Starting phenix.real_space_refine (version: dev) on Fri Feb 24 20:55:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ows_20216/02_2023/6ows_20216_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ows_20216/02_2023/6ows_20216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ows_20216/02_2023/6ows_20216.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ows_20216/02_2023/6ows_20216.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ows_20216/02_2023/6ows_20216_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ows_20216/02_2023/6ows_20216_updated.pdb" } resolution = 2.98 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= 1.000 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 Process input model Symmetric amino acids flipped Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 7": "NH1" <-> "NH2" Residue "A ARG 8": "NH1" <-> "NH2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A ASP 156": "OD1" <-> "OD2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A ASP 429": "OD1" <-> "OD2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A ARG 632": "NH1" <-> "NH2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ARG 771": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ARG 813": "NH1" <-> "NH2" Residue "A ARG 833": "NH1" <-> "NH2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A ARG 961": "NH1" <-> "NH2" Residue "A ARG 963": "NH1" <-> "NH2" Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 7": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ASP 156": "OD1" <-> "OD2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B ASP 429": "OD1" <-> "OD2" Residue "B ARG 583": "NH1" <-> "NH2" Residue "B ARG 585": "NH1" <-> "NH2" Residue "B ARG 632": "NH1" <-> "NH2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B ARG 724": "NH1" <-> "NH2" Residue "B ARG 758": "NH1" <-> "NH2" Residue "B ARG 771": "NH1" <-> "NH2" Residue "B ARG 809": "NH1" <-> "NH2" Residue "B ARG 813": "NH1" <-> "NH2" Residue "B ARG 833": "NH1" <-> "NH2" Residue "B ARG 910": "NH1" <-> "NH2" Residue "B ARG 961": "NH1" <-> "NH2" Residue "B ARG 963": "NH1" <-> "NH2" Residue "C PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 418": "NH1" <-> "NH2" Residue "C ASP 429": "OD1" <-> "OD2" Residue "C ARG 583": "NH1" <-> "NH2" Residue "C ARG 585": "NH1" <-> "NH2" Residue "C ARG 632": "NH1" <-> "NH2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C ARG 724": "NH1" <-> "NH2" Residue "C ARG 758": "NH1" <-> "NH2" Residue "C ARG 771": "NH1" <-> "NH2" Residue "C ARG 809": "NH1" <-> "NH2" Residue "C ARG 813": "NH1" <-> "NH2" Residue "C ARG 833": "NH1" <-> "NH2" Residue "C ARG 910": "NH1" <-> "NH2" Residue "C ARG 961": "NH1" <-> "NH2" Residue "C ARG 963": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 23651 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7807 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 46, 'TRANS': 976} Chain: "B" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7807 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 46, 'TRANS': 976} Chain: "C" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7807 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 46, 'TRANS': 976} Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "B" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Time building chain proxies: 13.28, per 1000 atoms: 0.56 Number of scatterers: 23651 At special positions: 0 Unit cell: (116.6, 120.84, 142.04, 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 135 16.00 P 6 15.00 O 4368 8.00 N 3825 7.00 C 15317 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: 9.24 Conformation dependent library (CDL) restraints added in 3.3 seconds 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5718 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 21 sheets defined 48.7% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.02 Creating SS restraints... Processing helix chain 'A' and resid 3 through 5 No H-bonds generated for 'chain 'A' and resid 3 through 5' Processing helix chain 'A' and resid 9 through 24 removed outlier: 3.888A pdb=" N ILE A 15 " --> pdb=" O PHE A 11 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 60 removed outlier: 3.544A pdb=" N ASP A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 69 removed outlier: 3.635A pdb=" N ARG A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.579A pdb=" N LYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 162 through 165 No H-bonds generated for 'chain 'A' and resid 162 through 165' Processing helix chain 'A' and resid 190 through 194 removed outlier: 3.714A pdb=" N VAL A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 190 through 194' Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.861A pdb=" N ASN A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 299 through 313 removed outlier: 3.560A pdb=" N GLU A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 359 removed outlier: 3.604A pdb=" N VAL A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 358 " --> pdb=" O VAL A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 385 removed outlier: 4.064A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix removed outlier: 4.210A pdb=" N VAL A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix removed outlier: 3.864A pdb=" N THR A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 405 removed outlier: 4.450A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 422 removed outlier: 4.484A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 450 removed outlier: 3.647A pdb=" N SER A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 3.938A pdb=" N LEU A 447 " --> pdb=" O ILE A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 461 through 486 removed outlier: 3.787A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A 477 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 509 through 531 removed outlier: 3.979A pdb=" N PHE A 513 " --> pdb=" O PHE A 509 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU A 525 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 526 " --> pdb=" O LYS A 522 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 555 removed outlier: 3.606A pdb=" N VAL A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE A 541 " --> pdb=" O PRO A 537 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 542 " --> pdb=" O MET A 538 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A 554 " --> pdb=" O PHE A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 592 Processing helix chain 'A' and resid 636 through 646 removed outlier: 4.069A pdb=" N SER A 641 " --> pdb=" O SER A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 666 No H-bonds generated for 'chain 'A' and resid 664 through 666' Processing helix chain 'A' and resid 684 through 697 removed outlier: 4.057A pdb=" N ASP A 692 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.621A pdb=" N ASP A 739 " --> pdb=" O SER A 735 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 740 " --> pdb=" O ASP A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 744 No H-bonds generated for 'chain 'A' and resid 742 through 744' Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' 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 792 through 794 No H-bonds generated for 'chain 'A' and resid 792 through 794' Processing helix chain 'A' and resid 828 through 841 removed outlier: 3.893A pdb=" N GLU A 836 " --> pdb=" O MET A 832 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA A 840 " --> pdb=" O GLU A 836 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS A 841 " --> pdb=" O GLN A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 861 Processing helix chain 'A' and resid 864 through 880 removed outlier: 3.508A pdb=" N MET A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL A 875 " --> pdb=" O SER A 871 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 880 " --> pdb=" O PHE A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 890 No H-bonds generated for 'chain 'A' and resid 888 through 890' Processing helix chain 'A' and resid 896 through 908 removed outlier: 4.177A pdb=" N GLY A 902 " --> pdb=" O LEU A 898 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 905 " --> pdb=" O PHE A 901 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 945 removed outlier: 3.587A pdb=" N ALA A 930 " --> pdb=" O ILE A 926 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE A 936 " --> pdb=" O ASN A 932 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 959 removed outlier: 3.655A pdb=" N THR A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 955 " --> pdb=" O ILE A 951 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 956 " --> pdb=" O GLU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 973 Processing helix chain 'A' and resid 977 through 980 No H-bonds generated for 'chain 'A' and resid 977 through 980' Processing helix chain 'A' and resid 988 through 1010 removed outlier: 4.033A pdb=" N LEU A 993 " --> pdb=" O THR A 989 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE A1010 " --> pdb=" O ILE A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1020 removed outlier: 3.791A pdb=" N ILE A1017 " --> pdb=" O PRO A1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 5 No H-bonds generated for 'chain 'B' and resid 3 through 5' Processing helix chain 'B' and resid 9 through 24 removed outlier: 3.888A pdb=" N ILE B 15 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 60 removed outlier: 3.544A pdb=" N ASP B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 69 removed outlier: 3.634A pdb=" N ARG B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 69 " --> pdb=" O ILE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 113 removed outlier: 3.579A pdb=" N LYS B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 123 No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 162 through 165 No H-bonds generated for 'chain 'B' and resid 162 through 165' Processing helix chain 'B' and resid 190 through 194 removed outlier: 3.713A pdb=" N VAL B 194 " --> pdb=" O PRO B 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 190 through 194' Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 243 through 248 removed outlier: 3.861A pdb=" N ASN B 248 " --> pdb=" O GLU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 299 through 313 removed outlier: 3.560A pdb=" N GLU B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 313 " --> pdb=" O LYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 359 removed outlier: 3.605A pdb=" N VAL B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 358 " --> pdb=" O VAL B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 385 removed outlier: 4.063A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix removed outlier: 4.209A pdb=" N VAL B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 373 - end of helix removed outlier: 3.864A pdb=" N THR B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 382 " --> pdb=" O GLY B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 405 removed outlier: 4.450A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 422 removed outlier: 4.484A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 450 removed outlier: 3.647A pdb=" N SER B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 439 " --> pdb=" O MET B 435 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N SER B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Proline residue: B 441 - end of helix removed outlier: 4.041A pdb=" N LEU B 447 " --> pdb=" O ILE B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 461 through 486 removed outlier: 3.787A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 493 Processing helix chain 'B' and resid 509 through 531 removed outlier: 3.979A pdb=" N PHE B 513 " --> pdb=" O PHE B 509 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU B 525 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 526 " --> pdb=" O LYS B 522 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 531 " --> pdb=" O MET B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 555 removed outlier: 3.607A pdb=" N VAL B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE B 541 " --> pdb=" O PRO B 537 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 542 " --> pdb=" O MET B 538 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL B 544 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 549 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 554 " --> pdb=" O PHE B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 592 Processing helix chain 'B' and resid 636 through 646 removed outlier: 4.068A pdb=" N SER B 641 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 666 No H-bonds generated for 'chain 'B' and resid 664 through 666' Processing helix chain 'B' and resid 684 through 697 removed outlier: 4.058A pdb=" N ASP B 692 " --> pdb=" O LEU B 688 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 729 Processing helix chain 'B' and resid 734 through 740 removed outlier: 3.620A pdb=" N ASP B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 740 " --> pdb=" O ASP B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 744 No H-bonds generated for 'chain 'B' and resid 742 through 744' Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' 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 792 through 794 No H-bonds generated for 'chain 'B' and resid 792 through 794' Processing helix chain 'B' and resid 828 through 841 removed outlier: 3.892A pdb=" N GLU B 836 " --> pdb=" O MET B 832 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA B 840 " --> pdb=" O GLU B 836 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS B 841 " --> pdb=" O GLN B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 861 Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.508A pdb=" N MET B 872 " --> pdb=" O LEU B 868 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL B 875 " --> pdb=" O SER B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 890 No H-bonds generated for 'chain 'B' and resid 888 through 890' Processing helix chain 'B' and resid 896 through 908 removed outlier: 4.176A pdb=" N GLY B 902 " --> pdb=" O LEU B 898 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 905 " --> pdb=" O PHE B 901 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 945 removed outlier: 3.569A pdb=" N ALA B 930 " --> pdb=" O ILE B 926 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 936 " --> pdb=" O ASN B 932 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 959 removed outlier: 3.656A pdb=" N THR B 954 " --> pdb=" O LEU B 950 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 955 " --> pdb=" O ILE B 951 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 956 " --> pdb=" O GLU B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 973 Processing helix chain 'B' and resid 977 through 980 No H-bonds generated for 'chain 'B' and resid 977 through 980' Processing helix chain 'B' and resid 988 through 1010 removed outlier: 4.032A pdb=" N LEU B 993 " --> pdb=" O THR B 989 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 999 " --> pdb=" O THR B 995 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE B1010 " --> pdb=" O ILE B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1020 removed outlier: 3.792A pdb=" N ILE B1017 " --> pdb=" O PRO B1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B1020 " --> pdb=" O PHE B1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 5 No H-bonds generated for 'chain 'C' and resid 3 through 5' Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.888A pdb=" N ILE C 15 " --> pdb=" O PHE C 11 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 20 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 60 removed outlier: 3.544A pdb=" N ASP C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 69 removed outlier: 3.634A pdb=" N ARG C 67 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 69 " --> pdb=" O ILE C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.579A pdb=" N LYS C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS C 112 " --> pdb=" O GLN C 108 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 123 No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 162 through 165 No H-bonds generated for 'chain 'C' and resid 162 through 165' Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.715A pdb=" N VAL C 194 " --> pdb=" O PRO C 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 190 through 194' Processing helix chain 'C' and resid 200 through 210 Processing helix chain 'C' and resid 243 through 248 removed outlier: 3.861A pdb=" N ASN C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) 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 313 removed outlier: 3.560A pdb=" N GLU C 304 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 313 " --> pdb=" O LYS C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 359 removed outlier: 3.604A pdb=" N VAL C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 385 removed outlier: 4.064A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 4.210A pdb=" N VAL C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix removed outlier: 3.863A pdb=" N THR C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL C 382 " --> pdb=" O GLY C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 405 removed outlier: 4.449A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 422 removed outlier: 4.484A pdb=" N VAL C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 450 removed outlier: 3.646A pdb=" N SER C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU C 437 " --> pdb=" O LYS C 433 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 439 " --> pdb=" O MET C 435 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Proline residue: C 441 - end of helix removed outlier: 4.041A pdb=" N LEU C 447 " --> pdb=" O ILE C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 458 No H-bonds generated for 'chain 'C' and resid 456 through 458' Processing helix chain 'C' and resid 461 through 486 removed outlier: 3.786A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER C 477 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE C 478 " --> pdb=" O MET C 474 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 Processing helix chain 'C' and resid 509 through 531 removed outlier: 3.979A pdb=" N PHE C 513 " --> pdb=" O PHE C 509 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 515 " --> pdb=" O ALA C 511 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU C 525 " --> pdb=" O THR C 521 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 531 " --> pdb=" O MET C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 555 removed outlier: 3.605A pdb=" N VAL C 540 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE C 541 " --> pdb=" O PRO C 537 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 542 " --> pdb=" O MET C 538 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C 544 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 549 " --> pdb=" O ILE C 545 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C 554 " --> pdb=" O PHE C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 592 Processing helix chain 'C' and resid 636 through 646 removed outlier: 4.069A pdb=" N SER C 641 " --> pdb=" O SER C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 666 No H-bonds generated for 'chain 'C' and resid 664 through 666' Processing helix chain 'C' and resid 684 through 697 removed outlier: 4.056A pdb=" N ASP C 692 " --> pdb=" O LEU C 688 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 Processing helix chain 'C' and resid 734 through 740 removed outlier: 3.621A pdb=" N ASP C 739 " --> pdb=" O SER C 735 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 740 " --> pdb=" O ASP C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 744 No H-bonds generated for 'chain 'C' and resid 742 through 744' Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' 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 792 through 794 No H-bonds generated for 'chain 'C' and resid 792 through 794' Processing helix chain 'C' and resid 828 through 841 removed outlier: 3.893A pdb=" N GLU C 836 " --> pdb=" O MET C 832 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA C 840 " --> pdb=" O GLU C 836 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS C 841 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 861 Processing helix chain 'C' and resid 864 through 880 removed outlier: 3.506A pdb=" N MET C 872 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL C 875 " --> pdb=" O SER C 871 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 880 " --> pdb=" O PHE C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 890 No H-bonds generated for 'chain 'C' and resid 888 through 890' Processing helix chain 'C' and resid 896 through 908 removed outlier: 4.175A pdb=" N GLY C 902 " --> pdb=" O LEU C 898 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 905 " --> pdb=" O PHE C 901 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 945 removed outlier: 3.588A pdb=" N ALA C 930 " --> pdb=" O ILE C 926 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE C 936 " --> pdb=" O ASN C 932 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C 939 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 950 through 959 removed outlier: 3.656A pdb=" N THR C 954 " --> pdb=" O LEU C 950 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 955 " --> pdb=" O ILE C 951 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 956 " --> pdb=" O GLU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 973 Processing helix chain 'C' and resid 977 through 980 No H-bonds generated for 'chain 'C' and resid 977 through 980' Processing helix chain 'C' and resid 988 through 1010 removed outlier: 4.032A pdb=" N LEU C 993 " --> pdb=" O THR C 989 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL C 997 " --> pdb=" O LEU C 993 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C 999 " --> pdb=" O THR C 995 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE C1010 " --> pdb=" O ILE C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1020 removed outlier: 3.792A pdb=" N ILE C1017 " --> pdb=" O PRO C1013 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C1020 " --> pdb=" O PHE C1016 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 128 through 130 Processing sheet with id= B, first strand: chain 'A' and resid 322 through 328 removed outlier: 7.215A pdb=" N LEU A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.479A pdb=" N MET A 759 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N MET A 184 " --> pdb=" O MET A 759 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLN A 761 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE A 186 " --> pdb=" O GLN A 761 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE A 763 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL A 188 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLN A 765 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN A 751 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A 764 " --> pdb=" O TYR A 749 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR A 749 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL A 766 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N SER A 747 " --> pdb=" O VAL A 766 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 278 through 280 removed outlier: 6.702A pdb=" N THR A 625 " --> pdb=" O LYS A 602 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASN A 604 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE A 623 " --> pdb=" O ASN A 604 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA A 606 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 621 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU A 608 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL A 619 " --> pdb=" O LEU A 608 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 620 " --> pdb=" O PHE A 573 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 672 through 677 removed outlier: 4.293A pdb=" N ILE A 821 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N MET A 706 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 715 through 722 removed outlier: 3.638A pdb=" N GLY A 715 " --> pdb=" O ALA A 803 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 801 " --> pdb=" O ASN A 717 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 781 through 783 Processing sheet with id= H, first strand: chain 'B' and resid 128 through 130 Processing sheet with id= I, first strand: chain 'B' and resid 322 through 328 removed outlier: 7.215A pdb=" N LEU B 139 " --> pdb=" O PRO B 326 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.480A pdb=" N MET B 759 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N MET B 184 " --> pdb=" O MET B 759 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN B 761 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE B 186 " --> pdb=" O GLN B 761 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 763 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL B 188 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLN B 765 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN B 751 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 764 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR B 749 " --> pdb=" O VAL B 764 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL B 766 " --> pdb=" O SER B 747 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N SER B 747 " --> pdb=" O VAL B 766 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 278 through 280 removed outlier: 6.701A pdb=" N THR B 625 " --> pdb=" O LYS B 602 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASN B 604 " --> pdb=" O PHE B 623 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE B 623 " --> pdb=" O ASN B 604 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA B 606 " --> pdb=" O VAL B 621 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B 621 " --> pdb=" O ALA B 606 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU B 608 " --> pdb=" O VAL B 619 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL B 619 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 620 " --> pdb=" O PHE B 573 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 672 through 677 removed outlier: 4.291A pdb=" N ILE B 821 " --> pdb=" O MET B 706 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N MET B 706 " --> pdb=" O ILE B 821 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 715 through 722 removed outlier: 3.639A pdb=" N GLY B 715 " --> pdb=" O ALA B 803 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B 801 " --> pdb=" O ASN B 717 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 781 through 783 Processing sheet with id= O, first strand: chain 'C' and resid 128 through 130 Processing sheet with id= P, first strand: chain 'C' and resid 322 through 328 removed outlier: 7.215A pdb=" N LEU C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.479A pdb=" N MET C 759 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N MET C 184 " --> pdb=" O MET C 759 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN C 761 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE C 186 " --> pdb=" O GLN C 761 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 763 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL C 188 " --> pdb=" O ILE C 763 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLN C 765 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN C 751 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL C 764 " --> pdb=" O TYR C 749 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR C 749 " --> pdb=" O VAL C 764 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL C 766 " --> pdb=" O SER C 747 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N SER C 747 " --> pdb=" O VAL C 766 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 278 through 280 removed outlier: 6.703A pdb=" N THR C 625 " --> pdb=" O LYS C 602 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASN C 604 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE C 623 " --> pdb=" O ASN C 604 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA C 606 " --> pdb=" O VAL C 621 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL C 621 " --> pdb=" O ALA C 606 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU C 608 " --> pdb=" O VAL C 619 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL C 619 " --> pdb=" O LEU C 608 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA C 620 " --> pdb=" O PHE C 573 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 672 through 677 removed outlier: 4.292A pdb=" N ILE C 821 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N MET C 706 " --> pdb=" O ILE C 821 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 715 through 722 removed outlier: 3.638A pdb=" N GLY C 715 " --> pdb=" O ALA C 803 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN C 801 " --> pdb=" O ASN C 717 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 781 through 783 950 hydrogen bonds defined for protein. 2799 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: 8.52 Time building geometry restraints manager: 9.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 3864 1.28 - 1.41: 5389 1.41 - 1.54: 14475 1.54 - 1.68: 83 1.68 - 1.81: 264 Bond restraints: 24075 Sorted by residual: bond pdb=" C LYS C 468 " pdb=" O LYS C 468 " ideal model delta sigma weight residual 1.236 1.152 0.084 1.15e-02 7.56e+03 5.39e+01 bond pdb=" CA ASP B 578 " pdb=" C ASP B 578 " ideal model delta sigma weight residual 1.524 1.440 0.084 1.29e-02 6.01e+03 4.27e+01 bond pdb=" C ALA A 579 " pdb=" O ALA A 579 " ideal model delta sigma weight residual 1.236 1.157 0.079 1.21e-02 6.83e+03 4.21e+01 bond pdb=" C ASP B 578 " pdb=" O ASP B 578 " ideal model delta sigma weight residual 1.235 1.144 0.091 1.40e-02 5.10e+03 4.19e+01 bond pdb=" C ALA C 579 " pdb=" O ALA C 579 " ideal model delta sigma weight residual 1.235 1.167 0.068 1.22e-02 6.72e+03 3.13e+01 ... (remaining 24070 not shown) Histogram of bond angle deviations from ideal: 96.82 - 105.02: 569 105.02 - 113.22: 13455 113.22 - 121.42: 13213 121.42 - 129.61: 5248 129.61 - 137.81: 116 Bond angle restraints: 32601 Sorted by residual: angle pdb=" C LEU B 222 " pdb=" N PRO B 223 " pdb=" CA PRO B 223 " ideal model delta sigma weight residual 119.76 103.76 16.00 1.03e+00 9.43e-01 2.41e+02 angle pdb=" N PRO B 223 " pdb=" CA PRO B 223 " pdb=" C PRO B 223 " ideal model delta sigma weight residual 111.14 96.82 14.32 1.56e+00 4.11e-01 8.42e+01 angle pdb=" N ARG C 724 " pdb=" CA ARG C 724 " pdb=" C ARG C 724 " ideal model delta sigma weight residual 111.28 119.81 -8.53 1.09e+00 8.42e-01 6.12e+01 angle pdb=" N ARG B 724 " pdb=" CA ARG B 724 " pdb=" C ARG B 724 " ideal model delta sigma weight residual 111.28 118.83 -7.55 1.09e+00 8.42e-01 4.79e+01 angle pdb=" N ARG A 724 " pdb=" CA ARG A 724 " pdb=" C ARG A 724 " ideal model delta sigma weight residual 111.28 118.77 -7.49 1.09e+00 8.42e-01 4.72e+01 ... (remaining 32596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.86: 13642 24.86 - 49.72: 836 49.72 - 74.58: 102 74.58 - 99.43: 12 99.43 - 124.29: 3 Dihedral angle restraints: 14595 sinusoidal: 5754 harmonic: 8841 Sorted by residual: dihedral pdb=" CA ASP C 221 " pdb=" C ASP C 221 " pdb=" N LEU C 222 " pdb=" CA LEU C 222 " ideal model delta harmonic sigma weight residual -180.00 -150.01 -29.99 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ASP A 221 " pdb=" C ASP A 221 " pdb=" N LEU A 222 " pdb=" CA LEU A 222 " ideal model delta harmonic sigma weight residual -180.00 -150.10 -29.90 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA ARG B 632 " pdb=" C ARG B 632 " pdb=" N THR B 633 " pdb=" CA THR B 633 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 14592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 3732 0.121 - 0.242: 131 0.242 - 0.364: 8 0.364 - 0.485: 6 0.485 - 0.606: 2 Chirality restraints: 3879 Sorted by residual: chirality pdb=" CA TYR B 883 " pdb=" N TYR B 883 " pdb=" C TYR B 883 " pdb=" CB TYR B 883 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.19e+00 chirality pdb=" CA TYR C 883 " pdb=" N TYR C 883 " pdb=" C TYR C 883 " pdb=" CB TYR C 883 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.09e+00 chirality pdb=" CA ARG C 724 " pdb=" N ARG C 724 " pdb=" C ARG C 724 " pdb=" CB ARG C 724 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.02e+00 ... (remaining 3876 not shown) Planarity restraints: 4086 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 883 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C TYR B 883 " -0.067 2.00e-02 2.50e+03 pdb=" O TYR B 883 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU B 884 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 576 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.26e+01 pdb=" C PRO B 576 " 0.062 2.00e-02 2.50e+03 pdb=" O PRO B 576 " -0.022 2.00e-02 2.50e+03 pdb=" N SER B 577 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 575 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.17e+01 pdb=" C LEU C 575 " -0.059 2.00e-02 2.50e+03 pdb=" O LEU C 575 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO C 576 " 0.020 2.00e-02 2.50e+03 ... (remaining 4083 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4099 2.75 - 3.29: 21053 3.29 - 3.83: 36771 3.83 - 4.36: 45047 4.36 - 4.90: 77267 Nonbonded interactions: 184237 Sorted by model distance: nonbonded pdb=" NZ LYS C 468 " pdb=" O13 PTY C1102 " model vdw 2.216 2.520 nonbonded pdb=" O THR C 471 " pdb=" OG SER C 475 " model vdw 2.230 2.440 nonbonded pdb=" O THR A 471 " pdb=" OG SER A 475 " model vdw 2.230 2.440 nonbonded pdb=" O THR B 471 " pdb=" OG SER B 475 " model vdw 2.231 2.440 nonbonded pdb=" OD1 ASP C 723 " pdb=" OE1 GLU C 725 " model vdw 2.233 3.040 ... (remaining 184232 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 1023 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 C18 or name C2 \ or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C5 or name C6 or name C8 or name \ N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or na \ me O4 or name O7 or name P1 )) or (resid 1102 and (name C1 or name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C2 or name C20 or name C3 or name C30 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C5 \ or name C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 \ or name O14 or name O30 or name O4 or name O7 or name P1 )))) selection = (chain 'B' and (resid 1 through 1023 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 C18 or name C2 \ or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C5 or name C6 or name C8 or name \ N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or na \ me O4 or name O7 or name P1 )) or resid 1102)) selection = (chain 'C' and (resid 1 through 1023 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 C18 or name C2 \ or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C5 or name C6 or name C8 or name \ N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or na \ me O4 or name O7 or name P1 )) or (resid 1102 and (name C1 or name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C2 or name C20 or name C3 or name C30 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C5 \ or name C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 \ or name O14 or name O30 or name O4 or name O7 or name P1 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 135 5.16 5 C 15317 2.51 5 N 3825 2.21 5 O 4368 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 4.420 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: 22.410 Check model and map are aligned: 0.370 Process input model: 60.220 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.210 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.009 0.115 24075 Z= 0.587 Angle : 1.042 17.700 32601 Z= 0.562 Chirality : 0.061 0.606 3879 Planarity : 0.008 0.081 4086 Dihedral : 15.558 124.293 8877 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.69 % Favored : 96.15 % Rotamer Outliers : 6.03 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % 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: -5.39 (0.11), residues: 3063 helix: -4.36 (0.06), residues: 1530 sheet: -2.77 (0.19), residues: 498 loop : -2.16 (0.17), residues: 1035 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 521 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 155 outliers final: 31 residues processed: 639 average time/residue: 1.3247 time to fit residues: 975.4533 Evaluate side-chains 319 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 288 time to evaluate : 2.785 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 28 residues processed: 4 average time/residue: 0.3475 time to fit residues: 6.2335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 128 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 277 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 205 ASN A 237 GLN A 248 ASN A 574 GLN A 586 ASN A 593 ASN A 617 GLN A 644 ASN A 779 ASN A 788 GLN B 44 ASN B 120 GLN B 205 ASN B 237 GLN B 248 ASN B 586 ASN B 593 ASN B 617 GLN B 644 ASN B 717 ASN B 779 ASN B 805 GLN C 44 ASN C 74 ASN C 120 GLN C 205 ASN C 237 GLN C 248 ASN C 292 GLN C 574 GLN C 586 ASN C 593 ASN C 617 GLN C 644 ASN C 717 ASN C 779 ASN C 805 GLN C 863 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 24075 Z= 0.225 Angle : 0.646 10.130 32601 Z= 0.327 Chirality : 0.042 0.160 3879 Planarity : 0.005 0.072 4086 Dihedral : 8.018 106.627 3354 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 4.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.68 (0.13), residues: 3063 helix: -2.57 (0.10), residues: 1617 sheet: -2.08 (0.19), residues: 537 loop : -1.82 (0.19), residues: 909 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 302 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 36 residues processed: 380 average time/residue: 1.4163 time to fit residues: 618.9874 Evaluate side-chains 290 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 254 time to evaluate : 2.975 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 33 residues processed: 3 average time/residue: 0.2625 time to fit residues: 5.5544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 278 optimal weight: 2.9990 chunk 300 optimal weight: 0.9980 chunk 247 optimal weight: 0.8980 chunk 276 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 223 optimal weight: 0.0980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN B 108 GLN B 120 GLN B 292 GLN B 590 GLN B 788 GLN C 120 GLN C 292 GLN C 788 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 24075 Z= 0.202 Angle : 0.591 10.590 32601 Z= 0.294 Chirality : 0.041 0.145 3879 Planarity : 0.004 0.057 4086 Dihedral : 6.959 85.923 3354 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 4.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.22 (0.14), residues: 3063 helix: -1.25 (0.12), residues: 1593 sheet: -1.31 (0.21), residues: 510 loop : -1.57 (0.19), residues: 960 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 285 time to evaluate : 2.844 Fit side-chains outliers start: 112 outliers final: 40 residues processed: 373 average time/residue: 1.3045 time to fit residues: 563.7327 Evaluate side-chains 290 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 250 time to evaluate : 2.779 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 37 residues processed: 3 average time/residue: 0.2286 time to fit residues: 4.8265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 2.9990 chunk 209 optimal weight: 0.0970 chunk 144 optimal weight: 0.0870 chunk 30 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 279 optimal weight: 0.0870 chunk 295 optimal weight: 0.0980 chunk 145 optimal weight: 0.9980 chunk 264 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN B 74 ASN B 120 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 859 GLN B 863 GLN C 120 GLN C 292 GLN C 361 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 24075 Z= 0.140 Angle : 0.549 11.146 32601 Z= 0.271 Chirality : 0.040 0.204 3879 Planarity : 0.004 0.052 4086 Dihedral : 6.325 59.948 3354 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 3.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.39 (0.15), residues: 3063 helix: -0.49 (0.13), residues: 1572 sheet: -0.93 (0.21), residues: 543 loop : -1.33 (0.19), residues: 948 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 286 time to evaluate : 2.984 Fit side-chains outliers start: 89 outliers final: 43 residues processed: 360 average time/residue: 1.3778 time to fit residues: 574.0885 Evaluate side-chains 292 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 249 time to evaluate : 3.070 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 40 residues processed: 5 average time/residue: 1.0002 time to fit residues: 10.0255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 220 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 252 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 265 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN B 120 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN B 604 ASN B 691 GLN B 701 ASN C 108 GLN C 120 GLN C 292 GLN C 691 GLN C 701 ASN C 717 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.066 24075 Z= 0.498 Angle : 0.722 11.289 32601 Z= 0.359 Chirality : 0.049 0.201 3879 Planarity : 0.004 0.043 4086 Dihedral : 6.889 61.147 3354 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.10 % Favored : 96.80 % Rotamer Outliers : 4.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.51 (0.15), residues: 3063 helix: -0.55 (0.13), residues: 1596 sheet: -1.02 (0.21), residues: 561 loop : -1.47 (0.19), residues: 906 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 240 time to evaluate : 2.910 Fit side-chains outliers start: 125 outliers final: 58 residues processed: 339 average time/residue: 1.3298 time to fit residues: 522.3819 Evaluate side-chains 287 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 229 time to evaluate : 2.905 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 51 residues processed: 8 average time/residue: 0.5077 time to fit residues: 9.6772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 2.9990 chunk 266 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 73 optimal weight: 0.2980 chunk 296 optimal weight: 0.9980 chunk 245 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 292 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 24075 Z= 0.198 Angle : 0.579 12.026 32601 Z= 0.286 Chirality : 0.042 0.188 3879 Planarity : 0.004 0.044 4086 Dihedral : 6.342 59.677 3354 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 3.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.15), residues: 3063 helix: -0.02 (0.13), residues: 1584 sheet: -0.57 (0.22), residues: 510 loop : -1.28 (0.19), residues: 969 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 243 time to evaluate : 2.633 Fit side-chains outliers start: 98 outliers final: 56 residues processed: 325 average time/residue: 1.4123 time to fit residues: 530.1652 Evaluate side-chains 287 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 231 time to evaluate : 2.963 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 53 residues processed: 3 average time/residue: 1.0842 time to fit residues: 7.9186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 168 optimal weight: 0.0030 chunk 216 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 249 optimal weight: 0.0270 chunk 165 optimal weight: 2.9990 chunk 294 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.5850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN B 805 GLN C 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 24075 Z= 0.175 Angle : 0.569 12.535 32601 Z= 0.279 Chirality : 0.041 0.142 3879 Planarity : 0.004 0.043 4086 Dihedral : 5.999 57.574 3354 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 3.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.15), residues: 3063 helix: 0.26 (0.14), residues: 1587 sheet: -0.35 (0.22), residues: 510 loop : -1.07 (0.20), residues: 966 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 244 time to evaluate : 3.071 Fit side-chains outliers start: 83 outliers final: 58 residues processed: 316 average time/residue: 1.3327 time to fit residues: 486.0912 Evaluate side-chains 288 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 230 time to evaluate : 2.932 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 55 residues processed: 3 average time/residue: 0.5673 time to fit residues: 6.2755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 176 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 57 optimal weight: 0.0050 chunk 187 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 231 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN B 120 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 24075 Z= 0.182 Angle : 0.577 12.907 32601 Z= 0.281 Chirality : 0.041 0.239 3879 Planarity : 0.004 0.043 4086 Dihedral : 5.881 59.675 3354 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 3.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.16), residues: 3063 helix: 0.41 (0.14), residues: 1587 sheet: -0.29 (0.22), residues: 543 loop : -0.87 (0.20), residues: 933 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 241 time to evaluate : 2.656 Fit side-chains outliers start: 89 outliers final: 64 residues processed: 314 average time/residue: 1.3616 time to fit residues: 496.6502 Evaluate side-chains 294 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 230 time to evaluate : 3.033 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 59 residues processed: 5 average time/residue: 1.2985 time to fit residues: 11.6073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 0.3980 chunk 257 optimal weight: 0.6980 chunk 274 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 248 optimal weight: 0.5980 chunk 259 optimal weight: 2.9990 chunk 273 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 24075 Z= 0.182 Angle : 0.579 12.613 32601 Z= 0.282 Chirality : 0.041 0.295 3879 Planarity : 0.004 0.042 4086 Dihedral : 5.738 56.502 3354 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.16), residues: 3063 helix: 0.50 (0.14), residues: 1590 sheet: -0.20 (0.22), residues: 543 loop : -0.83 (0.20), residues: 930 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 236 time to evaluate : 2.666 Fit side-chains outliers start: 74 outliers final: 59 residues processed: 302 average time/residue: 1.3908 time to fit residues: 485.2015 Evaluate side-chains 289 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 230 time to evaluate : 3.016 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 57 residues processed: 2 average time/residue: 0.2376 time to fit residues: 4.8852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.9990 chunk 177 optimal weight: 0.0010 chunk 137 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 304 optimal weight: 0.5980 chunk 280 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 25 optimal weight: 0.0050 chunk 187 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 overall best weight: 0.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 24075 Z= 0.172 Angle : 0.582 12.697 32601 Z= 0.281 Chirality : 0.041 0.295 3879 Planarity : 0.004 0.042 4086 Dihedral : 5.594 59.728 3354 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.16), residues: 3063 helix: 0.62 (0.14), residues: 1593 sheet: 0.07 (0.23), residues: 507 loop : -0.88 (0.20), residues: 963 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 240 time to evaluate : 2.815 Fit side-chains outliers start: 60 outliers final: 56 residues processed: 297 average time/residue: 1.4511 time to fit residues: 498.5652 Evaluate side-chains 290 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 234 time to evaluate : 3.115 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 56 residues processed: 0 time to fit residues: 4.0891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 243 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 249 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.0060 chunk 213 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.117028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.091158 restraints weight = 38393.635| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.24 r_work: 0.3058 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 24075 Z= 0.190 Angle : 0.591 12.667 32601 Z= 0.286 Chirality : 0.041 0.281 3879 Planarity : 0.004 0.042 4086 Dihedral : 5.552 59.253 3354 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.16), residues: 3063 helix: 0.66 (0.14), residues: 1593 sheet: -0.08 (0.22), residues: 543 loop : -0.81 (0.20), residues: 927 =============================================================================== Job complete usr+sys time: 8992.29 seconds wall clock time: 161 minutes 25.63 seconds (9685.63 seconds total)