Starting phenix.real_space_refine on Sun Mar 17 11:42:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va1_8650/03_2024/5va1_8650.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va1_8650/03_2024/5va1_8650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va1_8650/03_2024/5va1_8650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va1_8650/03_2024/5va1_8650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va1_8650/03_2024/5va1_8650.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va1_8650/03_2024/5va1_8650.pdb" } resolution = 3.7 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= 0.002 sd= 0.003 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 11484 2.51 5 N 3008 2.21 5 O 3028 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 TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 92": "NH1" <-> "NH2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 534": "NH1" <-> "NH2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "B ARG 4": "NH1" <-> "NH2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 488": "NH1" <-> "NH2" Residue "B TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 534": "NH1" <-> "NH2" Residue "B ARG 672": "NH1" <-> "NH2" Residue "C ARG 4": "NH1" <-> "NH2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 488": "NH1" <-> "NH2" Residue "C TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C ARG 672": "NH1" <-> "NH2" Residue "D ARG 4": "NH1" <-> "NH2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 488": "NH1" <-> "NH2" Residue "D TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 534": "NH1" <-> "NH2" Residue "D ARG 672": "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: 17628 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4407 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 537} Chain breaks: 5 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 63 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: 4407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4407 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 537} Chain breaks: 5 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 63 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: 4407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4407 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 537} Chain breaks: 5 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 63 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: 4407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4407 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 537} Chain breaks: 5 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 63 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: 9.18, per 1000 atoms: 0.52 Number of scatterers: 17628 At special positions: 0 Unit cell: (146.87, 146.77, 121.283, 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 3028 8.00 N 3008 7.00 C 11484 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: 6.28 Conformation dependent library (CDL) restraints added in 3.1 seconds 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4200 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 12 sheets defined 61.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 13 through 26 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.532A pdb=" N CYS A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.567A pdb=" N GLN A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 431 removed outlier: 3.763A pdb=" N TRP A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 450 through 473 removed outlier: 3.564A pdb=" N VAL A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 472 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 494 removed outlier: 3.566A pdb=" N ILE A 489 " --> pdb=" O HIS A 485 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 505 removed outlier: 3.765A pdb=" N VAL A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.534A pdb=" N ALA A 527 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 removed outlier: 3.851A pdb=" N ALA A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 removed outlier: 3.894A pdb=" N TYR A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 575 removed outlier: 3.605A pdb=" N VAL A 549 " --> pdb=" O TYR A 545 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 550 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 572 " --> pdb=" O TRP A 568 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 593 removed outlier: 3.624A pdb=" N ASN A 588 " --> pdb=" O GLY A 584 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 623 removed outlier: 3.549A pdb=" N ALA A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 667 removed outlier: 3.870A pdb=" N PHE A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 688 removed outlier: 3.583A pdb=" N HIS A 674 " --> pdb=" O THR A 670 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 680 " --> pdb=" O GLN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 709 removed outlier: 4.037A pdb=" N ARG A 696 " --> pdb=" O PRO A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 removed outlier: 3.714A pdb=" N VAL A 716 " --> pdb=" O ASP A 712 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 733 Processing helix chain 'A' and resid 733 through 740 removed outlier: 3.924A pdb=" N HIS A 739 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 758 removed outlier: 3.871A pdb=" N LYS A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 813 removed outlier: 4.658A pdb=" N TYR A 812 " --> pdb=" O PRO A 808 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 808 through 813' Processing helix chain 'A' and resid 834 through 845 removed outlier: 3.743A pdb=" N GLU A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 841 " --> pdb=" O ASP A 837 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET A 844 " --> pdb=" O GLU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 856 removed outlier: 3.823A pdb=" N ASP A 850 " --> pdb=" O PRO A 846 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 854 " --> pdb=" O ASP A 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 26 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.532A pdb=" N CYS B 49 " --> pdb=" O ASN B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 75 through 89 removed outlier: 3.567A pdb=" N GLN B 81 " --> pdb=" O ARG B 77 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 431 removed outlier: 3.763A pdb=" N TRP B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Proline residue: B 426 - end of helix Processing helix chain 'B' and resid 450 through 473 removed outlier: 3.564A pdb=" N VAL B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B 472 " --> pdb=" O LEU B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 494 removed outlier: 3.566A pdb=" N ILE B 489 " --> pdb=" O HIS B 485 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS B 492 " --> pdb=" O ARG B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 505 removed outlier: 3.765A pdb=" N VAL B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 504 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 531 removed outlier: 3.534A pdb=" N ALA B 527 " --> pdb=" O LEU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 538 removed outlier: 3.851A pdb=" N ALA B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 removed outlier: 3.894A pdb=" N TYR B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 575 removed outlier: 3.605A pdb=" N VAL B 549 " --> pdb=" O TYR B 545 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 550 " --> pdb=" O GLY B 546 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY B 572 " --> pdb=" O TRP B 568 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU B 575 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 593 removed outlier: 3.624A pdb=" N ASN B 588 " --> pdb=" O GLY B 584 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 623 removed outlier: 3.549A pdb=" N ALA B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 667 removed outlier: 3.870A pdb=" N PHE B 656 " --> pdb=" O TYR B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 688 removed outlier: 3.583A pdb=" N HIS B 674 " --> pdb=" O THR B 670 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 680 " --> pdb=" O GLN B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 709 removed outlier: 4.037A pdb=" N ARG B 696 " --> pdb=" O PRO B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 removed outlier: 3.714A pdb=" N VAL B 716 " --> pdb=" O ASP B 712 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 733 Processing helix chain 'B' and resid 733 through 740 removed outlier: 3.924A pdb=" N HIS B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 758 removed outlier: 3.871A pdb=" N LYS B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 813 removed outlier: 4.658A pdb=" N TYR B 812 " --> pdb=" O PRO B 808 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 813 " --> pdb=" O LEU B 809 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 808 through 813' Processing helix chain 'B' and resid 834 through 845 removed outlier: 3.743A pdb=" N GLU B 840 " --> pdb=" O ASP B 836 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 841 " --> pdb=" O ASP B 837 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET B 844 " --> pdb=" O GLU B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 856 removed outlier: 3.823A pdb=" N ASP B 850 " --> pdb=" O PRO B 846 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS B 851 " --> pdb=" O GLU B 847 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER B 854 " --> pdb=" O ASP B 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 26 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.532A pdb=" N CYS C 49 " --> pdb=" O ASN C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 75 through 89 removed outlier: 3.567A pdb=" N GLN C 81 " --> pdb=" O ARG C 77 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 86 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 431 removed outlier: 3.763A pdb=" N TRP C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Proline residue: C 426 - end of helix Processing helix chain 'C' and resid 450 through 473 removed outlier: 3.564A pdb=" N VAL C 455 " --> pdb=" O PRO C 451 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE C 471 " --> pdb=" O ILE C 467 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG C 472 " --> pdb=" O LEU C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 494 removed outlier: 3.566A pdb=" N ILE C 489 " --> pdb=" O HIS C 485 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL C 491 " --> pdb=" O GLY C 487 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS C 492 " --> pdb=" O ARG C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 505 removed outlier: 3.765A pdb=" N VAL C 503 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C 504 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA C 505 " --> pdb=" O ASP C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 531 removed outlier: 3.534A pdb=" N ALA C 527 " --> pdb=" O LEU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 538 removed outlier: 3.851A pdb=" N ALA C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 removed outlier: 3.894A pdb=" N TYR C 542 " --> pdb=" O LYS C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 575 removed outlier: 3.605A pdb=" N VAL C 549 " --> pdb=" O TYR C 545 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 550 " --> pdb=" O GLY C 546 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 572 " --> pdb=" O TRP C 568 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU C 575 " --> pdb=" O ILE C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 593 removed outlier: 3.624A pdb=" N ASN C 588 " --> pdb=" O GLY C 584 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP C 591 " --> pdb=" O HIS C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 623 removed outlier: 3.549A pdb=" N ALA C 614 " --> pdb=" O LYS C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 667 removed outlier: 3.870A pdb=" N PHE C 656 " --> pdb=" O TYR C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 688 removed outlier: 3.583A pdb=" N HIS C 674 " --> pdb=" O THR C 670 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 680 " --> pdb=" O GLN C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 709 removed outlier: 4.037A pdb=" N ARG C 696 " --> pdb=" O PRO C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 718 removed outlier: 3.714A pdb=" N VAL C 716 " --> pdb=" O ASP C 712 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 717 " --> pdb=" O MET C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 733 Processing helix chain 'C' and resid 733 through 740 removed outlier: 3.924A pdb=" N HIS C 739 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 758 removed outlier: 3.871A pdb=" N LYS C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 813 removed outlier: 4.658A pdb=" N TYR C 812 " --> pdb=" O PRO C 808 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA C 813 " --> pdb=" O LEU C 809 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 808 through 813' Processing helix chain 'C' and resid 834 through 845 removed outlier: 3.743A pdb=" N GLU C 840 " --> pdb=" O ASP C 836 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 841 " --> pdb=" O ASP C 837 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET C 844 " --> pdb=" O GLU C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 856 removed outlier: 3.823A pdb=" N ASP C 850 " --> pdb=" O PRO C 846 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS C 851 " --> pdb=" O GLU C 847 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER C 854 " --> pdb=" O ASP C 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 45 through 53 removed outlier: 3.532A pdb=" N CYS D 49 " --> pdb=" O ASN D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 75 through 89 removed outlier: 3.567A pdb=" N GLN D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 431 removed outlier: 3.763A pdb=" N TRP D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Proline residue: D 426 - end of helix Processing helix chain 'D' and resid 450 through 473 removed outlier: 3.564A pdb=" N VAL D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG D 472 " --> pdb=" O LEU D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 494 removed outlier: 3.566A pdb=" N ILE D 489 " --> pdb=" O HIS D 485 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 490 " --> pdb=" O PRO D 486 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL D 491 " --> pdb=" O GLY D 487 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS D 492 " --> pdb=" O ARG D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 505 removed outlier: 3.765A pdb=" N VAL D 503 " --> pdb=" O LEU D 499 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA D 504 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA D 505 " --> pdb=" O ASP D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 531 removed outlier: 3.534A pdb=" N ALA D 527 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 538 removed outlier: 3.851A pdb=" N ALA D 536 " --> pdb=" O LEU D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 543 removed outlier: 3.894A pdb=" N TYR D 542 " --> pdb=" O LYS D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 575 removed outlier: 3.605A pdb=" N VAL D 549 " --> pdb=" O TYR D 545 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU D 550 " --> pdb=" O GLY D 546 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY D 572 " --> pdb=" O TRP D 568 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU D 575 " --> pdb=" O ILE D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 593 removed outlier: 3.624A pdb=" N ASN D 588 " --> pdb=" O GLY D 584 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 623 removed outlier: 3.549A pdb=" N ALA D 614 " --> pdb=" O LYS D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 667 removed outlier: 3.870A pdb=" N PHE D 656 " --> pdb=" O TYR D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 688 removed outlier: 3.583A pdb=" N HIS D 674 " --> pdb=" O THR D 670 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 680 " --> pdb=" O GLN D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 709 removed outlier: 4.037A pdb=" N ARG D 696 " --> pdb=" O PRO D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 718 removed outlier: 3.714A pdb=" N VAL D 716 " --> pdb=" O ASP D 712 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU D 717 " --> pdb=" O MET D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 733 Processing helix chain 'D' and resid 733 through 740 removed outlier: 3.924A pdb=" N HIS D 739 " --> pdb=" O SER D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 758 removed outlier: 3.871A pdb=" N LYS D 757 " --> pdb=" O ALA D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 813 removed outlier: 4.658A pdb=" N TYR D 812 " --> pdb=" O PRO D 808 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA D 813 " --> pdb=" O LEU D 809 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 808 through 813' Processing helix chain 'D' and resid 834 through 845 removed outlier: 3.743A pdb=" N GLU D 840 " --> pdb=" O ASP D 836 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL D 841 " --> pdb=" O ASP D 837 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET D 844 " --> pdb=" O GLU D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 856 removed outlier: 3.823A pdb=" N ASP D 850 " --> pdb=" O PRO D 846 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS D 851 " --> pdb=" O GLU D 847 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER D 854 " --> pdb=" O ASP D 850 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.274A pdb=" N ILE A 31 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N CYS A 44 " --> pdb=" O PHE A 29 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N PHE A 29 " --> pdb=" O CYS A 44 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS A 28 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 30 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET A 124 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 130 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 112 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG A 92 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 759 through 763 removed outlier: 3.908A pdb=" N LEU A 830 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 803 " --> pdb=" O ILE A 782 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 860 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 806 " --> pdb=" O PHE A 860 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 768 through 770 removed outlier: 7.088A pdb=" N VAL A 822 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.274A pdb=" N ILE B 31 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N CYS B 44 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N PHE B 29 " --> pdb=" O CYS B 44 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS B 28 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 30 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET B 124 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 130 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 112 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG B 92 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 759 through 763 removed outlier: 3.908A pdb=" N LEU B 830 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP B 803 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE B 860 " --> pdb=" O ILE B 804 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 806 " --> pdb=" O PHE B 860 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 768 through 770 removed outlier: 7.088A pdb=" N VAL B 822 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 41 through 44 removed outlier: 6.274A pdb=" N ILE C 31 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N CYS C 44 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N PHE C 29 " --> pdb=" O CYS C 44 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS C 28 " --> pdb=" O PHE C 129 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE C 30 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET C 124 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C 130 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 112 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG C 92 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 759 through 763 removed outlier: 3.908A pdb=" N LEU C 830 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP C 803 " --> pdb=" O ILE C 782 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE C 860 " --> pdb=" O ILE C 804 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 806 " --> pdb=" O PHE C 860 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 768 through 770 removed outlier: 7.088A pdb=" N VAL C 822 " --> pdb=" O LEU C 769 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 41 through 44 removed outlier: 6.274A pdb=" N ILE D 31 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N CYS D 44 " --> pdb=" O PHE D 29 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N PHE D 29 " --> pdb=" O CYS D 44 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS D 28 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE D 30 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET D 124 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU D 130 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL D 112 " --> pdb=" O ARG D 92 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG D 92 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 759 through 763 removed outlier: 3.908A pdb=" N LEU D 830 " --> pdb=" O THR D 761 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP D 803 " --> pdb=" O ILE D 782 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE D 860 " --> pdb=" O ILE D 804 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 806 " --> pdb=" O PHE D 860 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 768 through 770 removed outlier: 7.088A pdb=" N VAL D 822 " --> pdb=" O LEU D 769 " (cutoff:3.500A) 940 hydrogen bonds defined for protein. 2688 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: 5.03 Time building geometry restraints manager: 6.89 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: 5512 1.34 - 1.46: 2352 1.46 - 1.58: 10040 1.58 - 1.69: 0 1.69 - 1.81: 152 Bond restraints: 18056 Sorted by residual: bond pdb=" N GLY B 603 " pdb=" CA GLY B 603 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.68e+00 bond pdb=" N GLY A 603 " pdb=" CA GLY A 603 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.68e+00 bond pdb=" N GLY D 603 " pdb=" CA GLY D 603 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.68e+00 bond pdb=" N GLY C 603 " pdb=" CA GLY C 603 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.68e+00 bond pdb=" CA PRO B 764 " pdb=" C PRO B 764 " ideal model delta sigma weight residual 1.517 1.540 -0.023 9.30e-03 1.16e+04 6.32e+00 ... (remaining 18051 not shown) Histogram of bond angle deviations from ideal: 100.92 - 107.53: 644 107.53 - 114.14: 9884 114.14 - 120.74: 7480 120.74 - 127.35: 6324 127.35 - 133.95: 180 Bond angle restraints: 24512 Sorted by residual: angle pdb=" N ASN D 691 " pdb=" CA ASN D 691 " pdb=" C ASN D 691 " ideal model delta sigma weight residual 112.75 118.20 -5.45 1.36e+00 5.41e-01 1.60e+01 angle pdb=" N ASN B 691 " pdb=" CA ASN B 691 " pdb=" C ASN B 691 " ideal model delta sigma weight residual 112.75 118.20 -5.45 1.36e+00 5.41e-01 1.60e+01 angle pdb=" N ASN A 691 " pdb=" CA ASN A 691 " pdb=" C ASN A 691 " ideal model delta sigma weight residual 112.75 118.20 -5.45 1.36e+00 5.41e-01 1.60e+01 angle pdb=" N ASN C 691 " pdb=" CA ASN C 691 " pdb=" C ASN C 691 " ideal model delta sigma weight residual 112.75 118.20 -5.45 1.36e+00 5.41e-01 1.60e+01 angle pdb=" N ASN B 629 " pdb=" CA ASN B 629 " pdb=" C ASN B 629 " ideal model delta sigma weight residual 111.14 107.14 4.00 1.08e+00 8.57e-01 1.37e+01 ... (remaining 24507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.03: 9312 12.03 - 24.06: 860 24.06 - 36.09: 288 36.09 - 48.12: 96 48.12 - 60.16: 24 Dihedral angle restraints: 10580 sinusoidal: 4072 harmonic: 6508 Sorted by residual: 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 180.00 160.61 19.39 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA GLY D 628 " pdb=" C GLY D 628 " pdb=" N ASN D 629 " pdb=" CA ASN D 629 " ideal model delta harmonic sigma weight residual 180.00 160.61 19.39 0 5.00e+00 4.00e-02 1.50e+01 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 180.00 160.61 19.39 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 10577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1712 0.046 - 0.091: 720 0.091 - 0.137: 216 0.137 - 0.182: 104 0.182 - 0.228: 40 Chirality restraints: 2792 Sorted by residual: chirality pdb=" CA ILE A 804 " pdb=" N ILE A 804 " pdb=" C ILE A 804 " pdb=" CB ILE A 804 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ILE D 804 " pdb=" N ILE D 804 " pdb=" C ILE D 804 " pdb=" CB ILE D 804 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ILE B 804 " pdb=" N ILE B 804 " pdb=" C ILE B 804 " pdb=" CB ILE B 804 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 2789 not shown) Planarity restraints: 3080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 450 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO B 451 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 451 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 451 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 450 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO C 451 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 451 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 451 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 450 " -0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO A 451 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 451 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 451 " -0.018 5.00e-02 4.00e+02 ... (remaining 3077 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 16 2.35 - 2.99: 7492 2.99 - 3.63: 24892 3.63 - 4.26: 36240 4.26 - 4.90: 63270 Nonbonded interactions: 131910 Sorted by model distance: nonbonded pdb=" CG2 ILE C 42 " pdb=" O VAL D 796 " model vdw 1.715 3.460 nonbonded pdb=" CG2 ILE A 42 " pdb=" O VAL B 796 " model vdw 1.715 3.460 nonbonded pdb=" CG2 ILE B 42 " pdb=" O VAL C 796 " model vdw 1.715 3.460 nonbonded pdb=" O VAL A 796 " pdb=" CG2 ILE D 42 " model vdw 1.715 3.460 nonbonded pdb=" NH1 ARG C 752 " pdb=" NE2 HIS D 771 " model vdw 1.963 3.200 ... (remaining 131905 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 4.750 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 44.760 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.100 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 18056 Z= 0.498 Angle : 1.020 6.103 24512 Z= 0.703 Chirality : 0.063 0.228 2792 Planarity : 0.004 0.032 3080 Dihedral : 11.845 60.156 6380 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.30 % Allowed : 5.83 % Favored : 92.87 % 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: -3.52 (0.14), residues: 2192 helix: -2.21 (0.11), residues: 1124 sheet: -2.62 (0.37), residues: 132 loop : -2.27 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 585 HIS 0.004 0.001 HIS A 674 PHE 0.011 0.001 PHE D 68 TYR 0.011 0.001 TYR D 652 ARG 0.002 0.000 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 719 time to evaluate : 1.969 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: A 4 ARG cc_start: 0.9090 (ttp-170) cc_final: 0.8504 (ttt180) REVERT: A 130 GLU cc_start: 0.9714 (tp30) cc_final: 0.9514 (pm20) REVERT: A 407 LYS cc_start: 0.9550 (tptm) cc_final: 0.9159 (tptp) REVERT: A 466 ASP cc_start: 0.9632 (t0) cc_final: 0.9354 (t0) REVERT: A 541 ARG cc_start: 0.9271 (ttm170) cc_final: 0.8417 (ttp80) REVERT: A 542 TYR cc_start: 0.9264 (m-80) cc_final: 0.8022 (m-80) REVERT: A 576 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7897 (tp40) REVERT: A 640 PHE cc_start: 0.9684 (t80) cc_final: 0.9364 (t80) REVERT: A 668 SER cc_start: 0.9591 (t) cc_final: 0.9341 (m) REVERT: A 677 MET cc_start: 0.9883 (tpp) cc_final: 0.9645 (tpp) REVERT: A 679 ARG cc_start: 0.9798 (mtt180) cc_final: 0.9588 (mtt180) REVERT: A 681 ARG cc_start: 0.9736 (mtt180) cc_final: 0.9390 (ptp-110) REVERT: A 682 GLU cc_start: 0.9686 (mt-10) cc_final: 0.9442 (pt0) REVERT: A 695 GLN cc_start: 0.9667 (mt0) cc_final: 0.9352 (mp10) REVERT: A 698 GLU cc_start: 0.9691 (mt-10) cc_final: 0.9479 (pt0) REVERT: A 702 GLN cc_start: 0.9699 (mt0) cc_final: 0.9485 (mm-40) REVERT: A 714 ASN cc_start: 0.9774 (m-40) cc_final: 0.9442 (p0) REVERT: A 723 CYS cc_start: 0.9433 (m) cc_final: 0.8706 (p) REVERT: A 729 CYS cc_start: 0.9529 (m) cc_final: 0.8719 (p) REVERT: A 734 ARG cc_start: 0.9735 (ptt180) cc_final: 0.9476 (mtm110) REVERT: A 739 HIS cc_start: 0.9843 (m-70) cc_final: 0.9634 (m90) REVERT: A 748 LYS cc_start: 0.9866 (mttt) cc_final: 0.9568 (tttm) REVERT: A 756 MET cc_start: 0.9134 (mmm) cc_final: 0.8833 (mmm) REVERT: A 782 ILE cc_start: 0.9756 (mt) cc_final: 0.9452 (tp) REVERT: A 821 ASP cc_start: 0.9309 (m-30) cc_final: 0.9026 (p0) REVERT: A 854 SER cc_start: 0.9799 (t) cc_final: 0.9590 (p) REVERT: A 857 GLU cc_start: 0.9416 (mt-10) cc_final: 0.9123 (mm-30) REVERT: B 4 ARG cc_start: 0.9067 (ttp-170) cc_final: 0.8457 (ttt180) REVERT: B 31 ILE cc_start: 0.9799 (mt) cc_final: 0.9578 (pt) REVERT: B 126 ILE cc_start: 0.9785 (mt) cc_final: 0.9584 (tt) REVERT: B 130 GLU cc_start: 0.9723 (tp30) cc_final: 0.9488 (pm20) REVERT: B 407 LYS cc_start: 0.9573 (tptm) cc_final: 0.9205 (tptp) REVERT: B 415 LEU cc_start: 0.9955 (tt) cc_final: 0.9715 (tt) REVERT: B 466 ASP cc_start: 0.9687 (t0) cc_final: 0.9311 (t0) REVERT: B 541 ARG cc_start: 0.9287 (ttm170) cc_final: 0.8508 (ttp80) REVERT: B 542 TYR cc_start: 0.9262 (m-80) cc_final: 0.8157 (m-80) REVERT: B 576 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8156 (tp40) REVERT: B 588 ASN cc_start: 0.9739 (t0) cc_final: 0.9423 (t0) REVERT: B 592 GLN cc_start: 0.9142 (mt0) cc_final: 0.8894 (mt0) REVERT: B 620 SER cc_start: 0.9693 (p) cc_final: 0.9459 (t) REVERT: B 677 MET cc_start: 0.9871 (tpp) cc_final: 0.9630 (tpp) REVERT: B 681 ARG cc_start: 0.9728 (mtt180) cc_final: 0.9373 (ptp-110) REVERT: B 682 GLU cc_start: 0.9707 (mt-10) cc_final: 0.9479 (pt0) REVERT: B 695 GLN cc_start: 0.9625 (mt0) cc_final: 0.9308 (mp10) REVERT: B 698 GLU cc_start: 0.9656 (mt-10) cc_final: 0.9419 (pt0) REVERT: B 702 GLN cc_start: 0.9685 (mt0) cc_final: 0.9442 (mm-40) REVERT: B 705 TRP cc_start: 0.9450 (t60) cc_final: 0.9223 (t60) REVERT: B 714 ASN cc_start: 0.9793 (m-40) cc_final: 0.9508 (p0) REVERT: B 723 CYS cc_start: 0.9405 (m) cc_final: 0.8611 (p) REVERT: B 729 CYS cc_start: 0.9526 (m) cc_final: 0.8746 (p) REVERT: B 734 ARG cc_start: 0.9746 (ptt180) cc_final: 0.9484 (mtm110) REVERT: B 739 HIS cc_start: 0.9837 (m-70) cc_final: 0.9636 (m90) REVERT: B 748 LYS cc_start: 0.9894 (mttt) cc_final: 0.9614 (tttm) REVERT: B 756 MET cc_start: 0.9073 (mmm) cc_final: 0.8771 (mmm) REVERT: B 782 ILE cc_start: 0.9754 (mt) cc_final: 0.9447 (tp) REVERT: B 821 ASP cc_start: 0.9306 (m-30) cc_final: 0.9061 (p0) REVERT: B 854 SER cc_start: 0.9771 (t) cc_final: 0.9541 (p) REVERT: B 857 GLU cc_start: 0.9398 (mt-10) cc_final: 0.9061 (mm-30) REVERT: C 4 ARG cc_start: 0.9049 (ttp-170) cc_final: 0.8496 (ttt180) REVERT: C 130 GLU cc_start: 0.9721 (tp30) cc_final: 0.9509 (pm20) REVERT: C 407 LYS cc_start: 0.9562 (tptm) cc_final: 0.9189 (tptp) REVERT: C 466 ASP cc_start: 0.9655 (t0) cc_final: 0.9405 (t0) REVERT: C 501 ASP cc_start: 0.9460 (m-30) cc_final: 0.9050 (p0) REVERT: C 541 ARG cc_start: 0.9241 (ttm170) cc_final: 0.8504 (ttp80) REVERT: C 542 TYR cc_start: 0.9323 (m-80) cc_final: 0.8065 (m-80) REVERT: C 576 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8003 (tp40) REVERT: C 588 ASN cc_start: 0.9710 (t0) cc_final: 0.9390 (t0) REVERT: C 592 GLN cc_start: 0.9238 (mt0) cc_final: 0.8936 (mt0) REVERT: C 620 SER cc_start: 0.9642 (p) cc_final: 0.9430 (t) REVERT: C 677 MET cc_start: 0.9864 (tpp) cc_final: 0.9536 (tpp) REVERT: C 681 ARG cc_start: 0.9724 (mtt180) cc_final: 0.9366 (ptp-110) REVERT: C 682 GLU cc_start: 0.9696 (mt-10) cc_final: 0.9463 (pt0) REVERT: C 695 GLN cc_start: 0.9631 (mt0) cc_final: 0.9356 (mp10) REVERT: C 697 LEU cc_start: 0.9936 (mt) cc_final: 0.9634 (pp) REVERT: C 698 GLU cc_start: 0.9643 (mt-10) cc_final: 0.9437 (pt0) REVERT: C 699 GLU cc_start: 0.9703 (pt0) cc_final: 0.9498 (pt0) REVERT: C 702 GLN cc_start: 0.9677 (mt0) cc_final: 0.9420 (mm-40) REVERT: C 705 TRP cc_start: 0.9469 (t60) cc_final: 0.9227 (t60) REVERT: C 714 ASN cc_start: 0.9800 (m-40) cc_final: 0.9488 (p0) REVERT: C 723 CYS cc_start: 0.9364 (m) cc_final: 0.8700 (p) REVERT: C 729 CYS cc_start: 0.9544 (m) cc_final: 0.8783 (p) REVERT: C 748 LYS cc_start: 0.9900 (mttt) cc_final: 0.9632 (tttm) REVERT: C 756 MET cc_start: 0.9115 (mmm) cc_final: 0.8835 (mmm) REVERT: C 782 ILE cc_start: 0.9704 (mt) cc_final: 0.9358 (tp) REVERT: C 821 ASP cc_start: 0.9254 (m-30) cc_final: 0.9041 (p0) REVERT: C 854 SER cc_start: 0.9801 (t) cc_final: 0.9560 (p) REVERT: C 857 GLU cc_start: 0.9391 (mt-10) cc_final: 0.9067 (mm-30) REVERT: D 4 ARG cc_start: 0.9089 (ttp-170) cc_final: 0.8535 (ttt180) REVERT: D 31 ILE cc_start: 0.9806 (mt) cc_final: 0.9538 (tp) REVERT: D 124 MET cc_start: 0.9335 (mmt) cc_final: 0.9086 (mmm) REVERT: D 407 LYS cc_start: 0.9529 (tptm) cc_final: 0.9134 (tptp) REVERT: D 415 LEU cc_start: 0.9945 (tt) cc_final: 0.9683 (tt) REVERT: D 466 ASP cc_start: 0.9603 (t0) cc_final: 0.9338 (t0) REVERT: D 501 ASP cc_start: 0.9415 (m-30) cc_final: 0.9078 (p0) REVERT: D 541 ARG cc_start: 0.9214 (ttm170) cc_final: 0.8411 (ttp80) REVERT: D 542 TYR cc_start: 0.9328 (m-80) cc_final: 0.8195 (m-80) REVERT: D 576 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7764 (tp40) REVERT: D 655 ILE cc_start: 0.9616 (tt) cc_final: 0.9415 (tp) REVERT: D 677 MET cc_start: 0.9876 (tpp) cc_final: 0.9558 (tpp) REVERT: D 679 ARG cc_start: 0.9807 (mtt180) cc_final: 0.9597 (mtt180) REVERT: D 681 ARG cc_start: 0.9731 (mtt180) cc_final: 0.9395 (ptp-110) REVERT: D 682 GLU cc_start: 0.9681 (mt-10) cc_final: 0.9448 (pt0) REVERT: D 695 GLN cc_start: 0.9674 (mt0) cc_final: 0.9376 (mp10) REVERT: D 698 GLU cc_start: 0.9673 (mt-10) cc_final: 0.9417 (pt0) REVERT: D 702 GLN cc_start: 0.9683 (mt0) cc_final: 0.9453 (mm-40) REVERT: D 714 ASN cc_start: 0.9779 (m-40) cc_final: 0.9392 (p0) REVERT: D 723 CYS cc_start: 0.9371 (m) cc_final: 0.8786 (p) REVERT: D 729 CYS cc_start: 0.9538 (m) cc_final: 0.8752 (p) REVERT: D 748 LYS cc_start: 0.9875 (mttt) cc_final: 0.9582 (tttm) REVERT: D 756 MET cc_start: 0.9156 (mmm) cc_final: 0.8869 (mmm) REVERT: D 782 ILE cc_start: 0.9711 (mt) cc_final: 0.9356 (tp) REVERT: D 821 ASP cc_start: 0.9255 (m-30) cc_final: 0.9012 (p0) REVERT: D 837 ASP cc_start: 0.9537 (m-30) cc_final: 0.9322 (m-30) REVERT: D 857 GLU cc_start: 0.9410 (mt-10) cc_final: 0.9122 (mm-30) outliers start: 24 outliers final: 0 residues processed: 735 average time/residue: 0.3035 time to fit residues: 326.3140 Evaluate side-chains 542 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 538 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain B residue 576 GLN Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain D residue 576 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 94 optimal weight: 30.0000 chunk 57 optimal weight: 20.0000 chunk 114 optimal weight: 30.0000 chunk 90 optimal weight: 5.9990 chunk 175 optimal weight: 50.0000 chunk 67 optimal weight: 40.0000 chunk 106 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 70 HIS ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN B 61 GLN B 70 HIS ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN B 588 ASN ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 ASN C 61 GLN C 70 HIS C 576 GLN C 588 ASN ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 ASN D 70 HIS D 576 GLN ** D 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18056 Z= 0.239 Angle : 0.715 11.012 24512 Z= 0.352 Chirality : 0.044 0.162 2792 Planarity : 0.005 0.041 3080 Dihedral : 4.792 28.974 2440 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.43 % Allowed : 14.85 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.17), residues: 2192 helix: -0.04 (0.14), residues: 1220 sheet: -1.69 (0.34), residues: 168 loop : -1.54 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 497 HIS 0.008 0.001 HIS C 831 PHE 0.024 0.002 PHE A 557 TYR 0.016 0.001 TYR B 545 ARG 0.007 0.001 ARG C 734 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 523 time to evaluate : 1.982 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: A 4 ARG cc_start: 0.9250 (ttp-170) cc_final: 0.8670 (ttt90) REVERT: A 124 MET cc_start: 0.9756 (mmm) cc_final: 0.8973 (tpp) REVERT: A 130 GLU cc_start: 0.9714 (tp30) cc_final: 0.9482 (pm20) REVERT: A 466 ASP cc_start: 0.9681 (t0) cc_final: 0.9386 (t0) REVERT: A 470 ASN cc_start: 0.9292 (m-40) cc_final: 0.8814 (m110) REVERT: A 542 TYR cc_start: 0.8830 (m-80) cc_final: 0.8373 (m-80) REVERT: A 677 MET cc_start: 0.9882 (tpp) cc_final: 0.9575 (tpp) REVERT: A 681 ARG cc_start: 0.9651 (mtt180) cc_final: 0.9414 (mtm110) REVERT: A 691 ASN cc_start: 0.9843 (m-40) cc_final: 0.9640 (p0) REVERT: A 705 TRP cc_start: 0.9456 (t60) cc_final: 0.9232 (t60) REVERT: A 723 CYS cc_start: 0.9109 (m) cc_final: 0.8888 (p) REVERT: A 729 CYS cc_start: 0.9220 (m) cc_final: 0.8830 (m) REVERT: A 748 LYS cc_start: 0.9864 (mttt) cc_final: 0.9628 (tttm) REVERT: A 756 MET cc_start: 0.9198 (mmm) cc_final: 0.8761 (mmm) REVERT: A 836 ASP cc_start: 0.9301 (OUTLIER) cc_final: 0.9067 (p0) REVERT: A 837 ASP cc_start: 0.9536 (m-30) cc_final: 0.9322 (m-30) REVERT: B 4 ARG cc_start: 0.9239 (ttp-170) cc_final: 0.8669 (ttt90) REVERT: B 466 ASP cc_start: 0.9715 (t0) cc_final: 0.9508 (t0) REVERT: B 542 TYR cc_start: 0.8816 (m-80) cc_final: 0.8431 (m-80) REVERT: B 588 ASN cc_start: 0.9580 (t0) cc_final: 0.9351 (t0) REVERT: B 592 GLN cc_start: 0.8663 (mt0) cc_final: 0.8295 (mt0) REVERT: B 677 MET cc_start: 0.9876 (tpp) cc_final: 0.9470 (tpp) REVERT: B 681 ARG cc_start: 0.9642 (mtt180) cc_final: 0.9393 (ptp-110) REVERT: B 682 GLU cc_start: 0.9767 (mt-10) cc_final: 0.9563 (pt0) REVERT: B 691 ASN cc_start: 0.9820 (m-40) cc_final: 0.9595 (p0) REVERT: B 723 CYS cc_start: 0.9034 (m) cc_final: 0.8774 (p) REVERT: B 729 CYS cc_start: 0.9396 (m) cc_final: 0.8947 (m) REVERT: B 748 LYS cc_start: 0.9875 (mttt) cc_final: 0.9654 (tttm) REVERT: B 756 MET cc_start: 0.9184 (mmm) cc_final: 0.8776 (mmm) REVERT: B 857 GLU cc_start: 0.9446 (mt-10) cc_final: 0.9245 (mm-30) REVERT: C 4 ARG cc_start: 0.9262 (ttp-170) cc_final: 0.8704 (ttt90) REVERT: C 31 ILE cc_start: 0.9725 (pt) cc_final: 0.9478 (tp) REVERT: C 466 ASP cc_start: 0.9691 (t0) cc_final: 0.9370 (t0) REVERT: C 470 ASN cc_start: 0.9303 (m-40) cc_final: 0.8827 (m110) REVERT: C 500 ILE cc_start: 0.8918 (mm) cc_final: 0.8663 (pt) REVERT: C 542 TYR cc_start: 0.8868 (m-80) cc_final: 0.8416 (m-80) REVERT: C 677 MET cc_start: 0.9877 (tpp) cc_final: 0.9486 (tpp) REVERT: C 681 ARG cc_start: 0.9645 (mtt180) cc_final: 0.9401 (ptp-110) REVERT: C 682 GLU cc_start: 0.9758 (mt-10) cc_final: 0.9529 (pt0) REVERT: C 691 ASN cc_start: 0.9828 (m-40) cc_final: 0.9610 (p0) REVERT: C 697 LEU cc_start: 0.9915 (mt) cc_final: 0.9669 (pp) REVERT: C 723 CYS cc_start: 0.9080 (m) cc_final: 0.8840 (p) REVERT: C 727 ASP cc_start: 0.9499 (m-30) cc_final: 0.9286 (m-30) REVERT: C 729 CYS cc_start: 0.9402 (m) cc_final: 0.8932 (m) REVERT: C 748 LYS cc_start: 0.9862 (mttt) cc_final: 0.9636 (tttm) REVERT: C 756 MET cc_start: 0.9245 (mmm) cc_final: 0.8881 (mmm) REVERT: D 4 ARG cc_start: 0.9276 (ttp-170) cc_final: 0.8678 (ttt90) REVERT: D 466 ASP cc_start: 0.9653 (t0) cc_final: 0.9359 (t0) REVERT: D 470 ASN cc_start: 0.9304 (m-40) cc_final: 0.8839 (m110) REVERT: D 500 ILE cc_start: 0.8869 (mm) cc_final: 0.8626 (pt) REVERT: D 542 TYR cc_start: 0.8907 (m-80) cc_final: 0.8393 (m-80) REVERT: D 677 MET cc_start: 0.9868 (tpp) cc_final: 0.9609 (tpp) REVERT: D 691 ASN cc_start: 0.9844 (m-40) cc_final: 0.9531 (t0) REVERT: D 727 ASP cc_start: 0.9533 (m-30) cc_final: 0.9308 (m-30) REVERT: D 729 CYS cc_start: 0.9320 (m) cc_final: 0.8845 (m) REVERT: D 748 LYS cc_start: 0.9856 (mttt) cc_final: 0.9626 (tttm) REVERT: D 756 MET cc_start: 0.9273 (mmm) cc_final: 0.8897 (mmm) REVERT: D 832 LYS cc_start: 0.9551 (OUTLIER) cc_final: 0.9326 (mtpp) REVERT: D 836 ASP cc_start: 0.9332 (OUTLIER) cc_final: 0.8992 (p0) outliers start: 45 outliers final: 26 residues processed: 535 average time/residue: 0.2783 time to fit residues: 224.3305 Evaluate side-chains 461 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 432 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 836 ASP Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain D residue 479 ASN Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 836 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 138 optimal weight: 30.0000 chunk 56 optimal weight: 60.0000 chunk 203 optimal weight: 6.9990 chunk 220 optimal weight: 8.9990 chunk 181 optimal weight: 30.0000 chunk 202 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 163 optimal weight: 40.0000 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 33 ASN ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18056 Z= 0.211 Angle : 0.678 12.357 24512 Z= 0.332 Chirality : 0.043 0.170 2792 Planarity : 0.004 0.045 3080 Dihedral : 4.333 17.452 2428 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.97 % Allowed : 17.28 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2192 helix: 0.41 (0.15), residues: 1228 sheet: -1.36 (0.35), residues: 168 loop : -1.41 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 705 HIS 0.006 0.001 HIS D 687 PHE 0.027 0.002 PHE D 640 TYR 0.016 0.001 TYR B 616 ARG 0.006 0.001 ARG D 679 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 461 time to evaluate : 2.210 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: A 4 ARG cc_start: 0.9195 (ttp-170) cc_final: 0.8664 (ttm-80) REVERT: A 466 ASP cc_start: 0.9671 (t0) cc_final: 0.9330 (t0) REVERT: A 470 ASN cc_start: 0.9066 (m-40) cc_final: 0.8573 (m-40) REVERT: A 542 TYR cc_start: 0.8852 (m-80) cc_final: 0.8411 (m-80) REVERT: A 623 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8784 (p) REVERT: A 668 SER cc_start: 0.9612 (t) cc_final: 0.9376 (m) REVERT: A 677 MET cc_start: 0.9876 (tpp) cc_final: 0.9508 (tpp) REVERT: A 681 ARG cc_start: 0.9662 (mtt180) cc_final: 0.9381 (mmm160) REVERT: A 691 ASN cc_start: 0.9840 (m-40) cc_final: 0.9523 (t0) REVERT: A 705 TRP cc_start: 0.9381 (t60) cc_final: 0.9151 (t60) REVERT: A 729 CYS cc_start: 0.9195 (m) cc_final: 0.8700 (m) REVERT: A 748 LYS cc_start: 0.9867 (mttt) cc_final: 0.9633 (ttpp) REVERT: A 756 MET cc_start: 0.9111 (mmm) cc_final: 0.8703 (mmm) REVERT: B 4 ARG cc_start: 0.9184 (ttp-170) cc_final: 0.8687 (ttm-80) REVERT: B 8 VAL cc_start: 0.9355 (m) cc_final: 0.9118 (p) REVERT: B 542 TYR cc_start: 0.8811 (m-80) cc_final: 0.8441 (m-80) REVERT: B 681 ARG cc_start: 0.9570 (mtt180) cc_final: 0.9234 (ttp-110) REVERT: B 691 ASN cc_start: 0.9813 (m-40) cc_final: 0.9596 (p0) REVERT: B 729 CYS cc_start: 0.9324 (m) cc_final: 0.8776 (m) REVERT: B 748 LYS cc_start: 0.9872 (mttt) cc_final: 0.9645 (ttpp) REVERT: B 756 MET cc_start: 0.9066 (mmm) cc_final: 0.8678 (mmm) REVERT: C 4 ARG cc_start: 0.9239 (ttp-170) cc_final: 0.8665 (ttt90) REVERT: C 31 ILE cc_start: 0.9722 (pt) cc_final: 0.9494 (tp) REVERT: C 542 TYR cc_start: 0.8872 (m-80) cc_final: 0.8467 (m-80) REVERT: C 677 MET cc_start: 0.9717 (tpp) cc_final: 0.9497 (tpp) REVERT: C 681 ARG cc_start: 0.9573 (mtt180) cc_final: 0.9232 (ttp-110) REVERT: C 691 ASN cc_start: 0.9816 (m-40) cc_final: 0.9488 (t0) REVERT: C 748 LYS cc_start: 0.9855 (mttt) cc_final: 0.9635 (ttpp) REVERT: C 756 MET cc_start: 0.9088 (mmm) cc_final: 0.8850 (mmm) REVERT: C 857 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8893 (mm-30) REVERT: D 4 ARG cc_start: 0.9298 (ttp-170) cc_final: 0.8725 (ttt90) REVERT: D 462 MET cc_start: 0.9696 (mmm) cc_final: 0.9457 (mmm) REVERT: D 466 ASP cc_start: 0.9636 (t0) cc_final: 0.9277 (t0) REVERT: D 470 ASN cc_start: 0.9080 (m-40) cc_final: 0.8575 (m-40) REVERT: D 542 TYR cc_start: 0.8844 (m-80) cc_final: 0.8437 (m-80) REVERT: D 677 MET cc_start: 0.9696 (tpp) cc_final: 0.9421 (tpp) REVERT: D 680 VAL cc_start: 0.9922 (t) cc_final: 0.9657 (m) REVERT: D 681 ARG cc_start: 0.9518 (mtt180) cc_final: 0.9313 (mmm160) REVERT: D 691 ASN cc_start: 0.9836 (m-40) cc_final: 0.9537 (t0) REVERT: D 729 CYS cc_start: 0.9201 (m) cc_final: 0.8743 (m) REVERT: D 748 LYS cc_start: 0.9861 (mttt) cc_final: 0.9631 (ttpp) REVERT: D 756 MET cc_start: 0.9113 (mmm) cc_final: 0.8733 (mmm) outliers start: 55 outliers final: 43 residues processed: 491 average time/residue: 0.2574 time to fit residues: 195.8972 Evaluate side-chains 463 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 419 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 676 GLN Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 836 ASP Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain D residue 479 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 822 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 10.0000 chunk 153 optimal weight: 40.0000 chunk 105 optimal weight: 8.9990 chunk 22 optimal weight: 0.0770 chunk 97 optimal weight: 30.0000 chunk 136 optimal weight: 20.0000 chunk 204 optimal weight: 30.0000 chunk 216 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 193 optimal weight: 1.9990 chunk 58 optimal weight: 50.0000 overall best weight: 6.2148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN C 629 ASN ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18056 Z= 0.190 Angle : 0.654 12.338 24512 Z= 0.320 Chirality : 0.043 0.154 2792 Planarity : 0.004 0.034 3080 Dihedral : 4.195 17.256 2428 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.00 % Allowed : 17.82 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2192 helix: 0.58 (0.15), residues: 1200 sheet: -1.00 (0.36), residues: 168 loop : -1.13 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 705 HIS 0.006 0.001 HIS B 831 PHE 0.019 0.002 PHE A 557 TYR 0.015 0.001 TYR B 616 ARG 0.005 0.000 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 448 time to evaluate : 2.078 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: A 4 ARG cc_start: 0.9221 (ttp-170) cc_final: 0.8631 (ttm-80) REVERT: A 124 MET cc_start: 0.9817 (mmm) cc_final: 0.9083 (tpp) REVERT: A 542 TYR cc_start: 0.8900 (m-80) cc_final: 0.8456 (m-80) REVERT: A 668 SER cc_start: 0.9590 (t) cc_final: 0.9345 (m) REVERT: A 677 MET cc_start: 0.9864 (tpp) cc_final: 0.9514 (tpp) REVERT: A 681 ARG cc_start: 0.9657 (mtt180) cc_final: 0.9385 (mmm160) REVERT: A 691 ASN cc_start: 0.9872 (m-40) cc_final: 0.9607 (t0) REVERT: A 705 TRP cc_start: 0.9298 (t60) cc_final: 0.9065 (t60) REVERT: A 729 CYS cc_start: 0.9145 (m) cc_final: 0.8658 (m) REVERT: A 748 LYS cc_start: 0.9866 (mttt) cc_final: 0.9637 (tttm) REVERT: A 756 MET cc_start: 0.9062 (mmm) cc_final: 0.8654 (mmm) REVERT: A 780 TYR cc_start: 0.9588 (m-80) cc_final: 0.9381 (m-80) REVERT: B 4 ARG cc_start: 0.9188 (ttp-170) cc_final: 0.8576 (ttt90) REVERT: B 542 TYR cc_start: 0.8862 (m-80) cc_final: 0.8523 (m-80) REVERT: B 677 MET cc_start: 0.9792 (tpp) cc_final: 0.9425 (tpp) REVERT: B 691 ASN cc_start: 0.9808 (m-40) cc_final: 0.9466 (t0) REVERT: B 729 CYS cc_start: 0.9086 (m) cc_final: 0.8535 (m) REVERT: B 748 LYS cc_start: 0.9875 (mttt) cc_final: 0.9652 (ttpp) REVERT: B 756 MET cc_start: 0.8969 (mmm) cc_final: 0.8575 (mmm) REVERT: C 4 ARG cc_start: 0.9264 (ttp-170) cc_final: 0.8736 (ttm-80) REVERT: C 124 MET cc_start: 0.9824 (mmm) cc_final: 0.9102 (tpp) REVERT: C 410 TRP cc_start: 0.9576 (OUTLIER) cc_final: 0.9347 (t60) REVERT: C 462 MET cc_start: 0.9637 (mmp) cc_final: 0.9342 (tpt) REVERT: C 542 TYR cc_start: 0.8911 (m-80) cc_final: 0.8606 (m-80) REVERT: C 638 LYS cc_start: 0.9767 (mttt) cc_final: 0.9524 (mttm) REVERT: C 677 MET cc_start: 0.9692 (tpp) cc_final: 0.9408 (tpp) REVERT: C 681 ARG cc_start: 0.9551 (mtt180) cc_final: 0.9278 (mmm160) REVERT: C 691 ASN cc_start: 0.9815 (m-40) cc_final: 0.9481 (t0) REVERT: C 697 LEU cc_start: 0.9778 (mt) cc_final: 0.9499 (pp) REVERT: C 748 LYS cc_start: 0.9853 (mttt) cc_final: 0.9630 (ttpp) REVERT: C 756 MET cc_start: 0.9049 (mmm) cc_final: 0.8817 (mmm) REVERT: C 856 LEU cc_start: 0.9647 (tt) cc_final: 0.9444 (pp) REVERT: C 857 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8637 (mm-30) REVERT: D 4 ARG cc_start: 0.9293 (ttp-170) cc_final: 0.8708 (ttt90) REVERT: D 542 TYR cc_start: 0.8943 (m-80) cc_final: 0.8535 (m-80) REVERT: D 574 MET cc_start: 0.7398 (mmt) cc_final: 0.7026 (ppp) REVERT: D 638 LYS cc_start: 0.9754 (mttt) cc_final: 0.9500 (mttm) REVERT: D 677 MET cc_start: 0.9643 (tpp) cc_final: 0.9379 (tpp) REVERT: D 680 VAL cc_start: 0.9912 (t) cc_final: 0.9645 (m) REVERT: D 691 ASN cc_start: 0.9834 (m-40) cc_final: 0.9550 (t0) REVERT: D 729 CYS cc_start: 0.9061 (m) cc_final: 0.8337 (m) REVERT: D 748 LYS cc_start: 0.9861 (mttt) cc_final: 0.9630 (ttpp) REVERT: D 756 MET cc_start: 0.8994 (mmm) cc_final: 0.8616 (mmm) outliers start: 74 outliers final: 60 residues processed: 484 average time/residue: 0.2579 time to fit residues: 192.3597 Evaluate side-chains 464 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 403 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 676 GLN Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 714 ASN Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 836 ASP Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 733 ASN Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 479 ASN Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 714 ASN Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 836 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 30.0000 chunk 122 optimal weight: 30.0000 chunk 3 optimal weight: 30.0000 chunk 161 optimal weight: 50.0000 chunk 89 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 0 optimal weight: 60.0000 chunk 110 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 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 470 ASN ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18056 Z= 0.203 Angle : 0.677 11.014 24512 Z= 0.331 Chirality : 0.044 0.242 2792 Planarity : 0.004 0.039 3080 Dihedral : 4.180 16.831 2428 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.27 % Allowed : 19.38 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2192 helix: 0.53 (0.15), residues: 1208 sheet: -0.68 (0.37), residues: 168 loop : -0.81 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 410 HIS 0.006 0.001 HIS B 831 PHE 0.018 0.002 PHE D 557 TYR 0.016 0.001 TYR D 493 ARG 0.010 0.000 ARG B 681 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 429 time to evaluate : 1.950 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: A 4 ARG cc_start: 0.9205 (ttp-170) cc_final: 0.8636 (ttm-80) REVERT: A 541 ARG cc_start: 0.9202 (tpp80) cc_final: 0.8668 (ttp80) REVERT: A 542 TYR cc_start: 0.8940 (m-80) cc_final: 0.8448 (m-80) REVERT: A 638 LYS cc_start: 0.9705 (mttt) cc_final: 0.9279 (mmtm) REVERT: A 668 SER cc_start: 0.9577 (t) cc_final: 0.9325 (m) REVERT: A 677 MET cc_start: 0.9850 (tpp) cc_final: 0.9492 (tpp) REVERT: A 681 ARG cc_start: 0.9651 (mtt180) cc_final: 0.9391 (mmm160) REVERT: A 691 ASN cc_start: 0.9876 (m-40) cc_final: 0.9502 (t0) REVERT: A 699 GLU cc_start: 0.9734 (pt0) cc_final: 0.9485 (pp20) REVERT: A 705 TRP cc_start: 0.9259 (t60) cc_final: 0.9010 (t60) REVERT: A 729 CYS cc_start: 0.9173 (m) cc_final: 0.8694 (m) REVERT: A 748 LYS cc_start: 0.9867 (mttt) cc_final: 0.9643 (tttm) REVERT: A 756 MET cc_start: 0.8998 (mmm) cc_final: 0.8615 (mmm) REVERT: A 799 LEU cc_start: 0.9566 (mm) cc_final: 0.9316 (mm) REVERT: B 4 ARG cc_start: 0.9213 (ttp-170) cc_final: 0.8668 (ttm-80) REVERT: B 410 TRP cc_start: 0.9570 (OUTLIER) cc_final: 0.9308 (t60) REVERT: B 462 MET cc_start: 0.9723 (mmp) cc_final: 0.9484 (tpt) REVERT: B 542 TYR cc_start: 0.8864 (m-80) cc_final: 0.8567 (m-80) REVERT: B 638 LYS cc_start: 0.9680 (mttt) cc_final: 0.9205 (mmtm) REVERT: B 681 ARG cc_start: 0.9348 (mmm160) cc_final: 0.8979 (mmm160) REVERT: B 729 CYS cc_start: 0.9170 (m) cc_final: 0.8654 (m) REVERT: B 748 LYS cc_start: 0.9873 (mttt) cc_final: 0.9650 (ttpp) REVERT: B 756 MET cc_start: 0.8997 (mmm) cc_final: 0.8604 (mmm) REVERT: C 4 ARG cc_start: 0.9276 (ttp-170) cc_final: 0.8604 (ttt90) REVERT: C 124 MET cc_start: 0.9815 (mmm) cc_final: 0.9133 (tpp) REVERT: C 462 MET cc_start: 0.9628 (mmp) cc_final: 0.9412 (tpt) REVERT: C 542 TYR cc_start: 0.8940 (m-80) cc_final: 0.8653 (m-80) REVERT: C 574 MET cc_start: 0.7314 (mmt) cc_final: 0.7006 (ppp) REVERT: C 638 LYS cc_start: 0.9784 (mttt) cc_final: 0.9292 (mmtm) REVERT: C 677 MET cc_start: 0.9682 (tpp) cc_final: 0.9480 (tpp) REVERT: C 681 ARG cc_start: 0.9549 (mtt180) cc_final: 0.9245 (ptm-80) REVERT: C 691 ASN cc_start: 0.9818 (m-40) cc_final: 0.9503 (t0) REVERT: C 748 LYS cc_start: 0.9854 (mttt) cc_final: 0.9636 (ttpp) REVERT: C 756 MET cc_start: 0.9036 (mmm) cc_final: 0.8802 (mmm) REVERT: D 4 ARG cc_start: 0.9282 (ttp-170) cc_final: 0.8681 (ttt90) REVERT: D 542 TYR cc_start: 0.8979 (m-80) cc_final: 0.8701 (m-80) REVERT: D 574 MET cc_start: 0.7425 (mmt) cc_final: 0.7126 (ppp) REVERT: D 638 LYS cc_start: 0.9772 (mttt) cc_final: 0.9537 (mttm) REVERT: D 668 SER cc_start: 0.9569 (t) cc_final: 0.9305 (m) REVERT: D 677 MET cc_start: 0.9657 (tpp) cc_final: 0.9281 (tpp) REVERT: D 691 ASN cc_start: 0.9842 (m-40) cc_final: 0.9583 (t0) REVERT: D 729 CYS cc_start: 0.9084 (m) cc_final: 0.8412 (m) REVERT: D 748 LYS cc_start: 0.9861 (mttt) cc_final: 0.9637 (ttpp) REVERT: D 756 MET cc_start: 0.8965 (mmm) cc_final: 0.8577 (mmm) REVERT: D 784 ARG cc_start: 0.9353 (mtm110) cc_final: 0.9106 (ptm-80) outliers start: 79 outliers final: 66 residues processed: 469 average time/residue: 0.2741 time to fit residues: 195.9789 Evaluate side-chains 458 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 391 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain B residue 410 TRP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 676 GLN Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 714 ASN Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 836 ASP Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 827 TYR Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain D residue 479 ASN Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 733 ASN Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 822 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 30.0000 chunk 194 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 127 optimal weight: 5.9990 chunk 53 optimal weight: 40.0000 chunk 216 optimal weight: 30.0000 chunk 179 optimal weight: 50.0000 chunk 100 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 overall best weight: 11.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18056 Z= 0.275 Angle : 0.698 11.086 24512 Z= 0.351 Chirality : 0.045 0.257 2792 Planarity : 0.004 0.042 3080 Dihedral : 4.349 17.594 2428 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.92 % Favored : 97.90 % Rotamer: Outliers : 4.32 % Allowed : 21.81 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2192 helix: 0.51 (0.15), residues: 1212 sheet: -0.43 (0.39), residues: 168 loop : -0.50 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 705 HIS 0.007 0.002 HIS A 831 PHE 0.021 0.002 PHE D 551 TYR 0.018 0.002 TYR D 707 ARG 0.007 0.001 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 418 time to evaluate : 2.160 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: A 4 ARG cc_start: 0.9262 (ttp-170) cc_final: 0.8673 (ttm-80) REVERT: A 124 MET cc_start: 0.9832 (mmm) cc_final: 0.9122 (tpp) REVERT: A 538 LYS cc_start: 0.9689 (mmtt) cc_final: 0.9213 (mppt) REVERT: A 541 ARG cc_start: 0.9200 (tpp80) cc_final: 0.8992 (tpp80) REVERT: A 542 TYR cc_start: 0.9017 (m-80) cc_final: 0.8537 (m-80) REVERT: A 638 LYS cc_start: 0.9734 (mttt) cc_final: 0.9297 (mmtm) REVERT: A 668 SER cc_start: 0.9561 (t) cc_final: 0.9324 (m) REVERT: A 677 MET cc_start: 0.9848 (tpp) cc_final: 0.9528 (tpp) REVERT: A 681 ARG cc_start: 0.9657 (mtt180) cc_final: 0.9336 (ttm110) REVERT: A 699 GLU cc_start: 0.9729 (pt0) cc_final: 0.9462 (pp20) REVERT: A 705 TRP cc_start: 0.9302 (t60) cc_final: 0.9008 (t60) REVERT: A 729 CYS cc_start: 0.9262 (m) cc_final: 0.8827 (m) REVERT: A 748 LYS cc_start: 0.9865 (mttt) cc_final: 0.9653 (ttpp) REVERT: A 756 MET cc_start: 0.9019 (mmm) cc_final: 0.8619 (mmm) REVERT: A 768 THR cc_start: 0.8774 (p) cc_final: 0.8366 (t) REVERT: A 857 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8714 (mp0) REVERT: B 4 ARG cc_start: 0.9207 (ttp-170) cc_final: 0.8530 (ttm-80) REVERT: B 410 TRP cc_start: 0.9568 (OUTLIER) cc_final: 0.9276 (t60) REVERT: B 462 MET cc_start: 0.9727 (mmp) cc_final: 0.9467 (tpt) REVERT: B 538 LYS cc_start: 0.9664 (mmtt) cc_final: 0.9166 (mppt) REVERT: B 541 ARG cc_start: 0.9199 (tpp80) cc_final: 0.8666 (ttp80) REVERT: B 542 TYR cc_start: 0.8888 (m-80) cc_final: 0.8435 (m-80) REVERT: B 638 LYS cc_start: 0.9697 (mttt) cc_final: 0.9235 (mmtm) REVERT: B 677 MET cc_start: 0.9705 (tpp) cc_final: 0.9500 (tpp) REVERT: B 705 TRP cc_start: 0.9200 (t60) cc_final: 0.8967 (t60) REVERT: B 729 CYS cc_start: 0.9217 (m) cc_final: 0.8721 (m) REVERT: B 748 LYS cc_start: 0.9872 (mttt) cc_final: 0.9662 (ttpp) REVERT: B 756 MET cc_start: 0.9005 (mmm) cc_final: 0.8603 (mmm) REVERT: C 4 ARG cc_start: 0.9270 (ttp-170) cc_final: 0.8539 (ttm-80) REVERT: C 542 TYR cc_start: 0.9008 (m-80) cc_final: 0.8741 (m-80) REVERT: C 574 MET cc_start: 0.7396 (mmt) cc_final: 0.7125 (ppp) REVERT: C 638 LYS cc_start: 0.9802 (mttt) cc_final: 0.9340 (mmtm) REVERT: C 677 MET cc_start: 0.9665 (tpp) cc_final: 0.9375 (tpp) REVERT: C 681 ARG cc_start: 0.9547 (mtt180) cc_final: 0.9162 (ttm110) REVERT: C 691 ASN cc_start: 0.9826 (m-40) cc_final: 0.9509 (t0) REVERT: C 756 MET cc_start: 0.9046 (mmm) cc_final: 0.8816 (mmm) REVERT: D 4 ARG cc_start: 0.9269 (ttp-170) cc_final: 0.8672 (ttm-80) REVERT: D 538 LYS cc_start: 0.9678 (mmtt) cc_final: 0.9220 (mppt) REVERT: D 541 ARG cc_start: 0.9195 (tpp80) cc_final: 0.8990 (tpp80) REVERT: D 542 TYR cc_start: 0.9017 (m-80) cc_final: 0.8633 (m-80) REVERT: D 574 MET cc_start: 0.7484 (mmt) cc_final: 0.7183 (ppp) REVERT: D 638 LYS cc_start: 0.9796 (mttt) cc_final: 0.9201 (mmtm) REVERT: D 668 SER cc_start: 0.9571 (t) cc_final: 0.9312 (m) REVERT: D 681 ARG cc_start: 0.9561 (mmm-85) cc_final: 0.9094 (mmm160) REVERT: D 691 ASN cc_start: 0.9841 (m-40) cc_final: 0.9571 (t0) REVERT: D 729 CYS cc_start: 0.9113 (m) cc_final: 0.8773 (m) REVERT: D 857 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8738 (mp0) outliers start: 80 outliers final: 70 residues processed: 460 average time/residue: 0.2828 time to fit residues: 197.6641 Evaluate side-chains 461 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 390 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain B residue 410 TRP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 714 ASN Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 836 ASP Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 733 ASN Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain D residue 479 ASN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 722 GLU Chi-restraints excluded: chain D residue 733 ASN Chi-restraints excluded: chain D residue 758 PHE Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 836 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 9.9990 chunk 24 optimal weight: 30.0000 chunk 123 optimal weight: 50.0000 chunk 158 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 chunk 182 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 135 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 ASN B 33 ASN ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN C 588 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.6388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18056 Z= 0.194 Angle : 0.735 11.445 24512 Z= 0.349 Chirality : 0.045 0.263 2792 Planarity : 0.004 0.033 3080 Dihedral : 4.248 19.192 2428 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.10 % Allowed : 23.27 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.18), residues: 2192 helix: 0.52 (0.15), residues: 1220 sheet: 0.20 (0.35), residues: 244 loop : -0.57 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 585 HIS 0.005 0.001 HIS D 687 PHE 0.027 0.001 PHE C 48 TYR 0.015 0.001 TYR B 616 ARG 0.007 0.000 ARG B 823 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 419 time to evaluate : 1.984 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: A 4 ARG cc_start: 0.9262 (ttp-170) cc_final: 0.8657 (ttm-80) REVERT: A 124 MET cc_start: 0.9823 (mmm) cc_final: 0.9119 (tpp) REVERT: A 538 LYS cc_start: 0.9688 (mmtt) cc_final: 0.9211 (mppt) REVERT: A 541 ARG cc_start: 0.9245 (tpp80) cc_final: 0.9015 (tpp80) REVERT: A 542 TYR cc_start: 0.8946 (m-80) cc_final: 0.8498 (m-80) REVERT: A 574 MET cc_start: 0.7337 (mmt) cc_final: 0.7045 (ppp) REVERT: A 638 LYS cc_start: 0.9734 (mttt) cc_final: 0.9294 (mmtm) REVERT: A 668 SER cc_start: 0.9527 (t) cc_final: 0.9272 (m) REVERT: A 677 MET cc_start: 0.9846 (tpp) cc_final: 0.9505 (tpp) REVERT: A 681 ARG cc_start: 0.9630 (mtt180) cc_final: 0.9344 (ttm110) REVERT: A 699 GLU cc_start: 0.9733 (pt0) cc_final: 0.9481 (pp20) REVERT: A 705 TRP cc_start: 0.9309 (t60) cc_final: 0.8998 (t60) REVERT: A 729 CYS cc_start: 0.9222 (m) cc_final: 0.8770 (m) REVERT: A 748 LYS cc_start: 0.9867 (mttt) cc_final: 0.9644 (tttm) REVERT: A 756 MET cc_start: 0.9002 (mmm) cc_final: 0.8608 (mmm) REVERT: B 4 ARG cc_start: 0.9232 (ttp-170) cc_final: 0.8548 (ttm-80) REVERT: B 541 ARG cc_start: 0.9256 (tpp80) cc_final: 0.8710 (ttp80) REVERT: B 542 TYR cc_start: 0.8849 (m-80) cc_final: 0.8509 (m-80) REVERT: B 638 LYS cc_start: 0.9686 (mttt) cc_final: 0.9266 (mmtm) REVERT: B 705 TRP cc_start: 0.9251 (t60) cc_final: 0.8983 (t60) REVERT: B 729 CYS cc_start: 0.9155 (m) cc_final: 0.8632 (m) REVERT: B 748 LYS cc_start: 0.9875 (mttt) cc_final: 0.9661 (tttm) REVERT: B 756 MET cc_start: 0.8981 (mmm) cc_final: 0.8589 (mmm) REVERT: C 4 ARG cc_start: 0.9267 (ttp-170) cc_final: 0.8667 (ttm-80) REVERT: C 124 MET cc_start: 0.9840 (mmm) cc_final: 0.9150 (tpp) REVERT: C 538 LYS cc_start: 0.9656 (mmtt) cc_final: 0.9172 (mppt) REVERT: C 541 ARG cc_start: 0.9239 (tpp80) cc_final: 0.9006 (tpp80) REVERT: C 542 TYR cc_start: 0.8948 (m-80) cc_final: 0.8632 (m-80) REVERT: C 574 MET cc_start: 0.7366 (mmt) cc_final: 0.7133 (ppp) REVERT: C 638 LYS cc_start: 0.9805 (mttt) cc_final: 0.9195 (mmtm) REVERT: C 677 MET cc_start: 0.9641 (tpp) cc_final: 0.9325 (tpp) REVERT: C 681 ARG cc_start: 0.9524 (mtt180) cc_final: 0.9265 (mmm160) REVERT: C 691 ASN cc_start: 0.9824 (m-40) cc_final: 0.9505 (t0) REVERT: C 697 LEU cc_start: 0.9768 (mt) cc_final: 0.9464 (pp) REVERT: C 756 MET cc_start: 0.9016 (mmm) cc_final: 0.8796 (mmm) REVERT: D 4 ARG cc_start: 0.9274 (ttp-170) cc_final: 0.8655 (mtp180) REVERT: D 42 ILE cc_start: 0.9844 (pt) cc_final: 0.9520 (tt) REVERT: D 407 LYS cc_start: 0.9482 (tptm) cc_final: 0.9088 (tptp) REVERT: D 538 LYS cc_start: 0.9676 (mmtt) cc_final: 0.9201 (mppt) REVERT: D 541 ARG cc_start: 0.9218 (tpp80) cc_final: 0.7942 (ttp80) REVERT: D 542 TYR cc_start: 0.8959 (m-80) cc_final: 0.8540 (m-80) REVERT: D 574 MET cc_start: 0.7450 (mmt) cc_final: 0.7189 (ppp) REVERT: D 638 LYS cc_start: 0.9681 (mttt) cc_final: 0.9205 (mmtm) REVERT: D 658 ASN cc_start: 0.9031 (m-40) cc_final: 0.8799 (m110) REVERT: D 677 MET cc_start: 0.9752 (tpt) cc_final: 0.9539 (tpt) REVERT: D 691 ASN cc_start: 0.9842 (m-40) cc_final: 0.9569 (t0) REVERT: D 705 TRP cc_start: 0.9160 (t60) cc_final: 0.8860 (t60) REVERT: D 729 CYS cc_start: 0.9281 (m) cc_final: 0.8782 (m) REVERT: D 756 MET cc_start: 0.9533 (tpp) cc_final: 0.9192 (mmm) REVERT: D 799 LEU cc_start: 0.9852 (mm) cc_final: 0.9524 (mm) outliers start: 76 outliers final: 62 residues processed: 459 average time/residue: 0.2824 time to fit residues: 195.1874 Evaluate side-chains 456 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 394 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 827 TYR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 676 GLN Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 714 ASN Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain D residue 479 ASN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 722 GLU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 836 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 30.0000 chunk 86 optimal weight: 20.0000 chunk 128 optimal weight: 6.9990 chunk 65 optimal weight: 30.0000 chunk 42 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 137 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 106 optimal weight: 40.0000 chunk 20 optimal weight: 0.9980 chunk 169 optimal weight: 10.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.6547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18056 Z= 0.199 Angle : 0.752 12.736 24512 Z= 0.357 Chirality : 0.045 0.256 2792 Planarity : 0.004 0.099 3080 Dihedral : 4.246 22.520 2428 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.46 % Allowed : 24.24 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.18), residues: 2192 helix: 0.55 (0.15), residues: 1220 sheet: 0.33 (0.35), residues: 244 loop : -0.50 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 705 HIS 0.006 0.001 HIS D 687 PHE 0.026 0.002 PHE A 551 TYR 0.015 0.001 TYR B 616 ARG 0.013 0.000 ARG B 681 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 414 time to evaluate : 2.082 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: A 4 ARG cc_start: 0.9290 (ttp-170) cc_final: 0.8519 (ttt180) REVERT: A 124 MET cc_start: 0.9813 (mmm) cc_final: 0.9118 (tpp) REVERT: A 538 LYS cc_start: 0.9687 (mmtt) cc_final: 0.9213 (mppt) REVERT: A 541 ARG cc_start: 0.9251 (tpp80) cc_final: 0.9004 (tpp80) REVERT: A 542 TYR cc_start: 0.8949 (m-80) cc_final: 0.8533 (m-80) REVERT: A 574 MET cc_start: 0.7334 (mmt) cc_final: 0.7039 (ppp) REVERT: A 638 LYS cc_start: 0.9743 (mttt) cc_final: 0.9346 (mmtm) REVERT: A 658 ASN cc_start: 0.8973 (m-40) cc_final: 0.8730 (m110) REVERT: A 677 MET cc_start: 0.9851 (tpp) cc_final: 0.9470 (tpp) REVERT: A 681 ARG cc_start: 0.9628 (mtt180) cc_final: 0.9354 (ttm110) REVERT: A 699 GLU cc_start: 0.9735 (pt0) cc_final: 0.9489 (pp20) REVERT: A 705 TRP cc_start: 0.9301 (t60) cc_final: 0.8963 (t60) REVERT: A 729 CYS cc_start: 0.9224 (m) cc_final: 0.8800 (m) REVERT: A 748 LYS cc_start: 0.9866 (mttt) cc_final: 0.9643 (ttpp) REVERT: A 756 MET cc_start: 0.9044 (mmm) cc_final: 0.8654 (mmm) REVERT: B 4 ARG cc_start: 0.9220 (ttp-170) cc_final: 0.8503 (ttm-80) REVERT: B 541 ARG cc_start: 0.9263 (tpp80) cc_final: 0.8704 (ttp80) REVERT: B 542 TYR cc_start: 0.8828 (m-80) cc_final: 0.8504 (m-80) REVERT: B 574 MET cc_start: 0.7360 (mmt) cc_final: 0.7062 (ppp) REVERT: B 638 LYS cc_start: 0.9705 (mttt) cc_final: 0.9310 (mmtm) REVERT: B 677 MET cc_start: 0.9734 (tpp) cc_final: 0.9292 (mmm) REVERT: B 705 TRP cc_start: 0.9284 (t60) cc_final: 0.8907 (t60) REVERT: B 729 CYS cc_start: 0.9183 (m) cc_final: 0.8672 (m) REVERT: B 748 LYS cc_start: 0.9874 (mttt) cc_final: 0.9656 (ttpp) REVERT: B 756 MET cc_start: 0.8995 (mmm) cc_final: 0.8612 (mmm) REVERT: C 4 ARG cc_start: 0.9242 (ttp-170) cc_final: 0.8474 (ttm-80) REVERT: C 124 MET cc_start: 0.9830 (mmm) cc_final: 0.9133 (tpp) REVERT: C 538 LYS cc_start: 0.9659 (mmtt) cc_final: 0.9177 (mppt) REVERT: C 541 ARG cc_start: 0.9234 (tpp80) cc_final: 0.8980 (tpp80) REVERT: C 542 TYR cc_start: 0.8946 (m-80) cc_final: 0.8650 (m-80) REVERT: C 574 MET cc_start: 0.7396 (mmt) cc_final: 0.7165 (ppp) REVERT: C 638 LYS cc_start: 0.9678 (mttt) cc_final: 0.9260 (mmtm) REVERT: C 677 MET cc_start: 0.9639 (tpp) cc_final: 0.9323 (tpp) REVERT: C 681 ARG cc_start: 0.9528 (mtt180) cc_final: 0.9275 (mmm160) REVERT: C 691 ASN cc_start: 0.9822 (m-40) cc_final: 0.9494 (t0) REVERT: C 756 MET cc_start: 0.9058 (mmm) cc_final: 0.8857 (mmm) REVERT: D 4 ARG cc_start: 0.9279 (ttp-170) cc_final: 0.8668 (ttt90) REVERT: D 407 LYS cc_start: 0.9461 (tptm) cc_final: 0.9073 (tptp) REVERT: D 538 LYS cc_start: 0.9671 (mmtt) cc_final: 0.9184 (mppt) REVERT: D 541 ARG cc_start: 0.9213 (tpp80) cc_final: 0.7949 (ttp80) REVERT: D 542 TYR cc_start: 0.8969 (m-80) cc_final: 0.8538 (m-80) REVERT: D 574 MET cc_start: 0.7465 (mmt) cc_final: 0.7219 (ppp) REVERT: D 638 LYS cc_start: 0.9698 (mttt) cc_final: 0.9265 (mmtm) REVERT: D 658 ASN cc_start: 0.9031 (m-40) cc_final: 0.8789 (m110) REVERT: D 691 ASN cc_start: 0.9839 (m-40) cc_final: 0.9571 (t0) REVERT: D 705 TRP cc_start: 0.9188 (t60) cc_final: 0.8917 (t60) REVERT: D 756 MET cc_start: 0.9547 (tpp) cc_final: 0.9310 (mmm) outliers start: 64 outliers final: 55 residues processed: 442 average time/residue: 0.2805 time to fit residues: 187.7675 Evaluate side-chains 445 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 390 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 827 TYR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 676 GLN Chi-restraints excluded: chain B residue 714 ASN Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 827 TYR Chi-restraints excluded: chain D residue 479 ASN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 822 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 30.0000 chunk 206 optimal weight: 0.9990 chunk 188 optimal weight: 20.0000 chunk 201 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 61 optimal weight: 40.0000 chunk 181 optimal weight: 6.9990 chunk 190 optimal weight: 50.0000 chunk 200 optimal weight: 20.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.6649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18056 Z= 0.190 Angle : 0.790 14.263 24512 Z= 0.371 Chirality : 0.046 0.266 2792 Planarity : 0.004 0.040 3080 Dihedral : 4.193 20.782 2428 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.97 % Allowed : 25.38 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.18), residues: 2192 helix: 0.52 (0.15), residues: 1220 sheet: 0.45 (0.37), residues: 224 loop : -0.52 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 585 HIS 0.005 0.001 HIS D 687 PHE 0.025 0.002 PHE A 640 TYR 0.018 0.001 TYR A 707 ARG 0.005 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 415 time to evaluate : 1.982 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: A 4 ARG cc_start: 0.9290 (ttp-170) cc_final: 0.8472 (ttt180) REVERT: A 124 MET cc_start: 0.9805 (mmm) cc_final: 0.9113 (tpp) REVERT: A 538 LYS cc_start: 0.9687 (mmtt) cc_final: 0.9209 (mppt) REVERT: A 541 ARG cc_start: 0.9269 (tpp80) cc_final: 0.9017 (tpp80) REVERT: A 542 TYR cc_start: 0.8905 (m-80) cc_final: 0.8523 (m-80) REVERT: A 574 MET cc_start: 0.7320 (mmt) cc_final: 0.7065 (ppp) REVERT: A 638 LYS cc_start: 0.9749 (mttt) cc_final: 0.9382 (mmtm) REVERT: A 658 ASN cc_start: 0.8922 (m-40) cc_final: 0.8677 (m110) REVERT: A 677 MET cc_start: 0.9849 (tpp) cc_final: 0.9478 (tpp) REVERT: A 681 ARG cc_start: 0.9621 (mtt180) cc_final: 0.9358 (ttm110) REVERT: A 699 GLU cc_start: 0.9728 (pt0) cc_final: 0.9489 (pp20) REVERT: A 705 TRP cc_start: 0.9273 (t60) cc_final: 0.8943 (t60) REVERT: A 729 CYS cc_start: 0.9155 (m) cc_final: 0.8677 (m) REVERT: A 748 LYS cc_start: 0.9866 (mttt) cc_final: 0.9637 (ttpp) REVERT: A 756 MET cc_start: 0.9043 (mmm) cc_final: 0.8680 (mmm) REVERT: A 798 ILE cc_start: 0.9908 (mp) cc_final: 0.9696 (tp) REVERT: B 4 ARG cc_start: 0.9203 (ttp-170) cc_final: 0.8741 (ptm160) REVERT: B 541 ARG cc_start: 0.9250 (tpp80) cc_final: 0.9012 (tpp80) REVERT: B 542 TYR cc_start: 0.8808 (m-80) cc_final: 0.8538 (m-80) REVERT: B 574 MET cc_start: 0.7344 (mmt) cc_final: 0.7074 (ppp) REVERT: B 638 LYS cc_start: 0.9700 (mttt) cc_final: 0.9346 (mmtm) REVERT: B 677 MET cc_start: 0.9700 (tpp) cc_final: 0.9354 (mmm) REVERT: B 705 TRP cc_start: 0.9303 (t60) cc_final: 0.8954 (t60) REVERT: B 729 CYS cc_start: 0.9159 (m) cc_final: 0.8642 (m) REVERT: B 748 LYS cc_start: 0.9874 (mttt) cc_final: 0.9656 (tttm) REVERT: B 756 MET cc_start: 0.8995 (mmm) cc_final: 0.8611 (mmm) REVERT: C 4 ARG cc_start: 0.9211 (ttp-170) cc_final: 0.8420 (ttm-80) REVERT: C 124 MET cc_start: 0.9829 (mmm) cc_final: 0.9128 (tpp) REVERT: C 538 LYS cc_start: 0.9659 (mmtt) cc_final: 0.9195 (mppt) REVERT: C 541 ARG cc_start: 0.9245 (tpp80) cc_final: 0.8988 (tpp80) REVERT: C 542 TYR cc_start: 0.8907 (m-80) cc_final: 0.8661 (m-80) REVERT: C 574 MET cc_start: 0.7391 (mmt) cc_final: 0.7182 (ppp) REVERT: C 638 LYS cc_start: 0.9691 (mttt) cc_final: 0.9323 (mmtm) REVERT: C 677 MET cc_start: 0.9629 (tpp) cc_final: 0.9330 (tpp) REVERT: C 691 ASN cc_start: 0.9812 (m-40) cc_final: 0.9484 (t0) REVERT: C 733 ASN cc_start: 0.8806 (m-40) cc_final: 0.8369 (t0) REVERT: C 756 MET cc_start: 0.9046 (mmm) cc_final: 0.8835 (mmm) REVERT: D 4 ARG cc_start: 0.9270 (ttp-170) cc_final: 0.8655 (ttt90) REVERT: D 538 LYS cc_start: 0.9671 (mmtt) cc_final: 0.9209 (mppt) REVERT: D 541 ARG cc_start: 0.9234 (tpp80) cc_final: 0.8983 (tpp80) REVERT: D 542 TYR cc_start: 0.8940 (m-80) cc_final: 0.8580 (m-80) REVERT: D 574 MET cc_start: 0.7454 (mmt) cc_final: 0.7209 (ppp) REVERT: D 638 LYS cc_start: 0.9707 (mttt) cc_final: 0.9332 (mmtm) REVERT: D 658 ASN cc_start: 0.8974 (m-40) cc_final: 0.8732 (m110) REVERT: D 691 ASN cc_start: 0.9838 (m-40) cc_final: 0.9564 (t0) REVERT: D 705 TRP cc_start: 0.9175 (t60) cc_final: 0.8927 (t60) REVERT: D 756 MET cc_start: 0.9566 (tpp) cc_final: 0.9316 (mmm) outliers start: 55 outliers final: 50 residues processed: 438 average time/residue: 0.2953 time to fit residues: 197.0383 Evaluate side-chains 447 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 397 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 676 GLN Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 714 ASN Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain D residue 479 ASN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 722 GLU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 777 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 8.9990 chunk 212 optimal weight: 7.9990 chunk 129 optimal weight: 30.0000 chunk 100 optimal weight: 20.0000 chunk 147 optimal weight: 9.9990 chunk 223 optimal weight: 40.0000 chunk 205 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 108 optimal weight: 30.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.6848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18056 Z= 0.239 Angle : 0.807 14.079 24512 Z= 0.386 Chirality : 0.046 0.209 2792 Planarity : 0.004 0.068 3080 Dihedral : 4.340 25.641 2428 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 21.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.19 % Favored : 97.72 % Rotamer: Outliers : 3.02 % Allowed : 25.65 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.18), residues: 2192 helix: 0.51 (0.15), residues: 1208 sheet: 0.38 (0.36), residues: 224 loop : -0.56 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 705 HIS 0.005 0.001 HIS A 687 PHE 0.033 0.002 PHE D 551 TYR 0.018 0.001 TYR A 707 ARG 0.014 0.000 ARG C 681 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 401 time to evaluate : 1.676 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: A 4 ARG cc_start: 0.9294 (ttp-170) cc_final: 0.8450 (ttt180) REVERT: A 124 MET cc_start: 0.9803 (mmm) cc_final: 0.9126 (tpp) REVERT: A 538 LYS cc_start: 0.9677 (mmtt) cc_final: 0.9412 (mppt) REVERT: A 541 ARG cc_start: 0.9236 (tpp80) cc_final: 0.8887 (tpp80) REVERT: A 574 MET cc_start: 0.7366 (mmt) cc_final: 0.7095 (ppp) REVERT: A 638 LYS cc_start: 0.9775 (mttt) cc_final: 0.9385 (mmtm) REVERT: A 658 ASN cc_start: 0.8912 (m-40) cc_final: 0.8664 (m110) REVERT: A 677 MET cc_start: 0.9854 (tpp) cc_final: 0.9488 (tpp) REVERT: A 681 ARG cc_start: 0.9629 (mtt180) cc_final: 0.9363 (ttm110) REVERT: A 699 GLU cc_start: 0.9745 (pt0) cc_final: 0.9504 (pp20) REVERT: A 705 TRP cc_start: 0.9282 (t60) cc_final: 0.8936 (t60) REVERT: A 729 CYS cc_start: 0.9213 (m) cc_final: 0.8769 (m) REVERT: A 748 LYS cc_start: 0.9866 (mttt) cc_final: 0.9649 (ttpp) REVERT: A 756 MET cc_start: 0.9074 (mmm) cc_final: 0.8710 (mmm) REVERT: B 4 ARG cc_start: 0.9199 (ttp-170) cc_final: 0.8711 (ptm160) REVERT: B 541 ARG cc_start: 0.9227 (tpp80) cc_final: 0.8986 (tpp80) REVERT: B 542 TYR cc_start: 0.8839 (m-80) cc_final: 0.8562 (m-80) REVERT: B 574 MET cc_start: 0.7414 (mmt) cc_final: 0.7135 (ppp) REVERT: B 638 LYS cc_start: 0.9722 (mttt) cc_final: 0.9353 (mmtm) REVERT: B 677 MET cc_start: 0.9725 (tpp) cc_final: 0.9369 (mmm) REVERT: B 705 TRP cc_start: 0.9321 (t60) cc_final: 0.8967 (t60) REVERT: B 729 CYS cc_start: 0.9223 (m) cc_final: 0.8726 (m) REVERT: B 748 LYS cc_start: 0.9872 (mttt) cc_final: 0.9656 (ttpp) REVERT: B 756 MET cc_start: 0.9052 (mmm) cc_final: 0.8668 (mmm) REVERT: C 4 ARG cc_start: 0.9196 (ttp-170) cc_final: 0.8383 (ttm-80) REVERT: C 124 MET cc_start: 0.9828 (mmm) cc_final: 0.9134 (tpp) REVERT: C 541 ARG cc_start: 0.9219 (tpp80) cc_final: 0.8961 (tpp80) REVERT: C 574 MET cc_start: 0.7432 (mmt) cc_final: 0.7225 (ppp) REVERT: C 638 LYS cc_start: 0.9715 (mttt) cc_final: 0.9315 (mmtm) REVERT: C 681 ARG cc_start: 0.9659 (ttm110) cc_final: 0.9420 (mmm160) REVERT: C 691 ASN cc_start: 0.9811 (m-40) cc_final: 0.9491 (t0) REVERT: C 756 MET cc_start: 0.9080 (mmm) cc_final: 0.8870 (mmm) REVERT: D 4 ARG cc_start: 0.9271 (ttp-170) cc_final: 0.8658 (ttt90) REVERT: D 60 MET cc_start: 0.9383 (mmp) cc_final: 0.9127 (mmm) REVERT: D 538 LYS cc_start: 0.9660 (mmtt) cc_final: 0.9186 (mppt) REVERT: D 541 ARG cc_start: 0.9214 (tpp80) cc_final: 0.8964 (tpp80) REVERT: D 542 TYR cc_start: 0.8963 (m-80) cc_final: 0.8587 (m-80) REVERT: D 574 MET cc_start: 0.7476 (mmt) cc_final: 0.7219 (ppp) REVERT: D 638 LYS cc_start: 0.9747 (mttt) cc_final: 0.9320 (mmtm) REVERT: D 658 ASN cc_start: 0.8975 (m-40) cc_final: 0.8732 (m110) REVERT: D 691 ASN cc_start: 0.9835 (m-40) cc_final: 0.9559 (t0) REVERT: D 729 CYS cc_start: 0.9352 (m) cc_final: 0.8751 (m) REVERT: D 756 MET cc_start: 0.9564 (tpp) cc_final: 0.9230 (mmm) outliers start: 56 outliers final: 51 residues processed: 423 average time/residue: 0.2841 time to fit residues: 182.1082 Evaluate side-chains 443 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 392 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 676 GLN Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain D residue 479 ASN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 722 GLU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 777 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 9.9990 chunk 189 optimal weight: 30.0000 chunk 54 optimal weight: 5.9990 chunk 163 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 0.2980 chunk 177 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.065758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.050242 restraints weight = 85773.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.052001 restraints weight = 46773.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.053240 restraints weight = 31534.051| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.6890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18056 Z= 0.196 Angle : 0.816 13.755 24512 Z= 0.384 Chirality : 0.046 0.186 2792 Planarity : 0.004 0.056 3080 Dihedral : 4.268 20.201 2428 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.92 % Allowed : 26.13 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.18), residues: 2192 helix: 0.53 (0.15), residues: 1208 sheet: 0.43 (0.36), residues: 224 loop : -0.53 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 585 HIS 0.004 0.001 HIS C 703 PHE 0.023 0.002 PHE C 48 TYR 0.027 0.001 TYR A 707 ARG 0.011 0.000 ARG C 681 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6613.36 seconds wall clock time: 117 minutes 29.89 seconds (7049.89 seconds total)