Starting phenix.real_space_refine on Sun Mar 17 11:23:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va2_8651/03_2024/5va2_8651.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va2_8651/03_2024/5va2_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_8651/03_2024/5va2_8651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va2_8651/03_2024/5va2_8651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va2_8651/03_2024/5va2_8651.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va2_8651/03_2024/5va2_8651.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.436 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 11456 2.51 5 N 2996 2.21 5 O 3016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 "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 "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" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17576 Number of models: 1 Model: "" Number of chains: 4 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: "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: "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 Time building chain proxies: 9.73, per 1000 atoms: 0.55 Number of scatterers: 17576 At special positions: 0 Unit cell: (149.566, 149.566, 120.569, 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 108 16.00 O 3016 8.00 N 2996 7.00 C 11456 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: 6.10 Conformation dependent library (CDL) restraints added in 3.6 seconds 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4184 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 12 sheets defined 59.5% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 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: 3.967A 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: 3.615A 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: 3.856A 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: 3.864A 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: 3.688A 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: 3.592A 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: 3.586A 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: 3.630A 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: 3.608A pdb=" N GLN B 592 " --> pdb=" O ASN B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 623 removed outlier: 3.539A 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: 3.544A 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 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: 3.622A pdb=" N VAL B 113 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 3.551A 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: 3.931A 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: 4.032A 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: 3.635A 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) 784 hydrogen bonds defined for protein. 2280 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: 4.99 Time building geometry restraints manager: 6.71 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: 5492 1.34 - 1.46: 2324 1.46 - 1.58: 10032 1.58 - 1.69: 0 1.69 - 1.81: 152 Bond restraints: 18000 Sorted by residual: 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 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 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 7.32e+00 bond pdb=" N GLY C 603 " pdb=" CA GLY C 603 " ideal model delta sigma weight residual 1.451 1.493 -0.042 1.60e-02 3.91e+03 6.86e+00 ... (remaining 17995 not shown) Histogram of bond angle deviations from ideal: 100.88 - 107.50: 632 107.50 - 114.12: 9808 114.12 - 120.73: 7420 120.73 - 127.35: 6384 127.35 - 133.96: 188 Bond angle restraints: 24432 Sorted by residual: 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 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 B 8 " pdb=" CA VAL B 8 " pdb=" CB VAL B 8 " ideal model delta sigma weight residual 111.74 107.32 4.42 9.40e-01 1.13e+00 2.21e+01 angle pdb=" N ALA A 813 " pdb=" CA ALA A 813 " pdb=" C ALA A 813 " ideal model delta sigma weight residual 112.24 117.27 -5.03 1.28e+00 6.10e-01 1.54e+01 ... (remaining 24427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.46: 9124 12.46 - 24.92: 1048 24.92 - 37.38: 248 37.38 - 49.83: 92 49.83 - 62.29: 28 Dihedral angle restraints: 10540 sinusoidal: 4056 harmonic: 6484 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 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA GLY A 628 " pdb=" C GLY A 628 " pdb=" N ASN A 629 " pdb=" CA ASN A 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 10537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1856 0.052 - 0.104: 608 0.104 - 0.156: 240 0.156 - 0.208: 76 0.208 - 0.260: 8 Chirality restraints: 2788 Sorted by residual: 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 chirality pdb=" CA ILE B 593 " pdb=" N ILE B 593 " pdb=" C ILE B 593 " pdb=" CB ILE B 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 2785 not shown) Planarity restraints: 3064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 113 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO B 114 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 114 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 114 " -0.019 5.00e-02 4.00e+02 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 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 3061 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 32 2.27 - 2.92: 6496 2.92 - 3.58: 24000 3.58 - 4.24: 36950 4.24 - 4.90: 65184 Nonbonded interactions: 132662 Sorted by model distance: nonbonded pdb=" NH1 ARG C 752 " pdb=" CD2 HIS D 771 " model vdw 1.607 3.340 nonbonded pdb=" NH1 ARG B 752 " pdb=" CD2 HIS C 771 " model vdw 1.607 3.340 nonbonded pdb=" CD2 HIS A 771 " pdb=" NH1 ARG D 752 " model vdw 1.607 3.340 nonbonded pdb=" NH1 ARG A 752 " pdb=" CD2 HIS B 771 " model vdw 1.607 3.340 nonbonded pdb=" CG HIS A 771 " pdb=" NH1 ARG D 752 " model vdw 1.799 3.340 ... (remaining 132657 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.910 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 44.830 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 0.044 18000 Z= 0.514 Angle : 1.081 9.371 24432 Z= 0.725 Chirality : 0.064 0.260 2788 Planarity : 0.004 0.034 3064 Dihedral : 12.468 62.292 6356 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 1.65 % Allowed : 7.69 % Favored : 90.66 % Rotamer: Outliers : 1.08 % Allowed : 6.49 % Favored : 92.42 % 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 (0.14), residues: 2184 helix: -2.20 (0.11), residues: 1104 sheet: -4.06 (0.30), residues: 128 loop : -2.67 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 705 HIS 0.005 0.001 HIS A 587 PHE 0.011 0.001 PHE D 494 TYR 0.013 0.001 TYR D 652 ARG 0.003 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 896 time to evaluate : 1.971 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 revert: symmetry clash REVERT: A 30 ILE cc_start: 0.9743 (pt) cc_final: 0.9540 (mm) REVERT: A 31 ILE cc_start: 0.9799 (mt) cc_final: 0.9576 (mp) REVERT: A 42 ILE cc_start: 0.9629 (pt) cc_final: 0.9355 (pt) REVERT: A 43 TYR cc_start: 0.9498 (t80) cc_final: 0.9249 (t80) REVERT: A 59 VAL cc_start: 0.9734 (t) cc_final: 0.9390 (p) REVERT: A 95 GLU cc_start: 0.9575 (tt0) cc_final: 0.9160 (tm-30) REVERT: A 109 LEU cc_start: 0.9510 (tp) cc_final: 0.8919 (pp) REVERT: A 400 ILE cc_start: 0.9078 (mm) cc_final: 0.8875 (tp) REVERT: A 506 ILE cc_start: 0.9200 (mt) cc_final: 0.8911 (pt) REVERT: A 524 LEU cc_start: 0.9527 (mt) cc_final: 0.9213 (mt) REVERT: A 533 VAL cc_start: 0.9449 (t) cc_final: 0.9165 (p) REVERT: A 574 MET cc_start: 0.8306 (mtt) cc_final: 0.7818 (ppp) REVERT: A 575 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8233 (tp30) REVERT: A 588 ASN cc_start: 0.9626 (t0) cc_final: 0.9252 (m-40) REVERT: A 612 VAL cc_start: 0.9734 (t) cc_final: 0.9465 (p) REVERT: A 638 LYS cc_start: 0.9677 (mttt) cc_final: 0.9245 (mtpp) REVERT: A 644 VAL cc_start: 0.9597 (t) cc_final: 0.9359 (p) REVERT: A 645 MET cc_start: 0.9538 (mtp) cc_final: 0.9198 (ttp) REVERT: A 677 MET cc_start: 0.9866 (tpp) cc_final: 0.9405 (tmm) REVERT: A 681 ARG cc_start: 0.9618 (mtt180) cc_final: 0.9361 (mtm180) REVERT: A 689 ILE cc_start: 0.8779 (mt) cc_final: 0.8465 (mt) REVERT: A 691 ASN cc_start: 0.9641 (m-40) cc_final: 0.9367 (m110) REVERT: A 711 ILE cc_start: 0.7764 (mt) cc_final: 0.5323 (mm) REVERT: A 712 ASP cc_start: 0.9388 (m-30) cc_final: 0.9017 (p0) REVERT: A 729 CYS cc_start: 0.9708 (m) cc_final: 0.9485 (m) REVERT: A 737 LEU cc_start: 0.9780 (mp) cc_final: 0.9454 (mp) REVERT: A 751 LEU cc_start: 0.9559 (mt) cc_final: 0.9228 (pp) REVERT: A 761 THR cc_start: 0.8837 (p) cc_final: 0.8602 (t) REVERT: A 775 LEU cc_start: 0.8759 (mt) cc_final: 0.8371 (mm) REVERT: A 782 ILE cc_start: 0.9569 (mt) cc_final: 0.9027 (tt) REVERT: A 798 ILE cc_start: 0.9816 (mp) cc_final: 0.9421 (mm) REVERT: A 832 LYS cc_start: 0.9711 (tttt) cc_final: 0.9448 (ttpp) REVERT: A 833 ILE cc_start: 0.9586 (pt) cc_final: 0.9113 (pt) REVERT: A 840 GLU cc_start: 0.9734 (mt-10) cc_final: 0.9462 (tp30) REVERT: A 844 MET cc_start: 0.9629 (mmp) cc_final: 0.9410 (mtm) REVERT: B 42 ILE cc_start: 0.9570 (pt) cc_final: 0.9276 (pt) REVERT: B 59 VAL cc_start: 0.9741 (t) cc_final: 0.9393 (p) REVERT: B 95 GLU cc_start: 0.9597 (tt0) cc_final: 0.9227 (tm-30) REVERT: B 109 LEU cc_start: 0.9500 (tp) cc_final: 0.8926 (pp) REVERT: B 400 ILE cc_start: 0.9068 (mm) cc_final: 0.8859 (tp) REVERT: B 501 ASP cc_start: 0.9307 (m-30) cc_final: 0.7205 (m-30) REVERT: B 506 ILE cc_start: 0.9277 (mt) cc_final: 0.8934 (pt) REVERT: B 524 LEU cc_start: 0.9525 (mt) cc_final: 0.9257 (mm) REVERT: B 533 VAL cc_start: 0.9473 (t) cc_final: 0.9182 (p) REVERT: B 574 MET cc_start: 0.8332 (mtt) cc_final: 0.7826 (ppp) REVERT: B 575 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8138 (tp30) REVERT: B 612 VAL cc_start: 0.9714 (t) cc_final: 0.9433 (p) REVERT: B 638 LYS cc_start: 0.9638 (mttt) cc_final: 0.9186 (mtpp) REVERT: B 644 VAL cc_start: 0.9566 (t) cc_final: 0.9334 (p) REVERT: B 645 MET cc_start: 0.9529 (mtp) cc_final: 0.9242 (ttp) REVERT: B 677 MET cc_start: 0.9877 (tpp) cc_final: 0.9454 (tmm) REVERT: B 681 ARG cc_start: 0.9622 (mtt180) cc_final: 0.9341 (mtm180) REVERT: B 683 PHE cc_start: 0.9872 (t80) cc_final: 0.9622 (t80) REVERT: B 691 ASN cc_start: 0.9650 (m-40) cc_final: 0.9367 (m110) REVERT: B 711 ILE cc_start: 0.7861 (mt) cc_final: 0.5538 (mm) REVERT: B 712 ASP cc_start: 0.9455 (m-30) cc_final: 0.9066 (p0) REVERT: B 717 LEU cc_start: 0.9637 (tt) cc_final: 0.9389 (tp) REVERT: B 729 CYS cc_start: 0.9691 (m) cc_final: 0.9462 (m) REVERT: B 737 LEU cc_start: 0.9803 (mp) cc_final: 0.9488 (mp) REVERT: B 748 LYS cc_start: 0.9875 (mttt) cc_final: 0.9658 (tmmt) REVERT: B 751 LEU cc_start: 0.9564 (mt) cc_final: 0.9274 (pp) REVERT: B 781 PHE cc_start: 0.9775 (m-80) cc_final: 0.9563 (m-80) REVERT: B 782 ILE cc_start: 0.9566 (mt) cc_final: 0.9090 (tt) REVERT: B 798 ILE cc_start: 0.9804 (mp) cc_final: 0.9571 (tp) REVERT: B 804 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.9008 (tp) REVERT: B 832 LYS cc_start: 0.9685 (tttt) cc_final: 0.9437 (ttpp) REVERT: B 833 ILE cc_start: 0.9531 (pt) cc_final: 0.9082 (pt) REVERT: C 31 ILE cc_start: 0.9779 (mt) cc_final: 0.9548 (mp) REVERT: C 42 ILE cc_start: 0.9575 (pt) cc_final: 0.9309 (pt) REVERT: C 43 TYR cc_start: 0.9460 (t80) cc_final: 0.9236 (t80) REVERT: C 59 VAL cc_start: 0.9750 (t) cc_final: 0.9237 (p) REVERT: C 95 GLU cc_start: 0.9586 (tt0) cc_final: 0.9208 (tm-30) REVERT: C 109 LEU cc_start: 0.9495 (tp) cc_final: 0.8928 (pp) REVERT: C 400 ILE cc_start: 0.9033 (mm) cc_final: 0.8819 (tp) REVERT: C 501 ASP cc_start: 0.9336 (m-30) cc_final: 0.6770 (m-30) REVERT: C 533 VAL cc_start: 0.9413 (t) cc_final: 0.9050 (p) REVERT: C 574 MET cc_start: 0.8278 (mtt) cc_final: 0.7700 (ppp) REVERT: C 575 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8113 (tp30) REVERT: C 588 ASN cc_start: 0.9632 (t0) cc_final: 0.9260 (m-40) REVERT: C 638 LYS cc_start: 0.9663 (mttt) cc_final: 0.9225 (mtpp) REVERT: C 645 MET cc_start: 0.9522 (mtp) cc_final: 0.9277 (ttp) REVERT: C 677 MET cc_start: 0.9890 (tpp) cc_final: 0.9456 (tmm) REVERT: C 681 ARG cc_start: 0.9614 (mtt180) cc_final: 0.9345 (mtm180) REVERT: C 683 PHE cc_start: 0.9880 (t80) cc_final: 0.9624 (t80) REVERT: C 691 ASN cc_start: 0.9652 (m-40) cc_final: 0.9232 (m110) REVERT: C 695 GLN cc_start: 0.9770 (mt0) cc_final: 0.9463 (mp10) REVERT: C 698 GLU cc_start: 0.9737 (mt-10) cc_final: 0.9501 (mp0) REVERT: C 711 ILE cc_start: 0.7694 (mt) cc_final: 0.5422 (mm) REVERT: C 712 ASP cc_start: 0.9354 (m-30) cc_final: 0.8987 (p0) REVERT: C 717 LEU cc_start: 0.9607 (tt) cc_final: 0.9321 (tp) REVERT: C 729 CYS cc_start: 0.9703 (m) cc_final: 0.9482 (m) REVERT: C 737 LEU cc_start: 0.9812 (mp) cc_final: 0.9520 (mp) REVERT: C 748 LYS cc_start: 0.9876 (mttt) cc_final: 0.9653 (tmmt) REVERT: C 751 LEU cc_start: 0.9561 (mt) cc_final: 0.9250 (pp) REVERT: C 781 PHE cc_start: 0.9767 (m-80) cc_final: 0.9548 (m-80) REVERT: C 782 ILE cc_start: 0.9528 (mt) cc_final: 0.9016 (tt) REVERT: C 798 ILE cc_start: 0.9782 (mp) cc_final: 0.9542 (tp) REVERT: C 804 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9121 (tp) REVERT: C 821 ASP cc_start: 0.9207 (m-30) cc_final: 0.8960 (p0) REVERT: C 825 LEU cc_start: 0.9278 (mt) cc_final: 0.9075 (mp) REVERT: C 832 LYS cc_start: 0.9699 (tttt) cc_final: 0.9452 (ttpp) REVERT: C 833 ILE cc_start: 0.9589 (pt) cc_final: 0.9154 (pt) REVERT: C 840 GLU cc_start: 0.9716 (mt-10) cc_final: 0.9504 (tp30) REVERT: D 42 ILE cc_start: 0.9645 (pt) cc_final: 0.9201 (pt) REVERT: D 43 TYR cc_start: 0.9485 (t80) cc_final: 0.9157 (t80) REVERT: D 59 VAL cc_start: 0.9735 (t) cc_final: 0.9532 (p) REVERT: D 95 GLU cc_start: 0.9551 (tt0) cc_final: 0.9132 (tm-30) REVERT: D 109 LEU cc_start: 0.9506 (tp) cc_final: 0.8928 (pp) REVERT: D 400 ILE cc_start: 0.9036 (mm) cc_final: 0.8829 (tp) REVERT: D 506 ILE cc_start: 0.9299 (mt) cc_final: 0.9097 (pt) REVERT: D 524 LEU cc_start: 0.9498 (mt) cc_final: 0.9188 (mm) REVERT: D 533 VAL cc_start: 0.9391 (t) cc_final: 0.9099 (p) REVERT: D 574 MET cc_start: 0.8187 (mtt) cc_final: 0.7661 (ppp) REVERT: D 575 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8182 (tp30) REVERT: D 612 VAL cc_start: 0.9742 (t) cc_final: 0.9492 (p) REVERT: D 638 LYS cc_start: 0.9703 (mttt) cc_final: 0.9266 (mtpp) REVERT: D 644 VAL cc_start: 0.9665 (t) cc_final: 0.9456 (p) REVERT: D 645 MET cc_start: 0.9528 (mtp) cc_final: 0.9228 (ttp) REVERT: D 677 MET cc_start: 0.9880 (tpp) cc_final: 0.9468 (tmm) REVERT: D 681 ARG cc_start: 0.9618 (mtt180) cc_final: 0.9402 (mtm180) REVERT: D 689 ILE cc_start: 0.8657 (mt) cc_final: 0.8312 (mt) REVERT: D 691 ASN cc_start: 0.9642 (m-40) cc_final: 0.9233 (m110) REVERT: D 695 GLN cc_start: 0.9763 (mt0) cc_final: 0.9464 (mp10) REVERT: D 698 GLU cc_start: 0.9728 (mt-10) cc_final: 0.9472 (mp0) REVERT: D 711 ILE cc_start: 0.7572 (mt) cc_final: 0.5168 (mm) REVERT: D 712 ASP cc_start: 0.9278 (m-30) cc_final: 0.8888 (p0) REVERT: D 729 CYS cc_start: 0.9716 (m) cc_final: 0.9468 (m) REVERT: D 737 LEU cc_start: 0.9790 (mp) cc_final: 0.9439 (mp) REVERT: D 748 LYS cc_start: 0.9882 (mttt) cc_final: 0.9666 (tmmt) REVERT: D 751 LEU cc_start: 0.9570 (mt) cc_final: 0.9067 (pp) REVERT: D 775 LEU cc_start: 0.8770 (mt) cc_final: 0.8116 (mm) REVERT: D 781 PHE cc_start: 0.9785 (m-80) cc_final: 0.9585 (m-80) REVERT: D 782 ILE cc_start: 0.9530 (mt) cc_final: 0.9023 (tt) REVERT: D 798 ILE cc_start: 0.9795 (mp) cc_final: 0.9555 (tp) REVERT: D 821 ASP cc_start: 0.9225 (m-30) cc_final: 0.9018 (p0) REVERT: D 832 LYS cc_start: 0.9722 (tttt) cc_final: 0.9449 (ttpp) REVERT: D 833 ILE cc_start: 0.9635 (pt) cc_final: 0.9184 (pt) REVERT: D 840 GLU cc_start: 0.9738 (mt-10) cc_final: 0.9448 (tp30) REVERT: D 844 MET cc_start: 0.9628 (mmp) cc_final: 0.9345 (mtm) outliers start: 20 outliers final: 0 residues processed: 912 average time/residue: 0.3158 time to fit residues: 412.3931 Evaluate side-chains 592 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 590 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain C residue 804 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 172 optimal weight: 30.0000 chunk 66 optimal weight: 30.0000 chunk 104 optimal weight: 20.0000 chunk 128 optimal weight: 1.9990 chunk 199 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 HIS B 12 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS C 12 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN ** C 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 HIS C 834 HIS D 12 ASN D 470 ASN D 834 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18000 Z= 0.246 Angle : 0.802 9.790 24432 Z= 0.403 Chirality : 0.046 0.173 2788 Planarity : 0.005 0.055 3064 Dihedral : 5.362 33.474 2424 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.72 % Favored : 94.55 % Rotamer: Outliers : 4.00 % Allowed : 19.26 % Favored : 76.73 % 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: -2.17 (0.17), residues: 2184 helix: -0.82 (0.13), residues: 1216 sheet: -2.57 (0.33), residues: 152 loop : -2.02 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 497 HIS 0.009 0.002 HIS A 771 PHE 0.019 0.002 PHE B 617 TYR 0.021 0.002 TYR B 700 ARG 0.009 0.001 ARG D 752 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 624 time to evaluate : 1.748 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: A 31 ILE cc_start: 0.9791 (mt) cc_final: 0.9588 (mp) REVERT: A 43 TYR cc_start: 0.9483 (t80) cc_final: 0.9192 (t80) REVERT: A 472 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8582 (tpp80) REVERT: A 533 VAL cc_start: 0.9479 (t) cc_final: 0.9103 (p) REVERT: A 574 MET cc_start: 0.8422 (mtt) cc_final: 0.7948 (ppp) REVERT: A 677 MET cc_start: 0.9841 (tpp) cc_final: 0.9278 (tpp) REVERT: A 678 LEU cc_start: 0.9802 (mt) cc_final: 0.9509 (mt) REVERT: A 681 ARG cc_start: 0.9539 (mtt180) cc_final: 0.9071 (mtm110) REVERT: A 702 GLN cc_start: 0.9642 (mt0) cc_final: 0.9407 (pp30) REVERT: A 711 ILE cc_start: 0.7033 (mt) cc_final: 0.4508 (mm) REVERT: A 840 GLU cc_start: 0.9700 (mt-10) cc_final: 0.9488 (tm-30) REVERT: A 844 MET cc_start: 0.9737 (mmp) cc_final: 0.9317 (mtm) REVERT: B 472 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8681 (tpp80) REVERT: B 533 VAL cc_start: 0.9496 (t) cc_final: 0.9078 (p) REVERT: B 534 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.9104 (mmm160) REVERT: B 574 MET cc_start: 0.8407 (mtt) cc_final: 0.7894 (ppp) REVERT: B 677 MET cc_start: 0.9857 (tpp) cc_final: 0.9285 (tpp) REVERT: B 678 LEU cc_start: 0.9808 (mt) cc_final: 0.9355 (mt) REVERT: B 680 VAL cc_start: 0.9802 (p) cc_final: 0.9580 (m) REVERT: B 681 ARG cc_start: 0.9565 (mtt180) cc_final: 0.9132 (mtm110) REVERT: B 682 GLU cc_start: 0.9641 (pt0) cc_final: 0.9401 (tm-30) REVERT: B 702 GLN cc_start: 0.9615 (mt0) cc_final: 0.9411 (pp30) REVERT: B 712 ASP cc_start: 0.9514 (m-30) cc_final: 0.9215 (p0) REVERT: B 823 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8244 (mmp80) REVERT: C 43 TYR cc_start: 0.9443 (t80) cc_final: 0.9238 (t80) REVERT: C 59 VAL cc_start: 0.9289 (t) cc_final: 0.8945 (t) REVERT: C 472 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8606 (tpp80) REVERT: C 533 VAL cc_start: 0.9435 (t) cc_final: 0.9183 (p) REVERT: C 574 MET cc_start: 0.8365 (mtt) cc_final: 0.7840 (ppp) REVERT: C 575 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8160 (tp30) REVERT: C 619 PHE cc_start: 0.9813 (OUTLIER) cc_final: 0.9236 (t80) REVERT: C 677 MET cc_start: 0.9858 (tpp) cc_final: 0.9509 (mmm) REVERT: C 711 ILE cc_start: 0.6969 (mt) cc_final: 0.4302 (mm) REVERT: C 712 ASP cc_start: 0.9436 (m-30) cc_final: 0.9163 (p0) REVERT: C 840 GLU cc_start: 0.9685 (mt-10) cc_final: 0.9445 (tm-30) REVERT: C 844 MET cc_start: 0.9678 (mmp) cc_final: 0.9329 (mtm) REVERT: D 59 VAL cc_start: 0.9430 (t) cc_final: 0.9168 (m) REVERT: D 424 PHE cc_start: 0.9681 (m-80) cc_final: 0.9453 (m-80) REVERT: D 472 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8534 (tpp80) REVERT: D 533 VAL cc_start: 0.9435 (t) cc_final: 0.9021 (p) REVERT: D 574 MET cc_start: 0.8313 (mtt) cc_final: 0.7823 (ppp) REVERT: D 575 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8221 (tp30) REVERT: D 619 PHE cc_start: 0.9836 (OUTLIER) cc_final: 0.9250 (t80) REVERT: D 677 MET cc_start: 0.9865 (tpp) cc_final: 0.9615 (tmm) REVERT: D 681 ARG cc_start: 0.9544 (mtt180) cc_final: 0.9285 (mmm160) REVERT: D 682 GLU cc_start: 0.9664 (pt0) cc_final: 0.9446 (tm-30) REVERT: D 840 GLU cc_start: 0.9709 (mt-10) cc_final: 0.9474 (tm-30) REVERT: D 844 MET cc_start: 0.9708 (mmp) cc_final: 0.9367 (mtm) outliers start: 74 outliers final: 40 residues processed: 669 average time/residue: 0.2869 time to fit residues: 284.1933 Evaluate side-chains 541 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 493 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 HIS Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 472 ARG Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain B residue 7 HIS Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 472 ARG Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 472 ARG Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 789 ILE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 804 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 20.0000 chunk 62 optimal weight: 50.0000 chunk 166 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 55 optimal weight: 50.0000 chunk 200 optimal weight: 8.9990 chunk 216 optimal weight: 6.9990 chunk 178 optimal weight: 20.0000 chunk 198 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 160 optimal weight: 4.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 70 HIS A 562 HIS A 629 ASN A 664 GLN A 688 GLN A 691 ASN A 739 HIS B 12 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS B 470 ASN B 664 GLN B 688 GLN B 691 ASN B 739 HIS C 12 ASN C 61 GLN C 70 HIS C 75 GLN C 562 HIS C 664 GLN C 676 GLN C 688 GLN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS D 12 ASN D 70 HIS D 562 HIS ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 GLN D 688 GLN D 691 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18000 Z= 0.223 Angle : 0.761 12.663 24432 Z= 0.378 Chirality : 0.047 0.236 2788 Planarity : 0.004 0.089 3064 Dihedral : 4.923 18.851 2420 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.17 % Favored : 95.10 % Rotamer: Outliers : 5.47 % Allowed : 20.62 % Favored : 73.92 % 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: -1.53 (0.17), residues: 2184 helix: -0.34 (0.14), residues: 1196 sheet: -1.76 (0.37), residues: 152 loop : -1.73 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 410 HIS 0.006 0.001 HIS B 731 PHE 0.027 0.002 PHE D 48 TYR 0.017 0.002 TYR C 700 ARG 0.012 0.001 ARG C 537 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 515 time to evaluate : 1.878 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: A 472 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8546 (tpp80) REVERT: A 533 VAL cc_start: 0.9503 (t) cc_final: 0.9274 (p) REVERT: A 677 MET cc_start: 0.9851 (tpp) cc_final: 0.9404 (tmm) REVERT: A 678 LEU cc_start: 0.9785 (mt) cc_final: 0.9569 (mt) REVERT: A 702 GLN cc_start: 0.9685 (mt0) cc_final: 0.9414 (pp30) REVERT: A 711 ILE cc_start: 0.6216 (mt) cc_final: 0.5570 (mm) REVERT: A 809 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9179 (mp) REVERT: B 411 ASP cc_start: 0.9337 (t70) cc_final: 0.8941 (t0) REVERT: B 472 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8646 (tpp80) REVERT: B 541 ARG cc_start: 0.9021 (tpp80) cc_final: 0.8797 (tpp80) REVERT: B 677 MET cc_start: 0.9858 (tpp) cc_final: 0.9401 (tpp) REVERT: B 678 LEU cc_start: 0.9803 (mt) cc_final: 0.9324 (mt) REVERT: B 680 VAL cc_start: 0.9805 (p) cc_final: 0.9585 (m) REVERT: B 681 ARG cc_start: 0.9558 (mtt180) cc_final: 0.9088 (mtm110) REVERT: B 682 GLU cc_start: 0.9635 (pt0) cc_final: 0.9333 (tp30) REVERT: B 712 ASP cc_start: 0.9535 (m-30) cc_final: 0.9242 (p0) REVERT: B 809 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9174 (mp) REVERT: C 411 ASP cc_start: 0.9412 (t70) cc_final: 0.8600 (t70) REVERT: C 472 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8616 (tpp80) REVERT: C 533 VAL cc_start: 0.9416 (t) cc_final: 0.8860 (p) REVERT: C 534 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8722 (mmm160) REVERT: C 541 ARG cc_start: 0.9033 (tpt-90) cc_final: 0.8664 (tpt-90) REVERT: C 574 MET cc_start: 0.8332 (mtt) cc_final: 0.8101 (tpt) REVERT: C 645 MET cc_start: 0.9666 (ttm) cc_final: 0.9174 (ttm) REVERT: C 691 ASN cc_start: 0.9849 (p0) cc_final: 0.9532 (m110) REVERT: C 712 ASP cc_start: 0.9502 (m-30) cc_final: 0.9214 (p0) REVERT: C 809 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9178 (mp) REVERT: D 424 PHE cc_start: 0.9647 (m-80) cc_final: 0.9446 (m-80) REVERT: D 472 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8520 (tpp80) REVERT: D 538 LYS cc_start: 0.9053 (mmtm) cc_final: 0.8848 (mmtm) REVERT: D 574 MET cc_start: 0.8295 (mtt) cc_final: 0.8056 (tpt) REVERT: D 619 PHE cc_start: 0.9823 (OUTLIER) cc_final: 0.9358 (t80) REVERT: D 677 MET cc_start: 0.9874 (tpp) cc_final: 0.9625 (tmm) REVERT: D 681 ARG cc_start: 0.9545 (mtt180) cc_final: 0.9252 (mmm160) REVERT: D 695 GLN cc_start: 0.9736 (mt0) cc_final: 0.9500 (mm110) REVERT: D 698 GLU cc_start: 0.9667 (pt0) cc_final: 0.9299 (pp20) REVERT: D 762 HIS cc_start: 0.8277 (m-70) cc_final: 0.8043 (m170) REVERT: D 784 ARG cc_start: 0.9469 (mtp-110) cc_final: 0.9262 (mtm110) REVERT: D 809 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9139 (mp) outliers start: 101 outliers final: 53 residues processed: 589 average time/residue: 0.2759 time to fit residues: 243.9584 Evaluate side-chains 535 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 472 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 472 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 472 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 817 LYS Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 534 ARG Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 472 ARG Chi-restraints excluded: chain D residue 479 ASN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 711 ILE Chi-restraints excluded: chain D residue 789 ILE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 804 ILE Chi-restraints excluded: chain D residue 809 LEU Chi-restraints excluded: chain D residue 822 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 30.0000 chunk 150 optimal weight: 30.0000 chunk 103 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 40.0000 chunk 104 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 overall best weight: 5.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 HIS B 588 ASN B 629 ASN B 658 ASN B 691 ASN B 762 HIS ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN C 658 ASN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 HIS ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 HIS D 629 ASN D 658 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18000 Z= 0.201 Angle : 0.718 12.713 24432 Z= 0.355 Chirality : 0.044 0.161 2788 Planarity : 0.004 0.042 3064 Dihedral : 4.687 19.480 2420 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.64 % Allowed : 4.21 % Favored : 95.15 % Rotamer: Outliers : 3.79 % Allowed : 23.38 % Favored : 72.84 % 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: -1.36 (0.17), residues: 2184 helix: -0.33 (0.14), residues: 1220 sheet: -1.42 (0.36), residues: 156 loop : -1.51 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 410 HIS 0.006 0.001 HIS B 731 PHE 0.021 0.001 PHE A 424 TYR 0.015 0.001 TYR A 616 ARG 0.009 0.001 ARG C 679 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 519 time to evaluate : 2.019 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: A 59 VAL cc_start: 0.9499 (t) cc_final: 0.9167 (t) REVERT: A 411 ASP cc_start: 0.9419 (t70) cc_final: 0.9093 (t0) REVERT: A 533 VAL cc_start: 0.9423 (t) cc_final: 0.9193 (p) REVERT: A 538 LYS cc_start: 0.9123 (mmtm) cc_final: 0.8897 (mmtm) REVERT: A 677 MET cc_start: 0.9829 (tpp) cc_final: 0.9443 (tmm) REVERT: A 678 LEU cc_start: 0.9788 (mt) cc_final: 0.9549 (mt) REVERT: A 681 ARG cc_start: 0.9564 (mtm180) cc_final: 0.9261 (mtm180) REVERT: A 711 ILE cc_start: 0.6105 (mt) cc_final: 0.5526 (mm) REVERT: A 809 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9056 (mp) REVERT: A 840 GLU cc_start: 0.9640 (tp30) cc_final: 0.9232 (tp30) REVERT: B 410 TRP cc_start: 0.9271 (t60) cc_final: 0.8988 (t60) REVERT: B 411 ASP cc_start: 0.9303 (t70) cc_final: 0.8925 (t0) REVERT: B 541 ARG cc_start: 0.9037 (tpp80) cc_final: 0.8775 (tpp80) REVERT: B 645 MET cc_start: 0.9611 (ptm) cc_final: 0.9169 (ptm) REVERT: B 658 ASN cc_start: 0.9038 (m110) cc_final: 0.8813 (m110) REVERT: B 677 MET cc_start: 0.9855 (tpp) cc_final: 0.9579 (tmm) REVERT: B 678 LEU cc_start: 0.9789 (mt) cc_final: 0.9497 (mt) REVERT: B 681 ARG cc_start: 0.9562 (mtt180) cc_final: 0.9160 (tpm170) REVERT: B 682 GLU cc_start: 0.9641 (pt0) cc_final: 0.9371 (tp30) REVERT: B 702 GLN cc_start: 0.9647 (mt0) cc_final: 0.9413 (pp30) REVERT: B 712 ASP cc_start: 0.9562 (m-30) cc_final: 0.9293 (p0) REVERT: B 784 ARG cc_start: 0.9274 (mtp85) cc_final: 0.8945 (ptm160) REVERT: B 809 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9134 (mp) REVERT: C 411 ASP cc_start: 0.9350 (t70) cc_final: 0.8575 (t70) REVERT: C 472 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8595 (tpp80) REVERT: C 541 ARG cc_start: 0.9098 (tpt-90) cc_final: 0.8728 (tpt-90) REVERT: C 619 PHE cc_start: 0.9823 (OUTLIER) cc_final: 0.9436 (t80) REVERT: C 645 MET cc_start: 0.9647 (ttm) cc_final: 0.9423 (ttm) REVERT: C 658 ASN cc_start: 0.8980 (m110) cc_final: 0.8744 (m110) REVERT: C 677 MET cc_start: 0.9761 (tpp) cc_final: 0.9291 (mtm) REVERT: C 681 ARG cc_start: 0.9332 (mtm-85) cc_final: 0.9005 (mtm-85) REVERT: C 809 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9148 (mp) REVERT: D 60 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8798 (pmm) REVERT: D 411 ASP cc_start: 0.9425 (t70) cc_final: 0.9011 (t0) REVERT: D 424 PHE cc_start: 0.9654 (m-80) cc_final: 0.9441 (m-80) REVERT: D 472 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8519 (tpp80) REVERT: D 538 LYS cc_start: 0.9142 (mmtm) cc_final: 0.8892 (mmtm) REVERT: D 541 ARG cc_start: 0.9072 (tpp80) cc_final: 0.8783 (tpp80) REVERT: D 574 MET cc_start: 0.8256 (mtt) cc_final: 0.8027 (tpt) REVERT: D 617 PHE cc_start: 0.9726 (t80) cc_final: 0.9482 (t80) REVERT: D 658 ASN cc_start: 0.8970 (m110) cc_final: 0.8735 (m110) REVERT: D 677 MET cc_start: 0.9867 (tpp) cc_final: 0.9282 (tmm) REVERT: D 681 ARG cc_start: 0.9526 (mtt180) cc_final: 0.9071 (mmm-85) REVERT: D 702 GLN cc_start: 0.9680 (mt0) cc_final: 0.9405 (pp30) REVERT: D 809 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9047 (mp) outliers start: 70 outliers final: 44 residues processed: 567 average time/residue: 0.2803 time to fit residues: 239.0016 Evaluate side-chains 532 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 480 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 ARG Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 472 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 762 HIS Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 834 HIS Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 637 GLU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 762 HIS Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 472 ARG Chi-restraints excluded: chain D residue 479 ASN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 711 ILE Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 809 LEU Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 858 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 30.0000 chunk 120 optimal weight: 30.0000 chunk 3 optimal weight: 40.0000 chunk 158 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 108 optimal weight: 20.0000 chunk 190 optimal weight: 30.0000 chunk 53 optimal weight: 0.2980 overall best weight: 7.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 658 ASN A 691 ASN A 851 HIS ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS B 834 HIS B 851 HIS C 12 ASN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 HIS ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 691 ASN D 762 HIS D 851 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.6004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18000 Z= 0.222 Angle : 0.726 13.110 24432 Z= 0.361 Chirality : 0.045 0.222 2788 Planarity : 0.004 0.034 3064 Dihedral : 4.640 20.105 2420 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.85 % Favored : 94.78 % Rotamer: Outliers : 4.60 % Allowed : 25.97 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.17), residues: 2184 helix: -0.32 (0.14), residues: 1184 sheet: -0.97 (0.36), residues: 164 loop : -1.68 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 410 HIS 0.014 0.001 HIS B 834 PHE 0.026 0.002 PHE A 640 TYR 0.016 0.002 TYR A 616 ARG 0.005 0.001 ARG C 679 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 507 time to evaluate : 1.960 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: A 411 ASP cc_start: 0.9433 (t70) cc_final: 0.9005 (t0) REVERT: A 472 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8569 (tpm170) REVERT: A 533 VAL cc_start: 0.9426 (t) cc_final: 0.9191 (p) REVERT: A 538 LYS cc_start: 0.9184 (mmtm) cc_final: 0.8950 (mmtm) REVERT: A 623 THR cc_start: 0.9379 (OUTLIER) cc_final: 0.9132 (p) REVERT: A 658 ASN cc_start: 0.9031 (m110) cc_final: 0.8808 (m110) REVERT: A 677 MET cc_start: 0.9831 (tpp) cc_final: 0.9306 (tmm) REVERT: A 678 LEU cc_start: 0.9784 (mt) cc_final: 0.9488 (mt) REVERT: A 681 ARG cc_start: 0.9562 (mtm180) cc_final: 0.9084 (mtp85) REVERT: A 702 GLN cc_start: 0.9679 (mt0) cc_final: 0.9408 (pp30) REVERT: A 711 ILE cc_start: 0.6103 (mt) cc_final: 0.5466 (mp) REVERT: A 809 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8978 (mp) REVERT: A 844 MET cc_start: 0.8879 (mtm) cc_final: 0.8410 (ptt) REVERT: B 411 ASP cc_start: 0.9287 (t70) cc_final: 0.8825 (t0) REVERT: B 472 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8590 (tpp80) REVERT: B 541 ARG cc_start: 0.9027 (tpp80) cc_final: 0.8787 (tpp80) REVERT: B 623 THR cc_start: 0.9446 (OUTLIER) cc_final: 0.9212 (p) REVERT: B 645 MET cc_start: 0.9518 (ptm) cc_final: 0.8996 (ptm) REVERT: B 658 ASN cc_start: 0.9030 (m110) cc_final: 0.8807 (m110) REVERT: B 677 MET cc_start: 0.9855 (tpp) cc_final: 0.9201 (tmm) REVERT: B 678 LEU cc_start: 0.9788 (mt) cc_final: 0.9327 (mt) REVERT: B 681 ARG cc_start: 0.9561 (mtt180) cc_final: 0.9106 (mmm-85) REVERT: B 682 GLU cc_start: 0.9651 (pt0) cc_final: 0.9339 (tp30) REVERT: B 702 GLN cc_start: 0.9632 (mt0) cc_final: 0.9388 (pp30) REVERT: B 712 ASP cc_start: 0.9584 (m-30) cc_final: 0.9366 (p0) REVERT: B 809 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9047 (mp) REVERT: C 411 ASP cc_start: 0.9332 (t70) cc_final: 0.8541 (t70) REVERT: C 472 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8550 (tpp80) REVERT: C 541 ARG cc_start: 0.9148 (tpt-90) cc_final: 0.8819 (tpt-90) REVERT: C 619 PHE cc_start: 0.9816 (OUTLIER) cc_final: 0.9427 (t80) REVERT: C 623 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.8964 (p) REVERT: C 658 ASN cc_start: 0.8962 (m110) cc_final: 0.8730 (m110) REVERT: C 677 MET cc_start: 0.9765 (tpp) cc_final: 0.9542 (mtm) REVERT: C 691 ASN cc_start: 0.9798 (p0) cc_final: 0.9550 (m-40) REVERT: C 809 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9141 (mp) REVERT: C 821 ASP cc_start: 0.8868 (p0) cc_final: 0.8585 (m-30) REVERT: D 60 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.8856 (pmm) REVERT: D 411 ASP cc_start: 0.9439 (t70) cc_final: 0.9106 (t0) REVERT: D 472 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8580 (tpm170) REVERT: D 538 LYS cc_start: 0.9235 (mmtm) cc_final: 0.9007 (mmtm) REVERT: D 541 ARG cc_start: 0.9062 (tpp80) cc_final: 0.8764 (tpp80) REVERT: D 574 MET cc_start: 0.8262 (mtt) cc_final: 0.8034 (tpt) REVERT: D 658 ASN cc_start: 0.8951 (m110) cc_final: 0.8720 (m110) REVERT: D 677 MET cc_start: 0.9887 (tpp) cc_final: 0.9575 (tmm) REVERT: D 681 ARG cc_start: 0.9532 (mtt180) cc_final: 0.9201 (mmm160) REVERT: D 702 GLN cc_start: 0.9695 (mt0) cc_final: 0.9415 (pp30) REVERT: D 809 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9019 (mp) outliers start: 85 outliers final: 48 residues processed: 558 average time/residue: 0.2685 time to fit residues: 227.0838 Evaluate side-chains 537 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 476 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 ARG Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain B residue 472 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 762 HIS Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 834 HIS Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 637 GLU Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 472 ARG Chi-restraints excluded: chain D residue 479 ASN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 714 ASN Chi-restraints excluded: chain D residue 762 HIS Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 809 LEU Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 858 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 7.9990 chunk 191 optimal weight: 6.9990 chunk 42 optimal weight: 40.0000 chunk 124 optimal weight: 6.9990 chunk 52 optimal weight: 40.0000 chunk 212 optimal weight: 20.0000 chunk 176 optimal weight: 50.0000 chunk 98 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 676 GLN A 691 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 HIS ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 762 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.6213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18000 Z= 0.203 Angle : 0.726 13.171 24432 Z= 0.358 Chirality : 0.045 0.174 2788 Planarity : 0.003 0.032 3064 Dihedral : 4.545 20.408 2420 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.53 % Favored : 95.10 % Rotamer: Outliers : 4.22 % Allowed : 27.65 % Favored : 68.13 % 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: -1.33 (0.17), residues: 2184 helix: -0.32 (0.14), residues: 1172 sheet: -0.70 (0.38), residues: 164 loop : -1.59 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 410 HIS 0.010 0.001 HIS B 834 PHE 0.028 0.002 PHE A 424 TYR 0.016 0.001 TYR B 43 ARG 0.007 0.000 ARG B 784 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 503 time to evaluate : 1.914 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: A 411 ASP cc_start: 0.9411 (t70) cc_final: 0.9029 (t0) REVERT: A 472 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8559 (tpm170) REVERT: A 533 VAL cc_start: 0.9415 (t) cc_final: 0.9169 (p) REVERT: A 538 LYS cc_start: 0.9207 (mmtm) cc_final: 0.8974 (mmtm) REVERT: A 645 MET cc_start: 0.9681 (ptm) cc_final: 0.9312 (ptm) REVERT: A 658 ASN cc_start: 0.9036 (m110) cc_final: 0.8816 (m110) REVERT: A 677 MET cc_start: 0.9823 (tpp) cc_final: 0.9303 (tmm) REVERT: A 678 LEU cc_start: 0.9772 (mt) cc_final: 0.9500 (mt) REVERT: A 681 ARG cc_start: 0.9555 (mtm180) cc_final: 0.9092 (mtp85) REVERT: A 702 GLN cc_start: 0.9680 (mt0) cc_final: 0.9418 (pp30) REVERT: A 711 ILE cc_start: 0.6068 (mt) cc_final: 0.5529 (mp) REVERT: A 809 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8943 (mp) REVERT: A 844 MET cc_start: 0.8811 (mtm) cc_final: 0.8574 (ptp) REVERT: B 410 TRP cc_start: 0.9270 (t60) cc_final: 0.8997 (t60) REVERT: B 411 ASP cc_start: 0.9267 (t70) cc_final: 0.8957 (t0) REVERT: B 472 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8543 (tpp80) REVERT: B 541 ARG cc_start: 0.9052 (tpp80) cc_final: 0.8725 (tpp80) REVERT: B 619 PHE cc_start: 0.9828 (OUTLIER) cc_final: 0.9470 (t80) REVERT: B 623 THR cc_start: 0.9470 (OUTLIER) cc_final: 0.9138 (p) REVERT: B 658 ASN cc_start: 0.9015 (m110) cc_final: 0.8791 (m110) REVERT: B 677 MET cc_start: 0.9849 (tpp) cc_final: 0.9280 (tmm) REVERT: B 678 LEU cc_start: 0.9785 (mt) cc_final: 0.9539 (pp) REVERT: B 681 ARG cc_start: 0.9552 (mtt180) cc_final: 0.9112 (mmm-85) REVERT: B 682 GLU cc_start: 0.9660 (pt0) cc_final: 0.9401 (tp30) REVERT: B 702 GLN cc_start: 0.9630 (mt0) cc_final: 0.9378 (pp30) REVERT: B 712 ASP cc_start: 0.9597 (m-30) cc_final: 0.9342 (p0) REVERT: B 809 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8960 (mp) REVERT: B 827 TYR cc_start: 0.9366 (m-80) cc_final: 0.9043 (t80) REVERT: C 411 ASP cc_start: 0.9307 (OUTLIER) cc_final: 0.8538 (t70) REVERT: C 472 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8537 (tpp80) REVERT: C 541 ARG cc_start: 0.9191 (tpt-90) cc_final: 0.8855 (tpt-90) REVERT: C 658 ASN cc_start: 0.8940 (m110) cc_final: 0.8709 (m110) REVERT: C 677 MET cc_start: 0.9822 (tpp) cc_final: 0.9320 (tmm) REVERT: C 678 LEU cc_start: 0.9798 (pp) cc_final: 0.9570 (pp) REVERT: C 686 PHE cc_start: 0.9151 (t80) cc_final: 0.8518 (t80) REVERT: C 691 ASN cc_start: 0.9812 (p0) cc_final: 0.9553 (t0) REVERT: C 809 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9110 (mp) REVERT: C 821 ASP cc_start: 0.8865 (p0) cc_final: 0.8593 (m-30) REVERT: C 827 TYR cc_start: 0.9469 (m-80) cc_final: 0.9086 (t80) REVERT: D 60 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.8854 (pmm) REVERT: D 411 ASP cc_start: 0.9437 (t70) cc_final: 0.9085 (t0) REVERT: D 472 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8483 (tpp80) REVERT: D 538 LYS cc_start: 0.9255 (mmtm) cc_final: 0.9044 (mmtm) REVERT: D 574 MET cc_start: 0.8250 (mtt) cc_final: 0.8018 (tpt) REVERT: D 658 ASN cc_start: 0.8929 (m110) cc_final: 0.8697 (m110) REVERT: D 677 MET cc_start: 0.9885 (tpp) cc_final: 0.9277 (tmm) REVERT: D 681 ARG cc_start: 0.9518 (mtt180) cc_final: 0.9059 (mmm-85) REVERT: D 702 GLN cc_start: 0.9691 (mt0) cc_final: 0.9401 (pp30) REVERT: D 809 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9054 (mp) REVERT: D 821 ASP cc_start: 0.8851 (p0) cc_final: 0.8621 (m-30) outliers start: 78 outliers final: 51 residues processed: 547 average time/residue: 0.2635 time to fit residues: 221.3796 Evaluate side-chains 542 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 479 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 ARG Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain B residue 472 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 762 HIS Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 637 GLU Chi-restraints excluded: chain C residue 698 GLU Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 762 HIS Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 472 ARG Chi-restraints excluded: chain D residue 479 ASN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 711 ILE Chi-restraints excluded: chain D residue 714 ASN Chi-restraints excluded: chain D residue 762 HIS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 809 LEU Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 858 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 155 optimal weight: 30.0000 chunk 120 optimal weight: 40.0000 chunk 179 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 212 optimal weight: 40.0000 chunk 132 optimal weight: 40.0000 chunk 129 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 GLN A 691 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS ** B 834 HIS ** 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 12 ASN D 676 GLN D 762 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18000 Z= 0.195 Angle : 0.756 14.374 24432 Z= 0.370 Chirality : 0.046 0.279 2788 Planarity : 0.003 0.032 3064 Dihedral : 4.468 20.393 2420 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.62 % Favored : 95.01 % Rotamer: Outliers : 4.44 % Allowed : 29.38 % Favored : 66.18 % 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: -1.30 (0.17), residues: 2184 helix: -0.39 (0.14), residues: 1160 sheet: -0.59 (0.39), residues: 164 loop : -1.44 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 410 HIS 0.012 0.001 HIS B 762 PHE 0.035 0.002 PHE D 640 TYR 0.028 0.001 TYR C 707 ARG 0.007 0.000 ARG D 784 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 503 time to evaluate : 1.991 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: A 411 ASP cc_start: 0.9405 (t70) cc_final: 0.9020 (t0) REVERT: A 472 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8456 (tpp80) REVERT: A 533 VAL cc_start: 0.9405 (t) cc_final: 0.9154 (p) REVERT: A 538 LYS cc_start: 0.9244 (mmtm) cc_final: 0.9007 (mmtm) REVERT: A 658 ASN cc_start: 0.9023 (m110) cc_final: 0.8800 (m110) REVERT: A 677 MET cc_start: 0.9813 (tpp) cc_final: 0.9289 (tmm) REVERT: A 678 LEU cc_start: 0.9754 (mt) cc_final: 0.9497 (mt) REVERT: A 681 ARG cc_start: 0.9535 (mtm180) cc_final: 0.9088 (mtm180) REVERT: A 702 GLN cc_start: 0.9688 (mt0) cc_final: 0.9424 (pp30) REVERT: A 711 ILE cc_start: 0.6113 (mt) cc_final: 0.3955 (mp) REVERT: A 809 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.9007 (mp) REVERT: A 821 ASP cc_start: 0.9167 (p0) cc_final: 0.8942 (m-30) REVERT: B 12 ASN cc_start: 0.9609 (t0) cc_final: 0.9362 (t0) REVERT: B 410 TRP cc_start: 0.9195 (t60) cc_final: 0.8990 (t60) REVERT: B 411 ASP cc_start: 0.9291 (t70) cc_final: 0.8975 (t0) REVERT: B 541 ARG cc_start: 0.9071 (tpp80) cc_final: 0.8772 (tpp80) REVERT: B 645 MET cc_start: 0.9692 (ptm) cc_final: 0.9297 (ptm) REVERT: B 658 ASN cc_start: 0.8987 (m110) cc_final: 0.8764 (m110) REVERT: B 677 MET cc_start: 0.9842 (tpp) cc_final: 0.9257 (tmm) REVERT: B 678 LEU cc_start: 0.9782 (mt) cc_final: 0.9563 (pp) REVERT: B 681 ARG cc_start: 0.9545 (mtt180) cc_final: 0.9083 (mmm-85) REVERT: B 682 GLU cc_start: 0.9666 (pt0) cc_final: 0.9451 (tm-30) REVERT: B 702 GLN cc_start: 0.9619 (mt0) cc_final: 0.9367 (pp30) REVERT: B 712 ASP cc_start: 0.9606 (m-30) cc_final: 0.9361 (p0) REVERT: B 809 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8942 (mp) REVERT: B 827 TYR cc_start: 0.9339 (m-80) cc_final: 0.8994 (t80) REVERT: C 411 ASP cc_start: 0.9302 (OUTLIER) cc_final: 0.8509 (t70) REVERT: C 472 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8518 (tpp80) REVERT: C 541 ARG cc_start: 0.9223 (tpt-90) cc_final: 0.8887 (tpt-90) REVERT: C 619 PHE cc_start: 0.9815 (OUTLIER) cc_final: 0.9431 (t80) REVERT: C 658 ASN cc_start: 0.8930 (m110) cc_final: 0.8703 (m110) REVERT: C 677 MET cc_start: 0.9835 (tpp) cc_final: 0.9483 (tmm) REVERT: C 686 PHE cc_start: 0.8785 (t80) cc_final: 0.8469 (t80) REVERT: C 687 HIS cc_start: 0.8978 (m-70) cc_final: 0.8207 (m-70) REVERT: C 691 ASN cc_start: 0.9816 (p0) cc_final: 0.9559 (t0) REVERT: C 762 HIS cc_start: 0.8343 (m90) cc_final: 0.7424 (m170) REVERT: C 809 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9130 (mp) REVERT: C 821 ASP cc_start: 0.8862 (p0) cc_final: 0.8593 (m-30) REVERT: C 827 TYR cc_start: 0.9452 (m-80) cc_final: 0.9071 (t80) REVERT: D 411 ASP cc_start: 0.9409 (t70) cc_final: 0.8960 (t0) REVERT: D 472 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8450 (tpp80) REVERT: D 541 ARG cc_start: 0.9108 (tpp80) cc_final: 0.8863 (tpp80) REVERT: D 574 MET cc_start: 0.8227 (mtt) cc_final: 0.7996 (tpt) REVERT: D 658 ASN cc_start: 0.8924 (m110) cc_final: 0.8694 (m110) REVERT: D 677 MET cc_start: 0.9880 (tpp) cc_final: 0.9215 (tmm) REVERT: D 681 ARG cc_start: 0.9507 (mtt180) cc_final: 0.9004 (mmm-85) REVERT: D 702 GLN cc_start: 0.9676 (mt0) cc_final: 0.9384 (pp30) REVERT: D 809 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9073 (mp) outliers start: 82 outliers final: 52 residues processed: 542 average time/residue: 0.2520 time to fit residues: 211.7889 Evaluate side-chains 547 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 486 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 ARG Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 762 HIS Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 698 GLU Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 472 ARG Chi-restraints excluded: chain D residue 479 ASN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 698 GLU Chi-restraints excluded: chain D residue 714 ASN Chi-restraints excluded: chain D residue 762 HIS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 809 LEU Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 858 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 126 optimal weight: 0.3980 chunk 63 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 19 optimal weight: 0.0980 chunk 166 optimal weight: 6.9990 chunk 192 optimal weight: 30.0000 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 GLN A 691 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 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 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 GLN D 762 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.6560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18000 Z= 0.195 Angle : 0.775 14.415 24432 Z= 0.374 Chirality : 0.045 0.207 2788 Planarity : 0.004 0.033 3064 Dihedral : 4.450 20.333 2420 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.49 % Favored : 95.15 % Rotamer: Outliers : 4.00 % Allowed : 30.41 % Favored : 65.58 % 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: -1.23 (0.17), residues: 2184 helix: -0.44 (0.14), residues: 1196 sheet: -0.67 (0.35), residues: 212 loop : -1.23 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 410 HIS 0.012 0.001 HIS B 762 PHE 0.040 0.002 PHE C 640 TYR 0.036 0.001 TYR B 700 ARG 0.008 0.000 ARG D 784 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 493 time to evaluate : 1.996 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: A 411 ASP cc_start: 0.9407 (t70) cc_final: 0.9028 (t0) REVERT: A 472 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8441 (tpp80) REVERT: A 533 VAL cc_start: 0.9395 (t) cc_final: 0.9134 (p) REVERT: A 538 LYS cc_start: 0.9269 (mmtm) cc_final: 0.9055 (mmtm) REVERT: A 658 ASN cc_start: 0.9006 (m110) cc_final: 0.8785 (m110) REVERT: A 677 MET cc_start: 0.9808 (tpp) cc_final: 0.9166 (tmm) REVERT: A 678 LEU cc_start: 0.9749 (mt) cc_final: 0.9479 (mt) REVERT: A 681 ARG cc_start: 0.9533 (mtm180) cc_final: 0.8919 (mmm-85) REVERT: A 702 GLN cc_start: 0.9690 (mt0) cc_final: 0.9432 (pp30) REVERT: A 711 ILE cc_start: 0.6054 (OUTLIER) cc_final: 0.5298 (mp) REVERT: A 809 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8968 (mp) REVERT: A 821 ASP cc_start: 0.9168 (p0) cc_final: 0.8964 (m-30) REVERT: B 12 ASN cc_start: 0.9619 (t0) cc_final: 0.9339 (t0) REVERT: B 411 ASP cc_start: 0.9309 (t70) cc_final: 0.8971 (t0) REVERT: B 541 ARG cc_start: 0.9089 (tpp80) cc_final: 0.8816 (tpp80) REVERT: B 619 PHE cc_start: 0.9815 (OUTLIER) cc_final: 0.9562 (t80) REVERT: B 658 ASN cc_start: 0.8963 (m110) cc_final: 0.8741 (m110) REVERT: B 677 MET cc_start: 0.9832 (tpp) cc_final: 0.9255 (tmm) REVERT: B 678 LEU cc_start: 0.9778 (mt) cc_final: 0.9531 (pp) REVERT: B 681 ARG cc_start: 0.9544 (mtt180) cc_final: 0.9066 (mmm-85) REVERT: B 682 GLU cc_start: 0.9672 (pt0) cc_final: 0.9405 (tp30) REVERT: B 702 GLN cc_start: 0.9593 (mt0) cc_final: 0.9306 (pp30) REVERT: B 712 ASP cc_start: 0.9626 (m-30) cc_final: 0.9405 (p0) REVERT: B 784 ARG cc_start: 0.9401 (mtp-110) cc_final: 0.9088 (mtp-110) REVERT: B 809 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8948 (mp) REVERT: B 827 TYR cc_start: 0.9321 (m-80) cc_final: 0.9011 (t80) REVERT: C 109 LEU cc_start: 0.9477 (tp) cc_final: 0.9042 (pp) REVERT: C 411 ASP cc_start: 0.9316 (OUTLIER) cc_final: 0.8614 (t70) REVERT: C 472 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8490 (tpp80) REVERT: C 541 ARG cc_start: 0.9238 (tpt-90) cc_final: 0.8914 (tpt-90) REVERT: C 619 PHE cc_start: 0.9804 (OUTLIER) cc_final: 0.9411 (t80) REVERT: C 658 ASN cc_start: 0.8914 (m110) cc_final: 0.8689 (m110) REVERT: C 677 MET cc_start: 0.9831 (tpp) cc_final: 0.9483 (tmm) REVERT: C 691 ASN cc_start: 0.9813 (p0) cc_final: 0.9549 (t0) REVERT: C 809 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9143 (mp) REVERT: C 821 ASP cc_start: 0.8869 (p0) cc_final: 0.8600 (m-30) REVERT: D 411 ASP cc_start: 0.9385 (t70) cc_final: 0.9001 (t0) REVERT: D 472 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8430 (tpp80) REVERT: D 541 ARG cc_start: 0.9114 (tpp80) cc_final: 0.8887 (tpp80) REVERT: D 574 MET cc_start: 0.8233 (mtt) cc_final: 0.7980 (tpt) REVERT: D 619 PHE cc_start: 0.9834 (OUTLIER) cc_final: 0.9476 (t80) REVERT: D 658 ASN cc_start: 0.8922 (m110) cc_final: 0.8693 (m110) REVERT: D 677 MET cc_start: 0.9869 (tpp) cc_final: 0.9213 (tmm) REVERT: D 681 ARG cc_start: 0.9497 (mtt180) cc_final: 0.9021 (mmm-85) REVERT: D 702 GLN cc_start: 0.9669 (mt0) cc_final: 0.9366 (pp30) REVERT: D 809 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9058 (mp) REVERT: D 821 ASP cc_start: 0.8777 (p0) cc_final: 0.8445 (m-30) outliers start: 74 outliers final: 48 residues processed: 532 average time/residue: 0.2572 time to fit residues: 210.7627 Evaluate side-chains 541 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 481 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 ARG Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 714 ASN Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 698 GLU Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 472 ARG Chi-restraints excluded: chain D residue 479 ASN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 698 GLU Chi-restraints excluded: chain D residue 714 ASN Chi-restraints excluded: chain D residue 762 HIS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 809 LEU Chi-restraints excluded: chain D residue 858 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 9.9990 chunk 185 optimal weight: 30.0000 chunk 197 optimal weight: 5.9990 chunk 118 optimal weight: 50.0000 chunk 86 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 60 optimal weight: 30.0000 chunk 178 optimal weight: 20.0000 chunk 186 optimal weight: 0.0570 chunk 196 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 overall best weight: 4.6106 ------------------------------------------------------------------------------- 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 676 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 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 12 ASN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 GLN D 762 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.6671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18000 Z= 0.201 Angle : 0.800 13.598 24432 Z= 0.385 Chirality : 0.047 0.281 2788 Planarity : 0.003 0.034 3064 Dihedral : 4.449 20.052 2420 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.49 % Favored : 95.15 % Rotamer: Outliers : 3.84 % Allowed : 31.17 % Favored : 64.99 % 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: -1.26 (0.17), residues: 2184 helix: -0.50 (0.14), residues: 1212 sheet: -0.64 (0.36), residues: 212 loop : -1.21 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 410 HIS 0.007 0.001 HIS C 762 PHE 0.035 0.002 PHE D 424 TYR 0.040 0.001 TYR B 700 ARG 0.009 0.000 ARG D 784 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 494 time to evaluate : 2.107 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: A 12 ASN cc_start: 0.9522 (m-40) cc_final: 0.9310 (t0) REVERT: A 411 ASP cc_start: 0.9402 (t70) cc_final: 0.9122 (t0) REVERT: A 472 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8424 (tpp80) REVERT: A 533 VAL cc_start: 0.9382 (t) cc_final: 0.9113 (p) REVERT: A 538 LYS cc_start: 0.9289 (mmtm) cc_final: 0.9072 (mmtm) REVERT: A 619 PHE cc_start: 0.9847 (OUTLIER) cc_final: 0.9518 (t80) REVERT: A 658 ASN cc_start: 0.8978 (m110) cc_final: 0.8759 (m110) REVERT: A 677 MET cc_start: 0.9806 (tpp) cc_final: 0.9186 (tmm) REVERT: A 678 LEU cc_start: 0.9746 (mt) cc_final: 0.9487 (mt) REVERT: A 681 ARG cc_start: 0.9525 (mtm180) cc_final: 0.8898 (mmm-85) REVERT: A 702 GLN cc_start: 0.9689 (mt0) cc_final: 0.9433 (pp30) REVERT: A 711 ILE cc_start: 0.6289 (OUTLIER) cc_final: 0.5645 (mp) REVERT: A 809 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8945 (mp) REVERT: B 12 ASN cc_start: 0.9634 (t0) cc_final: 0.9369 (t0) REVERT: B 411 ASP cc_start: 0.9285 (t70) cc_final: 0.8980 (t0) REVERT: B 541 ARG cc_start: 0.9117 (tpp80) cc_final: 0.8850 (tpp80) REVERT: B 619 PHE cc_start: 0.9813 (OUTLIER) cc_final: 0.9565 (t80) REVERT: B 645 MET cc_start: 0.9683 (ptm) cc_final: 0.9322 (ptm) REVERT: B 658 ASN cc_start: 0.8942 (m110) cc_final: 0.8720 (m110) REVERT: B 677 MET cc_start: 0.9826 (tpp) cc_final: 0.9497 (tmm) REVERT: B 681 ARG cc_start: 0.9535 (mtt180) cc_final: 0.9303 (mtm180) REVERT: B 682 GLU cc_start: 0.9671 (pt0) cc_final: 0.9397 (tp30) REVERT: B 712 ASP cc_start: 0.9704 (m-30) cc_final: 0.9461 (p0) REVERT: B 784 ARG cc_start: 0.9401 (mtp-110) cc_final: 0.9066 (mtp-110) REVERT: B 821 ASP cc_start: 0.9227 (m-30) cc_final: 0.9003 (p0) REVERT: B 827 TYR cc_start: 0.9297 (m-80) cc_final: 0.8970 (t80) REVERT: C 109 LEU cc_start: 0.9473 (tp) cc_final: 0.9035 (pp) REVERT: C 411 ASP cc_start: 0.9307 (OUTLIER) cc_final: 0.8613 (t70) REVERT: C 541 ARG cc_start: 0.9247 (tpt-90) cc_final: 0.8940 (tpt-90) REVERT: C 619 PHE cc_start: 0.9806 (OUTLIER) cc_final: 0.9391 (t80) REVERT: C 658 ASN cc_start: 0.8909 (m110) cc_final: 0.8683 (m110) REVERT: C 677 MET cc_start: 0.9826 (tpp) cc_final: 0.9483 (tmm) REVERT: C 691 ASN cc_start: 0.9810 (p0) cc_final: 0.9538 (t0) REVERT: C 809 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9123 (mp) REVERT: C 821 ASP cc_start: 0.8885 (p0) cc_final: 0.8621 (m-30) REVERT: D 411 ASP cc_start: 0.9358 (t70) cc_final: 0.8950 (t0) REVERT: D 472 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8402 (tpp80) REVERT: D 541 ARG cc_start: 0.9131 (tpp80) cc_final: 0.8908 (tpp80) REVERT: D 574 MET cc_start: 0.8255 (mtt) cc_final: 0.7993 (tpt) REVERT: D 619 PHE cc_start: 0.9835 (OUTLIER) cc_final: 0.9537 (t80) REVERT: D 658 ASN cc_start: 0.8912 (m110) cc_final: 0.8682 (m110) REVERT: D 677 MET cc_start: 0.9866 (tpp) cc_final: 0.9166 (tmm) REVERT: D 681 ARG cc_start: 0.9492 (mtt180) cc_final: 0.8972 (mmm-85) REVERT: D 702 GLN cc_start: 0.9663 (mt0) cc_final: 0.9351 (pp30) REVERT: D 809 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9053 (mp) REVERT: D 821 ASP cc_start: 0.8786 (p0) cc_final: 0.8439 (m-30) outliers start: 71 outliers final: 45 residues processed: 531 average time/residue: 0.2705 time to fit residues: 223.2524 Evaluate side-chains 535 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 479 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 ARG Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 501 ASP Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 698 GLU Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 472 ARG Chi-restraints excluded: chain D residue 479 ASN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 698 GLU Chi-restraints excluded: chain D residue 714 ASN Chi-restraints excluded: chain D residue 762 HIS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 809 LEU Chi-restraints excluded: chain D residue 858 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 chunk 99 optimal weight: 30.0000 chunk 145 optimal weight: 9.9990 chunk 219 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 134 optimal weight: 30.0000 chunk 107 optimal weight: 40.0000 chunk 138 optimal weight: 20.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 GLN A 691 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN ** 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 676 GLN ** D 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 : 0.004 0.046 18000 Z= 0.236 Angle : 0.842 14.816 24432 Z= 0.405 Chirality : 0.047 0.259 2788 Planarity : 0.004 0.040 3064 Dihedral : 4.518 21.446 2420 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 25.60 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.53 % Favored : 95.10 % Rotamer: Outliers : 3.35 % Allowed : 32.14 % Favored : 64.50 % 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: -1.25 (0.17), residues: 2184 helix: -0.47 (0.14), residues: 1176 sheet: -0.71 (0.36), residues: 212 loop : -1.18 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP B 410 HIS 0.014 0.001 HIS D 762 PHE 0.045 0.002 PHE D 640 TYR 0.032 0.002 TYR B 700 ARG 0.009 0.000 ARG D 784 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 487 time to evaluate : 2.156 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: A 411 ASP cc_start: 0.9369 (t70) cc_final: 0.9000 (t0) REVERT: A 533 VAL cc_start: 0.9370 (t) cc_final: 0.9145 (p) REVERT: A 619 PHE cc_start: 0.9855 (OUTLIER) cc_final: 0.9529 (t80) REVERT: A 658 ASN cc_start: 0.8992 (m110) cc_final: 0.8775 (m110) REVERT: A 677 MET cc_start: 0.9811 (tpp) cc_final: 0.9155 (tmm) REVERT: A 678 LEU cc_start: 0.9746 (mt) cc_final: 0.9515 (mt) REVERT: A 681 ARG cc_start: 0.9527 (mtm180) cc_final: 0.8910 (mmm-85) REVERT: A 702 GLN cc_start: 0.9688 (mt0) cc_final: 0.9432 (pp30) REVERT: A 809 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8929 (mp) REVERT: B 12 ASN cc_start: 0.9647 (m-40) cc_final: 0.9391 (t0) REVERT: B 411 ASP cc_start: 0.9262 (t70) cc_final: 0.8957 (t0) REVERT: B 541 ARG cc_start: 0.9120 (tpp80) cc_final: 0.8848 (tpp80) REVERT: B 619 PHE cc_start: 0.9824 (OUTLIER) cc_final: 0.9594 (t80) REVERT: B 645 MET cc_start: 0.9677 (ptm) cc_final: 0.9377 (ptm) REVERT: B 658 ASN cc_start: 0.8941 (m110) cc_final: 0.8720 (m110) REVERT: B 677 MET cc_start: 0.9857 (tpp) cc_final: 0.9503 (tmm) REVERT: B 681 ARG cc_start: 0.9553 (mtt180) cc_final: 0.9309 (mtm180) REVERT: B 712 ASP cc_start: 0.9706 (m-30) cc_final: 0.9468 (p0) REVERT: B 821 ASP cc_start: 0.9264 (m-30) cc_final: 0.9004 (p0) REVERT: B 827 TYR cc_start: 0.9310 (m-80) cc_final: 0.8954 (t80) REVERT: C 109 LEU cc_start: 0.9485 (tp) cc_final: 0.9037 (pp) REVERT: C 411 ASP cc_start: 0.9288 (OUTLIER) cc_final: 0.8580 (t70) REVERT: C 541 ARG cc_start: 0.9241 (tpt-90) cc_final: 0.8927 (tpt-90) REVERT: C 619 PHE cc_start: 0.9813 (OUTLIER) cc_final: 0.9441 (t80) REVERT: C 658 ASN cc_start: 0.8900 (m110) cc_final: 0.8673 (m110) REVERT: C 677 MET cc_start: 0.9824 (tpp) cc_final: 0.9481 (tmm) REVERT: C 809 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9095 (mp) REVERT: C 821 ASP cc_start: 0.8897 (p0) cc_final: 0.8626 (m-30) REVERT: D 12 ASN cc_start: 0.9626 (m-40) cc_final: 0.9217 (t0) REVERT: D 411 ASP cc_start: 0.9331 (t70) cc_final: 0.9011 (t0) REVERT: D 541 ARG cc_start: 0.9140 (tpp80) cc_final: 0.8923 (tpp80) REVERT: D 574 MET cc_start: 0.8261 (mtt) cc_final: 0.7993 (tpt) REVERT: D 619 PHE cc_start: 0.9845 (OUTLIER) cc_final: 0.9569 (t80) REVERT: D 658 ASN cc_start: 0.8910 (m110) cc_final: 0.8681 (m110) REVERT: D 677 MET cc_start: 0.9884 (tpp) cc_final: 0.9259 (tmm) REVERT: D 681 ARG cc_start: 0.9508 (mtt180) cc_final: 0.9008 (mmm-85) REVERT: D 702 GLN cc_start: 0.9678 (mt0) cc_final: 0.9361 (pp30) REVERT: D 809 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9020 (mp) REVERT: D 821 ASP cc_start: 0.8827 (p0) cc_final: 0.8466 (m-30) outliers start: 62 outliers final: 41 residues processed: 523 average time/residue: 0.2548 time to fit residues: 206.6406 Evaluate side-chains 526 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 477 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 501 ASP Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 698 GLU Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 479 ASN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 698 GLU Chi-restraints excluded: chain D residue 714 ASN Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 809 LEU Chi-restraints excluded: chain D residue 858 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 160 optimal weight: 40.0000 chunk 25 optimal weight: 30.0000 chunk 48 optimal weight: 5.9990 chunk 174 optimal weight: 30.0000 chunk 73 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 22 optimal weight: 40.0000 chunk 32 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 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 12 ASN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 GLN D 762 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.065527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.053574 restraints weight = 99097.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.055113 restraints weight = 62622.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.056244 restraints weight = 44543.273| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.6980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18000 Z= 0.220 Angle : 0.852 14.831 24432 Z= 0.408 Chirality : 0.048 0.269 2788 Planarity : 0.004 0.035 3064 Dihedral : 4.530 21.399 2420 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 24.60 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.90 % Favored : 94.73 % Rotamer: Outliers : 3.14 % Allowed : 32.74 % Favored : 64.12 % 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: -1.25 (0.17), residues: 2184 helix: -0.50 (0.14), residues: 1184 sheet: -0.70 (0.35), residues: 212 loop : -1.17 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP C 410 HIS 0.006 0.001 HIS C 762 PHE 0.044 0.002 PHE D 640 TYR 0.028 0.002 TYR B 700 ARG 0.008 0.000 ARG D 784 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5727.67 seconds wall clock time: 102 minutes 52.22 seconds (6172.22 seconds total)