Starting phenix.real_space_refine (version: dev) on Wed Dec 14 18:22:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va2_8651/12_2022/5va2_8651.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va2_8651/12_2022/5va2_8651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va2_8651/12_2022/5va2_8651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va2_8651/12_2022/5va2_8651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va2_8651/12_2022/5va2_8651.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va2_8651/12_2022/5va2_8651.pdb" } resolution = 3.8 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= 0.436 sd= 0.853 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 "B ARG 4": "NH1" <-> "NH2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B ARG 488": "NH1" <-> "NH2" Residue "B ARG 534": "NH1" <-> "NH2" Residue "B ARG 541": "NH1" <-> "NH2" Residue "B ARG 672": "NH1" <-> "NH2" Residue "B GLU 722": "OE1" <-> "OE2" Residue "B TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 823": "NH1" <-> "NH2" Residue "A ARG 4": "NH1" <-> "NH2" Residue "A ARG 5": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 534": "NH1" <-> "NH2" Residue "A ARG 541": "NH1" <-> "NH2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 823": "NH1" <-> "NH2" Residue "C ARG 4": "NH1" <-> "NH2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C ARG 488": "NH1" <-> "NH2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C ARG 541": "NH1" <-> "NH2" Residue "C ARG 672": "NH1" <-> "NH2" Residue "C GLU 722": "OE1" <-> "OE2" Residue "C TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 823": "NH1" <-> "NH2" Residue "D ARG 4": "NH1" <-> "NH2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D ARG 488": "NH1" <-> "NH2" Residue "D ARG 534": "NH1" <-> "NH2" Residue "D ARG 541": "NH1" <-> "NH2" Residue "D ARG 672": "NH1" <-> "NH2" Residue "D GLU 722": "OE1" <-> "OE2" Residue "D TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 823": "NH1" <-> "NH2" Residue "E ARG 4": "NH1" <-> "NH2" Residue "E ARG 5": "NH1" <-> "NH2" Residue "E ARG 488": "NH1" <-> "NH2" Residue "E ARG 534": "NH1" <-> "NH2" Residue "E ARG 541": "NH1" <-> "NH2" Residue "E ARG 672": "NH1" <-> "NH2" Residue "E GLU 722": "OE1" <-> "OE2" Residue "E TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 823": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 21970 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4394 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 536} Chain breaks: 5 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4394 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 536} Chain breaks: 5 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "C" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4394 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 536} Chain breaks: 5 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4394 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 536} Chain breaks: 5 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "E" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4394 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 536} Chain breaks: 5 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Time building chain proxies: 12.22, per 1000 atoms: 0.56 Number of scatterers: 21970 At special positions: 0 Unit cell: (173.061, 197.129, 172.174, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 3770 8.00 N 3745 7.00 C 14320 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: 8.11 Conformation dependent library (CDL) restraints added in 3.1 seconds 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5230 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 15 sheets defined 59.5% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 13 through 26 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.684A pdb=" N CYS A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.696A pdb=" N GLN A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 433 removed outlier: 3.967A pdb=" N VAL A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Proline residue: A 426 - end of helix removed outlier: 3.579A pdb=" N PHE A 431 " --> pdb=" O TYR A 427 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 473 removed outlier: 4.317A pdb=" N LEU A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 459 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 498 removed outlier: 3.993A pdb=" N HIS A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE A 498 " --> pdb=" O PHE A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 505 removed outlier: 3.792A pdb=" N VAL A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.688A pdb=" N ALA A 527 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 538 through 543 removed outlier: 4.030A pdb=" N TYR A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 543' Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 547 through 575 removed outlier: 4.146A pdb=" N PHE A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 558 " --> pdb=" O MET A 554 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 572 " --> pdb=" O TRP A 568 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 593 removed outlier: 3.630A pdb=" N ASN A 588 " --> pdb=" O GLY A 584 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 592 " --> pdb=" O ASN A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 623 removed outlier: 3.539A pdb=" N ALA A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 667 removed outlier: 3.655A pdb=" N ALA A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 688 removed outlier: 3.615A pdb=" N HIS A 674 " --> pdb=" O THR A 670 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 709 removed outlier: 3.880A pdb=" N ARG A 696 " --> pdb=" O PRO A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 Processing helix chain 'A' and resid 721 through 733 Processing helix chain 'A' and resid 733 through 738 Processing helix chain 'A' and resid 740 through 745 removed outlier: 3.767A pdb=" N GLY A 745 " --> pdb=" O LYS A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 758 removed outlier: 3.614A pdb=" N ARG A 752 " --> pdb=" O LYS A 748 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 845 removed outlier: 3.830A pdb=" N GLU A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 841 " --> pdb=" O ASP A 837 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET A 844 " --> pdb=" O GLU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 856 Processing helix chain 'B' and resid 13 through 26 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.684A pdb=" N CYS B 49 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 75 through 89 removed outlier: 3.696A pdb=" N GLN B 81 " --> pdb=" O ARG B 77 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 433 removed outlier: 3.968A pdb=" N VAL B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Proline residue: B 426 - end of helix removed outlier: 3.579A pdb=" N PHE B 431 " --> pdb=" O TYR B 427 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 473 removed outlier: 4.317A pdb=" N LEU B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 498 removed outlier: 3.993A pdb=" N HIS B 492 " --> pdb=" O ARG B 488 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE B 498 " --> pdb=" O PHE B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 505 removed outlier: 3.792A pdb=" N VAL B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 531 removed outlier: 3.687A pdb=" N ALA B 527 " --> pdb=" O LEU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 537 Processing helix chain 'B' and resid 538 through 543 removed outlier: 4.030A pdb=" N TYR B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 538 through 543' Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 547 through 575 removed outlier: 4.146A pdb=" N PHE B 551 " --> pdb=" O ALA B 547 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 558 " --> pdb=" O MET B 554 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY B 572 " --> pdb=" O TRP B 568 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU B 575 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 593 removed outlier: 3.629A pdb=" N ASN B 588 " --> pdb=" O GLY B 584 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 592 " --> pdb=" O ASN B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 623 removed outlier: 3.540A pdb=" N ALA B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 667 removed outlier: 3.655A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE B 656 " --> pdb=" O TYR B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 688 removed outlier: 3.615A pdb=" N HIS B 674 " --> pdb=" O THR B 670 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 709 removed outlier: 3.880A pdb=" N ARG B 696 " --> pdb=" O PRO B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 Processing helix chain 'B' and resid 721 through 733 Processing helix chain 'B' and resid 733 through 738 Processing helix chain 'B' and resid 740 through 745 removed outlier: 3.767A pdb=" N GLY B 745 " --> pdb=" O LYS B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 758 removed outlier: 3.614A pdb=" N ARG B 752 " --> pdb=" O LYS B 748 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 753 " --> pdb=" O GLY B 749 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 845 removed outlier: 3.830A pdb=" N GLU B 840 " --> pdb=" O ASP B 836 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 841 " --> pdb=" O ASP B 837 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET B 844 " --> pdb=" O GLU B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 856 Processing helix chain 'C' and resid 13 through 26 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.684A pdb=" N CYS C 49 " --> pdb=" O ASN C 45 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 75 through 89 removed outlier: 3.696A pdb=" N GLN C 81 " --> pdb=" O ARG C 77 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 433 removed outlier: 3.967A pdb=" N VAL C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) Proline residue: C 426 - end of helix removed outlier: 3.579A pdb=" N PHE C 431 " --> pdb=" O TYR C 427 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU C 432 " --> pdb=" O SER C 428 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU C 433 " --> pdb=" O ALA C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 473 removed outlier: 4.317A pdb=" N LEU C 457 " --> pdb=" O ALA C 453 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 459 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET C 462 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE C 464 " --> pdb=" O ASP C 460 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE C 467 " --> pdb=" O PHE C 463 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU C 468 " --> pdb=" O ILE C 464 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 471 " --> pdb=" O ILE C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 498 removed outlier: 3.993A pdb=" N HIS C 492 " --> pdb=" O ARG C 488 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE C 498 " --> pdb=" O PHE C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 505 removed outlier: 3.792A pdb=" N VAL C 503 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 505 " --> pdb=" O ASP C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 531 removed outlier: 3.688A pdb=" N ALA C 527 " --> pdb=" O LEU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 537 Processing helix chain 'C' and resid 538 through 543 removed outlier: 4.030A pdb=" N TYR C 542 " --> pdb=" O LYS C 538 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 543 " --> pdb=" O LEU C 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 538 through 543' Processing helix chain 'C' and resid 544 through 546 No H-bonds generated for 'chain 'C' and resid 544 through 546' Processing helix chain 'C' and resid 547 through 575 removed outlier: 4.146A pdb=" N PHE C 551 " --> pdb=" O ALA C 547 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 558 " --> pdb=" O MET C 554 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY C 572 " --> pdb=" O TRP C 568 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU C 575 " --> pdb=" O ILE C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 593 removed outlier: 3.630A pdb=" N ASN C 588 " --> pdb=" O GLY C 584 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP C 591 " --> pdb=" O HIS C 587 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN C 592 " --> pdb=" O ASN C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 623 removed outlier: 3.539A pdb=" N ALA C 614 " --> pdb=" O LYS C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 667 removed outlier: 3.655A pdb=" N ALA C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE C 656 " --> pdb=" O TYR C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 688 removed outlier: 3.615A pdb=" N HIS C 674 " --> pdb=" O THR C 670 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 709 removed outlier: 3.880A pdb=" N ARG C 696 " --> pdb=" O PRO C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 718 Processing helix chain 'C' and resid 721 through 733 Processing helix chain 'C' and resid 733 through 738 Processing helix chain 'C' and resid 740 through 745 removed outlier: 3.767A pdb=" N GLY C 745 " --> pdb=" O LYS C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 758 removed outlier: 3.614A pdb=" N ARG C 752 " --> pdb=" O LYS C 748 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 753 " --> pdb=" O GLY C 749 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 845 removed outlier: 3.830A pdb=" N GLU C 840 " --> pdb=" O ASP C 836 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 841 " --> pdb=" O ASP C 837 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET C 844 " --> pdb=" O GLU C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 856 Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 45 through 53 removed outlier: 3.684A pdb=" N CYS D 49 " --> pdb=" O ASN D 45 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 75 through 89 removed outlier: 3.696A pdb=" N GLN D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 433 removed outlier: 3.967A pdb=" N VAL D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 415 " --> pdb=" O ASP D 411 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR D 420 " --> pdb=" O LEU D 416 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR D 421 " --> pdb=" O LEU D 417 " (cutoff:3.500A) Proline residue: D 426 - end of helix removed outlier: 3.579A pdb=" N PHE D 431 " --> pdb=" O TYR D 427 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 432 " --> pdb=" O SER D 428 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU D 433 " --> pdb=" O ALA D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 473 removed outlier: 4.317A pdb=" N LEU D 457 " --> pdb=" O ALA D 453 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE D 458 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL D 459 " --> pdb=" O VAL D 455 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE D 463 " --> pdb=" O VAL D 459 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE D 464 " --> pdb=" O ASP D 460 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE D 467 " --> pdb=" O PHE D 463 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU D 468 " --> pdb=" O ILE D 464 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 498 removed outlier: 3.993A pdb=" N HIS D 492 " --> pdb=" O ARG D 488 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE D 498 " --> pdb=" O PHE D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 505 removed outlier: 3.792A pdb=" N VAL D 503 " --> pdb=" O LEU D 499 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 505 " --> pdb=" O ASP D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 531 removed outlier: 3.688A pdb=" N ALA D 527 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 537 Processing helix chain 'D' and resid 538 through 543 removed outlier: 4.030A pdb=" N TYR D 542 " --> pdb=" O LYS D 538 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 543 " --> pdb=" O LEU D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 538 through 543' Processing helix chain 'D' and resid 544 through 546 No H-bonds generated for 'chain 'D' and resid 544 through 546' Processing helix chain 'D' and resid 547 through 575 removed outlier: 4.146A pdb=" N PHE D 551 " --> pdb=" O ALA D 547 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 558 " --> pdb=" O MET D 554 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY D 572 " --> pdb=" O TRP D 568 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU D 575 " --> pdb=" O ILE D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 593 removed outlier: 3.630A pdb=" N ASN D 588 " --> pdb=" O GLY D 584 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN D 592 " --> pdb=" O ASN D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 623 removed outlier: 3.539A pdb=" N ALA D 614 " --> pdb=" O LYS D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 667 removed outlier: 3.655A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE D 656 " --> pdb=" O TYR D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 688 removed outlier: 3.615A pdb=" N HIS D 674 " --> pdb=" O THR D 670 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 709 removed outlier: 3.880A pdb=" N ARG D 696 " --> pdb=" O PRO D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 718 Processing helix chain 'D' and resid 721 through 733 Processing helix chain 'D' and resid 733 through 738 Processing helix chain 'D' and resid 740 through 745 removed outlier: 3.767A pdb=" N GLY D 745 " --> pdb=" O LYS D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 758 removed outlier: 3.614A pdb=" N ARG D 752 " --> pdb=" O LYS D 748 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D 753 " --> pdb=" O GLY D 749 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS D 757 " --> pdb=" O ALA D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 845 removed outlier: 3.830A pdb=" N GLU D 840 " --> pdb=" O ASP D 836 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL D 841 " --> pdb=" O ASP D 837 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET D 844 " --> pdb=" O GLU D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 856 Processing helix chain 'E' and resid 13 through 26 Processing helix chain 'E' and resid 45 through 53 removed outlier: 3.684A pdb=" N CYS E 49 " --> pdb=" O ASN E 45 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'E' and resid 75 through 89 removed outlier: 3.696A pdb=" N GLN E 81 " --> pdb=" O ARG E 77 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 433 removed outlier: 3.967A pdb=" N VAL E 409 " --> pdb=" O PRO E 405 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 415 " --> pdb=" O ASP E 411 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR E 420 " --> pdb=" O LEU E 416 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR E 421 " --> pdb=" O LEU E 417 " (cutoff:3.500A) Proline residue: E 426 - end of helix removed outlier: 3.579A pdb=" N PHE E 431 " --> pdb=" O TYR E 427 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU E 432 " --> pdb=" O SER E 428 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU E 433 " --> pdb=" O ALA E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 473 removed outlier: 4.317A pdb=" N LEU E 457 " --> pdb=" O ALA E 453 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE E 458 " --> pdb=" O VAL E 454 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL E 459 " --> pdb=" O VAL E 455 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET E 462 " --> pdb=" O ILE E 458 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE E 463 " --> pdb=" O VAL E 459 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE E 464 " --> pdb=" O ASP E 460 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE E 467 " --> pdb=" O PHE E 463 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU E 468 " --> pdb=" O ILE E 464 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE E 471 " --> pdb=" O ILE E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 498 removed outlier: 3.993A pdb=" N HIS E 492 " --> pdb=" O ARG E 488 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE E 498 " --> pdb=" O PHE E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 505 removed outlier: 3.792A pdb=" N VAL E 503 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA E 505 " --> pdb=" O ASP E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 531 removed outlier: 3.688A pdb=" N ALA E 527 " --> pdb=" O LEU E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 537 Processing helix chain 'E' and resid 538 through 543 removed outlier: 4.030A pdb=" N TYR E 542 " --> pdb=" O LYS E 538 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER E 543 " --> pdb=" O LEU E 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 538 through 543' Processing helix chain 'E' and resid 544 through 546 No H-bonds generated for 'chain 'E' and resid 544 through 546' Processing helix chain 'E' and resid 547 through 575 removed outlier: 4.146A pdb=" N PHE E 551 " --> pdb=" O ALA E 547 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA E 558 " --> pdb=" O MET E 554 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY E 572 " --> pdb=" O TRP E 568 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU E 575 " --> pdb=" O ILE E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 593 removed outlier: 3.630A pdb=" N ASN E 588 " --> pdb=" O GLY E 584 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP E 591 " --> pdb=" O HIS E 587 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN E 592 " --> pdb=" O ASN E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 623 removed outlier: 3.539A pdb=" N ALA E 614 " --> pdb=" O LYS E 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 667 removed outlier: 3.655A pdb=" N ALA E 653 " --> pdb=" O SER E 649 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE E 656 " --> pdb=" O TYR E 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 688 removed outlier: 3.615A pdb=" N HIS E 674 " --> pdb=" O THR E 670 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR E 675 " --> pdb=" O ALA E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 690 through 709 removed outlier: 3.880A pdb=" N ARG E 696 " --> pdb=" O PRO E 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 712 through 718 Processing helix chain 'E' and resid 721 through 733 Processing helix chain 'E' and resid 733 through 738 Processing helix chain 'E' and resid 740 through 745 removed outlier: 3.767A pdb=" N GLY E 745 " --> pdb=" O LYS E 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 758 removed outlier: 3.614A pdb=" N ARG E 752 " --> pdb=" O LYS E 748 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA E 753 " --> pdb=" O GLY E 749 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS E 757 " --> pdb=" O ALA E 753 " (cutoff:3.500A) Processing helix chain 'E' and resid 835 through 845 removed outlier: 3.830A pdb=" N GLU E 840 " --> pdb=" O ASP E 836 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL E 841 " --> pdb=" O ASP E 837 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET E 844 " --> pdb=" O GLU E 840 " (cutoff:3.500A) Processing helix chain 'E' and resid 851 through 856 Processing sheet with id= 1, first strand: chain 'A' and resid 41 through 44 removed outlier: 7.182A pdb=" N VAL A 41 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASN A 33 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A 43 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET A 124 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 115 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 126 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 113 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 106 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE A 98 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS A 108 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE A 96 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 112 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG A 92 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 803 through 805 removed outlier: 3.706A pdb=" N ASP A 803 " --> pdb=" O ILE A 782 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 805 " --> pdb=" O TYR A 780 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 779 " --> pdb=" O ILE A 833 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.232A pdb=" N ILE A 787 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A 798 " --> pdb=" O ILE A 787 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 789 " --> pdb=" O VAL A 796 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 41 through 44 removed outlier: 7.182A pdb=" N VAL B 41 " --> pdb=" O ASN B 33 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASN B 33 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR B 43 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET B 124 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 115 " --> pdb=" O MET B 124 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 126 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 113 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 106 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE B 98 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS B 108 " --> pdb=" O ILE B 96 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE B 96 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 112 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG B 92 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 803 through 805 removed outlier: 3.706A pdb=" N ASP B 803 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 805 " --> pdb=" O TYR B 780 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 779 " --> pdb=" O ILE B 833 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 787 through 790 removed outlier: 6.232A pdb=" N ILE B 787 " --> pdb=" O ILE B 798 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE B 798 " --> pdb=" O ILE B 787 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 789 " --> pdb=" O VAL B 796 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 41 through 44 removed outlier: 7.182A pdb=" N VAL C 41 " --> pdb=" O ASN C 33 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASN C 33 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR C 43 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET C 124 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 115 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE C 126 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL C 113 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE C 106 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE C 98 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS C 108 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE C 96 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 112 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG C 92 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 803 through 805 removed outlier: 3.706A pdb=" N ASP C 803 " --> pdb=" O ILE C 782 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE C 805 " --> pdb=" O TYR C 780 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 779 " --> pdb=" O ILE C 833 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 787 through 790 removed outlier: 6.232A pdb=" N ILE C 787 " --> pdb=" O ILE C 798 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE C 798 " --> pdb=" O ILE C 787 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE C 789 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 41 through 44 removed outlier: 7.182A pdb=" N VAL D 41 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASN D 33 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR D 43 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET D 124 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL D 115 " --> pdb=" O MET D 124 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE D 126 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D 113 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE D 106 " --> pdb=" O PHE D 98 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE D 98 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS D 108 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE D 96 " --> pdb=" O CYS D 108 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL D 112 " --> pdb=" O ARG D 92 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG D 92 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 803 through 805 removed outlier: 3.706A pdb=" N ASP D 803 " --> pdb=" O ILE D 782 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 805 " --> pdb=" O TYR D 780 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 779 " --> pdb=" O ILE D 833 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 787 through 790 removed outlier: 6.232A pdb=" N ILE D 787 " --> pdb=" O ILE D 798 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE D 798 " --> pdb=" O ILE D 787 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE D 789 " --> pdb=" O VAL D 796 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 41 through 44 removed outlier: 7.182A pdb=" N VAL E 41 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASN E 33 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR E 43 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET E 124 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL E 115 " --> pdb=" O MET E 124 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE E 126 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL E 113 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE E 106 " --> pdb=" O PHE E 98 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE E 98 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS E 108 " --> pdb=" O ILE E 96 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE E 96 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL E 112 " --> pdb=" O ARG E 92 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG E 92 " --> pdb=" O VAL E 112 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 803 through 805 removed outlier: 3.706A pdb=" N ASP E 803 " --> pdb=" O ILE E 782 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE E 805 " --> pdb=" O TYR E 780 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU E 779 " --> pdb=" O ILE E 833 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 787 through 790 removed outlier: 6.232A pdb=" N ILE E 787 " --> pdb=" O ILE E 798 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE E 798 " --> pdb=" O ILE E 787 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE E 789 " --> pdb=" O VAL E 796 " (cutoff:3.500A) 980 hydrogen bonds defined for protein. 2850 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: 6.43 Time building geometry restraints manager: 8.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6865 1.34 - 1.46: 2906 1.46 - 1.58: 12539 1.58 - 1.69: 0 1.69 - 1.81: 190 Bond restraints: 22500 Sorted by residual: bond pdb=" CA PRO C 764 " pdb=" C PRO C 764 " ideal model delta sigma weight residual 1.517 1.542 -0.025 9.30e-03 1.16e+04 7.32e+00 bond pdb=" CA PRO E 764 " pdb=" C PRO E 764 " ideal model delta sigma weight residual 1.517 1.542 -0.025 9.30e-03 1.16e+04 7.32e+00 bond pdb=" CA PRO A 764 " pdb=" C PRO A 764 " ideal model delta sigma weight residual 1.517 1.542 -0.025 9.30e-03 1.16e+04 7.32e+00 bond pdb=" CA PRO D 764 " pdb=" C PRO D 764 " ideal model delta sigma weight residual 1.517 1.542 -0.025 9.30e-03 1.16e+04 7.32e+00 bond pdb=" CA PRO B 764 " pdb=" C PRO B 764 " ideal model delta sigma weight residual 1.517 1.542 -0.025 9.30e-03 1.16e+04 7.21e+00 ... (remaining 22495 not shown) Histogram of bond angle deviations from ideal: 100.88 - 107.50: 790 107.50 - 114.12: 12271 114.12 - 120.74: 9291 120.74 - 127.36: 7953 127.36 - 133.98: 235 Bond angle restraints: 30540 Sorted by residual: angle pdb=" C VAL B 8 " pdb=" CA VAL B 8 " pdb=" CB VAL B 8 " ideal model delta sigma weight residual 111.74 107.31 4.43 9.40e-01 1.13e+00 2.22e+01 angle pdb=" C VAL C 8 " pdb=" CA VAL C 8 " pdb=" CB VAL C 8 " ideal model delta sigma weight residual 111.74 107.32 4.42 9.40e-01 1.13e+00 2.21e+01 angle pdb=" C VAL E 8 " pdb=" CA VAL E 8 " pdb=" CB VAL E 8 " ideal model delta sigma weight residual 111.74 107.32 4.42 9.40e-01 1.13e+00 2.21e+01 angle pdb=" C VAL A 8 " pdb=" CA VAL A 8 " pdb=" CB VAL A 8 " ideal model delta sigma weight residual 111.74 107.32 4.42 9.40e-01 1.13e+00 2.21e+01 angle pdb=" C VAL D 8 " pdb=" CA VAL D 8 " pdb=" CB VAL D 8 " ideal model delta sigma weight residual 111.74 107.32 4.42 9.40e-01 1.13e+00 2.21e+01 ... (remaining 30535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.46: 11405 12.46 - 24.92: 1310 24.92 - 37.39: 310 37.39 - 49.85: 115 49.85 - 62.31: 35 Dihedral angle restraints: 13175 sinusoidal: 5070 harmonic: 8105 Sorted by residual: dihedral pdb=" CA GLY B 628 " pdb=" C GLY B 628 " pdb=" N ASN B 629 " pdb=" CA ASN B 629 " ideal model delta harmonic sigma weight residual 180.00 161.98 18.02 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA GLY E 628 " pdb=" C GLY E 628 " pdb=" N ASN E 629 " pdb=" CA ASN E 629 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA GLY C 628 " pdb=" C GLY C 628 " pdb=" N ASN C 629 " pdb=" CA ASN C 629 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 13172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2317 0.052 - 0.104: 763 0.104 - 0.156: 300 0.156 - 0.208: 95 0.208 - 0.260: 10 Chirality restraints: 3485 Sorted by residual: chirality pdb=" CA ILE E 593 " pdb=" N ILE E 593 " pdb=" C ILE E 593 " pdb=" CB ILE E 593 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ILE D 593 " pdb=" N ILE D 593 " pdb=" C ILE D 593 " pdb=" CB ILE D 593 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ILE C 593 " pdb=" N ILE C 593 " pdb=" C ILE C 593 " pdb=" CB ILE C 593 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 3482 not shown) Planarity restraints: 3830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 113 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 114 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 114 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 114 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 113 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO E 114 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 114 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 114 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 113 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO D 114 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 114 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 114 " -0.019 5.00e-02 4.00e+02 ... (remaining 3827 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 35 2.27 - 2.92: 8082 2.92 - 3.58: 29877 3.58 - 4.24: 45852 4.24 - 4.90: 80776 Nonbonded interactions: 164622 Sorted by model distance: nonbonded pdb=" NH1 ARG D 752 " pdb=" CD2 HIS E 771 " model vdw 1.607 3.340 nonbonded pdb=" NH1 ARG C 752 " pdb=" CD2 HIS D 771 " model vdw 1.607 3.340 nonbonded pdb=" CD2 HIS A 771 " pdb=" NH1 ARG E 752 " model vdw 1.607 3.340 nonbonded pdb=" NH1 ARG A 752 " pdb=" CD2 HIS C 771 " model vdw 1.607 3.340 nonbonded pdb=" NH1 ARG C 752 " pdb=" CG HIS D 771 " model vdw 1.799 3.340 ... (remaining 164617 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' 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: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 14320 2.51 5 N 3745 2.21 5 O 3770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.080 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: 6.340 Check model and map are aligned: 0.330 Convert atoms to be neutral: 0.180 Process input model: 53.460 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5761 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 : 0.008 0.045 22500 Z= 0.514 Angle : 1.081 9.371 30540 Z= 0.725 Chirality : 0.064 0.260 3485 Planarity : 0.004 0.034 3830 Dihedral : 12.468 62.311 7945 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 1.65 % Allowed : 7.69 % Favored : 90.66 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.13), residues: 2730 helix: -2.20 (0.10), residues: 1380 sheet: -4.06 (0.27), residues: 160 loop : -2.67 (0.16), residues: 1190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 905 time to evaluate : 2.669 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 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: 25 outliers final: 4 residues processed: 926 average time/residue: 0.3564 time to fit residues: 494.8622 Evaluate side-chains 561 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 557 time to evaluate : 2.732 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2062 time to fit residues: 5.2966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 8.9990 chunk 208 optimal weight: 0.0980 chunk 115 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 249 optimal weight: 0.0370 overall best weight: 2.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 470 ASN A 691 ASN A 834 HIS C 12 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN C 691 ASN D 12 ASN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 470 ASN D 676 GLN D 691 ASN D 834 HIS E 12 ASN E 470 ASN E 691 ASN E 834 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5930 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 22500 Z= 0.218 Angle : 0.814 9.921 30540 Z= 0.401 Chirality : 0.046 0.258 3485 Planarity : 0.005 0.043 3830 Dihedral : 5.174 21.136 3025 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.73 % Allowed : 5.20 % Favored : 94.07 % Rotamer Outliers : 3.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.15), residues: 2730 helix: -0.90 (0.12), residues: 1490 sheet: -2.59 (0.32), residues: 165 loop : -2.10 (0.19), residues: 1075 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 602 time to evaluate : 2.646 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 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: 90 outliers final: 46 residues processed: 664 average time/residue: 0.3223 time to fit residues: 328.8253 Evaluate side-chains 538 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 492 time to evaluate : 2.817 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.2191 time to fit residues: 21.3230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 138 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 68 optimal weight: 30.0000 chunk 250 optimal weight: 20.0000 chunk 270 optimal weight: 2.9990 chunk 222 optimal weight: 20.0000 chunk 248 optimal weight: 30.0000 chunk 85 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 810 ASN B 834 HIS A 12 ASN ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 562 HIS A 629 ASN A 664 GLN A 688 GLN A 709 ASN C 12 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 664 GLN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS ** C 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 61 GLN D 70 HIS D 664 GLN D 739 HIS ** D 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 70 HIS ** E 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 664 GLN E 688 GLN ** E 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 22500 Z= 0.219 Angle : 0.744 13.075 30540 Z= 0.367 Chirality : 0.045 0.246 3485 Planarity : 0.004 0.037 3830 Dihedral : 4.836 18.079 3025 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.70 % Allowed : 4.69 % Favored : 94.62 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.15), residues: 2730 helix: -0.45 (0.13), residues: 1515 sheet: -2.09 (0.31), residues: 205 loop : -1.76 (0.20), residues: 1010 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 511 time to evaluate : 2.578 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 outliers start: 72 outliers final: 33 residues processed: 559 average time/residue: 0.3057 time to fit residues: 268.8770 Evaluate side-chains 484 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 451 time to evaluate : 2.503 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1858 time to fit residues: 15.0568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 247 optimal weight: 20.0000 chunk 188 optimal weight: 8.9990 chunk 129 optimal weight: 40.0000 chunk 27 optimal weight: 30.0000 chunk 119 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 265 optimal weight: 20.0000 chunk 131 optimal weight: 40.0000 chunk 237 optimal weight: 30.0000 chunk 71 optimal weight: 2.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 739 HIS A 70 HIS A 658 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS C 562 HIS C 629 ASN C 658 ASN C 691 ASN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 HIS C 834 HIS C 851 HIS D 75 GLN D 629 ASN D 658 ASN D 762 HIS ** D 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 HIS E 75 GLN ** E 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 629 ASN E 658 ASN E 691 ASN ** E 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 834 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 22500 Z= 0.196 Angle : 0.705 13.627 30540 Z= 0.346 Chirality : 0.043 0.162 3485 Planarity : 0.004 0.055 3830 Dihedral : 4.600 18.468 3025 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.66 % Allowed : 4.18 % Favored : 95.16 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.16), residues: 2730 helix: -0.29 (0.13), residues: 1515 sheet: -1.02 (0.36), residues: 195 loop : -1.71 (0.19), residues: 1020 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 506 time to evaluate : 2.520 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 outliers start: 62 outliers final: 28 residues processed: 545 average time/residue: 0.2905 time to fit residues: 254.1908 Evaluate side-chains 486 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 458 time to evaluate : 2.633 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1905 time to fit residues: 13.5024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 221 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 3 optimal weight: 50.0000 chunk 197 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 0 optimal weight: 90.0000 chunk 135 optimal weight: 30.0000 chunk 238 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 HIS ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 HIS E 691 ASN E 762 HIS E 851 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6077 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 22500 Z= 0.190 Angle : 0.703 13.579 30540 Z= 0.344 Chirality : 0.044 0.233 3485 Planarity : 0.004 0.039 3830 Dihedral : 4.507 19.582 3025 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.20 % Favored : 94.32 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.16), residues: 2730 helix: -0.17 (0.13), residues: 1515 sheet: -0.57 (0.38), residues: 190 loop : -1.58 (0.19), residues: 1025 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 496 time to evaluate : 3.092 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 outliers start: 41 outliers final: 20 residues processed: 519 average time/residue: 0.2898 time to fit residues: 242.8857 Evaluate side-chains 483 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 463 time to evaluate : 2.534 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2115 time to fit residues: 10.9396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 89 optimal weight: 9.9990 chunk 239 optimal weight: 7.9990 chunk 52 optimal weight: 50.0000 chunk 156 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 266 optimal weight: 8.9990 chunk 220 optimal weight: 40.0000 chunk 123 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 139 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 HIS ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 HIS ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN D 695 GLN ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 HIS ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 691 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6106 moved from start: 0.6067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 22500 Z= 0.200 Angle : 0.716 13.673 30540 Z= 0.353 Chirality : 0.043 0.182 3485 Planarity : 0.004 0.036 3830 Dihedral : 4.470 20.102 3025 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.98 % Favored : 94.65 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2730 helix: -0.13 (0.13), residues: 1490 sheet: -0.40 (0.39), residues: 190 loop : -1.54 (0.19), residues: 1050 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 488 time to evaluate : 2.491 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 outliers start: 47 outliers final: 26 residues processed: 515 average time/residue: 0.2789 time to fit residues: 232.3881 Evaluate side-chains 491 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 465 time to evaluate : 2.333 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1845 time to fit residues: 12.1335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 50.0000 chunk 29 optimal weight: 50.0000 chunk 151 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 223 optimal weight: 40.0000 chunk 148 optimal weight: 8.9990 chunk 265 optimal weight: 30.0000 chunk 165 optimal weight: 50.0000 chunk 161 optimal weight: 40.0000 chunk 122 optimal weight: 8.9990 overall best weight: 11.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 HIS ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 691 ASN E 762 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.6417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 22500 Z= 0.254 Angle : 0.736 11.772 30540 Z= 0.369 Chirality : 0.045 0.262 3485 Planarity : 0.004 0.036 3830 Dihedral : 4.587 21.679 3025 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 24.96 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.46 % Favored : 94.21 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.16), residues: 2730 helix: -0.12 (0.13), residues: 1490 sheet: -0.44 (0.38), residues: 190 loop : -1.39 (0.19), residues: 1050 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 495 time to evaluate : 2.518 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 outliers start: 34 outliers final: 13 residues processed: 508 average time/residue: 0.2873 time to fit residues: 237.0704 Evaluate side-chains 475 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 462 time to evaluate : 2.648 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1922 time to fit residues: 8.2418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 163 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 52 optimal weight: 50.0000 chunk 51 optimal weight: 50.0000 chunk 168 optimal weight: 4.9990 chunk 180 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 208 optimal weight: 30.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 629 ASN ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 691 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.6595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 22500 Z= 0.207 Angle : 0.756 14.818 30540 Z= 0.367 Chirality : 0.045 0.214 3485 Planarity : 0.004 0.034 3830 Dihedral : 4.494 20.853 3025 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.73 % Favored : 94.95 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.16), residues: 2730 helix: -0.11 (0.13), residues: 1490 sheet: -0.56 (0.41), residues: 140 loop : -1.29 (0.19), residues: 1100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 486 time to evaluate : 2.502 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: 22 outliers final: 10 residues processed: 499 average time/residue: 0.2820 time to fit residues: 229.3819 Evaluate side-chains 480 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 470 time to evaluate : 2.622 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1855 time to fit residues: 7.1857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 241 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 231 optimal weight: 40.0000 chunk 246 optimal weight: 20.0000 chunk 148 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 chunk 193 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 223 optimal weight: 40.0000 chunk 233 optimal weight: 3.9990 chunk 162 optimal weight: 50.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 691 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.6717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 22500 Z= 0.186 Angle : 0.789 14.484 30540 Z= 0.380 Chirality : 0.046 0.298 3485 Planarity : 0.003 0.032 3830 Dihedral : 4.414 21.897 3025 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.73 % Favored : 94.95 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.16), residues: 2730 helix: -0.13 (0.13), residues: 1490 sheet: -0.48 (0.41), residues: 140 loop : -1.29 (0.18), residues: 1100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 483 time to evaluate : 2.797 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 outliers start: 18 outliers final: 8 residues processed: 492 average time/residue: 0.2922 time to fit residues: 234.2528 Evaluate side-chains 475 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 467 time to evaluate : 2.684 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1863 time to fit residues: 6.4165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 261 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 123 optimal weight: 0.0270 chunk 181 optimal weight: 0.7980 chunk 273 optimal weight: 6.9990 chunk 252 optimal weight: 40.0000 chunk 218 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 168 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 834 HIS ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 691 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.6773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 22500 Z= 0.185 Angle : 0.826 15.298 30540 Z= 0.395 Chirality : 0.046 0.252 3485 Planarity : 0.004 0.046 3830 Dihedral : 4.368 20.493 3025 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.76 % Favored : 94.91 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.16), residues: 2730 helix: -0.19 (0.13), residues: 1495 sheet: -0.31 (0.42), residues: 140 loop : -1.29 (0.18), residues: 1095 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5460 Ramachandran restraints generated. 2730 Oldfield, 0 Emsley, 2730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 477 time to evaluate : 2.270 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 outliers start: 1 outliers final: 0 residues processed: 478 average time/residue: 0.2873 time to fit residues: 224.0356 Evaluate side-chains 460 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 460 time to evaluate : 2.560 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 8.9990 chunk 66 optimal weight: 50.0000 chunk 201 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 218 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 224 optimal weight: 0.3980 chunk 27 optimal weight: 30.0000 chunk 40 optimal weight: 50.0000 chunk 191 optimal weight: 5.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN ** E 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 691 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.139083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.078044 restraints weight = 60933.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.078707 restraints weight = 47212.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.077896 restraints weight = 37086.616| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.6887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 22500 Z= 0.193 Angle : 0.823 14.270 30540 Z= 0.397 Chirality : 0.046 0.245 3485 Planarity : 0.004 0.037 3830 Dihedral : 4.342 20.718 3025 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.69 % Favored : 94.98 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.16), residues: 2730 helix: -0.15 (0.13), residues: 1495 sheet: -0.21 (0.43), residues: 140 loop : -1.28 (0.18), residues: 1095 =============================================================================== Job complete usr+sys time: 8208.18 seconds wall clock time: 146 minutes 59.22 seconds (8819.22 seconds total)