Starting phenix.real_space_refine on Mon Dec 11 11:20:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va1_8650/12_2023/5va1_8650.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va1_8650/12_2023/5va1_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_8650/12_2023/5va1_8650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va1_8650/12_2023/5va1_8650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va1_8650/12_2023/5va1_8650.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va1_8650/12_2023/5va1_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 9.90, per 1000 atoms: 0.56 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: 6.53 Conformation dependent library (CDL) restraints added in 3.2 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: 1.99 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: 5.68 Time building geometry restraints manager: 7.08 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.910 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 47.300 Find NCS groups from input model: 1.110 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.490 ------------------------------------------------------------------------------- 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 : 2.086 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 outliers start: 24 outliers final: 0 residues processed: 735 average time/residue: 0.3067 time to fit residues: 329.7254 Evaluate side-chains 476 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 476 time to evaluate : 2.155 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 114 optimal weight: 30.0000 chunk 90 optimal weight: 5.9990 chunk 175 optimal weight: 40.0000 chunk 67 optimal weight: 50.0000 chunk 106 optimal weight: 30.0000 chunk 130 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 70 HIS ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN B 70 HIS ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 ASN C 70 HIS ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 ASN D 70 HIS ** D 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4536 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= 0.232 Angle : 0.754 13.010 24512 Z= 0.368 Chirality : 0.046 0.163 2792 Planarity : 0.005 0.054 3080 Dihedral : 4.555 19.660 2428 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.81 % Allowed : 16.68 % Favored : 80.51 % 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: -1.22 (0.16), residues: 2192 helix: -0.10 (0.14), residues: 1196 sheet: -1.58 (0.34), residues: 168 loop : -1.57 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 705 HIS 0.008 0.001 HIS C 831 PHE 0.023 0.002 PHE A 557 TYR 0.015 0.001 TYR B 545 ARG 0.009 0.001 ARG A 541 *********************** 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 532 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 480 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 29 residues processed: 500 average time/residue: 0.2827 time to fit residues: 218.2184 Evaluate side-chains 437 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 408 time to evaluate : 2.128 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1755 time to fit residues: 12.1864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 138 optimal weight: 8.9990 chunk 56 optimal weight: 70.0000 chunk 203 optimal weight: 6.9990 chunk 220 optimal weight: 30.0000 chunk 181 optimal weight: 9.9990 chunk 202 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 overall best weight: 4.3186 ------------------------------------------------------------------------------- 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 676 GLN ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 ASN A 695 GLN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 GLN ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 ASN B 695 GLN ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 GLN ** D 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.5226 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= 0.186 Angle : 0.687 11.693 24512 Z= 0.339 Chirality : 0.044 0.175 2792 Planarity : 0.004 0.036 3080 Dihedral : 4.296 20.911 2428 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.21 % Allowed : 18.20 % Favored : 79.59 % 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: -0.74 (0.17), residues: 2192 helix: 0.38 (0.15), residues: 1216 sheet: -1.40 (0.34), residues: 188 loop : -1.53 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 705 HIS 0.006 0.001 HIS B 831 PHE 0.022 0.002 PHE B 557 TYR 0.016 0.001 TYR B 542 ARG 0.005 0.000 ARG D 814 *********************** 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 487 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 446 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 27 residues processed: 464 average time/residue: 0.2809 time to fit residues: 200.8871 Evaluate side-chains 412 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 385 time to evaluate : 2.194 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1718 time to fit residues: 11.6066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 20.0000 chunk 153 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 136 optimal weight: 20.0000 chunk 204 optimal weight: 7.9990 chunk 216 optimal weight: 30.0000 chunk 106 optimal weight: 10.0000 chunk 193 optimal weight: 30.0000 chunk 58 optimal weight: 30.0000 overall best weight: 10.9996 ------------------------------------------------------------------------------- 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 629 ASN ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 GLN B 33 ASN B 470 ASN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 629 ASN C 695 GLN D 33 ASN D 695 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18056 Z= 0.265 Angle : 0.704 12.296 24512 Z= 0.358 Chirality : 0.044 0.165 2792 Planarity : 0.004 0.083 3080 Dihedral : 4.323 17.710 2428 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.08 % Allowed : 19.38 % Favored : 77.54 % 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: -0.54 (0.17), residues: 2192 helix: 0.34 (0.15), residues: 1232 sheet: -1.11 (0.35), residues: 172 loop : -1.18 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C 705 HIS 0.007 0.001 HIS B 831 PHE 0.025 0.002 PHE A 640 TYR 0.016 0.002 TYR B 616 ARG 0.009 0.001 ARG C 681 *********************** 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 473 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 416 time to evaluate : 2.239 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 outliers start: 57 outliers final: 35 residues processed: 438 average time/residue: 0.2635 time to fit residues: 180.2952 Evaluate side-chains 406 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 371 time to evaluate : 2.258 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1831 time to fit residues: 13.9965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 50.0000 chunk 122 optimal weight: 20.0000 chunk 3 optimal weight: 50.0000 chunk 161 optimal weight: 30.0000 chunk 89 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 0 optimal weight: 70.0000 chunk 110 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 54 optimal weight: 0.0980 overall best weight: 5.8188 ------------------------------------------------------------------------------- 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** A 702 GLN B 470 ASN B 629 ASN ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN ** C 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 702 GLN D 33 ASN D 629 ASN ** D 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18056 Z= 0.201 Angle : 0.689 9.934 24512 Z= 0.342 Chirality : 0.045 0.307 2792 Planarity : 0.004 0.030 3080 Dihedral : 4.231 16.887 2428 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.51 % Allowed : 21.33 % Favored : 77.16 % 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: -0.07 (0.18), residues: 2192 helix: 0.59 (0.15), residues: 1184 sheet: -0.89 (0.36), residues: 172 loop : -0.63 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP C 705 HIS 0.005 0.001 HIS D 762 PHE 0.019 0.002 PHE D 557 TYR 0.016 0.001 TYR D 707 ARG 0.004 0.000 ARG D 823 *********************** 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 443 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 415 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 427 average time/residue: 0.2715 time to fit residues: 180.4283 Evaluate side-chains 381 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 365 time to evaluate : 2.092 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1626 time to fit residues: 7.6289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 216 optimal weight: 30.0000 chunk 179 optimal weight: 50.0000 chunk 100 optimal weight: 50.0000 chunk 18 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- 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 676 GLN ** 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 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN C 33 ASN ** D 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN D 695 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.6421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18056 Z= 0.221 Angle : 0.705 11.383 24512 Z= 0.352 Chirality : 0.046 0.281 2792 Planarity : 0.004 0.030 3080 Dihedral : 4.250 17.233 2428 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.19 % Favored : 97.72 % Rotamer: Outliers : 1.78 % Allowed : 22.89 % Favored : 75.32 % 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: 0.57 (0.15), residues: 1200 sheet: -0.67 (0.37), residues: 172 loop : -0.53 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP C 705 HIS 0.007 0.001 HIS B 703 PHE 0.019 0.002 PHE D 557 TYR 0.015 0.001 TYR A 616 ARG 0.006 0.000 ARG C 681 *********************** 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 427 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 394 time to evaluate : 1.995 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 outliers start: 33 outliers final: 24 residues processed: 404 average time/residue: 0.2502 time to fit residues: 160.5174 Evaluate side-chains 387 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 363 time to evaluate : 1.997 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1623 time to fit residues: 9.7434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 30.0000 chunk 24 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 chunk 158 optimal weight: 50.0000 chunk 122 optimal weight: 30.0000 chunk 182 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 215 optimal weight: 30.0000 chunk 135 optimal weight: 40.0000 chunk 131 optimal weight: 8.9990 chunk 99 optimal weight: 30.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 676 GLN ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN D 702 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.6605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18056 Z= 0.225 Angle : 0.728 15.010 24512 Z= 0.359 Chirality : 0.046 0.234 2792 Planarity : 0.004 0.035 3080 Dihedral : 4.281 18.951 2428 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.19 % Favored : 97.72 % Rotamer: Outliers : 1.13 % Allowed : 24.35 % Favored : 74.51 % 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: 0.07 (0.18), residues: 2192 helix: 0.58 (0.15), residues: 1192 sheet: -0.51 (0.39), residues: 172 loop : -0.46 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 705 HIS 0.011 0.001 HIS B 703 PHE 0.020 0.002 PHE D 557 TYR 0.028 0.001 TYR A 780 ARG 0.006 0.000 ARG D 784 *********************** 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 411 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 390 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 396 average time/residue: 0.2551 time to fit residues: 160.0800 Evaluate side-chains 370 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 359 time to evaluate : 2.036 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1667 time to fit residues: 5.9394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 128 optimal weight: 30.0000 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 147 optimal weight: 40.0000 chunk 106 optimal weight: 30.0000 chunk 20 optimal weight: 6.9990 chunk 169 optimal weight: 0.5980 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 GLN ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.6758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18056 Z= 0.198 Angle : 0.747 13.588 24512 Z= 0.361 Chirality : 0.046 0.258 2792 Planarity : 0.004 0.030 3080 Dihedral : 4.305 22.298 2428 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.86 % Allowed : 25.86 % Favored : 73.27 % 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: 0.14 (0.18), residues: 2192 helix: 0.56 (0.15), residues: 1204 sheet: -0.35 (0.40), residues: 172 loop : -0.34 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 705 HIS 0.010 0.001 HIS C 703 PHE 0.021 0.001 PHE A 551 TYR 0.017 0.001 TYR C 827 ARG 0.005 0.000 ARG C 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 409 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 393 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 395 average time/residue: 0.2685 time to fit residues: 168.5377 Evaluate side-chains 373 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 363 time to evaluate : 1.778 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1862 time to fit residues: 5.7758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 chunk 201 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 157 optimal weight: 30.0000 chunk 61 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 200 optimal weight: 0.0970 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 GLN ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 GLN ** D 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.6886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18056 Z= 0.189 Angle : 0.759 13.731 24512 Z= 0.366 Chirality : 0.046 0.231 2792 Planarity : 0.004 0.041 3080 Dihedral : 4.273 20.732 2428 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.76 % Allowed : 26.46 % Favored : 72.79 % 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: 0.14 (0.18), residues: 2192 helix: 0.55 (0.15), residues: 1208 sheet: -0.22 (0.40), residues: 172 loop : -0.34 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 705 HIS 0.009 0.001 HIS C 703 PHE 0.041 0.002 PHE B 701 TYR 0.022 0.001 TYR D 707 ARG 0.014 0.000 ARG C 681 *********************** 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 409 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 395 time to evaluate : 2.373 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 outliers start: 14 outliers final: 6 residues processed: 398 average time/residue: 0.2423 time to fit residues: 155.3527 Evaluate side-chains 381 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 375 time to evaluate : 2.016 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1598 time to fit residues: 4.3992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 7.9990 chunk 212 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 223 optimal weight: 8.9990 chunk 205 optimal weight: 9.9990 chunk 177 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 137 optimal weight: 0.5980 chunk 108 optimal weight: 9.9990 overall best weight: 6.5188 ------------------------------------------------------------------------------- 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 573 ASN A 676 GLN ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 ASN ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.7037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18056 Z= 0.223 Angle : 0.784 13.179 24512 Z= 0.380 Chirality : 0.047 0.243 2792 Planarity : 0.004 0.039 3080 Dihedral : 4.391 27.535 2428 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.19 % Favored : 97.76 % Rotamer: Outliers : 0.65 % Allowed : 27.75 % Favored : 71.60 % 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: 0.14 (0.18), residues: 2192 helix: 0.53 (0.15), residues: 1200 sheet: -0.23 (0.41), residues: 172 loop : -0.31 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 705 HIS 0.008 0.001 HIS B 703 PHE 0.042 0.002 PHE A 551 TYR 0.020 0.001 TYR D 707 ARG 0.010 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 382 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 370 time to evaluate : 2.131 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 outliers start: 12 outliers final: 9 residues processed: 371 average time/residue: 0.2701 time to fit residues: 163.2635 Evaluate side-chains 362 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 353 time to evaluate : 2.248 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1993 time to fit residues: 6.1540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 20.0000 chunk 189 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 177 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 182 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 573 ASN A 676 GLN ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 ASN ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 702 GLN ** D 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.059597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.044544 restraints weight = 88834.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.046358 restraints weight = 47943.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.047646 restraints weight = 31498.703| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.7153 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= 0.238 Angle : 0.786 12.879 24512 Z= 0.384 Chirality : 0.048 0.440 2792 Planarity : 0.004 0.030 3080 Dihedral : 4.441 25.698 2428 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.28 % Favored : 97.58 % Rotamer: Outliers : 0.43 % Allowed : 27.70 % Favored : 71.87 % 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: 0.09 (0.18), residues: 2192 helix: 0.52 (0.15), residues: 1188 sheet: -0.25 (0.40), residues: 172 loop : -0.36 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 705 HIS 0.008 0.001 HIS C 703 PHE 0.032 0.002 PHE B 701 TYR 0.020 0.001 TYR C 673 ARG 0.008 0.000 ARG C 681 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5708.67 seconds wall clock time: 103 minutes 37.74 seconds (6217.74 seconds total)