Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 20:58:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr7_24654/04_2023/7rr7_24654_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr7_24654/04_2023/7rr7_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_24654/04_2023/7rr7_24654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr7_24654/04_2023/7rr7_24654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr7_24654/04_2023/7rr7_24654_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr7_24654/04_2023/7rr7_24654_updated.pdb" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 125 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: 12.58, per 1000 atoms: 0.53 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: 9.78 Conformation dependent library (CDL) restraints added in 3.6 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: 3.81 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: 8.87 Time building geometry restraints manager: 10.59 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: 14130 34.22 - 68.43: 279 68.43 - 102.65: 24 102.65 - 136.86: 3 136.86 - 171.08: 7 Dihedral angle restraints: 14443 sinusoidal: 5694 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 14440 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: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.080 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 61.850 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.420 ------------------------------------------------------------------------------- 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 : 14.147 171.077 8829 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 % 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 *********************** 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 : 2.853 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. outliers start: 7 outliers final: 1 residues processed: 321 average time/residue: 0.3374 time to fit residues: 176.4319 Evaluate side-chains 258 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 2.739 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2496 time to fit residues: 4.1397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 6.9990 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: 0.0663 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= 0.172 Angle : 0.506 9.508 32673 Z= 0.251 Chirality : 0.040 0.138 3826 Planarity : 0.004 0.041 4124 Dihedral : 11.914 172.469 3566 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 0.97 % 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: 0.56 (0.16), residues: 3049 helix: 1.27 (0.14), residues: 1595 sheet: -0.87 (0.26), residues: 414 loop : -0.38 (0.21), residues: 1040 *********************** 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 307 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 283 time to evaluate : 2.827 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. outliers start: 24 outliers final: 10 residues processed: 293 average time/residue: 0.3231 time to fit residues: 159.2234 Evaluate side-chains 272 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 262 time to evaluate : 2.876 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2217 time to fit residues: 8.1240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 229 optimal weight: 0.6980 chunk 187 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 276 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 chunk 246 optimal weight: 9.9990 chunk 274 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 221 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 89 GLN C 744 ASN A 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.0887 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= 0.177 Angle : 0.488 6.982 32673 Z= 0.241 Chirality : 0.040 0.135 3826 Planarity : 0.003 0.041 4124 Dihedral : 11.172 177.831 3566 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 0.89 % 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: 0.64 (0.16), residues: 3049 helix: 1.33 (0.14), residues: 1609 sheet: -0.79 (0.25), residues: 425 loop : -0.34 (0.21), residues: 1015 *********************** 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 311 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 289 time to evaluate : 2.964 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. outliers start: 22 outliers final: 11 residues processed: 294 average time/residue: 0.3238 time to fit residues: 160.1528 Evaluate side-chains 272 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 261 time to evaluate : 2.873 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2432 time to fit residues: 8.7626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 143 optimal weight: 0.0870 chunk 30 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 185 optimal weight: 0.5980 chunk 277 optimal weight: 0.8980 chunk 293 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 263 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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: 0.8250 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 24140 Z= 0.150 Angle : 0.478 7.083 32673 Z= 0.236 Chirality : 0.040 0.144 3826 Planarity : 0.003 0.040 4124 Dihedral : 10.368 175.736 3566 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 0.93 % 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: 0.75 (0.16), residues: 3049 helix: 1.41 (0.14), residues: 1604 sheet: -0.75 (0.26), residues: 410 loop : -0.29 (0.21), residues: 1035 *********************** 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 306 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 283 time to evaluate : 2.801 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. outliers start: 23 outliers final: 9 residues processed: 295 average time/residue: 0.3226 time to fit residues: 160.5798 Evaluate side-chains 275 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 266 time to evaluate : 2.611 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2663 time to fit residues: 7.8606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 218 optimal weight: 0.4980 chunk 121 optimal weight: 0.9990 chunk 250 optimal weight: 0.7980 chunk 203 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 263 optimal weight: 0.1980 chunk 74 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 24140 Z= 0.145 Angle : 0.476 6.929 32673 Z= 0.233 Chirality : 0.039 0.156 3826 Planarity : 0.003 0.040 4124 Dihedral : 9.747 176.846 3566 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 1.01 % 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: 0.86 (0.16), residues: 3049 helix: 1.49 (0.14), residues: 1603 sheet: -0.69 (0.26), residues: 410 loop : -0.23 (0.21), residues: 1036 *********************** 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 314 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 289 time to evaluate : 2.652 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. outliers start: 25 outliers final: 12 residues processed: 303 average time/residue: 0.3212 time to fit residues: 164.6195 Evaluate side-chains 280 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 268 time to evaluate : 2.831 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2440 time to fit residues: 9.2684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 0.0980 chunk 264 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 136 optimal weight: 0.0170 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- 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 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 24140 Z= 0.168 Angle : 0.483 7.611 32673 Z= 0.237 Chirality : 0.040 0.157 3826 Planarity : 0.003 0.040 4124 Dihedral : 9.331 169.776 3566 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 0.81 % 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: 0.88 (0.16), residues: 3049 helix: 1.50 (0.14), residues: 1613 sheet: -0.64 (0.26), residues: 408 loop : -0.24 (0.21), residues: 1028 *********************** 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 296 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 276 time to evaluate : 2.836 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 288 average time/residue: 0.3364 time to fit residues: 161.4291 Evaluate side-chains 269 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 262 time to evaluate : 2.915 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2255 time to fit residues: 6.9809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 247 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 293 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 178 optimal weight: 0.3980 chunk 135 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.8251 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 24140 Z= 0.156 Angle : 0.485 7.494 32673 Z= 0.237 Chirality : 0.040 0.167 3826 Planarity : 0.003 0.040 4124 Dihedral : 8.958 166.651 3566 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 0.65 % 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: 0.93 (0.16), residues: 3049 helix: 1.55 (0.14), residues: 1608 sheet: -0.62 (0.26), residues: 410 loop : -0.23 (0.21), residues: 1031 *********************** 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 294 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 278 time to evaluate : 3.047 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 285 average time/residue: 0.3395 time to fit residues: 161.5461 Evaluate side-chains 272 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 264 time to evaluate : 2.688 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2478 time to fit residues: 7.1281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 174 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 57 optimal weight: 0.0050 chunk 56 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 144 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 overall best weight: 1.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 HIS C 74 ASN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 24140 Z= 0.225 Angle : 0.512 8.472 32673 Z= 0.250 Chirality : 0.041 0.162 3826 Planarity : 0.003 0.041 4124 Dihedral : 8.771 161.555 3566 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.73 % 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: 0.88 (0.16), residues: 3049 helix: 1.54 (0.14), residues: 1600 sheet: -0.67 (0.26), residues: 406 loop : -0.28 (0.21), residues: 1043 *********************** 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 290 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 272 time to evaluate : 2.925 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. outliers start: 18 outliers final: 9 residues processed: 281 average time/residue: 0.3371 time to fit residues: 159.7298 Evaluate side-chains 269 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 260 time to evaluate : 2.859 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2658 time to fit residues: 8.1786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 7.9990 chunk 280 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 chunk 273 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 246 optimal weight: 10.0000 chunk 258 optimal weight: 0.4980 chunk 272 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 526 HIS C 74 ASN C 125 GLN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1406 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= 0.224 Angle : 0.522 11.009 32673 Z= 0.255 Chirality : 0.041 0.179 3826 Planarity : 0.003 0.041 4124 Dihedral : 8.636 157.780 3566 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1602 sheet: -0.64 (0.26), residues: 398 loop : -0.31 (0.20), residues: 1049 *********************** 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 278 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 269 time to evaluate : 2.936 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 273 average time/residue: 0.3375 time to fit residues: 155.2849 Evaluate side-chains 263 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 259 time to evaluate : 3.684 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2312 time to fit residues: 5.4840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 136 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 302 optimal weight: 7.9990 chunk 278 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 186 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.8287 moved from start: 0.1452 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= 0.216 Angle : 0.530 11.679 32673 Z= 0.257 Chirality : 0.041 0.184 3826 Planarity : 0.003 0.041 4124 Dihedral : 8.484 153.128 3566 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.24 % 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: 1600 sheet: -0.60 (0.26), residues: 400 loop : -0.32 (0.20), residues: 1049 ********************** 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 269 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 263 time to evaluate : 2.807 Fit side-chains TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 264 average time/residue: 0.3326 time to fit residues: 148.5080 Evaluate side-chains 262 residues out of total 2494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 259 time to evaluate : 2.853 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2604 time to fit residues: 5.2486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 0.8980 chunk 256 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 222 optimal weight: 0.0170 chunk 35 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 241 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.116559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.092779 restraints weight = 40580.755| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.21 r_work: 0.3247 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 24140 Z= 0.151 Angle : 0.508 12.326 32673 Z= 0.245 Chirality : 0.040 0.175 3826 Planarity : 0.003 0.041 4124 Dihedral : 8.197 145.677 3566 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 0.24 % 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: 0.93 (0.16), residues: 3049 helix: 1.56 (0.14), residues: 1605 sheet: -0.60 (0.26), residues: 410 loop : -0.24 (0.21), residues: 1034 =============================================================================== Job complete usr+sys time: 4914.86 seconds wall clock time: 89 minutes 56.13 seconds (5396.13 seconds total)