 0.7791 (tp40) cc_final: 0.7313 (tp-100) REVERT: B 390 ILE cc_start: 0.8713 (mm) cc_final: 0.8449 (mt) REVERT: A 184 MET cc_start: 0.8784 (tpp) cc_final: 0.8559 (tpt) REVERT: A 541 TYR cc_start: 0.6551 (m-10) cc_final: 0.6183 (m-80) REVERT: A 546 LEU cc_start: 0.8287 (mp) cc_final: 0.7786 (tt) outliers start: 38 outliers final: 33 residues processed: 285 average time/residue: 0.3005 time to fit residues: 142.0454 Evaluate side-chains 283 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 250 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP 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 391 ASN Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 21 LEU 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 180 SER Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 649 MET Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 495 THR 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 982 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 0.9980 chunk 288 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 302 optimal weight: 10.0000 chunk 278 optimal weight: 2.9990 chunk 241 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 186 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1486 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= 0.170 Angle : 0.518 8.515 32673 Z= 0.252 Chirality : 0.040 0.157 3826 Planarity : 0.003 0.042 4124 Dihedral : 9.505 140.364 3652 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.37 % Allowed : 12.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.16), residues: 3049 helix: 1.50 (0.14), residues: 1600 sheet: -0.75 (0.26), residues: 411 loop : -0.31 (0.21), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 515 HIS 0.004 0.001 HIS B 526 PHE 0.018 0.001 PHE C 885 TYR 0.014 0.001 TYR B 49 ARG 0.003 0.000 ARG A 780 ********************** 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 297 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 263 time to evaluate : 2.661 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 390 ILE cc_start: 0.8682 (mm) cc_final: 0.8456 (mt) REVERT: A 184 MET cc_start: 0.8789 (tpp) cc_final: 0.8491 (tpt) REVERT: A 541 TYR cc_start: 0.6500 (m-10) cc_final: 0.6154 (m-80) REVERT: A 546 LEU cc_start: 0.8269 (mp) cc_final: 0.7775 (tt) outliers start: 34 outliers final: 29 residues processed: 285 average time/residue: 0.3085 time to fit residues: 147.6418 Evaluate side-chains 289 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 260 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP 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 391 ASN Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 649 MET Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 182 TYR 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 982 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 222 optimal weight: 0.0070 chunk 35 optimal weight: 0.0980 chunk 67 optimal weight: 0.0370 chunk 241 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 248 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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** A 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.116797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.093527 restraints weight = 40534.878| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.17 r_work: 0.3242 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24140 Z= 0.143 Angle : 0.503 12.065 32673 Z= 0.243 Chirality : 0.040 0.161 3826 Planarity : 0.003 0.042 4124 Dihedral : 9.080 121.239 3652 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.25 % Allowed : 13.20 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.16), residues: 3049 helix: 1.61 (0.14), residues: 1600 sheet: -0.68 (0.26), residues: 412 loop : -0.26 (0.21), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 515 HIS 0.005 0.001 HIS B 526 PHE 0.024 0.001 PHE A 380 TYR 0.013 0.001 TYR C 857 ARG 0.003 0.000 ARG B 971 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4734.71 seconds wall clock time: 86 minutes 7.33 seconds (5167.33 seconds total)