Starting phenix.real_space_refine on Sun Mar 17 04:08:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0h_20998/03_2024/6v0h_20998.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0h_20998/03_2024/6v0h_20998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0h_20998/03_2024/6v0h_20998.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0h_20998/03_2024/6v0h_20998.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0h_20998/03_2024/6v0h_20998.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0h_20998/03_2024/6v0h_20998.pdb" } resolution = 3.6 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= 0.000 sd= 0.007 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 24 5.16 5 C 10542 2.51 5 N 2922 2.21 5 O 3114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 547": "NH1" <-> "NH2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ARG 797": "NH1" <-> "NH2" Residue "A ARG 869": "NH1" <-> "NH2" Residue "B ARG 547": "NH1" <-> "NH2" Residue "B ARG 672": "NH1" <-> "NH2" Residue "B ARG 691": "NH1" <-> "NH2" Residue "B ARG 797": "NH1" <-> "NH2" Residue "B ARG 869": "NH1" <-> "NH2" Residue "C ARG 547": "NH1" <-> "NH2" Residue "C ARG 672": "NH1" <-> "NH2" Residue "C ARG 691": "NH1" <-> "NH2" Residue "C ARG 797": "NH1" <-> "NH2" Residue "C ARG 869": "NH1" <-> "NH2" Residue "D ARG 547": "NH1" <-> "NH2" Residue "D ARG 672": "NH1" <-> "NH2" Residue "D ARG 691": "NH1" <-> "NH2" Residue "D ARG 797": "NH1" <-> "NH2" Residue "D ARG 869": "NH1" <-> "NH2" Residue "E ARG 547": "NH1" <-> "NH2" Residue "E ARG 672": "NH1" <-> "NH2" Residue "E ARG 691": "NH1" <-> "NH2" Residue "E ARG 797": "NH1" <-> "NH2" Residue "E ARG 869": "NH1" <-> "NH2" Residue "F ARG 547": "NH1" <-> "NH2" Residue "F ARG 672": "NH1" <-> "NH2" Residue "F ARG 691": "NH1" <-> "NH2" Residue "F ARG 797": "NH1" <-> "NH2" Residue "F ARG 869": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16602 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2767 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 18, 'TRANS': 344} Chain: "B" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2767 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 18, 'TRANS': 344} Chain: "C" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2767 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 18, 'TRANS': 344} Chain: "D" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2767 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 18, 'TRANS': 344} Chain: "E" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2767 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 18, 'TRANS': 344} Chain: "F" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2767 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 18, 'TRANS': 344} Time building chain proxies: 7.83, per 1000 atoms: 0.47 Number of scatterers: 16602 At special positions: 0 Unit cell: (110.04, 111.35, 112.66, 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 24 16.00 O 3114 8.00 N 2922 7.00 C 10542 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: 5.52 Conformation dependent library (CDL) restraints added in 3.1 seconds 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 23 sheets defined 15.2% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 560 through 567 removed outlier: 3.869A pdb=" N ASN A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 612 through 617 Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.562A pdb=" N ILE A 714 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 744 removed outlier: 4.488A pdb=" N ARG A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 802 removed outlier: 3.843A pdb=" N VAL A 802 " --> pdb=" O GLN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 835 removed outlier: 4.107A pdb=" N ILE A 834 " --> pdb=" O PHE A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 870 removed outlier: 4.126A pdb=" N ARG A 869 " --> pdb=" O LYS A 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 567 removed outlier: 3.869A pdb=" N ASN B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 600 Processing helix chain 'B' and resid 612 through 617 Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 711 through 715 removed outlier: 3.562A pdb=" N ILE B 714 " --> pdb=" O LEU B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 744 removed outlier: 4.487A pdb=" N ARG B 743 " --> pdb=" O ILE B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 802 removed outlier: 3.843A pdb=" N VAL B 802 " --> pdb=" O GLN B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 835 removed outlier: 4.108A pdb=" N ILE B 834 " --> pdb=" O PHE B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 870 removed outlier: 4.127A pdb=" N ARG B 869 " --> pdb=" O LYS B 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 567 removed outlier: 3.810A pdb=" N ASN C 565 " --> pdb=" O PRO C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 600 Processing helix chain 'C' and resid 611 through 617 removed outlier: 3.966A pdb=" N GLN C 615 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 631 Processing helix chain 'C' and resid 711 through 715 removed outlier: 3.571A pdb=" N ILE C 714 " --> pdb=" O LEU C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 removed outlier: 4.483A pdb=" N ARG C 743 " --> pdb=" O ILE C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 802 removed outlier: 3.841A pdb=" N VAL C 802 " --> pdb=" O GLN C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 835 removed outlier: 4.508A pdb=" N ILE C 834 " --> pdb=" O PHE C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 870 removed outlier: 4.248A pdb=" N ARG C 869 " --> pdb=" O LYS C 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 567 removed outlier: 3.868A pdb=" N ASN D 565 " --> pdb=" O PRO D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 600 Processing helix chain 'D' and resid 612 through 617 Processing helix chain 'D' and resid 626 through 631 Processing helix chain 'D' and resid 711 through 715 removed outlier: 3.563A pdb=" N ILE D 714 " --> pdb=" O LEU D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 744 removed outlier: 4.486A pdb=" N ARG D 743 " --> pdb=" O ILE D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 802 removed outlier: 3.843A pdb=" N VAL D 802 " --> pdb=" O GLN D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 830 through 835 removed outlier: 4.107A pdb=" N ILE D 834 " --> pdb=" O PHE D 830 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 870 removed outlier: 4.126A pdb=" N ARG D 869 " --> pdb=" O LYS D 866 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 567 removed outlier: 3.869A pdb=" N ASN E 565 " --> pdb=" O PRO E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 600 Processing helix chain 'E' and resid 612 through 617 Processing helix chain 'E' and resid 626 through 631 Processing helix chain 'E' and resid 711 through 715 removed outlier: 3.563A pdb=" N ILE E 714 " --> pdb=" O LEU E 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 739 through 744 removed outlier: 4.486A pdb=" N ARG E 743 " --> pdb=" O ILE E 739 " (cutoff:3.500A) Processing helix chain 'E' and resid 798 through 802 removed outlier: 3.844A pdb=" N VAL E 802 " --> pdb=" O GLN E 799 " (cutoff:3.500A) Processing helix chain 'E' and resid 830 through 835 removed outlier: 4.108A pdb=" N ILE E 834 " --> pdb=" O PHE E 830 " (cutoff:3.500A) Processing helix chain 'E' and resid 865 through 870 removed outlier: 4.126A pdb=" N ARG E 869 " --> pdb=" O LYS E 866 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 567 removed outlier: 3.869A pdb=" N ASN F 565 " --> pdb=" O PRO F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 600 Processing helix chain 'F' and resid 612 through 617 Processing helix chain 'F' and resid 626 through 631 Processing helix chain 'F' and resid 711 through 715 removed outlier: 3.562A pdb=" N ILE F 714 " --> pdb=" O LEU F 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 739 through 744 removed outlier: 4.487A pdb=" N ARG F 743 " --> pdb=" O ILE F 739 " (cutoff:3.500A) Processing helix chain 'F' and resid 798 through 802 removed outlier: 3.843A pdb=" N VAL F 802 " --> pdb=" O GLN F 799 " (cutoff:3.500A) Processing helix chain 'F' and resid 830 through 835 removed outlier: 4.108A pdb=" N ILE F 834 " --> pdb=" O PHE F 830 " (cutoff:3.500A) Processing helix chain 'F' and resid 865 through 870 removed outlier: 4.126A pdb=" N ARG F 869 " --> pdb=" O LYS F 866 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 517 through 521 removed outlier: 6.506A pdb=" N ASP A 554 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL A 546 " --> pdb=" O ASP A 554 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP A 556 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL A 533 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 602 through 607 removed outlier: 9.260A pdb=" N TYR A 624 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N PHE A 573 " --> pdb=" O TYR A 624 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 636 through 641 removed outlier: 7.238A pdb=" N GLU A 674 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU A 668 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN A 676 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LEU A 666 " --> pdb=" O GLN A 676 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LYS A 678 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE A 653 " --> pdb=" O ILE A 660 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 721 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE A 696 " --> pdb=" O GLN A 735 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 748 through 754 removed outlier: 7.055A pdb=" N MET A 789 " --> pdb=" O MET A 779 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N MET A 779 " --> pdb=" O MET A 789 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA A 791 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE A 768 " --> pdb=" O GLU A 772 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA A 841 " --> pdb=" O VAL A 807 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 807 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A 808 " --> pdb=" O GLN A 861 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 517 through 521 removed outlier: 6.506A pdb=" N ASP B 554 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL B 546 " --> pdb=" O ASP B 554 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP B 556 " --> pdb=" O ILE B 544 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL B 533 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 602 through 607 removed outlier: 9.260A pdb=" N TYR B 624 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N PHE B 573 " --> pdb=" O TYR B 624 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 636 through 641 removed outlier: 7.238A pdb=" N GLU B 674 " --> pdb=" O LEU B 668 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU B 668 " --> pdb=" O GLU B 674 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN B 676 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU B 666 " --> pdb=" O GLN B 676 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LYS B 678 " --> pdb=" O GLN B 664 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE B 653 " --> pdb=" O ILE B 660 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 721 " --> pdb=" O ARG B 654 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE B 696 " --> pdb=" O GLN B 735 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 748 through 754 removed outlier: 7.055A pdb=" N MET B 789 " --> pdb=" O MET B 779 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N MET B 779 " --> pdb=" O MET B 789 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA B 791 " --> pdb=" O THR B 777 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE B 768 " --> pdb=" O GLU B 772 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 841 " --> pdb=" O VAL B 807 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL B 807 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE B 808 " --> pdb=" O GLN B 861 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 517 through 520 removed outlier: 6.492A pdb=" N ASP C 554 " --> pdb=" O VAL C 546 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL C 546 " --> pdb=" O ASP C 554 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASP C 556 " --> pdb=" O ILE C 544 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL C 533 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N TYR C 624 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N PHE C 573 " --> pdb=" O TYR C 624 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 636 through 641 removed outlier: 7.247A pdb=" N GLU C 674 " --> pdb=" O LEU C 668 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU C 668 " --> pdb=" O GLU C 674 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLN C 676 " --> pdb=" O LEU C 666 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU C 666 " --> pdb=" O GLN C 676 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LYS C 678 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE C 653 " --> pdb=" O ILE C 660 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 721 " --> pdb=" O ARG C 654 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE C 696 " --> pdb=" O GLN C 735 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N PHE C 732 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR C 638 " --> pdb=" O PHE C 732 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU C 734 " --> pdb=" O THR C 638 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N HIS C 640 " --> pdb=" O LEU C 734 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 748 through 754 removed outlier: 7.012A pdb=" N MET C 789 " --> pdb=" O MET C 779 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N MET C 779 " --> pdb=" O MET C 789 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA C 791 " --> pdb=" O THR C 777 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLU C 772 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE C 768 " --> pdb=" O GLU C 772 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA C 841 " --> pdb=" O VAL C 807 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL C 807 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE C 808 " --> pdb=" O GLN C 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 517 through 521 removed outlier: 6.505A pdb=" N ASP D 554 " --> pdb=" O VAL D 546 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL D 546 " --> pdb=" O ASP D 554 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP D 556 " --> pdb=" O ILE D 544 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL D 533 " --> pdb=" O VAL D 540 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 602 through 607 removed outlier: 9.260A pdb=" N TYR D 624 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N PHE D 573 " --> pdb=" O TYR D 624 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 636 through 641 removed outlier: 7.237A pdb=" N GLU D 674 " --> pdb=" O LEU D 668 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU D 668 " --> pdb=" O GLU D 674 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN D 676 " --> pdb=" O LEU D 666 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU D 666 " --> pdb=" O GLN D 676 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LYS D 678 " --> pdb=" O GLN D 664 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE D 653 " --> pdb=" O ILE D 660 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL D 721 " --> pdb=" O ARG D 654 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE D 696 " --> pdb=" O GLN D 735 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 748 through 754 removed outlier: 7.055A pdb=" N MET D 789 " --> pdb=" O MET D 779 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N MET D 779 " --> pdb=" O MET D 789 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA D 791 " --> pdb=" O THR D 777 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU D 772 " --> pdb=" O PHE D 768 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE D 768 " --> pdb=" O GLU D 772 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA D 841 " --> pdb=" O VAL D 807 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL D 807 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE D 808 " --> pdb=" O GLN D 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 517 through 521 removed outlier: 6.506A pdb=" N ASP E 554 " --> pdb=" O VAL E 546 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL E 546 " --> pdb=" O ASP E 554 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP E 556 " --> pdb=" O ILE E 544 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL E 533 " --> pdb=" O VAL E 540 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 602 through 607 removed outlier: 9.260A pdb=" N TYR E 624 " --> pdb=" O SER E 571 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N PHE E 573 " --> pdb=" O TYR E 624 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 636 through 641 removed outlier: 7.238A pdb=" N GLU E 674 " --> pdb=" O LEU E 668 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU E 668 " --> pdb=" O GLU E 674 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN E 676 " --> pdb=" O LEU E 666 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LEU E 666 " --> pdb=" O GLN E 676 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LYS E 678 " --> pdb=" O GLN E 664 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE E 653 " --> pdb=" O ILE E 660 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL E 721 " --> pdb=" O ARG E 654 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE E 696 " --> pdb=" O GLN E 735 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 748 through 754 removed outlier: 7.055A pdb=" N MET E 789 " --> pdb=" O MET E 779 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N MET E 779 " --> pdb=" O MET E 789 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA E 791 " --> pdb=" O THR E 777 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLU E 772 " --> pdb=" O PHE E 768 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE E 768 " --> pdb=" O GLU E 772 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA E 841 " --> pdb=" O VAL E 807 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL E 807 " --> pdb=" O ALA E 841 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE E 808 " --> pdb=" O GLN E 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 517 through 521 removed outlier: 6.506A pdb=" N ASP F 554 " --> pdb=" O VAL F 546 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL F 546 " --> pdb=" O ASP F 554 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP F 556 " --> pdb=" O ILE F 544 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL F 533 " --> pdb=" O VAL F 540 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 602 through 607 removed outlier: 9.260A pdb=" N TYR F 624 " --> pdb=" O SER F 571 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N PHE F 573 " --> pdb=" O TYR F 624 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 636 through 641 removed outlier: 7.237A pdb=" N GLU F 674 " --> pdb=" O LEU F 668 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU F 668 " --> pdb=" O GLU F 674 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLN F 676 " --> pdb=" O LEU F 666 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU F 666 " --> pdb=" O GLN F 676 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LYS F 678 " --> pdb=" O GLN F 664 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE F 653 " --> pdb=" O ILE F 660 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL F 721 " --> pdb=" O ARG F 654 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE F 696 " --> pdb=" O GLN F 735 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 748 through 754 removed outlier: 7.056A pdb=" N MET F 789 " --> pdb=" O MET F 779 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N MET F 779 " --> pdb=" O MET F 789 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA F 791 " --> pdb=" O THR F 777 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU F 772 " --> pdb=" O PHE F 768 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE F 768 " --> pdb=" O GLU F 772 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA F 841 " --> pdb=" O VAL F 807 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL F 807 " --> pdb=" O ALA F 841 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE F 808 " --> pdb=" O GLN F 861 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.92 Time building geometry restraints manager: 6.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2780 1.32 - 1.44: 4378 1.44 - 1.56: 9719 1.56 - 1.68: 7 1.68 - 1.80: 48 Bond restraints: 16932 Sorted by residual: bond pdb=" C VAL C 581 " pdb=" O VAL C 581 " ideal model delta sigma weight residual 1.234 1.198 0.035 1.17e-02 7.31e+03 9.14e+00 bond pdb=" CG LEU C 588 " pdb=" CD1 LEU C 588 " ideal model delta sigma weight residual 1.521 1.602 -0.081 3.30e-02 9.18e+02 5.96e+00 bond pdb=" CA THR C 589 " pdb=" CB THR C 589 " ideal model delta sigma weight residual 1.530 1.556 -0.026 1.57e-02 4.06e+03 2.64e+00 bond pdb=" CB VAL F 590 " pdb=" CG1 VAL F 590 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.51e+00 bond pdb=" CB VAL D 590 " pdb=" CG1 VAL D 590 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.50e+00 ... (remaining 16927 not shown) Histogram of bond angle deviations from ideal: 96.77 - 104.21: 265 104.21 - 111.66: 7593 111.66 - 119.10: 5945 119.10 - 126.55: 8960 126.55 - 133.99: 223 Bond angle restraints: 22986 Sorted by residual: angle pdb=" C PRO D 876 " pdb=" N LYS D 877 " pdb=" CA LYS D 877 " ideal model delta sigma weight residual 121.70 128.19 -6.49 1.80e+00 3.09e-01 1.30e+01 angle pdb=" C PRO E 876 " pdb=" N LYS E 877 " pdb=" CA LYS E 877 " ideal model delta sigma weight residual 121.70 128.16 -6.46 1.80e+00 3.09e-01 1.29e+01 angle pdb=" C PRO B 876 " pdb=" N LYS B 877 " pdb=" CA LYS B 877 " ideal model delta sigma weight residual 121.70 128.15 -6.45 1.80e+00 3.09e-01 1.29e+01 angle pdb=" C PRO F 876 " pdb=" N LYS F 877 " pdb=" CA LYS F 877 " ideal model delta sigma weight residual 121.70 128.15 -6.45 1.80e+00 3.09e-01 1.28e+01 angle pdb=" C PRO A 876 " pdb=" N LYS A 877 " pdb=" CA LYS A 877 " ideal model delta sigma weight residual 121.70 128.15 -6.45 1.80e+00 3.09e-01 1.28e+01 ... (remaining 22981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.05: 9611 15.05 - 30.09: 376 30.09 - 45.14: 81 45.14 - 60.18: 0 60.18 - 75.23: 12 Dihedral angle restraints: 10080 sinusoidal: 3948 harmonic: 6132 Sorted by residual: dihedral pdb=" CA THR C 846 " pdb=" C THR C 846 " pdb=" N PRO C 847 " pdb=" CA PRO C 847 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA THR B 846 " pdb=" C THR B 846 " pdb=" N PRO B 847 " pdb=" CA PRO B 847 " ideal model delta harmonic sigma weight residual 180.00 152.67 27.33 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA THR A 846 " pdb=" C THR A 846 " pdb=" N PRO A 847 " pdb=" CA PRO A 847 " ideal model delta harmonic sigma weight residual 180.00 152.68 27.32 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 10077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2070 0.065 - 0.129: 490 0.129 - 0.194: 66 0.194 - 0.259: 1 0.259 - 0.324: 1 Chirality restraints: 2628 Sorted by residual: chirality pdb=" CG LEU C 588 " pdb=" CB LEU C 588 " pdb=" CD1 LEU C 588 " pdb=" CD2 LEU C 588 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CG LEU C 767 " pdb=" CB LEU C 767 " pdb=" CD1 LEU C 767 " pdb=" CD2 LEU C 767 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA THR C 846 " pdb=" N THR C 846 " pdb=" C THR C 846 " pdb=" CB THR C 846 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.52e-01 ... (remaining 2625 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 587 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.74e+00 pdb=" C GLY C 587 " 0.051 2.00e-02 2.50e+03 pdb=" O GLY C 587 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU C 588 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 846 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO F 847 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO F 847 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 847 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 846 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO E 847 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO E 847 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 847 " 0.036 5.00e-02 4.00e+02 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 9 2.47 - 3.08: 10096 3.08 - 3.69: 22824 3.69 - 4.29: 33105 4.29 - 4.90: 55059 Nonbonded interactions: 121093 Sorted by model distance: nonbonded pdb=" O PHE B 833 " pdb=" OG1 THR C 829 " model vdw 1.866 2.440 nonbonded pdb=" NE2 GLN A 528 " pdb=" OE1 GLU B 539 " model vdw 2.297 2.520 nonbonded pdb=" NE2 GLN C 528 " pdb=" OE1 GLU D 539 " model vdw 2.341 2.520 nonbonded pdb=" N TYR C 535 " pdb=" O PHE C 538 " model vdw 2.386 2.520 nonbonded pdb=" N TYR F 535 " pdb=" O PHE F 538 " model vdw 2.401 2.520 ... (remaining 121088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.270 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: 0.010 Extract box with map and model: 5.390 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 41.370 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 16932 Z= 0.338 Angle : 0.845 10.272 22986 Z= 0.460 Chirality : 0.054 0.324 2628 Planarity : 0.007 0.064 2988 Dihedral : 9.305 75.229 6180 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: -3.68 (0.15), residues: 2166 helix: -4.40 (0.15), residues: 228 sheet: -2.05 (0.17), residues: 648 loop : -2.32 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 574 HIS 0.006 0.002 HIS A 558 PHE 0.038 0.003 PHE C 605 TYR 0.013 0.003 TYR A 798 ARG 0.004 0.001 ARG E 793 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 564 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 656 LEU cc_start: 0.9186 (mt) cc_final: 0.8939 (mp) REVERT: A 716 GLN cc_start: 0.8122 (tt0) cc_final: 0.7909 (pt0) REVERT: A 835 ARG cc_start: 0.6597 (mtt180) cc_final: 0.6319 (mtp180) REVERT: A 853 GLN cc_start: 0.7736 (mm110) cc_final: 0.7264 (mp10) REVERT: A 870 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7824 (mp0) REVERT: B 735 GLN cc_start: 0.7911 (mt0) cc_final: 0.7654 (mt0) REVERT: B 759 SER cc_start: 0.7571 (t) cc_final: 0.7297 (t) REVERT: B 842 THR cc_start: 0.7712 (m) cc_final: 0.7272 (p) REVERT: C 749 SER cc_start: 0.8976 (t) cc_final: 0.8763 (m) REVERT: C 833 PHE cc_start: 0.7378 (t80) cc_final: 0.7150 (t80) REVERT: D 620 LYS cc_start: 0.7440 (mtmt) cc_final: 0.7162 (mtpt) REVERT: D 853 GLN cc_start: 0.7720 (mm110) cc_final: 0.7278 (mp10) REVERT: E 518 SER cc_start: 0.9127 (m) cc_final: 0.8851 (t) REVERT: E 735 GLN cc_start: 0.7777 (mt0) cc_final: 0.7453 (mt0) REVERT: E 759 SER cc_start: 0.7804 (t) cc_final: 0.7416 (t) REVERT: E 771 LEU cc_start: 0.8762 (mt) cc_final: 0.8527 (mt) REVERT: E 798 TYR cc_start: 0.8490 (m-10) cc_final: 0.8233 (m-10) REVERT: E 809 TRP cc_start: 0.8525 (p90) cc_final: 0.8202 (p90) REVERT: E 833 PHE cc_start: 0.7576 (t80) cc_final: 0.7307 (t80) REVERT: F 518 SER cc_start: 0.9124 (m) cc_final: 0.8898 (t) REVERT: F 842 THR cc_start: 0.8041 (m) cc_final: 0.7728 (p) outliers start: 0 outliers final: 0 residues processed: 564 average time/residue: 0.3636 time to fit residues: 280.9212 Evaluate side-chains 311 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 90 optimal weight: 0.0670 chunk 55 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 169 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.1980 chunk 126 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 HIS A 570 ASN A 662 GLN B 558 HIS B 662 GLN B 716 GLN C 558 HIS C 662 GLN C 716 GLN D 558 HIS D 570 ASN D 662 GLN ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 HIS E 570 ASN E 662 GLN E 716 GLN F 558 HIS F 662 GLN ** F 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 716 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 16932 Z= 0.201 Angle : 0.612 7.997 22986 Z= 0.325 Chirality : 0.047 0.145 2628 Planarity : 0.005 0.046 2988 Dihedral : 5.386 20.332 2370 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.75 % Allowed : 11.34 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.16), residues: 2166 helix: -3.40 (0.31), residues: 192 sheet: -1.56 (0.17), residues: 774 loop : -1.89 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 809 HIS 0.003 0.001 HIS B 640 PHE 0.016 0.001 PHE F 833 TYR 0.017 0.002 TYR B 624 ARG 0.005 0.001 ARG C 869 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 325 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 646 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7510 (mtmt) REVERT: A 716 GLN cc_start: 0.8211 (tt0) cc_final: 0.7850 (pt0) REVERT: A 746 ASP cc_start: 0.6467 (t0) cc_final: 0.6152 (t0) REVERT: A 762 ILE cc_start: 0.8815 (mp) cc_final: 0.8609 (mm) REVERT: A 798 TYR cc_start: 0.8820 (m-80) cc_final: 0.8575 (m-80) REVERT: A 853 GLN cc_start: 0.7768 (mm110) cc_final: 0.7238 (mp10) REVERT: B 746 ASP cc_start: 0.6384 (t0) cc_final: 0.6007 (t0) REVERT: B 797 ARG cc_start: 0.8169 (mtm110) cc_final: 0.7937 (mtm110) REVERT: B 798 TYR cc_start: 0.8765 (m-80) cc_final: 0.8152 (m-80) REVERT: B 842 THR cc_start: 0.7800 (m) cc_final: 0.7362 (p) REVERT: C 749 SER cc_start: 0.8970 (t) cc_final: 0.8753 (m) REVERT: C 827 THR cc_start: 0.7901 (m) cc_final: 0.7527 (p) REVERT: D 599 LEU cc_start: 0.7400 (mp) cc_final: 0.7158 (mp) REVERT: D 646 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7551 (mtmt) REVERT: D 731 ASP cc_start: 0.7452 (m-30) cc_final: 0.7155 (m-30) REVERT: D 745 LEU cc_start: 0.8230 (mt) cc_final: 0.8015 (mt) REVERT: D 746 ASP cc_start: 0.6364 (t0) cc_final: 0.5923 (t0) REVERT: D 798 TYR cc_start: 0.8871 (m-80) cc_final: 0.8392 (m-80) REVERT: E 518 SER cc_start: 0.9084 (m) cc_final: 0.8738 (t) REVERT: E 606 ASP cc_start: 0.7711 (t0) cc_final: 0.7310 (t0) REVERT: E 695 ARG cc_start: 0.8068 (mtm180) cc_final: 0.7747 (mtp180) REVERT: E 798 TYR cc_start: 0.8574 (m-10) cc_final: 0.8313 (m-10) REVERT: E 809 TRP cc_start: 0.8600 (p90) cc_final: 0.8263 (p90) REVERT: E 842 THR cc_start: 0.8171 (m) cc_final: 0.7712 (p) REVERT: F 518 SER cc_start: 0.9002 (m) cc_final: 0.8764 (t) REVERT: F 842 THR cc_start: 0.8031 (m) cc_final: 0.7664 (p) outliers start: 48 outliers final: 30 residues processed: 344 average time/residue: 0.3004 time to fit residues: 150.7501 Evaluate side-chains 307 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 275 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 716 GLN Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 646 LYS Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 733 GLU Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain E residue 642 PHE Chi-restraints excluded: chain E residue 780 THR Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 859 LEU Chi-restraints excluded: chain F residue 569 SER Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 816 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 212 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 157 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 ASN E 570 ASN E 662 GLN E 716 GLN ** F 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 804 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16932 Z= 0.195 Angle : 0.559 7.844 22986 Z= 0.292 Chirality : 0.045 0.147 2628 Planarity : 0.005 0.078 2988 Dihedral : 4.940 18.115 2370 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.86 % Allowed : 13.92 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.17), residues: 2166 helix: -3.25 (0.27), residues: 240 sheet: -1.29 (0.17), residues: 750 loop : -1.75 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 809 HIS 0.003 0.001 HIS C 558 PHE 0.020 0.002 PHE F 833 TYR 0.017 0.002 TYR C 798 ARG 0.007 0.001 ARG D 691 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 305 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7595 (mtmt) REVERT: A 716 GLN cc_start: 0.8261 (tt0) cc_final: 0.8060 (pt0) REVERT: A 731 ASP cc_start: 0.7499 (m-30) cc_final: 0.7263 (m-30) REVERT: A 798 TYR cc_start: 0.8871 (m-80) cc_final: 0.8330 (m-80) REVERT: B 712 ASP cc_start: 0.7628 (p0) cc_final: 0.7423 (p0) REVERT: B 746 ASP cc_start: 0.6294 (t0) cc_final: 0.5807 (t0) REVERT: B 797 ARG cc_start: 0.8197 (mtm110) cc_final: 0.7991 (mtm110) REVERT: B 842 THR cc_start: 0.7914 (m) cc_final: 0.7516 (p) REVERT: C 798 TYR cc_start: 0.7920 (m-10) cc_final: 0.7632 (m-10) REVERT: D 646 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7692 (mtmt) REVERT: D 746 ASP cc_start: 0.6409 (t0) cc_final: 0.5879 (t0) REVERT: D 797 ARG cc_start: 0.8269 (mtm110) cc_final: 0.7835 (mtm110) REVERT: D 798 TYR cc_start: 0.8897 (m-80) cc_final: 0.8436 (m-80) REVERT: D 853 GLN cc_start: 0.7794 (mm110) cc_final: 0.7249 (mp10) REVERT: E 518 SER cc_start: 0.9055 (m) cc_final: 0.8692 (t) REVERT: E 606 ASP cc_start: 0.7402 (t0) cc_final: 0.7183 (t0) REVERT: E 695 ARG cc_start: 0.8080 (mtm180) cc_final: 0.7859 (ttm110) REVERT: E 809 TRP cc_start: 0.8612 (p90) cc_final: 0.8245 (p90) REVERT: E 842 THR cc_start: 0.8186 (m) cc_final: 0.7762 (p) REVERT: F 518 SER cc_start: 0.8961 (m) cc_final: 0.8689 (t) REVERT: F 842 THR cc_start: 0.8150 (m) cc_final: 0.7775 (p) outliers start: 50 outliers final: 24 residues processed: 324 average time/residue: 0.2999 time to fit residues: 142.2233 Evaluate side-chains 296 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 270 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 868 TRP Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 838 ILE Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain D residue 646 LYS Chi-restraints excluded: chain D residue 733 GLU Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 780 THR Chi-restraints excluded: chain E residue 859 LEU Chi-restraints excluded: chain F residue 569 SER Chi-restraints excluded: chain F residue 711 LEU Chi-restraints excluded: chain F residue 816 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 197 optimal weight: 0.9990 chunk 208 optimal weight: 0.0570 chunk 103 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 662 GLN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 ASN E 570 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 662 GLN E 716 GLN F 570 ASN ** F 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 831 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16932 Z= 0.201 Angle : 0.551 8.006 22986 Z= 0.285 Chirality : 0.045 0.158 2628 Planarity : 0.004 0.038 2988 Dihedral : 4.762 17.515 2370 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.04 % Allowed : 15.69 % Favored : 81.27 % 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: -2.41 (0.17), residues: 2166 helix: -3.04 (0.27), residues: 240 sheet: -1.12 (0.17), residues: 750 loop : -1.56 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 809 HIS 0.003 0.001 HIS C 558 PHE 0.025 0.002 PHE F 833 TYR 0.015 0.002 TYR F 624 ARG 0.008 0.000 ARG C 769 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 284 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7623 (mtmt) REVERT: A 746 ASP cc_start: 0.6498 (t0) cc_final: 0.6265 (t0) REVERT: B 606 ASP cc_start: 0.7765 (t0) cc_final: 0.7521 (t0) REVERT: B 746 ASP cc_start: 0.6305 (t0) cc_final: 0.5720 (t0) REVERT: B 842 THR cc_start: 0.8004 (m) cc_final: 0.7609 (p) REVERT: C 606 ASP cc_start: 0.7709 (t0) cc_final: 0.7468 (t0) REVERT: C 779 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7887 (ttt) REVERT: D 606 ASP cc_start: 0.7715 (t0) cc_final: 0.7432 (t0) REVERT: D 646 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7711 (mtmt) REVERT: D 746 ASP cc_start: 0.6391 (t0) cc_final: 0.5870 (t0) REVERT: D 756 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7180 (mt-10) REVERT: D 797 ARG cc_start: 0.8295 (mtm110) cc_final: 0.7907 (mtm110) REVERT: D 798 TYR cc_start: 0.8968 (m-80) cc_final: 0.8596 (m-80) REVERT: E 518 SER cc_start: 0.9047 (m) cc_final: 0.8658 (t) REVERT: E 695 ARG cc_start: 0.8104 (mtm180) cc_final: 0.7643 (ttm110) REVERT: E 809 TRP cc_start: 0.8608 (p90) cc_final: 0.8213 (p90) REVERT: E 833 PHE cc_start: 0.6841 (t80) cc_final: 0.6611 (t80) REVERT: E 842 THR cc_start: 0.8058 (m) cc_final: 0.7676 (p) REVERT: F 518 SER cc_start: 0.8931 (m) cc_final: 0.8662 (t) REVERT: F 842 THR cc_start: 0.8258 (m) cc_final: 0.7895 (p) outliers start: 53 outliers final: 31 residues processed: 304 average time/residue: 0.2746 time to fit residues: 125.5197 Evaluate side-chains 299 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 265 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 868 TRP Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 646 LYS Chi-restraints excluded: chain D residue 733 GLU Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 842 THR Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 780 THR Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 859 LEU Chi-restraints excluded: chain F residue 711 LEU Chi-restraints excluded: chain F residue 727 ASN Chi-restraints excluded: chain F residue 773 VAL Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 816 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 155 optimal weight: 0.4980 chunk 86 optimal weight: 0.0050 chunk 178 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 GLN A 853 GLN B 662 GLN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 716 GLN F 570 ASN F 702 GLN F 804 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16932 Z= 0.198 Angle : 0.538 9.924 22986 Z= 0.278 Chirality : 0.045 0.146 2628 Planarity : 0.004 0.036 2988 Dihedral : 4.637 17.184 2370 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.38 % Allowed : 16.21 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.17), residues: 2166 helix: -2.81 (0.28), residues: 240 sheet: -1.06 (0.17), residues: 810 loop : -1.50 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 809 HIS 0.002 0.001 HIS C 558 PHE 0.016 0.001 PHE E 833 TYR 0.011 0.001 TYR F 744 ARG 0.006 0.000 ARG F 797 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 277 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 646 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7740 (mtmt) REVERT: A 746 ASP cc_start: 0.6482 (t0) cc_final: 0.6259 (t0) REVERT: B 606 ASP cc_start: 0.7804 (t0) cc_final: 0.7490 (t0) REVERT: B 746 ASP cc_start: 0.6147 (t0) cc_final: 0.5733 (t0) REVERT: B 756 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7324 (mm-30) REVERT: B 833 PHE cc_start: 0.5657 (t80) cc_final: 0.5397 (t80) REVERT: B 842 THR cc_start: 0.8067 (m) cc_final: 0.7691 (p) REVERT: C 606 ASP cc_start: 0.7616 (t0) cc_final: 0.7359 (t0) REVERT: C 842 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7576 (p) REVERT: D 606 ASP cc_start: 0.7744 (t0) cc_final: 0.7524 (t0) REVERT: D 646 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7719 (mtmt) REVERT: D 733 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7447 (mm-30) REVERT: D 746 ASP cc_start: 0.6374 (t0) cc_final: 0.5836 (t0) REVERT: D 797 ARG cc_start: 0.8293 (mtm110) cc_final: 0.7994 (mtm110) REVERT: D 798 TYR cc_start: 0.8918 (m-80) cc_final: 0.8504 (m-80) REVERT: E 518 SER cc_start: 0.9014 (m) cc_final: 0.8605 (t) REVERT: E 540 VAL cc_start: 0.4439 (OUTLIER) cc_final: 0.4236 (t) REVERT: E 606 ASP cc_start: 0.7532 (t0) cc_final: 0.7269 (t0) REVERT: E 695 ARG cc_start: 0.8152 (mtm180) cc_final: 0.7831 (ttm110) REVERT: E 809 TRP cc_start: 0.8620 (p90) cc_final: 0.8189 (p90) REVERT: E 842 THR cc_start: 0.8069 (m) cc_final: 0.7653 (p) REVERT: F 518 SER cc_start: 0.8996 (m) cc_final: 0.8714 (t) REVERT: F 842 THR cc_start: 0.8325 (m) cc_final: 0.7961 (p) outliers start: 59 outliers final: 39 residues processed: 303 average time/residue: 0.2635 time to fit residues: 121.7622 Evaluate side-chains 306 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 261 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 868 TRP Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 646 LYS Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 733 GLU Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 714 ILE Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 780 THR Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain E residue 859 LEU Chi-restraints excluded: chain F residue 569 SER Chi-restraints excluded: chain F residue 711 LEU Chi-restraints excluded: chain F residue 727 ASN Chi-restraints excluded: chain F residue 773 VAL Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 804 ASN Chi-restraints excluded: chain F residue 816 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 4.9990 chunk 188 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN B 662 GLN B 832 GLN C 662 GLN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 ASN D 662 GLN E 662 GLN F 570 ASN F 662 GLN ** F 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 804 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 16932 Z= 0.299 Angle : 0.577 7.447 22986 Z= 0.302 Chirality : 0.046 0.165 2628 Planarity : 0.004 0.060 2988 Dihedral : 4.820 17.022 2370 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.01 % Allowed : 16.61 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.18), residues: 2166 helix: -2.71 (0.28), residues: 240 sheet: -1.24 (0.16), residues: 894 loop : -1.34 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 809 HIS 0.004 0.001 HIS C 800 PHE 0.023 0.002 PHE E 833 TYR 0.012 0.002 TYR E 814 ARG 0.007 0.000 ARG F 797 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 271 time to evaluate : 1.804 Fit side-chains revert: symmetry clash REVERT: A 606 ASP cc_start: 0.7996 (t0) cc_final: 0.7731 (t0) REVERT: A 646 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7771 (mtmt) REVERT: A 716 GLN cc_start: 0.8114 (pm20) cc_final: 0.7308 (pm20) REVERT: A 746 ASP cc_start: 0.6504 (t0) cc_final: 0.6291 (t0) REVERT: A 779 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7748 (ttm) REVERT: B 606 ASP cc_start: 0.7928 (t0) cc_final: 0.7693 (t0) REVERT: B 673 ASN cc_start: 0.7701 (p0) cc_final: 0.7482 (p0) REVERT: B 746 ASP cc_start: 0.5911 (t0) cc_final: 0.5577 (t0) REVERT: B 816 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7931 (mt) REVERT: B 830 PHE cc_start: 0.6342 (OUTLIER) cc_final: 0.5162 (p90) REVERT: B 833 PHE cc_start: 0.5819 (t80) cc_final: 0.5535 (t80) REVERT: B 842 THR cc_start: 0.8169 (m) cc_final: 0.7830 (p) REVERT: C 606 ASP cc_start: 0.7793 (t0) cc_final: 0.7571 (t0) REVERT: C 835 ARG cc_start: 0.6920 (mtt180) cc_final: 0.6670 (mpp80) REVERT: C 842 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.7780 (p) REVERT: D 646 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7743 (mtmt) REVERT: D 798 TYR cc_start: 0.8868 (m-80) cc_final: 0.8516 (m-80) REVERT: E 518 SER cc_start: 0.9000 (m) cc_final: 0.8731 (t) REVERT: E 606 ASP cc_start: 0.7586 (t0) cc_final: 0.7245 (t0) REVERT: E 695 ARG cc_start: 0.8281 (mtm180) cc_final: 0.7776 (mtp180) REVERT: E 809 TRP cc_start: 0.8672 (p90) cc_final: 0.8177 (p90) REVERT: E 842 THR cc_start: 0.8136 (m) cc_final: 0.7751 (p) REVERT: F 518 SER cc_start: 0.8981 (m) cc_final: 0.8725 (t) REVERT: F 771 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8674 (mt) REVERT: F 842 THR cc_start: 0.8419 (m) cc_final: 0.8074 (p) outliers start: 70 outliers final: 53 residues processed: 307 average time/residue: 0.2546 time to fit residues: 120.9577 Evaluate side-chains 317 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 257 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 868 TRP Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 580 LYS Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 646 LYS Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 727 ASN Chi-restraints excluded: chain D residue 733 GLU Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 830 PHE Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 714 ILE Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 780 THR Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain E residue 859 LEU Chi-restraints excluded: chain F residue 551 ASN Chi-restraints excluded: chain F residue 569 SER Chi-restraints excluded: chain F residue 711 LEU Chi-restraints excluded: chain F residue 727 ASN Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 773 VAL Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 802 VAL Chi-restraints excluded: chain F residue 816 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 662 GLN ** A 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN C 702 GLN F 570 ASN F 702 GLN F 710 HIS F 804 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 16932 Z= 0.440 Angle : 0.669 9.282 22986 Z= 0.351 Chirality : 0.048 0.192 2628 Planarity : 0.005 0.049 2988 Dihedral : 5.372 18.190 2370 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.87 % Allowed : 16.90 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.18), residues: 2166 helix: -2.87 (0.27), residues: 240 sheet: -1.41 (0.16), residues: 894 loop : -1.32 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 809 HIS 0.004 0.001 HIS E 558 PHE 0.023 0.002 PHE E 833 TYR 0.014 0.002 TYR F 624 ARG 0.008 0.001 ARG F 797 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 273 time to evaluate : 1.851 Fit side-chains REVERT: A 606 ASP cc_start: 0.8028 (t0) cc_final: 0.7814 (t0) REVERT: A 646 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7802 (mtmt) REVERT: A 716 GLN cc_start: 0.8186 (pm20) cc_final: 0.7476 (pm20) REVERT: A 779 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7747 (ttm) REVERT: A 816 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7611 (pp) REVERT: B 606 ASP cc_start: 0.7939 (t0) cc_final: 0.7698 (t0) REVERT: B 672 ARG cc_start: 0.7265 (mtm180) cc_final: 0.7039 (ptt180) REVERT: B 673 ASN cc_start: 0.7811 (p0) cc_final: 0.7589 (p0) REVERT: B 746 ASP cc_start: 0.5873 (t0) cc_final: 0.5590 (t0) REVERT: B 816 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7597 (mt) REVERT: B 830 PHE cc_start: 0.6709 (OUTLIER) cc_final: 0.5380 (p90) REVERT: B 842 THR cc_start: 0.8253 (m) cc_final: 0.7994 (p) REVERT: C 606 ASP cc_start: 0.7894 (t0) cc_final: 0.7674 (t0) REVERT: C 842 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8012 (p) REVERT: D 646 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7872 (mtmt) REVERT: D 798 TYR cc_start: 0.8851 (m-80) cc_final: 0.8478 (m-80) REVERT: E 518 SER cc_start: 0.8997 (m) cc_final: 0.8791 (t) REVERT: E 600 LYS cc_start: 0.4732 (OUTLIER) cc_final: 0.3355 (mmtt) REVERT: E 606 ASP cc_start: 0.7832 (t0) cc_final: 0.7554 (t0) REVERT: E 695 ARG cc_start: 0.8398 (mtm180) cc_final: 0.8122 (mtp180) REVERT: E 816 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7289 (mm) REVERT: E 830 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.5817 (p90) REVERT: E 842 THR cc_start: 0.8133 (m) cc_final: 0.7800 (p) REVERT: F 771 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8796 (mt) REVERT: F 842 THR cc_start: 0.8560 (m) cc_final: 0.8228 (p) outliers start: 85 outliers final: 56 residues processed: 322 average time/residue: 0.2584 time to fit residues: 127.8835 Evaluate side-chains 321 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 254 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 868 TRP Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 580 LYS Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 646 LYS Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 727 ASN Chi-restraints excluded: chain D residue 733 GLU Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 830 PHE Chi-restraints excluded: chain D residue 838 ILE Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 642 PHE Chi-restraints excluded: chain E residue 714 ILE Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 780 THR Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 830 PHE Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain E residue 859 LEU Chi-restraints excluded: chain F residue 551 ASN Chi-restraints excluded: chain F residue 569 SER Chi-restraints excluded: chain F residue 667 ASP Chi-restraints excluded: chain F residue 700 THR Chi-restraints excluded: chain F residue 711 LEU Chi-restraints excluded: chain F residue 727 ASN Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 773 VAL Chi-restraints excluded: chain F residue 779 MET Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 804 ASN Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain F residue 859 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 662 GLN A 716 GLN B 570 ASN C 662 GLN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 662 GLN D 832 GLN E 832 GLN F 570 ASN F 640 HIS F 676 GLN F 804 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16932 Z= 0.282 Angle : 0.593 9.014 22986 Z= 0.307 Chirality : 0.046 0.193 2628 Planarity : 0.004 0.049 2988 Dihedral : 5.041 18.130 2370 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.61 % Allowed : 18.04 % Favored : 78.35 % 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: -2.34 (0.18), residues: 2166 helix: -2.77 (0.27), residues: 240 sheet: -1.34 (0.16), residues: 894 loop : -1.27 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 809 HIS 0.002 0.001 HIS E 558 PHE 0.027 0.002 PHE C 833 TYR 0.016 0.002 TYR B 814 ARG 0.008 0.000 ARG F 797 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 270 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 606 ASP cc_start: 0.8202 (t0) cc_final: 0.7960 (t0) REVERT: A 646 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7705 (mtmt) REVERT: A 716 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7426 (pm20) REVERT: A 746 ASP cc_start: 0.6388 (t0) cc_final: 0.5885 (t0) REVERT: A 779 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7655 (ttm) REVERT: A 797 ARG cc_start: 0.8331 (mtm110) cc_final: 0.8118 (ttp80) REVERT: B 606 ASP cc_start: 0.7944 (t0) cc_final: 0.7711 (t0) REVERT: B 673 ASN cc_start: 0.7787 (p0) cc_final: 0.7575 (p0) REVERT: B 746 ASP cc_start: 0.5904 (t0) cc_final: 0.5644 (t0) REVERT: B 816 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7613 (mt) REVERT: B 830 PHE cc_start: 0.6382 (OUTLIER) cc_final: 0.5473 (p90) REVERT: B 833 PHE cc_start: 0.6118 (t80) cc_final: 0.5902 (t80) REVERT: B 842 THR cc_start: 0.8219 (m) cc_final: 0.7911 (p) REVERT: C 606 ASP cc_start: 0.7859 (t0) cc_final: 0.7659 (t0) REVERT: C 835 ARG cc_start: 0.6927 (mtt180) cc_final: 0.6714 (mpp80) REVERT: C 842 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.7975 (p) REVERT: D 646 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7747 (mtmt) REVERT: D 798 TYR cc_start: 0.8780 (m-80) cc_final: 0.8351 (m-80) REVERT: E 518 SER cc_start: 0.8911 (m) cc_final: 0.8669 (t) REVERT: E 606 ASP cc_start: 0.7893 (t0) cc_final: 0.7622 (t0) REVERT: E 695 ARG cc_start: 0.8370 (mtm180) cc_final: 0.8061 (mtp180) REVERT: E 816 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7256 (mm) REVERT: E 842 THR cc_start: 0.8140 (m) cc_final: 0.7783 (p) REVERT: F 771 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8791 (mt) REVERT: F 816 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7170 (mt) REVERT: F 842 THR cc_start: 0.8515 (m) cc_final: 0.8153 (p) outliers start: 63 outliers final: 41 residues processed: 304 average time/residue: 0.2666 time to fit residues: 123.4895 Evaluate side-chains 310 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 259 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 868 TRP Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain D residue 580 LYS Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 646 LYS Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 733 GLU Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 788 VAL Chi-restraints excluded: chain D residue 830 PHE Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 780 THR Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain E residue 859 LEU Chi-restraints excluded: chain F residue 551 ASN Chi-restraints excluded: chain F residue 569 SER Chi-restraints excluded: chain F residue 667 ASP Chi-restraints excluded: chain F residue 711 LEU Chi-restraints excluded: chain F residue 727 ASN Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 804 ASN Chi-restraints excluded: chain F residue 816 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 0.0980 chunk 181 optimal weight: 0.1980 chunk 194 optimal weight: 0.0010 chunk 116 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 59 optimal weight: 0.3980 chunk 175 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 GLN A 853 GLN B 570 ASN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 853 GLN E 662 GLN F 570 ASN F 662 GLN F 804 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 16932 Z= 0.166 Angle : 0.548 9.816 22986 Z= 0.280 Chirality : 0.045 0.159 2628 Planarity : 0.004 0.044 2988 Dihedral : 4.596 17.378 2370 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.98 % Allowed : 19.07 % Favored : 77.95 % 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: -2.17 (0.18), residues: 2166 helix: -2.67 (0.28), residues: 246 sheet: -1.10 (0.17), residues: 894 loop : -1.29 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 809 HIS 0.002 0.000 HIS F 800 PHE 0.018 0.001 PHE E 833 TYR 0.016 0.001 TYR A 718 ARG 0.008 0.000 ARG F 797 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 277 time to evaluate : 1.879 Fit side-chains REVERT: A 606 ASP cc_start: 0.8050 (t0) cc_final: 0.7811 (t0) REVERT: A 646 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7719 (mtmt) REVERT: A 695 ARG cc_start: 0.7996 (mtm180) cc_final: 0.7781 (mtp180) REVERT: A 746 ASP cc_start: 0.6370 (t0) cc_final: 0.5892 (t0) REVERT: B 606 ASP cc_start: 0.7997 (t0) cc_final: 0.7764 (t0) REVERT: B 746 ASP cc_start: 0.5821 (t0) cc_final: 0.5513 (t0) REVERT: B 816 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7490 (mt) REVERT: B 842 THR cc_start: 0.8130 (m) cc_final: 0.7755 (p) REVERT: C 646 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7882 (mtmt) REVERT: C 842 THR cc_start: 0.8306 (m) cc_final: 0.7839 (p) REVERT: D 646 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7739 (mtmt) REVERT: E 518 SER cc_start: 0.8802 (m) cc_final: 0.8491 (t) REVERT: E 600 LYS cc_start: 0.4672 (OUTLIER) cc_final: 0.3354 (mmtt) REVERT: E 606 ASP cc_start: 0.7816 (t0) cc_final: 0.7548 (t0) REVERT: E 695 ARG cc_start: 0.8278 (mtm180) cc_final: 0.7993 (mtp180) REVERT: E 809 TRP cc_start: 0.8617 (p90) cc_final: 0.8142 (p90) REVERT: E 816 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7204 (mm) REVERT: E 833 PHE cc_start: 0.6194 (t80) cc_final: 0.5604 (t80) REVERT: E 842 THR cc_start: 0.8028 (m) cc_final: 0.7588 (p) REVERT: F 771 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8696 (mt) REVERT: F 816 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7124 (mt) REVERT: F 842 THR cc_start: 0.8411 (m) cc_final: 0.8015 (p) outliers start: 52 outliers final: 33 residues processed: 303 average time/residue: 0.2609 time to fit residues: 120.7923 Evaluate side-chains 308 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 267 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 646 LYS Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain D residue 580 LYS Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 646 LYS Chi-restraints excluded: chain D residue 733 GLU Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 780 THR Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain E residue 859 LEU Chi-restraints excluded: chain F residue 569 SER Chi-restraints excluded: chain F residue 667 ASP Chi-restraints excluded: chain F residue 711 LEU Chi-restraints excluded: chain F residue 721 VAL Chi-restraints excluded: chain F residue 727 ASN Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 802 VAL Chi-restraints excluded: chain F residue 804 ASN Chi-restraints excluded: chain F residue 816 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 0.6980 chunk 125 optimal weight: 0.0370 chunk 97 optimal weight: 0.2980 chunk 142 optimal weight: 5.9990 chunk 215 optimal weight: 0.0270 chunk 198 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 136 optimal weight: 0.4980 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 570 ASN B 662 GLN C 702 GLN C 716 GLN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 ASN D 853 GLN E 662 GLN E 716 GLN F 570 ASN F 716 GLN F 804 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16932 Z= 0.167 Angle : 0.545 8.543 22986 Z= 0.279 Chirality : 0.045 0.215 2628 Planarity : 0.004 0.064 2988 Dihedral : 4.450 17.343 2370 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.52 % Allowed : 20.10 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.18), residues: 2166 helix: -2.41 (0.29), residues: 246 sheet: -1.03 (0.17), residues: 894 loop : -1.23 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 809 HIS 0.002 0.000 HIS C 558 PHE 0.042 0.001 PHE C 833 TYR 0.024 0.001 TYR B 814 ARG 0.009 0.000 ARG F 797 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 268 time to evaluate : 1.761 Fit side-chains REVERT: A 646 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7701 (mtmt) REVERT: A 716 GLN cc_start: 0.7869 (pm20) cc_final: 0.7241 (pm20) REVERT: A 746 ASP cc_start: 0.6380 (t0) cc_final: 0.5889 (t0) REVERT: B 606 ASP cc_start: 0.7982 (t0) cc_final: 0.7757 (t0) REVERT: B 746 ASP cc_start: 0.5860 (t0) cc_final: 0.5606 (t0) REVERT: B 816 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7474 (mt) REVERT: B 842 THR cc_start: 0.8120 (m) cc_final: 0.7741 (p) REVERT: C 646 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7893 (mtmt) REVERT: C 842 THR cc_start: 0.8240 (m) cc_final: 0.7774 (p) REVERT: D 646 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7720 (mtmt) REVERT: D 798 TYR cc_start: 0.8779 (m-80) cc_final: 0.8488 (m-80) REVERT: E 518 SER cc_start: 0.8804 (m) cc_final: 0.8381 (t) REVERT: E 600 LYS cc_start: 0.4728 (OUTLIER) cc_final: 0.3383 (mmtt) REVERT: E 606 ASP cc_start: 0.7815 (t0) cc_final: 0.7544 (t0) REVERT: E 673 ASN cc_start: 0.7417 (p0) cc_final: 0.7118 (p0) REVERT: E 695 ARG cc_start: 0.8270 (mtm180) cc_final: 0.7985 (mtp180) REVERT: E 746 ASP cc_start: 0.5758 (t0) cc_final: 0.5555 (t0) REVERT: E 809 TRP cc_start: 0.8629 (p90) cc_final: 0.8152 (p90) REVERT: E 816 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7192 (mm) REVERT: E 842 THR cc_start: 0.8066 (m) cc_final: 0.7607 (p) REVERT: F 771 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8637 (mt) REVERT: F 816 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7097 (mt) REVERT: F 835 ARG cc_start: 0.6511 (OUTLIER) cc_final: 0.6258 (mpp80) REVERT: F 842 THR cc_start: 0.8410 (m) cc_final: 0.8008 (p) outliers start: 44 outliers final: 31 residues processed: 293 average time/residue: 0.2652 time to fit residues: 117.6680 Evaluate side-chains 300 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 260 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 646 LYS Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain D residue 580 LYS Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 646 LYS Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 780 THR Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain E residue 859 LEU Chi-restraints excluded: chain F residue 569 SER Chi-restraints excluded: chain F residue 667 ASP Chi-restraints excluded: chain F residue 711 LEU Chi-restraints excluded: chain F residue 727 ASN Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 804 ASN Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain F residue 835 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 176 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 GLN A 853 GLN B 570 ASN B 662 GLN B 853 GLN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN F 804 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.174989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.141616 restraints weight = 23083.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.146409 restraints weight = 14044.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149662 restraints weight = 10076.356| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 16932 Z= 0.220 Angle : 0.554 7.850 22986 Z= 0.286 Chirality : 0.046 0.251 2628 Planarity : 0.004 0.055 2988 Dihedral : 4.487 18.150 2370 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.75 % Allowed : 20.27 % Favored : 76.98 % 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: -1.95 (0.18), residues: 2166 helix: -2.25 (0.30), residues: 240 sheet: -1.08 (0.17), residues: 894 loop : -1.09 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 809 HIS 0.002 0.001 HIS D 857 PHE 0.016 0.002 PHE F 833 TYR 0.027 0.001 TYR B 814 ARG 0.009 0.000 ARG F 797 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3460.88 seconds wall clock time: 62 minutes 55.91 seconds (3775.91 seconds total)