Starting phenix.real_space_refine (version: dev) on Fri Dec 23 01:01:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgu_10185/12_2022/6sgu_10185.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgu_10185/12_2022/6sgu_10185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgu_10185/12_2022/6sgu_10185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgu_10185/12_2022/6sgu_10185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgu_10185/12_2022/6sgu_10185.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgu_10185/12_2022/6sgu_10185.pdb" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 620": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 866": "OE1" <-> "OE2" Residue "A GLU 962": "OE1" <-> "OE2" Residue "A PHE 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 673": "OE1" <-> "OE2" Residue "C ARG 792": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 1032": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "E GLU 29": "OE1" <-> "OE2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 159": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 52169 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 15847 Classifications: {'peptide': 1033} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 987} Chain: "B" Number of atoms: 15849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 15849 Classifications: {'peptide': 1033} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 987} Chain: "C" Number of atoms: 15850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 15850 Classifications: {'peptide': 1033} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 45, 'TRANS': 987} Chain: "D" Number of atoms: 2336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2336 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 3, 'TRANS': 152} Chain: "E" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2287 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Time building chain proxies: 20.09, per 1000 atoms: 0.39 Number of scatterers: 52169 At special positions: 0 Unit cell: (151.58, 130.38, 144.16, 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 134 16.00 O 4825 8.00 N 4293 7.00 C 16623 6.00 H 26294 1.00 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: 41.27 Conformation dependent library (CDL) restraints added in 4.6 seconds 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6222 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 21 sheets defined 56.2% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 4.141A pdb=" N ASP A 7 " --> pdb=" O ASN A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 28 removed outlier: 4.082A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU A 28 " --> pdb=" O GLY A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 99 through 112 removed outlier: 3.561A pdb=" N LYS A 110 " --> pdb=" O GLN A 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.604A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.622A pdb=" N GLY A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 248' Processing helix chain 'A' and resid 298 through 312 removed outlier: 3.627A pdb=" N ALA A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 329 through 334 removed outlier: 3.670A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 359 removed outlier: 3.667A pdb=" N THR A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.513A pdb=" N THR A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 379 through 386 removed outlier: 3.508A pdb=" N ALA A 384 " --> pdb=" O PHE A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 422 removed outlier: 4.329A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 454 removed outlier: 4.034A pdb=" N ARG A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 452 " --> pdb=" O VAL A 448 " (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 463 through 488 removed outlier: 3.990A pdb=" N TYR A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU A 486 " --> pdb=" O VAL A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.645A pdb=" N GLU A 507 " --> pdb=" O ASP A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 538 removed outlier: 3.566A pdb=" N GLY A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TRP A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 558 removed outlier: 4.092A pdb=" N VAL A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 558 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 601 removed outlier: 3.605A pdb=" N THR A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 653 Processing helix chain 'A' and resid 692 through 708 removed outlier: 4.326A pdb=" N ALA A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 739 Processing helix chain 'A' and resid 743 through 755 removed outlier: 3.949A pdb=" N ASN A 747 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 788 removed outlier: 3.875A pdb=" N GLY A 787 " --> pdb=" O ASP A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 849 Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 873 through 893 removed outlier: 4.703A pdb=" N ILE A 879 " --> pdb=" O SER A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 903 removed outlier: 4.149A pdb=" N VAL A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 920 removed outlier: 3.768A pdb=" N VAL A 909 " --> pdb=" O VAL A 905 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 956 removed outlier: 3.709A pdb=" N LEU A 932 " --> pdb=" O GLN A 928 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE A 945 " --> pdb=" O ASN A 941 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 968 removed outlier: 3.584A pdb=" N ASP A 966 " --> pdb=" O GLU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 984 Processing helix chain 'A' and resid 986 through 991 removed outlier: 3.775A pdb=" N VAL A 990 " --> pdb=" O VAL A 986 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 991 " --> pdb=" O MET A 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 986 through 991' Processing helix chain 'A' and resid 996 through 1009 removed outlier: 3.988A pdb=" N ALA A1002 " --> pdb=" O GLY A 998 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A1007 " --> pdb=" O VAL A1003 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A1009 " --> pdb=" O THR A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1018 removed outlier: 3.659A pdb=" N THR A1013 " --> pdb=" O GLY A1009 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A1014 " --> pdb=" O GLY A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1033 removed outlier: 3.938A pdb=" N VAL A1024 " --> pdb=" O PHE A1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 8 removed outlier: 4.422A pdb=" N ASP B 7 " --> pdb=" O ASN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 28 removed outlier: 3.872A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 removed outlier: 3.565A pdb=" N VAL B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.579A pdb=" N GLN B 67 " --> pdb=" O GLN B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 114 through 118 removed outlier: 3.557A pdb=" N LEU B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 4.110A pdb=" N GLN B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 162 removed outlier: 3.547A pdb=" N ASN B 161 " --> pdb=" O TYR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 189 through 194 Processing helix chain 'B' and resid 201 through 210 Processing helix chain 'B' and resid 242 through 247 removed outlier: 3.520A pdb=" N PHE B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 312 Processing helix chain 'B' and resid 329 through 358 removed outlier: 3.891A pdb=" N ILE B 335 " --> pdb=" O PRO B 331 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 342 " --> pdb=" O HIS B 338 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR B 356 " --> pdb=" O PHE B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 367 through 386 Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 400 removed outlier: 4.128A pdb=" N MET B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 400 " --> pdb=" O PHE B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 424 removed outlier: 3.743A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 454 removed outlier: 4.171A pdb=" N GLY B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 438 " --> pdb=" O SER B 434 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.901A pdb=" N PHE B 459 " --> pdb=" O MET B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 488 removed outlier: 3.676A pdb=" N ILE B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 494 Processing helix chain 'B' and resid 511 through 537 removed outlier: 3.608A pdb=" N TRP B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 558 removed outlier: 3.973A pdb=" N LEU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 558 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 601 Processing helix chain 'B' and resid 633 through 637 Processing helix chain 'B' and resid 643 through 656 removed outlier: 4.276A pdb=" N MET B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 705 removed outlier: 3.595A pdb=" N LEU B 695 " --> pdb=" O GLY B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 739 removed outlier: 3.667A pdb=" N GLN B 737 " --> pdb=" O GLN B 733 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 739 " --> pdb=" O LYS B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 755 removed outlier: 3.552A pdb=" N THR B 748 " --> pdb=" O ASN B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 780 Processing helix chain 'B' and resid 785 through 788 Processing helix chain 'B' and resid 836 through 845 removed outlier: 4.082A pdb=" N ALA B 840 " --> pdb=" O SER B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 851 Processing helix chain 'B' and resid 861 through 866 removed outlier: 4.003A pdb=" N GLN B 865 " --> pdb=" O GLY B 861 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 866 " --> pdb=" O MET B 862 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 861 through 866' Processing helix chain 'B' and resid 871 through 893 removed outlier: 3.635A pdb=" N SER B 875 " --> pdb=" O ASN B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 903 Processing helix chain 'B' and resid 904 through 919 removed outlier: 3.890A pdb=" N GLY B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 909 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE B 910 " --> pdb=" O PRO B 906 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA B 912 " --> pdb=" O GLY B 908 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 917 " --> pdb=" O LEU B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 953 removed outlier: 3.744A pdb=" N LEU B 944 " --> pdb=" O LYS B 940 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 945 " --> pdb=" O ASN B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 992 removed outlier: 4.538A pdb=" N ARG B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Proline residue: B 974 - end of helix Proline residue: B 988 - end of helix Processing helix chain 'B' and resid 996 through 1017 removed outlier: 4.180A pdb=" N GLY B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B1013 " --> pdb=" O GLY B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1033 removed outlier: 3.773A pdb=" N VAL B1022 " --> pdb=" O ALA B1018 " (cutoff:3.500A) Proline residue: B1023 - end of helix Processing helix chain 'C' and resid 8 through 28 removed outlier: 3.685A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 removed outlier: 3.551A pdb=" N VAL C 57 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 99 through 112 removed outlier: 3.520A pdb=" N LYS C 110 " --> pdb=" O GLN C 106 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN C 112 " --> pdb=" O GLN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 190 through 193 Processing helix chain 'C' and resid 199 through 208 removed outlier: 3.617A pdb=" N ALA C 206 " --> pdb=" O ASP C 202 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 207 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 298 through 312 removed outlier: 3.501A pdb=" N ALA C 303 " --> pdb=" O ALA C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 359 removed outlier: 4.196A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE C 335 " --> pdb=" O PRO C 331 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS C 338 " --> pdb=" O LYS C 334 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 339 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 340 " --> pdb=" O SER C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 370 through 386 removed outlier: 3.617A pdb=" N VAL C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY C 378 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 406 removed outlier: 4.223A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 423 removed outlier: 3.705A pdb=" N VAL C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 435 Processing helix chain 'C' and resid 438 through 452 removed outlier: 3.888A pdb=" N LEU C 449 " --> pdb=" O ILE C 445 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 488 removed outlier: 3.574A pdb=" N GLY C 464 " --> pdb=" O GLY C 460 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE C 474 " --> pdb=" O PHE C 470 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA C 477 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 486 " --> pdb=" O VAL C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 496 Processing helix chain 'C' and resid 511 through 535 removed outlier: 3.589A pdb=" N TRP C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 558 removed outlier: 3.581A pdb=" N VAL C 557 " --> pdb=" O ALA C 553 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 558 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 601 Processing helix chain 'C' and resid 633 through 637 Processing helix chain 'C' and resid 639 through 642 removed outlier: 3.608A pdb=" N ASN C 642 " --> pdb=" O GLY C 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 639 through 642' Processing helix chain 'C' and resid 643 through 656 Processing helix chain 'C' and resid 691 through 706 Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.748A pdb=" N LEU C 750 " --> pdb=" O ILE C 746 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP C 754 " --> pdb=" O LEU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 788 Processing helix chain 'C' and resid 802 through 804 No H-bonds generated for 'chain 'C' and resid 802 through 804' Processing helix chain 'C' and resid 836 through 850 removed outlier: 3.663A pdb=" N ALA C 840 " --> pdb=" O SER C 836 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 845 " --> pdb=" O MET C 841 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS C 850 " --> pdb=" O GLN C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 880 removed outlier: 3.681A pdb=" N GLN C 865 " --> pdb=" O GLY C 861 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG C 867 " --> pdb=" O SER C 863 " (cutoff:3.500A) Proline residue: C 874 - end of helix removed outlier: 3.517A pdb=" N ALA C 878 " --> pdb=" O PRO C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 893 Processing helix chain 'C' and resid 895 through 903 removed outlier: 3.894A pdb=" N PHE C 899 " --> pdb=" O TRP C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 919 removed outlier: 3.839A pdb=" N GLY C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 919 " --> pdb=" O ALA C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 956 removed outlier: 4.477A pdb=" N ILE C 945 " --> pdb=" O ASN C 941 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 947 " --> pdb=" O ILE C 943 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 971 Processing helix chain 'C' and resid 971 through 985 Processing helix chain 'C' and resid 986 through 990 Processing helix chain 'C' and resid 996 through 1017 removed outlier: 4.362A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL C1016 " --> pdb=" O VAL C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1033 Proline residue: C1023 - end of helix Processing helix chain 'D' and resid 12 through 23 removed outlier: 3.794A pdb=" N LYS D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 36 Processing helix chain 'D' and resid 49 through 57 Processing helix chain 'D' and resid 62 through 67 Processing helix chain 'D' and resid 68 through 70 No H-bonds generated for 'chain 'D' and resid 68 through 70' Processing helix chain 'D' and resid 82 through 89 Processing helix chain 'D' and resid 92 through 100 removed outlier: 4.137A pdb=" N VAL D 98 " --> pdb=" O GLU D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 122 Processing helix chain 'D' and resid 125 through 134 Processing helix chain 'D' and resid 148 through 157 Processing helix chain 'D' and resid 158 through 165 Processing helix chain 'E' and resid 16 through 23 removed outlier: 3.827A pdb=" N GLU E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG E 23 " --> pdb=" O LEU E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 37 Processing helix chain 'E' and resid 49 through 58 Processing helix chain 'E' and resid 59 through 69 removed outlier: 3.769A pdb=" N VAL E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 91 Processing helix chain 'E' and resid 92 through 101 removed outlier: 4.529A pdb=" N VAL E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 123 removed outlier: 3.568A pdb=" N LEU E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 134 Processing helix chain 'E' and resid 150 through 156 removed outlier: 3.573A pdb=" N ASN E 156 " --> pdb=" O ILE E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 165 removed outlier: 3.651A pdb=" N ILE E 164 " --> pdb=" O ASP E 160 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.966A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 77 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 80 " --> pdb=" O ARG A 818 " (cutoff:3.500A) removed outlier: 12.587A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.966A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 77 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 80 " --> pdb=" O ARG A 818 " (cutoff:3.500A) removed outlier: 12.587A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A 686 " --> pdb=" O PRO A 823 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET A 825 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 684 " --> pdb=" O MET A 825 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 858 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 685 " --> pdb=" O GLY A 856 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.795A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASN A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.795A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 286 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET A 573 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 272 removed outlier: 3.519A pdb=" N GLU A 269 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR A 182 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS A 770 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN A 760 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL A 773 " --> pdb=" O TYR A 758 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TYR A 758 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 235 removed outlier: 5.951A pdb=" N ILE A 235 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE B 731 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 253 removed outlier: 3.826A pdb=" N LYS A 252 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 805 through 812 removed outlier: 4.097A pdb=" N SER C 233 " --> pdb=" O PRO A 725 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 790 through 792 Processing sheet with id=AB1, first strand: chain 'B' and resid 42 through 48 removed outlier: 3.970A pdb=" N THR B 93 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR B 77 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER B 80 " --> pdb=" O ARG B 818 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP B 681 " --> pdb=" O THR B 860 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 174 through 178 removed outlier: 4.170A pdb=" N GLY B 288 " --> pdb=" O PHE B 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 174 through 178 removed outlier: 4.170A pdb=" N GLY B 288 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.915A pdb=" N TYR B 182 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N TYR B 772 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N MET B 184 " --> pdb=" O TYR B 772 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N MET B 774 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE B 186 " --> pdb=" O MET B 774 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN B 760 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL B 773 " --> pdb=" O TYR B 758 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR B 758 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 217 through 219 removed outlier: 4.430A pdb=" N GLY B 217 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER B 233 " --> pdb=" O PHE C 727 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE C 729 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE B 235 " --> pdb=" O ILE C 729 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 790 through 792 Processing sheet with id=AB7, first strand: chain 'C' and resid 128 through 130 removed outlier: 12.794A pdb=" N ARG C 815 " --> pdb=" O GLU C 826 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU C 826 " --> pdb=" O ARG C 815 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU C 817 " --> pdb=" O SER C 824 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP C 681 " --> pdb=" O THR C 860 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 175 through 177 removed outlier: 4.660A pdb=" N ASN C 144 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 175 through 177 removed outlier: 3.564A pdb=" N ALA C 286 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER C 608 " --> pdb=" O SER C 630 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 266 through 272 removed outlier: 3.525A pdb=" N GLU C 269 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N TYR C 182 " --> pdb=" O LYS C 770 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N TYR C 772 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N MET C 184 " --> pdb=" O TYR C 772 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N MET C 774 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE C 186 " --> pdb=" O MET C 774 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN C 760 " --> pdb=" O VAL C 771 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 252 through 253 removed outlier: 3.753A pdb=" N LYS C 252 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 790 through 792 1428 hydrogen bonds defined for protein. 4104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.36 Time building geometry restraints manager: 43.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 26288 1.03 - 1.23: 14 1.23 - 1.42: 10638 1.42 - 1.62: 15455 1.62 - 1.81: 262 Bond restraints: 52657 Sorted by residual: bond pdb=" C MET B 355 " pdb=" O MET B 355 " ideal model delta sigma weight residual 1.236 1.194 0.042 1.29e-02 6.01e+03 1.04e+01 bond pdb=" C ASP E 27 " pdb=" O ASP E 27 " ideal model delta sigma weight residual 1.236 1.195 0.041 1.29e-02 6.01e+03 1.01e+01 bond pdb=" CA SER B 813 " pdb=" CB SER B 813 " ideal model delta sigma weight residual 1.531 1.489 0.042 1.37e-02 5.33e+03 9.49e+00 bond pdb=" N SER B 813 " pdb=" CA SER B 813 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.14e-02 7.69e+03 9.26e+00 bond pdb=" N GLU B 810 " pdb=" CA GLU B 810 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.20e-02 6.94e+03 8.41e+00 ... (remaining 52652 not shown) Histogram of bond angle deviations from ideal: 98.17 - 105.35: 541 105.35 - 112.52: 62075 112.52 - 119.70: 13552 119.70 - 126.88: 19084 126.88 - 134.06: 260 Bond angle restraints: 95512 Sorted by residual: angle pdb=" N ILE D 62 " pdb=" CA ILE D 62 " pdb=" C ILE D 62 " ideal model delta sigma weight residual 111.62 106.40 5.22 7.90e-01 1.60e+00 4.37e+01 angle pdb=" N ASN C 667 " pdb=" CA ASN C 667 " pdb=" C ASN C 667 " ideal model delta sigma weight residual 110.53 103.91 6.62 1.32e+00 5.74e-01 2.51e+01 angle pdb=" C SER B 813 " pdb=" N PRO B 814 " pdb=" CA PRO B 814 " ideal model delta sigma weight residual 119.84 126.06 -6.22 1.25e+00 6.40e-01 2.47e+01 angle pdb=" CA ALA A 232 " pdb=" C ALA A 232 " pdb=" O ALA A 232 " ideal model delta sigma weight residual 121.23 115.98 5.25 1.07e+00 8.73e-01 2.41e+01 angle pdb=" C PHE C 666 " pdb=" CA PHE C 666 " pdb=" CB PHE C 666 " ideal model delta sigma weight residual 109.38 99.61 9.77 2.03e+00 2.43e-01 2.32e+01 ... (remaining 95507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 18658 17.92 - 35.84: 1725 35.84 - 53.76: 310 53.76 - 71.67: 96 71.67 - 89.59: 44 Dihedral angle restraints: 20833 sinusoidal: 9643 harmonic: 11190 Sorted by residual: dihedral pdb=" CA GLN A 830 " pdb=" C GLN A 830 " pdb=" N ALA A 831 " pdb=" CA ALA A 831 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA PHE A 388 " pdb=" C PHE A 388 " pdb=" N SER A 389 " pdb=" CA SER A 389 " ideal model delta harmonic sigma weight residual -180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA PHE C 655 " pdb=" C PHE C 655 " pdb=" N SER C 656 " pdb=" CA SER C 656 " ideal model delta harmonic sigma weight residual 180.00 154.02 25.98 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 20830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3577 0.055 - 0.109: 555 0.109 - 0.163: 77 0.163 - 0.218: 1 0.218 - 0.272: 1 Chirality restraints: 4211 Sorted by residual: chirality pdb=" CA LEU A 219 " pdb=" N LEU A 219 " pdb=" C LEU A 219 " pdb=" CB LEU A 219 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA GLU B 810 " pdb=" N GLU B 810 " pdb=" C GLU B 810 " pdb=" CB GLU B 810 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" CA ILE A 827 " pdb=" N ILE A 827 " pdb=" C ILE A 827 " pdb=" CB ILE A 827 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 4208 not shown) Planarity restraints: 7856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 667 " 0.110 2.00e-02 2.50e+03 1.23e-01 2.28e+02 pdb=" CG ASN C 667 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN C 667 " -0.116 2.00e-02 2.50e+03 pdb=" ND2 ASN C 667 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN C 667 " -0.182 2.00e-02 2.50e+03 pdb="HD22 ASN C 667 " 0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 233 " -0.026 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" N ILE A 234 " 0.086 2.00e-02 2.50e+03 pdb=" CA ILE A 234 " -0.022 2.00e-02 2.50e+03 pdb=" H ILE A 234 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 355 " -0.020 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" N TYR B 356 " 0.064 2.00e-02 2.50e+03 pdb=" CA TYR B 356 " -0.016 2.00e-02 2.50e+03 pdb=" H TYR B 356 " -0.027 2.00e-02 2.50e+03 ... (remaining 7853 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.20: 4109 2.20 - 2.80: 112115 2.80 - 3.40: 141119 3.40 - 4.00: 191041 4.00 - 4.60: 299948 Nonbonded interactions: 748332 Sorted by model distance: nonbonded pdb=" O LEU B 578 " pdb="HD22 ASN B 623 " model vdw 1.605 1.850 nonbonded pdb=" O GLY B 221 " pdb="HH21 ARG C 780 " model vdw 1.609 1.850 nonbonded pdb=" O ALA C 401 " pdb=" H LEU C 404 " model vdw 1.625 1.850 nonbonded pdb=" O GLY C 930 " pdb=" HG1 THR C 934 " model vdw 1.626 1.850 nonbonded pdb="HH11 ARG B 8 " pdb=" OE2 GLU C 893 " model vdw 1.628 1.850 ... (remaining 748327 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 144 or (resid 145 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 146 through 1033)) selection = (chain 'B' and (resid 1 through 355 or (resid 356 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name HD \ 1 or name HD2 or name HE1 or name HE2)) or resid 357 through 666 or (resid 667 a \ nd (name N or name CA or name C or name O or name CB or name CG or name OD1 or n \ ame ND2 or name H or name HA or name HB2 or name HB3)) or resid 668 through 1033 \ )) selection = (chain 'C' and (resid 1 through 144 or (resid 145 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 146 through 355 or (resid 356 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2 or name CE1 or name CE2 or name CZ or name OH or name H or name HA or n \ ame HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2)) or resid 3 \ 57 through 666 or (resid 667 and (name N or name CA or name C or name O or name \ CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name H \ B3)) or resid 668 through 1033)) } ncs_group { reference = (chain 'D' and ((resid 15 and (name N or name CA or name C or name O or name HA2 \ or name HA3)) or resid 16 through 166)) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 134 5.16 5 C 16623 2.51 5 N 4293 2.21 5 O 4825 1.98 5 H 26294 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.760 Extract box with map and model: 9.790 Check model and map are aligned: 0.600 Convert atoms to be neutral: 0.360 Process input model: 140.690 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 26363 Z= 0.333 Angle : 0.720 9.768 35806 Z= 0.439 Chirality : 0.041 0.272 4211 Planarity : 0.004 0.067 4595 Dihedral : 12.693 89.592 9506 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.03 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.11), residues: 3397 helix: -2.75 (0.10), residues: 1749 sheet: -2.32 (0.22), residues: 405 loop : -3.11 (0.14), residues: 1243 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 745 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 739 time to evaluate : 3.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 742 average time/residue: 0.7890 time to fit residues: 906.7834 Evaluate side-chains 447 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 444 time to evaluate : 3.593 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 1.0089 time to fit residues: 9.1455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 286 optimal weight: 0.5980 chunk 256 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 307 optimal weight: 0.7980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 ASN A 747 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN B 733 GLN B 846 GLN C 58 GLN C 255 GLN C 360 GLN C 517 ASN C1000 GLN D 85 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 26363 Z= 0.334 Angle : 0.754 9.458 35806 Z= 0.399 Chirality : 0.047 0.241 4211 Planarity : 0.005 0.099 4595 Dihedral : 5.271 26.885 3608 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.13), residues: 3397 helix: -1.14 (0.12), residues: 1753 sheet: -1.78 (0.23), residues: 403 loop : -2.20 (0.16), residues: 1241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 577 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 516 time to evaluate : 3.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 37 residues processed: 548 average time/residue: 0.7171 time to fit residues: 626.0825 Evaluate side-chains 454 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 417 time to evaluate : 4.025 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 2 residues processed: 37 average time/residue: 0.5409 time to fit residues: 40.5664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 171 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 256 optimal weight: 9.9990 chunk 209 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 308 optimal weight: 2.9990 chunk 333 optimal weight: 8.9990 chunk 274 optimal weight: 3.9990 chunk 305 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 247 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN B 577 GLN C 181 GLN C 605 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 26363 Z= 0.258 Angle : 0.582 7.159 35806 Z= 0.308 Chirality : 0.041 0.166 4211 Planarity : 0.004 0.050 4595 Dihedral : 4.858 24.952 3608 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.14), residues: 3397 helix: -0.43 (0.12), residues: 1773 sheet: -1.56 (0.23), residues: 424 loop : -1.92 (0.17), residues: 1200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 456 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 426 time to evaluate : 3.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 446 average time/residue: 0.7390 time to fit residues: 524.9280 Evaluate side-chains 401 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 383 time to evaluate : 4.131 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 2 residues processed: 18 average time/residue: 0.5835 time to fit residues: 24.3514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 304 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 309 optimal weight: 5.9990 chunk 327 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 ASN C 605 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 26363 Z= 0.294 Angle : 0.612 7.178 35806 Z= 0.320 Chirality : 0.043 0.245 4211 Planarity : 0.004 0.061 4595 Dihedral : 4.836 25.095 3608 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.14), residues: 3397 helix: -0.09 (0.12), residues: 1786 sheet: -1.54 (0.24), residues: 420 loop : -1.75 (0.18), residues: 1191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 445 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 403 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 27 residues processed: 425 average time/residue: 0.7265 time to fit residues: 488.6148 Evaluate side-chains 394 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 367 time to evaluate : 3.238 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 2 residues processed: 27 average time/residue: 0.4752 time to fit residues: 27.4560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 272 optimal weight: 0.3980 chunk 186 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 243 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 279 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 294 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 846 GLN C 605 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 26363 Z= 0.212 Angle : 0.548 6.515 35806 Z= 0.287 Chirality : 0.040 0.160 4211 Planarity : 0.003 0.045 4595 Dihedral : 4.601 24.071 3608 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 3397 helix: 0.24 (0.13), residues: 1806 sheet: -1.43 (0.24), residues: 428 loop : -1.60 (0.18), residues: 1163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 414 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 387 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 18 residues processed: 406 average time/residue: 0.7196 time to fit residues: 465.7497 Evaluate side-chains 376 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 358 time to evaluate : 3.210 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 2 residues processed: 18 average time/residue: 0.4643 time to fit residues: 19.4889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 110 optimal weight: 2.9990 chunk 295 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 192 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 327 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.6395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 26363 Z= 0.241 Angle : 0.555 6.672 35806 Z= 0.289 Chirality : 0.041 0.162 4211 Planarity : 0.003 0.052 4595 Dihedral : 4.533 23.686 3608 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.15), residues: 3397 helix: 0.42 (0.13), residues: 1800 sheet: -1.42 (0.24), residues: 420 loop : -1.53 (0.18), residues: 1177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 406 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 381 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 395 average time/residue: 0.6978 time to fit residues: 439.4546 Evaluate side-chains 365 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 351 time to evaluate : 3.174 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.4724 time to fit residues: 16.1421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 316 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 276 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 326 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN C 415 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.6768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 26363 Z= 0.308 Angle : 0.582 6.787 35806 Z= 0.306 Chirality : 0.042 0.185 4211 Planarity : 0.004 0.063 4595 Dihedral : 4.599 23.983 3608 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.15), residues: 3397 helix: 0.42 (0.13), residues: 1812 sheet: -1.40 (0.24), residues: 419 loop : -1.51 (0.18), residues: 1166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 379 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 361 time to evaluate : 3.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 371 average time/residue: 0.7278 time to fit residues: 425.6691 Evaluate side-chains 357 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 346 time to evaluate : 3.190 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4891 time to fit residues: 13.6927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 202 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 256 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.6973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 26363 Z= 0.267 Angle : 0.561 6.884 35806 Z= 0.293 Chirality : 0.041 0.160 4211 Planarity : 0.004 0.062 4595 Dihedral : 4.538 23.694 3608 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3397 helix: 0.55 (0.13), residues: 1811 sheet: -1.37 (0.24), residues: 417 loop : -1.38 (0.18), residues: 1169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 379 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 363 time to evaluate : 3.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 373 average time/residue: 0.7308 time to fit residues: 430.7712 Evaluate side-chains 361 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 349 time to evaluate : 3.178 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.5076 time to fit residues: 14.8148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 297 optimal weight: 0.9980 chunk 313 optimal weight: 4.9990 chunk 285 optimal weight: 0.9980 chunk 304 optimal weight: 3.9990 chunk 312 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 239 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 287 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 GLN C 415 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 26363 Z= 0.164 Angle : 0.526 6.386 35806 Z= 0.273 Chirality : 0.040 0.158 4211 Planarity : 0.003 0.050 4595 Dihedral : 4.364 23.078 3608 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3397 helix: 0.75 (0.13), residues: 1805 sheet: -1.20 (0.24), residues: 419 loop : -1.22 (0.18), residues: 1173 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 382 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 373 time to evaluate : 3.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 378 average time/residue: 0.7538 time to fit residues: 455.3331 Evaluate side-chains 367 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 361 time to evaluate : 3.256 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.5240 time to fit residues: 9.8548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 303 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 321 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 chunk 337 optimal weight: 4.9990 chunk 310 optimal weight: 6.9990 chunk 268 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN C 120 GLN C 124 GLN C 151 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.7264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 26363 Z= 0.306 Angle : 0.575 6.754 35806 Z= 0.301 Chirality : 0.042 0.155 4211 Planarity : 0.004 0.063 4595 Dihedral : 4.491 23.421 3608 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3397 helix: 0.68 (0.13), residues: 1816 sheet: -1.39 (0.24), residues: 428 loop : -1.22 (0.18), residues: 1153 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 364 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 359 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 361 average time/residue: 0.7261 time to fit residues: 414.8118 Evaluate side-chains 357 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 353 time to evaluate : 3.208 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.5697 time to fit residues: 7.8493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 164 optimal weight: 5.9990 chunk 213 optimal weight: 0.5980 chunk 286 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 247 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 276 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.111800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.090976 restraints weight = 103515.467| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.78 r_work: 0.2837 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.7307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 26363 Z= 0.158 Angle : 0.524 6.417 35806 Z= 0.272 Chirality : 0.040 0.158 4211 Planarity : 0.003 0.054 4595 Dihedral : 4.322 22.723 3608 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3397 helix: 0.92 (0.13), residues: 1809 sheet: -1.19 (0.24), residues: 421 loop : -1.10 (0.18), residues: 1167 =============================================================================== Job complete usr+sys time: 10188.45 seconds wall clock time: 177 minutes 5.89 seconds (10625.89 seconds total)