Starting phenix.real_space_refine on Tue Mar 19 04:56:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6csx_7609/03_2024/6csx_7609_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6csx_7609/03_2024/6csx_7609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6csx_7609/03_2024/6csx_7609.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6csx_7609/03_2024/6csx_7609.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6csx_7609/03_2024/6csx_7609_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6csx_7609/03_2024/6csx_7609_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 129 5.16 5 C 15009 2.51 5 N 3748 2.21 5 O 4334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B ARG 432": "NH1" <-> "NH2" Residue "B ARG 518": "NH1" <-> "NH2" Residue "B ARG 540": "NH1" <-> "NH2" Residue "B ARG 767": "NH1" <-> "NH2" Residue "B ARG 867": "NH1" <-> "NH2" Residue "B ARG 969": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C ARG 418": "NH1" <-> "NH2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C ARG 540": "NH1" <-> "NH2" Residue "C PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C ARG 780": "NH1" <-> "NH2" Residue "C ARG 1030": "NH1" <-> "NH2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 767": "NH1" <-> "NH2" Residue "A ARG 973": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23232 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 7735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7735 Classifications: {'peptide': 1019} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 973} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 7685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7685 Classifications: {'peptide': 1015} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 968} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 7305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7305 Classifications: {'peptide': 965} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 919} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 216 Unusual residues: {'D12': 1, 'PTY': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 111 Unusual residues: {'PTY': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PTY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 180 Unusual residues: {'PTY': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 2, 'PTY:plan-2': 3} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 12.09, per 1000 atoms: 0.52 Number of scatterers: 23232 At special positions: 0 Unit cell: (117.852, 116.144, 144.326, 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 129 16.00 P 12 15.00 O 4334 8.00 N 3748 7.00 C 15009 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.75 Conformation dependent library (CDL) restraints added in 4.8 seconds 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5504 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 135 helices and 27 sheets defined 46.1% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.37 Creating SS restraints... Processing helix chain 'B' and resid 4 through 6 No H-bonds generated for 'chain 'B' and resid 4 through 6' Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.528A pdb=" N ILE B 15 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 62 through 66 Processing helix chain 'B' and resid 100 through 112 Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 161 Processing helix chain 'B' and resid 163 through 166 No H-bonds generated for 'chain 'B' and resid 163 through 166' Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.618A pdb=" N ALA B 206 " --> pdb=" O ASP B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.780A pdb=" N GLY B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 243 through 247' Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 299 through 312 removed outlier: 4.061A pdb=" N ALA B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 358 removed outlier: 3.648A pdb=" N ILE B 337 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 356 " --> pdb=" O PHE B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 365 No H-bonds generated for 'chain 'B' and resid 362 through 365' Processing helix chain 'B' and resid 367 through 383 removed outlier: 3.545A pdb=" N VAL B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 392 through 401 removed outlier: 3.793A pdb=" N MET B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 413 through 422 removed outlier: 3.587A pdb=" N ALA B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 437 removed outlier: 3.561A pdb=" N THR B 431 " --> pdb=" O PRO B 427 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 456 removed outlier: 3.696A pdb=" N SER B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 451 " --> pdb=" O MET B 447 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 464 through 486 removed outlier: 3.778A pdb=" N GLN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 494 No H-bonds generated for 'chain 'B' and resid 491 through 494' Processing helix chain 'B' and resid 519 through 522 No H-bonds generated for 'chain 'B' and resid 519 through 522' Processing helix chain 'B' and resid 527 through 555 removed outlier: 3.671A pdb=" N GLY B 533 " --> pdb=" O ASP B 529 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 536 " --> pdb=" O GLY B 532 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER B 537 " --> pdb=" O GLY B 533 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY B 539 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ARG B 540 " --> pdb=" O ARG B 536 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 544 " --> pdb=" O ARG B 540 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 547 " --> pdb=" O VAL B 543 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 600 removed outlier: 4.037A pdb=" N VAL B 590 " --> pdb=" O ARG B 586 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS B 596 " --> pdb=" O ASN B 592 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 597 " --> pdb=" O GLU B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 652 removed outlier: 4.224A pdb=" N MET B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 706 removed outlier: 3.521A pdb=" N GLN B 697 " --> pdb=" O GLU B 693 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 738 Processing helix chain 'B' and resid 743 through 755 removed outlier: 3.833A pdb=" N THR B 748 " --> pdb=" O ASN B 744 " (cutoff:3.500A) 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 785 through 788 Processing helix chain 'B' and resid 801 through 803 No H-bonds generated for 'chain 'B' and resid 801 through 803' Processing helix chain 'B' and resid 837 through 850 removed outlier: 3.687A pdb=" N GLU B 845 " --> pdb=" O MET B 841 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B 849 " --> pdb=" O GLU B 845 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS B 850 " --> pdb=" O GLN B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 868 Processing helix chain 'B' and resid 870 through 891 removed outlier: 4.430A pdb=" N ALA B 873 " --> pdb=" O GLY B 870 " (cutoff:3.500A) Proline residue: B 874 - end of helix removed outlier: 4.300A pdb=" N TYR B 877 " --> pdb=" O PRO B 874 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B 878 " --> pdb=" O SER B 875 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 882 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL B 884 " --> pdb=" O LEU B 881 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS B 887 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA B 890 " --> pdb=" O CYS B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 917 removed outlier: 5.161A pdb=" N VAL B 904 " --> pdb=" O SER B 900 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL B 905 " --> pdb=" O VAL B 901 " (cutoff:3.500A) Proline residue: B 906 - end of helix removed outlier: 3.582A pdb=" N VAL B 909 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 910 " --> pdb=" O PRO B 906 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 912 " --> pdb=" O GLY B 908 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 917 " --> pdb=" O LEU B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 954 removed outlier: 3.549A pdb=" N VAL B 929 " --> pdb=" O VAL B 925 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 932 " --> pdb=" O GLN B 928 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET B 953 " --> pdb=" O ALA B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 983 removed outlier: 3.542A pdb=" N ARG B 969 " --> pdb=" O LEU B 965 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET B 970 " --> pdb=" O ASP B 966 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ARG B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Proline residue: B 974 - end of helix removed outlier: 3.828A pdb=" N SER B 979 " --> pdb=" O ILE B 975 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B 982 " --> pdb=" O THR B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 991 removed outlier: 3.618A pdb=" N ILE B 991 " --> pdb=" O MET B 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 987 through 991' Processing helix chain 'B' and resid 997 through 1012 removed outlier: 3.623A pdb=" N ALA B1002 " --> pdb=" O GLY B 998 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B1005 " --> pdb=" O ASN B1001 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B1007 " --> pdb=" O VAL B1003 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY B1010 " --> pdb=" O GLY B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1032 Proline residue: B1023 - end of helix removed outlier: 3.774A pdb=" N VAL B1027 " --> pdb=" O PRO B1023 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG B1030 " --> pdb=" O PHE B1026 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG B1032 " --> pdb=" O VAL B1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 5 No H-bonds generated for 'chain 'C' and resid 2 through 5' Processing helix chain 'C' and resid 9 through 21 Processing helix chain 'C' and resid 26 through 29 Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 62 through 66 Processing helix chain 'C' and resid 102 through 106 Processing helix chain 'C' and resid 122 through 125 No H-bonds generated for 'chain 'C' and resid 122 through 125' Processing helix chain 'C' and resid 151 through 161 removed outlier: 3.665A pdb=" N VAL C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 200 through 210 Processing helix chain 'C' and resid 244 through 247 No H-bonds generated for 'chain 'C' and resid 244 through 247' 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: 3.619A pdb=" N ALA C 305 " --> pdb=" O ASP C 301 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N MET C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 336 Processing helix chain 'C' and resid 338 through 359 removed outlier: 3.515A pdb=" N LEU C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 385 removed outlier: 3.603A pdb=" N ALA C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix removed outlier: 3.621A pdb=" N VAL C 382 " --> pdb=" O GLY C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 405 removed outlier: 4.634A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 421 removed outlier: 6.411A pdb=" N ARG C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 445 through 451 removed outlier: 4.660A pdb=" N SER C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 468 through 471 No H-bonds generated for 'chain 'C' and resid 468 through 471' Processing helix chain 'C' and resid 479 through 485 removed outlier: 3.626A pdb=" N LEU C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 495 removed outlier: 3.592A pdb=" N THR C 495 " --> pdb=" O ALA C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 556 removed outlier: 3.529A pdb=" N TYR C 545 " --> pdb=" O TYR C 541 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 546 " --> pdb=" O LEU C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 599 removed outlier: 3.732A pdb=" N VAL C 590 " --> pdb=" O ARG C 586 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 599 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 636 No H-bonds generated for 'chain 'C' and resid 634 through 636' Processing helix chain 'C' and resid 640 through 642 No H-bonds generated for 'chain 'C' and resid 640 through 642' Processing helix chain 'C' and resid 644 through 657 removed outlier: 3.690A pdb=" N MET C 649 " --> pdb=" O GLU C 645 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG C 653 " --> pdb=" O MET C 649 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN C 657 " --> pdb=" O ARG C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 705 removed outlier: 3.536A pdb=" N LEU C 695 " --> pdb=" O GLY C 691 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN C 697 " --> pdb=" O GLU C 693 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 704 " --> pdb=" O ASN C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 743 through 754 removed outlier: 3.645A pdb=" N ALA C 752 " --> pdb=" O THR C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 779 No H-bonds generated for 'chain 'C' and resid 777 through 779' Processing helix chain 'C' and resid 783 through 788 removed outlier: 3.516A pdb=" N ILE C 786 " --> pdb=" O PRO C 783 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY C 787 " --> pdb=" O ASP C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 803 No H-bonds generated for 'chain 'C' and resid 801 through 803' Processing helix chain 'C' and resid 837 through 847 removed outlier: 3.899A pdb=" N GLU C 845 " --> pdb=" O MET C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 889 removed outlier: 3.579A pdb=" N GLU C 866 " --> pdb=" O MET C 862 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN C 871 " --> pdb=" O ARG C 867 " (cutoff:3.500A) Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 895 through 902 removed outlier: 3.716A pdb=" N PHE C 899 " --> pdb=" O TRP C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 919 removed outlier: 3.592A pdb=" N ILE C 910 " --> pdb=" O PRO C 906 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG C 919 " --> pdb=" O ALA C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 936 removed outlier: 3.560A pdb=" N LEU C 932 " --> pdb=" O GLN C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 941 No H-bonds generated for 'chain 'C' and resid 938 through 941' Processing helix chain 'C' and resid 946 through 952 Processing helix chain 'C' and resid 960 through 970 removed outlier: 4.381A pdb=" N ARG C 969 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET C 970 " --> pdb=" O ASP C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 990 removed outlier: 4.089A pdb=" N PHE C 982 " --> pdb=" O THR C 978 " (cutoff:3.500A) Proline residue: C 988 - end of helix Processing helix chain 'C' and resid 1002 through 1012 removed outlier: 4.407A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET C1011 " --> pdb=" O VAL C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1019 No H-bonds generated for 'chain 'C' and resid 1017 through 1019' Processing helix chain 'C' and resid 1022 through 1030 removed outlier: 3.535A pdb=" N ARG C1030 " --> pdb=" O PHE C1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 9 through 27 removed outlier: 3.702A pdb=" N ILE A 15 " --> pdb=" O PHE A 11 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 100 through 111 removed outlier: 3.754A pdb=" N VAL A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 108 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 110 " --> pdb=" O GLN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.699A pdb=" N GLN A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 160 removed outlier: 3.601A pdb=" N ASP A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 243 through 246 No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 299 through 316 removed outlier: 3.584A pdb=" N ALA A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 330 through 357 removed outlier: 3.798A pdb=" N ILE A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 365 No H-bonds generated for 'chain 'A' and resid 362 through 365' Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.615A pdb=" N ALA A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix removed outlier: 3.610A pdb=" N PHE A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 402 through 422 removed outlier: 3.900A pdb=" N ASP A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 448 removed outlier: 3.619A pdb=" N THR A 431 " --> pdb=" O PRO A 427 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 462 through 485 removed outlier: 4.003A pdb=" N ILE A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 541 through 555 removed outlier: 3.553A pdb=" N TYR A 545 " --> pdb=" O TYR A 541 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 600 removed outlier: 3.581A pdb=" N VAL A 590 " --> pdb=" O ARG A 586 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 644 through 655 removed outlier: 3.741A pdb=" N MET A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR A 652 " --> pdb=" O THR A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 707 removed outlier: 3.509A pdb=" N LEU A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 737 Processing helix chain 'A' and resid 743 through 754 removed outlier: 3.506A pdb=" N ASN A 747 " --> pdb=" O ILE A 743 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 779 No H-bonds generated for 'chain 'A' and resid 777 through 779' Processing helix chain 'A' and resid 783 through 788 removed outlier: 3.546A pdb=" N ILE A 786 " --> pdb=" O PRO A 783 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 787 " --> pdb=" O ASP A 784 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP A 788 " --> pdb=" O ASP A 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 783 through 788' Processing helix chain 'A' and resid 801 through 803 No H-bonds generated for 'chain 'A' and resid 801 through 803' Processing helix chain 'A' and resid 837 through 841 Processing helix chain 'A' and resid 844 through 847 No H-bonds generated for 'chain 'A' and resid 844 through 847' Processing helix chain 'A' and resid 862 through 868 removed outlier: 3.708A pdb=" N ARG A 867 " --> pdb=" O SER A 863 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU A 868 " --> pdb=" O TYR A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 892 removed outlier: 3.864A pdb=" N TYR A 877 " --> pdb=" O ALA A 873 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 883 " --> pdb=" O ILE A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 902 removed outlier: 3.868A pdb=" N MET A 902 " --> pdb=" O PHE A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 918 removed outlier: 3.894A pdb=" N ILE A 910 " --> pdb=" O PRO A 906 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 912 " --> pdb=" O GLY A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 945 removed outlier: 3.561A pdb=" N LEU A 932 " --> pdb=" O GLN A 928 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 943 " --> pdb=" O ALA A 939 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 984 removed outlier: 3.838A pdb=" N ILE A 983 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 984 " --> pdb=" O LEU A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 990 No H-bonds generated for 'chain 'A' and resid 987 through 990' Processing helix chain 'A' and resid 997 through 1015 removed outlier: 3.669A pdb=" N ALA A1002 " --> pdb=" O GLY A 998 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A1013 " --> pdb=" O GLY A1009 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A1014 " --> pdb=" O GLY A1010 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1020 No H-bonds generated for 'chain 'A' and resid 1017 through 1020' Processing sheet with id= A, first strand: chain 'B' and resid 128 through 131 removed outlier: 4.327A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN B 89 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR B 77 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 321 through 324 removed outlier: 3.580A pdb=" N VAL B 142 " --> pdb=" O SER B 287 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.613A pdb=" N VAL B 768 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N MET B 184 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LYS B 770 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE B 186 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR B 772 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N MET B 188 " --> pdb=" O TYR B 772 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N MET B 774 " --> pdb=" O MET B 188 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 278 through 281 removed outlier: 7.152A pdb=" N SER B 630 " --> pdb=" O GLU B 607 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL B 609 " --> pdb=" O PHE B 628 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE B 628 " --> pdb=" O VAL B 609 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA B 611 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE B 626 " --> pdb=" O ALA B 611 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASN B 613 " --> pdb=" O THR B 624 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N THR B 624 " --> pdb=" O ASN B 613 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 827 through 829 removed outlier: 3.854A pdb=" N GLY B 829 " --> pdb=" O PHE B 680 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 858 " --> pdb=" O GLU B 683 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 724 through 731 Processing sheet with id= G, first strand: chain 'B' and resid 790 through 792 Processing sheet with id= H, first strand: chain 'B' and resid 250 through 254 removed outlier: 7.222A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL B 253 " --> pdb=" O SER B 258 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N SER B 258 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.589A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN C 89 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR C 77 " --> pdb=" O THR C 93 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 322 through 324 removed outlier: 7.092A pdb=" N ILE C 291 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL C 139 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU C 289 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY C 141 " --> pdb=" O SER C 287 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER C 287 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE C 143 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.802A pdb=" N VAL C 768 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 9.360A pdb=" N MET C 184 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS C 770 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ILE C 186 " --> pdb=" O LYS C 770 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR C 772 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N MET C 188 " --> pdb=" O TYR C 772 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N MET C 774 " --> pdb=" O MET C 188 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 662 through 666 removed outlier: 3.503A pdb=" N MET C 573 " --> pdb=" O PHE C 666 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 681 through 683 Processing sheet with id= N, first strand: chain 'C' and resid 724 through 726 Processing sheet with id= O, first strand: chain 'C' and resid 729 through 731 Processing sheet with id= P, first strand: chain 'C' and resid 790 through 792 Processing sheet with id= Q, first strand: chain 'C' and resid 172 through 177 removed outlier: 6.601A pdb=" N LYS C 292 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 175 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLY C 290 " --> pdb=" O VAL C 175 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 215 through 219 removed outlier: 4.395A pdb=" N ALA C 216 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE C 234 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLN C 218 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA C 232 " --> pdb=" O GLN C 218 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 250 through 253 removed outlier: 7.103A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.070A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 12.167A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY A 829 " --> pdb=" O PHE A 680 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 321 through 324 removed outlier: 6.875A pdb=" N ILE A 291 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A 139 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU A 289 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 141 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER A 287 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 266 through 272 Processing sheet with id= W, first strand: chain 'A' and resid 284 through 286 removed outlier: 3.670A pdb=" N ALA A 286 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER A 630 " --> pdb=" O GLU A 607 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL A 609 " --> pdb=" O PHE A 628 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE A 628 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA A 611 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 626 " --> pdb=" O ALA A 611 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ASN A 613 " --> pdb=" O THR A 624 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N THR A 624 " --> pdb=" O ASN A 613 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET A 573 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 724 through 731 Processing sheet with id= Y, first strand: chain 'A' and resid 761 through 764 Processing sheet with id= Z, first strand: chain 'A' and resid 790 through 792 Processing sheet with id= AA, first strand: chain 'A' and resid 250 through 253 removed outlier: 6.880A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) 853 hydrogen bonds defined for protein. 2457 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.60 Time building geometry restraints manager: 9.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3810 1.30 - 1.43: 5777 1.43 - 1.56: 13770 1.56 - 1.68: 24 1.68 - 1.81: 252 Bond restraints: 23633 Sorted by residual: bond pdb=" N PRO C 852 " pdb=" CD PRO C 852 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.60e+01 bond pdb=" C8 PTY B1105 " pdb=" O7 PTY B1105 " ideal model delta sigma weight residual 1.331 1.408 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C8 PTY B1104 " pdb=" O7 PTY B1104 " ideal model delta sigma weight residual 1.331 1.407 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C8 PTY A1105 " pdb=" O7 PTY A1105 " ideal model delta sigma weight residual 1.331 1.406 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C30 PTY A1103 " pdb=" O4 PTY A1103 " ideal model delta sigma weight residual 1.331 1.403 -0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 23628 not shown) Histogram of bond angle deviations from ideal: 95.69 - 104.29: 446 104.29 - 112.88: 12672 112.88 - 121.47: 13345 121.47 - 130.07: 5432 130.07 - 138.66: 102 Bond angle restraints: 31997 Sorted by residual: angle pdb=" N VAL B 413 " pdb=" CA VAL B 413 " pdb=" C VAL B 413 " ideal model delta sigma weight residual 110.62 101.18 9.44 1.02e+00 9.61e-01 8.57e+01 angle pdb=" N GLN C 588 " pdb=" CA GLN C 588 " pdb=" C GLN C 588 " ideal model delta sigma weight residual 111.69 103.41 8.28 1.23e+00 6.61e-01 4.53e+01 angle pdb=" N VAL C 416 " pdb=" CA VAL C 416 " pdb=" C VAL C 416 " ideal model delta sigma weight residual 110.72 104.12 6.60 1.01e+00 9.80e-01 4.27e+01 angle pdb=" O11 PTY B1106 " pdb=" P1 PTY B1106 " pdb=" O14 PTY B1106 " ideal model delta sigma weight residual 92.90 111.81 -18.91 3.00e+00 1.11e-01 3.97e+01 angle pdb=" C VAL B 904 " pdb=" N VAL B 905 " pdb=" CA VAL B 905 " ideal model delta sigma weight residual 120.24 124.07 -3.83 6.30e-01 2.52e+00 3.70e+01 ... (remaining 31992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.00: 13750 28.00 - 56.00: 425 56.00 - 83.99: 49 83.99 - 111.99: 6 111.99 - 139.99: 6 Dihedral angle restraints: 14236 sinusoidal: 5660 harmonic: 8576 Sorted by residual: dihedral pdb=" CA LYS C 131 " pdb=" C LYS C 131 " pdb=" N SER C 132 " pdb=" CA SER C 132 " ideal model delta harmonic sigma weight residual -180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ALA C 446 " pdb=" C ALA C 446 " pdb=" N MET C 447 " pdb=" CA MET C 447 " ideal model delta harmonic sigma weight residual 180.00 151.53 28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" N ASN C 415 " pdb=" C ASN C 415 " pdb=" CA ASN C 415 " pdb=" CB ASN C 415 " ideal model delta harmonic sigma weight residual 122.80 136.99 -14.19 0 2.50e+00 1.60e-01 3.22e+01 ... (remaining 14233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 3358 0.096 - 0.192: 358 0.192 - 0.287: 30 0.287 - 0.383: 5 0.383 - 0.479: 2 Chirality restraints: 3753 Sorted by residual: chirality pdb=" CA LEU C 488 " pdb=" N LEU C 488 " pdb=" C LEU C 488 " pdb=" CB LEU C 488 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CA ASN C 415 " pdb=" N ASN C 415 " pdb=" C ASN C 415 " pdb=" CB ASN C 415 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CA VAL B 412 " pdb=" N VAL B 412 " pdb=" C VAL B 412 " pdb=" CB VAL B 412 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 3750 not shown) Planarity restraints: 4046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 717 " -0.080 5.00e-02 4.00e+02 1.23e-01 2.41e+01 pdb=" N PRO C 718 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO C 718 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO C 718 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 317 " 0.073 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO C 318 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO C 318 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO C 318 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 451 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C ALA C 451 " -0.065 2.00e-02 2.50e+03 pdb=" O ALA C 451 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL C 452 " 0.022 2.00e-02 2.50e+03 ... (remaining 4043 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 53 2.43 - 3.05: 13057 3.05 - 3.67: 34719 3.67 - 4.28: 54451 4.28 - 4.90: 88718 Nonbonded interactions: 190998 Sorted by model distance: nonbonded pdb=" O VAL C 452 " pdb=" CD2 PHE C 453 " model vdw 1.815 3.340 nonbonded pdb=" O PRO C 427 " pdb=" OG1 THR C 431 " model vdw 2.222 2.440 nonbonded pdb=" CE2 PHE C 317 " pdb=" CD2 LEU C 321 " model vdw 2.232 3.760 nonbonded pdb=" O TYR C 467 " pdb=" N SER C 471 " model vdw 2.235 2.520 nonbonded pdb=" O SER C 319 " pdb=" N LEU C 321 " model vdw 2.235 2.520 ... (remaining 190993 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 385 or (resid 386 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 387 through 413 or (resid 414 and (name N or name CA or name C o \ r name O or name CB )) or resid 415 through 602 or (resid 603 and (name N or nam \ e CA or name C or name O or name CB )) or resid 604 through 644 or (resid 645 th \ rough 646 and (name N or name CA or name C or name O or name CB )) or resid 647 \ through 1026 or (resid 1104 and (name C1 or name C11 or name C12 or name C13 or \ name C14 or name C8 or name O4 or name O7 )) or (resid 1105 and (name C11 or nam \ e C12 or name C13 or name C14 or name C5 or name C6 or name C8 or name O14 or na \ me O7 )) or (resid 1106 and (name C1 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 O30 or name O4 or n \ ame O7 )))) selection = (chain 'B' and (resid 1 through 413 or (resid 414 and (name N or name CA or name \ C or name O or name CB )) or resid 415 through 449 or (resid 450 and (name N or \ name CA or name C or name CB or name OG )) or resid 451 through 499 or resid 54 \ 0 through 602 or (resid 603 and (name N or name CA or name C or name O or name C \ B )) or resid 604 through 644 or (resid 645 through 646 and (name N or name CA o \ r name C or name O or name CB )) or resid 647 through 949 or resid 971 through 1 \ 026 or (resid 1105 and (name C1 or name C11 or name C12 or name C13 or name C14 \ or name C8 or name O4 or name O7 )) or (resid 1106 and (name C11 or name C12 or \ name C13 or name C14 or name C5 or name C6 or name C8 or name O14 or name O7 )) \ or (resid 1107 and (name C1 or name C30 or name C31 or name C32 or name C33 or n \ ame C34 or name C35 or name C36 or name C37 or name O30 or name O4 or name O7 )) \ )) selection = (chain 'C' and (resid 1 through 385 or (resid 386 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 387 through 449 or (resid 450 and (name N or name CA or name C o \ r name CB or name OG )) or resid 451 through 499 or resid 540 through 949 or res \ id 971 through 1026 or (resid 1101 and (name C1 or name C11 or name C12 or name \ C13 or name C14 or name C8 or name O4 or name O7 )) or (resid 1102 and (name C11 \ or name C12 or name C13 or name C14 or name C5 or name C6 or name C8 or name O1 \ 4 or name O7 )) or (resid 1103 and (name C1 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 O30 or name \ O4 or name O7 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 8.560 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 64.760 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 0.087 23633 Z= 0.581 Angle : 1.209 18.910 31997 Z= 0.603 Chirality : 0.062 0.479 3753 Planarity : 0.008 0.123 4046 Dihedral : 13.610 139.990 8732 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.80 % Favored : 93.67 % Rotamer: Outliers : 2.42 % Allowed : 4.07 % Favored : 93.51 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.04 % 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: -5.28 (0.11), residues: 2985 helix: -4.39 (0.06), residues: 1492 sheet: -2.36 (0.22), residues: 425 loop : -2.16 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 754 HIS 0.009 0.002 HIS C 692 PHE 0.052 0.003 PHE B 5 TYR 0.058 0.004 TYR B 49 ARG 0.019 0.002 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 524 time to evaluate : 2.656 Fit side-chains REVERT: B 28 LEU cc_start: 0.7933 (mp) cc_final: 0.7608 (pp) REVERT: B 176 GLN cc_start: 0.7216 (tp40) cc_final: 0.6828 (tm-30) REVERT: B 218 GLN cc_start: 0.8811 (mt0) cc_final: 0.8268 (mt0) REVERT: B 435 MET cc_start: 0.6948 (mmp) cc_final: 0.5932 (ptm) REVERT: B 558 ARG cc_start: 0.7724 (ttp80) cc_final: 0.7250 (ptt90) REVERT: B 953 MET cc_start: 0.7117 (mtt) cc_final: 0.6914 (mtm) REVERT: C 29 LYS cc_start: 0.7870 (mtpp) cc_final: 0.7663 (mtmt) REVERT: C 184 MET cc_start: 0.8956 (tpp) cc_final: 0.8244 (tpt) REVERT: C 413 VAL cc_start: 0.8890 (p) cc_final: 0.8606 (t) REVERT: C 519 MET cc_start: 0.5812 (pp-130) cc_final: 0.5491 (pp-130) REVERT: C 868 LEU cc_start: 0.8841 (tm) cc_final: 0.8498 (mm) REVERT: C 958 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6862 (pttt) REVERT: A 366 LEU cc_start: 0.8950 (tt) cc_final: 0.8618 (tt) outliers start: 59 outliers final: 19 residues processed: 574 average time/residue: 1.2941 time to fit residues: 850.3585 Evaluate side-chains 330 residues out of total 2439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 310 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 897 ILE Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 958 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 472 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 251 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 270 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 112 GLN B 211 ASN C 63 GLN C 68 ASN C 74 ASN C 125 GLN C 213 GLN C 231 ASN C 282 ASN C 298 ASN C 361 ASN C 469 GLN ** C 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 871 ASN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 ASN A 229 GLN A 231 ASN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN A 439 GLN A 469 GLN A 737 GLN A 928 GLN A 941 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23633 Z= 0.207 Angle : 0.639 10.227 31997 Z= 0.327 Chirality : 0.044 0.215 3753 Planarity : 0.005 0.072 4046 Dihedral : 12.009 157.082 3591 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.95 % Favored : 95.98 % Rotamer: Outliers : 4.89 % Allowed : 11.80 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.04 % 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: -3.44 (0.13), residues: 2985 helix: -2.66 (0.10), residues: 1486 sheet: -1.65 (0.24), residues: 420 loop : -1.59 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 789 HIS 0.003 0.001 HIS A 692 PHE 0.026 0.001 PHE B 5 TYR 0.020 0.001 TYR A 49 ARG 0.003 0.000 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 355 time to evaluate : 2.640 Fit side-chains REVERT: B 28 LEU cc_start: 0.8121 (mp) cc_final: 0.7720 (pp) REVERT: B 37 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8418 (t) REVERT: B 138 MET cc_start: 0.8245 (ptm) cc_final: 0.8045 (ptm) REVERT: B 176 GLN cc_start: 0.7149 (tp40) cc_final: 0.6917 (tm-30) REVERT: B 218 GLN cc_start: 0.8759 (mt0) cc_final: 0.8190 (mt0) REVERT: B 435 MET cc_start: 0.7209 (mmp) cc_final: 0.5949 (ttp) REVERT: B 456 MET cc_start: 0.8226 (ttt) cc_final: 0.8019 (ttt) REVERT: B 558 ARG cc_start: 0.7758 (ttp80) cc_final: 0.7157 (ptt90) REVERT: B 969 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7579 (ptm-80) REVERT: B 1030 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7399 (ptm-80) REVERT: C 519 MET cc_start: 0.5786 (pp-130) cc_final: 0.5436 (pp-130) REVERT: C 958 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7060 (pttt) REVERT: A 174 ASP cc_start: 0.7663 (p0) cc_final: 0.7223 (t0) REVERT: A 363 ARG cc_start: 0.7611 (ttm110) cc_final: 0.7280 (ttp-110) REVERT: A 418 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.6455 (ttt-90) REVERT: A 447 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.7100 (mpp) REVERT: A 858 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7565 (t0) outliers start: 119 outliers final: 28 residues processed: 435 average time/residue: 1.1773 time to fit residues: 596.3915 Evaluate side-chains 323 residues out of total 2439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 288 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 969 ARG Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 1030 ARG Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 958 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 858 ASP Chi-restraints excluded: chain A residue 984 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 150 optimal weight: 0.4980 chunk 83 optimal weight: 8.9990 chunk 225 optimal weight: 4.9990 chunk 184 optimal weight: 0.4980 chunk 74 optimal weight: 6.9990 chunk 271 optimal weight: 3.9990 chunk 292 optimal weight: 5.9990 chunk 241 optimal weight: 0.9990 chunk 268 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 217 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 846 GLN C 63 GLN ** C 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 ASN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN A 391 ASN A 830 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23633 Z= 0.198 Angle : 0.592 9.998 31997 Z= 0.298 Chirality : 0.043 0.183 3753 Planarity : 0.004 0.054 4046 Dihedral : 10.581 160.823 3568 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.31 % Rotamer: Outliers : 4.60 % Allowed : 14.18 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.04 % 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: -2.31 (0.15), residues: 2985 helix: -1.57 (0.12), residues: 1474 sheet: -1.23 (0.23), residues: 437 loop : -1.27 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 895 HIS 0.002 0.001 HIS C 692 PHE 0.023 0.001 PHE B 5 TYR 0.018 0.001 TYR C 49 ARG 0.007 0.000 ARG C 558 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 327 time to evaluate : 2.314 Fit side-chains REVERT: B 28 LEU cc_start: 0.8036 (mp) cc_final: 0.7673 (pp) REVERT: B 37 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8483 (t) REVERT: B 176 GLN cc_start: 0.7143 (tp40) cc_final: 0.6889 (tm-30) REVERT: B 218 GLN cc_start: 0.8753 (mt0) cc_final: 0.8186 (mt0) REVERT: B 435 MET cc_start: 0.6642 (mmp) cc_final: 0.5811 (ptm) REVERT: B 558 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7484 (ttt180) REVERT: B 825 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8235 (mtt) REVERT: B 987 MET cc_start: 0.7797 (tpt) cc_final: 0.7368 (mmm) REVERT: B 1008 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7983 (ttt) REVERT: B 1011 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.7056 (ttm) REVERT: C 117 LEU cc_start: 0.8270 (mt) cc_final: 0.7527 (tp) REVERT: C 229 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7277 (mp10) REVERT: C 429 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7033 (mt-10) REVERT: C 519 MET cc_start: 0.5919 (OUTLIER) cc_final: 0.5564 (pp-130) REVERT: C 542 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8292 (tp) REVERT: C 546 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8234 (tp) REVERT: C 682 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7597 (p90) REVERT: C 977 MET cc_start: 0.7983 (mmm) cc_final: 0.7348 (mmm) REVERT: A 174 ASP cc_start: 0.7734 (p0) cc_final: 0.7222 (t0) REVERT: A 363 ARG cc_start: 0.7670 (ttm110) cc_final: 0.7279 (ttp-110) REVERT: A 418 ARG cc_start: 0.6800 (OUTLIER) cc_final: 0.6348 (ttt-90) REVERT: A 447 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.7020 (mpp) REVERT: A 858 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7591 (t0) outliers start: 112 outliers final: 40 residues processed: 402 average time/residue: 1.1767 time to fit residues: 552.2310 Evaluate side-chains 342 residues out of total 2439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 290 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 784 ASP Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 1008 MET Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 682 PHE Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 858 ASP Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 984 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 267 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 272 optimal weight: 2.9990 chunk 288 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 257 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1000 GLN C 63 GLN C 596 HIS ** C 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 ASN A 58 GLN A 830 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23633 Z= 0.175 Angle : 0.567 9.844 31997 Z= 0.283 Chirality : 0.043 0.250 3753 Planarity : 0.004 0.047 4046 Dihedral : 9.757 148.500 3564 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.31 % Rotamer: Outliers : 3.90 % Allowed : 16.52 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.04 % 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: -1.67 (0.15), residues: 2985 helix: -1.00 (0.13), residues: 1477 sheet: -0.99 (0.24), residues: 436 loop : -1.02 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 895 HIS 0.002 0.000 HIS C 692 PHE 0.018 0.001 PHE B 5 TYR 0.014 0.001 TYR C 49 ARG 0.008 0.000 ARG C 558 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 318 time to evaluate : 2.589 Fit side-chains REVERT: B 28 LEU cc_start: 0.8022 (mp) cc_final: 0.7676 (pp) REVERT: B 37 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8518 (t) REVERT: B 176 GLN cc_start: 0.7159 (tp40) cc_final: 0.6893 (tm-30) REVERT: B 435 MET cc_start: 0.6845 (mmp) cc_final: 0.5993 (ttp) REVERT: B 685 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8867 (mm) REVERT: B 969 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7544 (ptm-80) REVERT: B 987 MET cc_start: 0.7794 (tpt) cc_final: 0.7402 (mmm) REVERT: B 1008 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7991 (ttt) REVERT: C 104 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8665 (tm-30) REVERT: C 117 LEU cc_start: 0.8161 (mt) cc_final: 0.7438 (tp) REVERT: C 229 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7264 (mp10) REVERT: C 429 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7087 (mt-10) REVERT: C 519 MET cc_start: 0.6122 (OUTLIER) cc_final: 0.5836 (pp-130) REVERT: C 546 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8179 (tp) REVERT: C 547 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8605 (mp) REVERT: C 682 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7569 (p90) REVERT: C 919 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7546 (ttm110) REVERT: A 174 ASP cc_start: 0.7662 (p0) cc_final: 0.7164 (t0) REVERT: A 363 ARG cc_start: 0.7718 (ttm110) cc_final: 0.7376 (ttp-110) REVERT: A 418 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.6255 (ttt-90) REVERT: A 447 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.7038 (mpp) REVERT: A 858 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7556 (t0) outliers start: 95 outliers final: 34 residues processed: 381 average time/residue: 1.1046 time to fit residues: 493.2512 Evaluate side-chains 336 residues out of total 2439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 289 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 784 ASP Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 969 ARG Chi-restraints excluded: chain B residue 1008 MET Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 682 PHE Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 744 ASN Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain C residue 1031 ARG Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 858 ASP Chi-restraints excluded: chain A residue 993 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 239 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 245 optimal weight: 6.9990 chunk 199 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 258 optimal weight: 2.9990 chunk 72 optimal weight: 0.0970 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 846 GLN ** C 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23633 Z= 0.193 Angle : 0.572 9.303 31997 Z= 0.284 Chirality : 0.043 0.249 3753 Planarity : 0.004 0.048 4046 Dihedral : 9.364 133.973 3562 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.69 % Favored : 96.21 % Rotamer: Outliers : 4.73 % Allowed : 16.56 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.04 % 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: -1.35 (0.15), residues: 2985 helix: -0.67 (0.13), residues: 1483 sheet: -0.86 (0.24), residues: 431 loop : -0.96 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 895 HIS 0.002 0.001 HIS C 692 PHE 0.017 0.001 PHE B 5 TYR 0.014 0.001 TYR C 49 ARG 0.009 0.000 ARG C 558 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 295 time to evaluate : 2.531 Fit side-chains REVERT: B 1 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.6646 (tpp) REVERT: B 28 LEU cc_start: 0.8034 (mp) cc_final: 0.7684 (pp) REVERT: B 37 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8454 (t) REVERT: B 176 GLN cc_start: 0.7142 (tp40) cc_final: 0.6875 (tm-30) REVERT: B 362 PHE cc_start: 0.8225 (t80) cc_final: 0.7888 (t80) REVERT: B 435 MET cc_start: 0.6923 (mmp) cc_final: 0.5983 (ttp) REVERT: B 685 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8912 (mm) REVERT: B 825 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8167 (mtt) REVERT: B 969 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7566 (ptm-80) REVERT: B 987 MET cc_start: 0.7792 (tpt) cc_final: 0.7414 (mmm) REVERT: C 104 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8633 (tm-30) REVERT: C 117 LEU cc_start: 0.8179 (mt) cc_final: 0.7463 (tp) REVERT: C 229 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7309 (mp10) REVERT: C 413 VAL cc_start: 0.9166 (p) cc_final: 0.8796 (t) REVERT: C 429 GLU cc_start: 0.7309 (mm-30) cc_final: 0.7097 (mt-10) REVERT: C 439 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: C 525 HIS cc_start: 0.5554 (t-90) cc_final: 0.4980 (t-90) REVERT: C 542 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8314 (tp) REVERT: C 546 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8208 (tp) REVERT: C 547 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8598 (mp) REVERT: C 682 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7508 (p90) REVERT: C 919 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7583 (ttm110) REVERT: A 95 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: A 174 ASP cc_start: 0.7682 (p0) cc_final: 0.7199 (t0) REVERT: A 363 ARG cc_start: 0.7613 (ttm110) cc_final: 0.7395 (ttp-110) REVERT: A 447 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.7056 (mpp) REVERT: A 569 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7984 (mt0) REVERT: A 858 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7654 (m-30) outliers start: 115 outliers final: 49 residues processed: 371 average time/residue: 1.1948 time to fit residues: 525.3930 Evaluate side-chains 349 residues out of total 2439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 284 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 784 ASP Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 969 ARG Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 682 PHE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 744 ASN Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 970 MET Chi-restraints excluded: chain C residue 993 THR Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain C residue 1031 ARG Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 858 ASP Chi-restraints excluded: chain A residue 993 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 96 optimal weight: 0.6980 chunk 259 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 169 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 288 optimal weight: 0.9990 chunk 239 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 GLN B 865 GLN ** C 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23633 Z= 0.151 Angle : 0.544 10.412 31997 Z= 0.270 Chirality : 0.042 0.257 3753 Planarity : 0.004 0.049 4046 Dihedral : 8.636 105.382 3562 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.55 % Favored : 96.38 % Rotamer: Outliers : 3.95 % Allowed : 17.51 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.04 % 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: -0.96 (0.15), residues: 2985 helix: -0.29 (0.14), residues: 1476 sheet: -0.70 (0.25), residues: 418 loop : -0.86 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 895 HIS 0.001 0.000 HIS C 692 PHE 0.017 0.001 PHE B 352 TYR 0.018 0.001 TYR C 545 ARG 0.009 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 327 time to evaluate : 2.793 Fit side-chains REVERT: B 28 LEU cc_start: 0.8041 (mp) cc_final: 0.7698 (pp) REVERT: B 37 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8545 (t) REVERT: B 140 VAL cc_start: 0.8910 (t) cc_final: 0.8642 (p) REVERT: B 362 PHE cc_start: 0.8250 (t80) cc_final: 0.7895 (t80) REVERT: B 435 MET cc_start: 0.6868 (mmp) cc_final: 0.6040 (ptt) REVERT: B 685 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8873 (mm) REVERT: B 825 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8139 (mtt) REVERT: B 969 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7523 (ptm-80) REVERT: B 987 MET cc_start: 0.7860 (tpt) cc_final: 0.7464 (mmm) REVERT: C 117 LEU cc_start: 0.8096 (mt) cc_final: 0.7432 (tp) REVERT: C 334 LYS cc_start: 0.8375 (ttmp) cc_final: 0.7882 (tptt) REVERT: C 439 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7193 (tm-30) REVERT: C 525 HIS cc_start: 0.5520 (t-90) cc_final: 0.4964 (t-90) REVERT: C 543 VAL cc_start: 0.8906 (t) cc_final: 0.8488 (m) REVERT: C 546 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8203 (tp) REVERT: C 547 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8587 (mp) REVERT: C 682 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7471 (p90) REVERT: C 919 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7580 (ttm110) REVERT: A 95 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7443 (mt-10) REVERT: A 174 ASP cc_start: 0.7536 (p0) cc_final: 0.7090 (t0) REVERT: A 447 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.7001 (mpp) REVERT: A 496 MET cc_start: 0.7744 (ptp) cc_final: 0.7500 (ptt) outliers start: 96 outliers final: 43 residues processed: 393 average time/residue: 1.1306 time to fit residues: 519.9858 Evaluate side-chains 350 residues out of total 2439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 296 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 969 ARG Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 458 PHE Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 682 PHE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 744 ASN Chi-restraints excluded: chain C residue 841 MET Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 970 MET Chi-restraints excluded: chain C residue 993 THR Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain C residue 1031 ARG Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 993 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 277 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 242 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 287 optimal weight: 0.5980 chunk 179 optimal weight: 8.9990 chunk 175 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 GLN B 667 ASN C 391 ASN ** C 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 GLN A 830 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23633 Z= 0.214 Angle : 0.586 11.466 31997 Z= 0.290 Chirality : 0.043 0.260 3753 Planarity : 0.004 0.048 4046 Dihedral : 8.575 83.417 3562 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.09 % Favored : 95.85 % Rotamer: Outliers : 3.99 % Allowed : 18.13 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.04 % 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: -0.83 (0.16), residues: 2985 helix: -0.19 (0.14), residues: 1487 sheet: -0.62 (0.24), residues: 420 loop : -0.80 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 187 HIS 0.002 0.001 HIS B 338 PHE 0.016 0.001 PHE B 5 TYR 0.024 0.001 TYR C 545 ARG 0.008 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 302 time to evaluate : 3.131 Fit side-chains REVERT: B 28 LEU cc_start: 0.8059 (mp) cc_final: 0.7707 (pp) REVERT: B 37 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8510 (t) REVERT: B 362 PHE cc_start: 0.8264 (t80) cc_final: 0.7866 (t80) REVERT: B 435 MET cc_start: 0.7329 (mmp) cc_final: 0.6110 (ptt) REVERT: B 685 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8995 (mm) REVERT: B 825 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8086 (mtt) REVERT: B 969 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7575 (ptm-80) REVERT: B 987 MET cc_start: 0.7870 (tpt) cc_final: 0.7464 (mmm) REVERT: C 117 LEU cc_start: 0.8144 (mt) cc_final: 0.7432 (tp) REVERT: C 229 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7288 (mp10) REVERT: C 413 VAL cc_start: 0.9141 (p) cc_final: 0.8853 (t) REVERT: C 439 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7294 (tm-30) REVERT: C 525 HIS cc_start: 0.5527 (t-90) cc_final: 0.4958 (t-90) REVERT: C 543 VAL cc_start: 0.8892 (t) cc_final: 0.8614 (t) REVERT: C 547 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8586 (mp) REVERT: C 682 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7564 (p90) REVERT: C 919 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7580 (ttm110) REVERT: A 115 MET cc_start: 0.8731 (tpt) cc_final: 0.7690 (tpt) REVERT: A 174 ASP cc_start: 0.7732 (p0) cc_final: 0.7338 (t0) REVERT: A 447 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6940 (mpp) REVERT: A 980 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8856 (mm) outliers start: 97 outliers final: 52 residues processed: 365 average time/residue: 1.1496 time to fit residues: 494.1463 Evaluate side-chains 350 residues out of total 2439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 287 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 969 ARG Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 458 PHE Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 682 PHE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 744 ASN Chi-restraints excluded: chain C residue 841 MET Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 970 MET Chi-restraints excluded: chain C residue 993 THR Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain C residue 1031 ARG Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 993 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.4733 > 50: distance: 21 - 25: 4.198 distance: 25 - 31: 8.091 distance: 26 - 29: 3.574 distance: 27 - 28: 8.769 distance: 27 - 32: 3.858 distance: 29 - 30: 9.337 distance: 33 - 34: 9.553 distance: 33 - 36: 10.169 distance: 34 - 35: 8.576 distance: 36 - 37: 6.249 distance: 37 - 38: 4.567 distance: 37 - 39: 5.688 distance: 42 - 49: 9.996 distance: 44 - 45: 7.241 distance: 46 - 47: 5.638 distance: 46 - 48: 4.914 distance: 50 - 51: 8.978 distance: 50 - 53: 14.176 distance: 51 - 52: 5.733 distance: 51 - 57: 7.762 distance: 54 - 55: 8.003 distance: 54 - 56: 12.204 distance: 57 - 58: 5.670 distance: 58 - 59: 3.184 distance: 58 - 61: 5.940 distance: 59 - 60: 13.356 distance: 59 - 66: 15.057 distance: 61 - 62: 14.164 distance: 62 - 63: 8.473 distance: 63 - 64: 10.483 distance: 63 - 65: 8.666 distance: 66 - 67: 10.105 distance: 67 - 68: 8.614 distance: 68 - 69: 21.152 distance: 68 - 70: 12.287 distance: 70 - 71: 15.803 distance: 71 - 72: 31.821 distance: 71 - 74: 19.083 distance: 72 - 73: 9.377 distance: 72 - 77: 17.466 distance: 74 - 75: 25.087 distance: 74 - 76: 15.298 distance: 77 - 78: 15.441 distance: 77 - 148: 18.763 distance: 78 - 81: 9.706 distance: 79 - 88: 3.927 distance: 80 - 145: 13.907 distance: 81 - 82: 13.319 distance: 82 - 83: 9.277 distance: 82 - 84: 7.900 distance: 83 - 85: 10.867 distance: 84 - 86: 8.894 distance: 85 - 87: 4.816 distance: 86 - 87: 9.778 distance: 88 - 203: 16.230 distance: 89 - 90: 9.365 distance: 90 - 91: 7.881 distance: 90 - 96: 4.113 distance: 91 - 200: 5.471 distance: 92 - 93: 14.977 distance: 93 - 94: 11.694 distance: 94 - 95: 12.925 distance: 96 - 97: 4.442 distance: 96 - 132: 8.026 distance: 97 - 98: 6.923 distance: 97 - 100: 5.390 distance: 98 - 99: 17.422 distance: 98 - 103: 3.985 distance: 99 - 129: 12.508 distance: 100 - 101: 8.112 distance: 100 - 102: 5.393 distance: 103 - 194: 3.368