Starting phenix.real_space_refine on Sun Mar 17 04:06:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0e_20995/03_2024/6v0e_20995.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0e_20995/03_2024/6v0e_20995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0e_20995/03_2024/6v0e_20995.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0e_20995/03_2024/6v0e_20995.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0e_20995/03_2024/6v0e_20995.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0e_20995/03_2024/6v0e_20995.pdb" } resolution = 3.06 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 564": "NH1" <-> "NH2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ARG 743": "NH1" <-> "NH2" Residue "A ARG 797": "NH1" <-> "NH2" Residue "A ARG 869": "NH1" <-> "NH2" Residue "B ARG 547": "NH1" <-> "NH2" Residue "B ARG 564": "NH1" <-> "NH2" Residue "B ARG 672": "NH1" <-> "NH2" Residue "B ARG 691": "NH1" <-> "NH2" Residue "B ARG 743": "NH1" <-> "NH2" Residue "B ARG 797": "NH1" <-> "NH2" Residue "B ARG 869": "NH1" <-> "NH2" Residue "C ARG 547": "NH1" <-> "NH2" Residue "C ARG 564": "NH1" <-> "NH2" Residue "C ARG 672": "NH1" <-> "NH2" Residue "C ARG 691": "NH1" <-> "NH2" Residue "C ARG 743": "NH1" <-> "NH2" Residue "C ARG 797": "NH1" <-> "NH2" Residue "C ARG 869": "NH1" <-> "NH2" Residue "D ARG 547": "NH1" <-> "NH2" Residue "D ARG 564": "NH1" <-> "NH2" Residue "D ARG 672": "NH1" <-> "NH2" Residue "D ARG 691": "NH1" <-> "NH2" Residue "D ARG 743": "NH1" <-> "NH2" Residue "D ARG 797": "NH1" <-> "NH2" Residue "D ARG 869": "NH1" <-> "NH2" Residue "E ARG 547": "NH1" <-> "NH2" Residue "E ARG 564": "NH1" <-> "NH2" Residue "E ARG 672": "NH1" <-> "NH2" Residue "E ARG 691": "NH1" <-> "NH2" Residue "E ARG 743": "NH1" <-> "NH2" Residue "E ARG 797": "NH1" <-> "NH2" Residue "E ARG 869": "NH1" <-> "NH2" Residue "F ARG 547": "NH1" <-> "NH2" Residue "F ARG 564": "NH1" <-> "NH2" Residue "F ARG 672": "NH1" <-> "NH2" Residue "F ARG 691": "NH1" <-> "NH2" Residue "F ARG 743": "NH1" <-> "NH2" Residue "F ARG 797": "NH1" <-> "NH2" Residue "F ARG 869": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 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: 9.17, per 1000 atoms: 0.55 Number of scatterers: 16602 At special positions: 0 Unit cell: (106.11, 108.73, 110.04, 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: 5.84 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: 48 helices and 18 sheets defined 12.7% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 560 through 564 Processing helix chain 'A' and resid 594 through 600 removed outlier: 3.521A pdb=" N ALA A 598 " --> pdb=" O PRO A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 617 removed outlier: 3.553A pdb=" N GLN A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 632 removed outlier: 3.501A pdb=" N ALA A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 741 through 745 removed outlier: 4.502A pdb=" N TYR A 744 " --> pdb=" O ASP A 741 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 745 " --> pdb=" O SER A 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 741 through 745' Processing helix chain 'A' and resid 798 through 802 Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 594 through 600 removed outlier: 3.521A pdb=" N ALA B 598 " --> pdb=" O PRO B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 617 removed outlier: 3.552A pdb=" N GLN B 615 " --> pdb=" O ALA B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 632 removed outlier: 3.502A pdb=" N ALA B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 715 Processing helix chain 'B' and resid 741 through 745 removed outlier: 4.502A pdb=" N TYR B 744 " --> pdb=" O ASP B 741 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 745 " --> pdb=" O SER B 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 741 through 745' Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 867 through 871 Processing helix chain 'C' and resid 560 through 564 Processing helix chain 'C' and resid 594 through 600 removed outlier: 3.521A pdb=" N ALA C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 617 removed outlier: 3.553A pdb=" N GLN C 615 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 632 removed outlier: 3.502A pdb=" N ALA C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 715 Processing helix chain 'C' and resid 741 through 745 removed outlier: 4.502A pdb=" N TYR C 744 " --> pdb=" O ASP C 741 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 745 " --> pdb=" O SER C 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 741 through 745' Processing helix chain 'C' and resid 798 through 802 Processing helix chain 'C' and resid 867 through 871 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 594 through 600 removed outlier: 3.521A pdb=" N ALA D 598 " --> pdb=" O PRO D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 617 removed outlier: 3.554A pdb=" N GLN D 615 " --> pdb=" O ALA D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 632 removed outlier: 3.502A pdb=" N ALA D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 715 Processing helix chain 'D' and resid 741 through 745 removed outlier: 4.501A pdb=" N TYR D 744 " --> pdb=" O ASP D 741 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 745 " --> pdb=" O SER D 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 741 through 745' Processing helix chain 'D' and resid 798 through 802 Processing helix chain 'D' and resid 867 through 871 Processing helix chain 'E' and resid 560 through 564 Processing helix chain 'E' and resid 594 through 600 removed outlier: 3.521A pdb=" N ALA E 598 " --> pdb=" O PRO E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 617 removed outlier: 3.553A pdb=" N GLN E 615 " --> pdb=" O ALA E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 632 removed outlier: 3.502A pdb=" N ALA E 630 " --> pdb=" O SER E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 711 through 715 Processing helix chain 'E' and resid 741 through 745 removed outlier: 4.502A pdb=" N TYR E 744 " --> pdb=" O ASP E 741 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU E 745 " --> pdb=" O SER E 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 741 through 745' Processing helix chain 'E' and resid 798 through 802 Processing helix chain 'E' and resid 867 through 871 Processing helix chain 'F' and resid 560 through 564 Processing helix chain 'F' and resid 594 through 600 removed outlier: 3.521A pdb=" N ALA F 598 " --> pdb=" O PRO F 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 617 removed outlier: 3.553A pdb=" N GLN F 615 " --> pdb=" O ALA F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 626 through 632 removed outlier: 3.501A pdb=" N ALA F 630 " --> pdb=" O SER F 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 711 through 715 Processing helix chain 'F' and resid 741 through 745 removed outlier: 4.501A pdb=" N TYR F 744 " --> pdb=" O ASP F 741 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 745 " --> pdb=" O SER F 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 741 through 745' Processing helix chain 'F' and resid 798 through 802 Processing helix chain 'F' and resid 867 through 871 Processing sheet with id=AA1, first strand: chain 'A' and resid 517 through 521 removed outlier: 3.610A pdb=" N VAL A 517 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 521 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N HIS A 558 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL A 543 " --> pdb=" O HIS A 558 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL A 533 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N TYR A 624 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE A 573 " --> pdb=" O TYR A 624 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 695 through 698 removed outlier: 6.512A pdb=" N ILE A 653 " --> pdb=" O ILE A 660 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS A 678 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU A 666 " --> pdb=" O GLN A 676 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLN A 676 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU A 668 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU A 674 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N PHE A 732 " --> pdb=" O GLN A 636 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THR A 638 " --> pdb=" O PHE A 732 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 749 through 754 removed outlier: 6.391A pdb=" N ARG A 793 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL A 776 " --> pdb=" O ARG A 793 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLU A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE A 768 " --> pdb=" O GLU A 772 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 841 " --> pdb=" O VAL A 807 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE A 808 " --> pdb=" O GLN A 861 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N PHE A 858 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE A 751 " --> pdb=" O PHE A 858 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU A 860 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU A 753 " --> pdb=" O LEU A 860 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 517 through 521 removed outlier: 3.609A pdb=" N VAL B 517 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 521 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N HIS B 558 " --> pdb=" O VAL B 543 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL B 543 " --> pdb=" O HIS B 558 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL B 533 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N TYR B 624 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE B 573 " --> pdb=" O TYR B 624 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 695 through 698 removed outlier: 6.513A pdb=" N ILE B 653 " --> pdb=" O ILE B 660 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS B 678 " --> pdb=" O GLN B 664 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU B 666 " --> pdb=" O GLN B 676 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLN B 676 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU B 668 " --> pdb=" O GLU B 674 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU B 674 " --> pdb=" O LEU B 668 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N PHE B 732 " --> pdb=" O GLN B 636 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THR B 638 " --> pdb=" O PHE B 732 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 749 through 754 removed outlier: 6.391A pdb=" N ARG B 793 " --> pdb=" O VAL B 776 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL B 776 " --> pdb=" O ARG B 793 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLU B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE B 768 " --> pdb=" O GLU B 772 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 841 " --> pdb=" O VAL B 807 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE B 808 " --> pdb=" O GLN B 861 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N PHE B 858 " --> pdb=" O SER B 749 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE B 751 " --> pdb=" O PHE B 858 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU B 860 " --> pdb=" O ILE B 751 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU B 753 " --> pdb=" O LEU B 860 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 517 through 521 removed outlier: 3.609A pdb=" N VAL C 517 " --> pdb=" O LEU C 557 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 521 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N HIS C 558 " --> pdb=" O VAL C 543 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL C 543 " --> pdb=" O HIS C 558 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL C 533 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N TYR C 624 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE C 573 " --> pdb=" O TYR C 624 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 695 through 698 removed outlier: 6.512A pdb=" N ILE C 653 " --> pdb=" O ILE C 660 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS C 678 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU C 666 " --> pdb=" O GLN C 676 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLN C 676 " --> pdb=" O LEU C 666 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU C 668 " --> pdb=" O GLU C 674 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU C 674 " --> pdb=" O LEU C 668 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N PHE C 732 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THR C 638 " --> pdb=" O PHE C 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 749 through 754 removed outlier: 6.392A pdb=" N ARG C 793 " --> pdb=" O VAL C 776 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL C 776 " --> pdb=" O ARG C 793 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLU C 772 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE C 768 " --> pdb=" O GLU C 772 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA C 841 " --> pdb=" O VAL C 807 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE C 808 " --> pdb=" O GLN C 861 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N PHE C 858 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE C 751 " --> pdb=" O PHE C 858 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU C 860 " --> pdb=" O ILE C 751 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLU C 753 " --> pdb=" O LEU C 860 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 517 through 521 removed outlier: 3.609A pdb=" N VAL D 517 " --> pdb=" O LEU D 557 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 521 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N HIS D 558 " --> pdb=" O VAL D 543 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL D 543 " --> pdb=" O HIS D 558 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL D 533 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N TYR D 624 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE D 573 " --> pdb=" O TYR D 624 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 695 through 698 removed outlier: 6.513A pdb=" N ILE D 653 " --> pdb=" O ILE D 660 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS D 678 " --> pdb=" O GLN D 664 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU D 666 " --> pdb=" O GLN D 676 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLN D 676 " --> pdb=" O LEU D 666 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU D 668 " --> pdb=" O GLU D 674 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU D 674 " --> pdb=" O LEU D 668 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N PHE D 732 " --> pdb=" O GLN D 636 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THR D 638 " --> pdb=" O PHE D 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 749 through 754 removed outlier: 6.392A pdb=" N ARG D 793 " --> pdb=" O VAL D 776 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL D 776 " --> pdb=" O ARG D 793 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLU D 772 " --> pdb=" O PHE D 768 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE D 768 " --> pdb=" O GLU D 772 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 841 " --> pdb=" O VAL D 807 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE D 808 " --> pdb=" O GLN D 861 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N PHE D 858 " --> pdb=" O SER D 749 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE D 751 " --> pdb=" O PHE D 858 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU D 860 " --> pdb=" O ILE D 751 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU D 753 " --> pdb=" O LEU D 860 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 517 through 521 removed outlier: 3.609A pdb=" N VAL E 517 " --> pdb=" O LEU E 557 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA E 521 " --> pdb=" O PHE E 553 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N HIS E 558 " --> pdb=" O VAL E 543 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL E 543 " --> pdb=" O HIS E 558 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL E 533 " --> pdb=" O VAL E 540 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N TYR E 624 " --> pdb=" O SER E 571 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE E 573 " --> pdb=" O TYR E 624 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 695 through 698 removed outlier: 6.513A pdb=" N ILE E 653 " --> pdb=" O ILE E 660 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LYS E 678 " --> pdb=" O GLN E 664 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU E 666 " --> pdb=" O GLN E 676 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLN E 676 " --> pdb=" O LEU E 666 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU E 668 " --> pdb=" O GLU E 674 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU E 674 " --> pdb=" O LEU E 668 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N PHE E 732 " --> pdb=" O GLN E 636 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THR E 638 " --> pdb=" O PHE E 732 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 749 through 754 removed outlier: 6.392A pdb=" N ARG E 793 " --> pdb=" O VAL E 776 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL E 776 " --> pdb=" O ARG E 793 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLU E 772 " --> pdb=" O PHE E 768 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE E 768 " --> pdb=" O GLU E 772 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA E 841 " --> pdb=" O VAL E 807 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE E 808 " --> pdb=" O GLN E 861 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N PHE E 858 " --> pdb=" O SER E 749 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE E 751 " --> pdb=" O PHE E 858 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU E 860 " --> pdb=" O ILE E 751 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU E 753 " --> pdb=" O LEU E 860 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 517 through 521 removed outlier: 3.609A pdb=" N VAL F 517 " --> pdb=" O LEU F 557 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA F 521 " --> pdb=" O PHE F 553 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N HIS F 558 " --> pdb=" O VAL F 543 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL F 543 " --> pdb=" O HIS F 558 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL F 533 " --> pdb=" O VAL F 540 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N TYR F 624 " --> pdb=" O SER F 571 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE F 573 " --> pdb=" O TYR F 624 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 695 through 698 removed outlier: 6.512A pdb=" N ILE F 653 " --> pdb=" O ILE F 660 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LYS F 678 " --> pdb=" O GLN F 664 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU F 666 " --> pdb=" O GLN F 676 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLN F 676 " --> pdb=" O LEU F 666 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU F 668 " --> pdb=" O GLU F 674 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU F 674 " --> pdb=" O LEU F 668 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N PHE F 732 " --> pdb=" O GLN F 636 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THR F 638 " --> pdb=" O PHE F 732 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 749 through 754 removed outlier: 6.391A pdb=" N ARG F 793 " --> pdb=" O VAL F 776 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL F 776 " --> pdb=" O ARG F 793 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLU F 772 " --> pdb=" O PHE F 768 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE F 768 " --> pdb=" O GLU F 772 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA F 841 " --> pdb=" O VAL F 807 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE F 808 " --> pdb=" O GLN F 861 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N PHE F 858 " --> pdb=" O SER F 749 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE F 751 " --> pdb=" O PHE F 858 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU F 860 " --> pdb=" O ILE F 751 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU F 753 " --> pdb=" O LEU F 860 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.59 Time building geometry restraints manager: 6.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5468 1.34 - 1.45: 2449 1.45 - 1.57: 8967 1.57 - 1.68: 0 1.68 - 1.80: 48 Bond restraints: 16932 Sorted by residual: bond pdb=" C VAL E 699 " pdb=" N THR E 700 " ideal model delta sigma weight residual 1.331 1.296 0.035 1.59e-02 3.96e+03 4.94e+00 bond pdb=" C VAL C 699 " pdb=" N THR C 700 " ideal model delta sigma weight residual 1.331 1.296 0.035 1.59e-02 3.96e+03 4.88e+00 bond pdb=" C VAL D 699 " pdb=" N THR D 700 " ideal model delta sigma weight residual 1.331 1.296 0.035 1.59e-02 3.96e+03 4.78e+00 bond pdb=" C VAL A 699 " pdb=" N THR A 700 " ideal model delta sigma weight residual 1.331 1.297 0.034 1.59e-02 3.96e+03 4.63e+00 bond pdb=" C VAL B 699 " pdb=" N THR B 700 " ideal model delta sigma weight residual 1.331 1.297 0.034 1.59e-02 3.96e+03 4.55e+00 ... (remaining 16927 not shown) Histogram of bond angle deviations from ideal: 97.71 - 104.98: 353 104.98 - 112.24: 8399 112.24 - 119.51: 5465 119.51 - 126.77: 8552 126.77 - 134.04: 217 Bond angle restraints: 22986 Sorted by residual: angle pdb=" C GLY A 828 " pdb=" N THR A 829 " pdb=" CA THR A 829 " ideal model delta sigma weight residual 122.82 128.01 -5.19 1.42e+00 4.96e-01 1.34e+01 angle pdb=" C GLY D 828 " pdb=" N THR D 829 " pdb=" CA THR D 829 " ideal model delta sigma weight residual 122.82 128.01 -5.19 1.42e+00 4.96e-01 1.33e+01 angle pdb=" C GLY B 828 " pdb=" N THR B 829 " pdb=" CA THR B 829 " ideal model delta sigma weight residual 122.82 127.99 -5.17 1.42e+00 4.96e-01 1.33e+01 angle pdb=" C GLY C 828 " pdb=" N THR C 829 " pdb=" CA THR C 829 " ideal model delta sigma weight residual 122.82 127.99 -5.17 1.42e+00 4.96e-01 1.33e+01 angle pdb=" C GLY E 828 " pdb=" N THR E 829 " pdb=" CA THR E 829 " ideal model delta sigma weight residual 122.82 127.98 -5.16 1.42e+00 4.96e-01 1.32e+01 ... (remaining 22981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.40: 9384 14.40 - 28.80: 546 28.80 - 43.19: 138 43.19 - 57.59: 0 57.59 - 71.99: 12 Dihedral angle restraints: 10080 sinusoidal: 3948 harmonic: 6132 Sorted by residual: dihedral pdb=" CA THR D 846 " pdb=" C THR D 846 " pdb=" N PRO D 847 " pdb=" CA PRO D 847 " ideal model delta harmonic sigma weight residual 180.00 152.63 27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA THR E 846 " pdb=" C THR E 846 " pdb=" N PRO E 847 " pdb=" CA PRO E 847 " ideal model delta harmonic sigma weight residual 180.00 152.63 27.37 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 180.00 152.66 27.34 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 10077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1658 0.048 - 0.096: 676 0.096 - 0.144: 230 0.144 - 0.192: 28 0.192 - 0.240: 36 Chirality restraints: 2628 Sorted by residual: chirality pdb=" CB VAL C 527 " pdb=" CA VAL C 527 " pdb=" CG1 VAL C 527 " pdb=" CG2 VAL C 527 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CB VAL E 527 " pdb=" CA VAL E 527 " pdb=" CG1 VAL E 527 " pdb=" CG2 VAL E 527 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL B 527 " pdb=" CA VAL B 527 " pdb=" CG1 VAL B 527 " pdb=" CG2 VAL B 527 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 2625 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 846 " 0.043 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO D 847 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 847 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 847 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 846 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO A 847 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 847 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 847 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 846 " 0.043 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO E 847 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 847 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 847 " 0.037 5.00e-02 4.00e+02 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2418 2.76 - 3.29: 14322 3.29 - 3.83: 26704 3.83 - 4.36: 31260 4.36 - 4.90: 55417 Nonbonded interactions: 130121 Sorted by model distance: nonbonded pdb=" OG SER A 759 " pdb=" O GLY B 828 " model vdw 2.220 2.440 nonbonded pdb=" OG SER D 759 " pdb=" O GLY E 828 " model vdw 2.220 2.440 nonbonded pdb=" OG SER E 759 " pdb=" O GLY F 828 " model vdw 2.239 2.440 nonbonded pdb=" OG SER B 759 " pdb=" O GLY C 828 " model vdw 2.247 2.440 nonbonded pdb=" O GLY A 828 " pdb=" OG SER F 759 " model vdw 2.284 2.440 ... (remaining 130116 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 individual isotropic 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: 1.050 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: 5.270 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 45.100 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 16932 Z= 0.564 Angle : 1.017 12.556 22986 Z= 0.543 Chirality : 0.062 0.240 2628 Planarity : 0.007 0.064 2988 Dihedral : 10.010 71.988 6180 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: -3.15 (0.15), residues: 2166 helix: -4.75 (0.10), residues: 198 sheet: -1.70 (0.16), residues: 816 loop : -1.82 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 868 HIS 0.007 0.002 HIS A 558 PHE 0.039 0.005 PHE C 605 TYR 0.018 0.003 TYR A 682 ARG 0.009 0.001 ARG F 564 *********************** 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 494 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.9108 (ttt) cc_final: 0.8905 (ttt) REVERT: A 817 ASP cc_start: 0.7696 (m-30) cc_final: 0.7014 (p0) REVERT: B 554 ASP cc_start: 0.7481 (t70) cc_final: 0.7243 (m-30) REVERT: B 817 ASP cc_start: 0.7428 (m-30) cc_final: 0.6975 (p0) REVERT: C 580 LYS cc_start: 0.8097 (tttt) cc_final: 0.7171 (mmmt) REVERT: C 792 MET cc_start: 0.8651 (ptp) cc_final: 0.8301 (ptp) REVERT: C 817 ASP cc_start: 0.7644 (m-30) cc_final: 0.7060 (p0) REVERT: D 651 MET cc_start: 0.9094 (ttt) cc_final: 0.8890 (ttt) REVERT: D 817 ASP cc_start: 0.7705 (m-30) cc_final: 0.7018 (p0) REVERT: E 554 ASP cc_start: 0.7454 (t70) cc_final: 0.7216 (m-30) REVERT: E 817 ASP cc_start: 0.7421 (m-30) cc_final: 0.6931 (p0) REVERT: F 792 MET cc_start: 0.8637 (ptp) cc_final: 0.8285 (ptp) REVERT: F 817 ASP cc_start: 0.7641 (m-30) cc_final: 0.7018 (p0) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.3228 time to fit residues: 224.4299 Evaluate side-chains 261 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.874 ------------------------------------------------------------------------------- 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: 1.9990 chunk 90 optimal weight: 0.0070 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 169 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 chunk 196 optimal weight: 0.7980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN A 591 GLN A 607 ASN ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 ASN A 831 ASN ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN C 607 ASN ** C 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN D 591 GLN D 607 ASN ** D 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 831 ASN ** E 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 ASN ** F 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16932 Z= 0.238 Angle : 0.651 8.568 22986 Z= 0.336 Chirality : 0.047 0.148 2628 Planarity : 0.005 0.040 2988 Dihedral : 5.953 20.016 2370 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.41 % Allowed : 11.45 % Favored : 86.14 % 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: -2.51 (0.17), residues: 2166 helix: -3.79 (0.20), residues: 210 sheet: -1.41 (0.17), residues: 786 loop : -1.34 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 868 HIS 0.003 0.001 HIS A 640 PHE 0.015 0.002 PHE A 808 TYR 0.016 0.002 TYR C 563 ARG 0.006 0.001 ARG C 691 *********************** 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 319 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 277 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 627 GLU cc_start: 0.7685 (tm-30) cc_final: 0.6017 (tm-30) REVERT: A 651 MET cc_start: 0.9051 (ttt) cc_final: 0.8795 (ttt) REVERT: A 818 PHE cc_start: 0.5989 (t80) cc_final: 0.5743 (t80) REVERT: C 580 LYS cc_start: 0.8037 (tttt) cc_final: 0.7149 (mmtt) REVERT: C 627 GLU cc_start: 0.7739 (tm-30) cc_final: 0.6084 (tm-30) REVERT: C 792 MET cc_start: 0.8703 (ptp) cc_final: 0.8291 (ptp) REVERT: D 627 GLU cc_start: 0.7691 (tm-30) cc_final: 0.6041 (tm-30) REVERT: D 651 MET cc_start: 0.9034 (ttt) cc_final: 0.8779 (ttt) REVERT: D 818 PHE cc_start: 0.6041 (t80) cc_final: 0.5765 (t80) REVERT: D 838 ILE cc_start: 0.9286 (mt) cc_final: 0.9055 (mt) REVERT: E 554 ASP cc_start: 0.7700 (t70) cc_final: 0.6998 (m-30) REVERT: E 817 ASP cc_start: 0.7400 (m-30) cc_final: 0.7058 (p0) REVERT: F 627 GLU cc_start: 0.7715 (tm-30) cc_final: 0.6102 (tm-30) REVERT: F 792 MET cc_start: 0.8702 (ptp) cc_final: 0.8295 (ptp) outliers start: 42 outliers final: 25 residues processed: 298 average time/residue: 0.2758 time to fit residues: 122.6854 Evaluate side-chains 248 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 223 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 796 LYS Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 712 ASP Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 796 LYS Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 712 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.0570 chunk 60 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 133 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 HIS B 640 HIS B 676 GLN C 607 ASN ** C 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 HIS ** D 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 HIS ** F 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16932 Z= 0.227 Angle : 0.603 7.349 22986 Z= 0.306 Chirality : 0.046 0.156 2628 Planarity : 0.004 0.035 2988 Dihedral : 5.523 19.761 2370 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.92 % Allowed : 14.20 % Favored : 82.88 % 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: -2.06 (0.18), residues: 2166 helix: -3.38 (0.23), residues: 210 sheet: -1.14 (0.17), residues: 846 loop : -1.00 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 809 HIS 0.002 0.001 HIS B 558 PHE 0.013 0.002 PHE F 605 TYR 0.021 0.001 TYR E 563 ARG 0.005 0.001 ARG F 597 *********************** 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 308 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 257 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 607 ASN cc_start: 0.7786 (m110) cc_final: 0.7213 (m-40) REVERT: A 627 GLU cc_start: 0.7595 (tm-30) cc_final: 0.5994 (tm-30) REVERT: A 818 PHE cc_start: 0.5951 (t80) cc_final: 0.5700 (t80) REVERT: B 627 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7248 (tp30) REVERT: B 817 ASP cc_start: 0.7797 (m-30) cc_final: 0.7079 (p0) REVERT: C 545 THR cc_start: 0.8207 (m) cc_final: 0.7982 (m) REVERT: C 580 LYS cc_start: 0.8031 (tttt) cc_final: 0.7292 (mmtt) REVERT: C 792 MET cc_start: 0.8703 (ptp) cc_final: 0.8210 (ptp) REVERT: D 627 GLU cc_start: 0.7603 (tm-30) cc_final: 0.6021 (tm-30) REVERT: D 818 PHE cc_start: 0.5977 (t80) cc_final: 0.5747 (t80) REVERT: D 835 ARG cc_start: 0.7474 (ptt-90) cc_final: 0.7180 (ptt-90) REVERT: E 627 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7204 (tp30) REVERT: F 545 THR cc_start: 0.8146 (m) cc_final: 0.7921 (m) REVERT: F 792 MET cc_start: 0.8697 (ptp) cc_final: 0.8243 (ptp) outliers start: 51 outliers final: 31 residues processed: 289 average time/residue: 0.2920 time to fit residues: 124.7855 Evaluate side-chains 255 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 224 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 796 LYS Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain F residue 532 VAL Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 665 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.6980 chunk 147 optimal weight: 0.0980 chunk 101 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN B 664 GLN ** C 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 676 GLN D 640 HIS E 591 GLN ** E 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 HIS F 676 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16932 Z= 0.211 Angle : 0.577 7.172 22986 Z= 0.294 Chirality : 0.045 0.160 2628 Planarity : 0.004 0.036 2988 Dihedral : 5.322 19.879 2370 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.15 % Allowed : 15.41 % Favored : 81.44 % 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: -1.62 (0.18), residues: 2166 helix: -2.61 (0.33), residues: 162 sheet: -1.03 (0.17), residues: 846 loop : -0.74 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 809 HIS 0.001 0.000 HIS C 558 PHE 0.012 0.002 PHE F 818 TYR 0.017 0.001 TYR D 563 ARG 0.004 0.000 ARG C 597 *********************** 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 303 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 248 time to evaluate : 1.976 Fit side-chains REVERT: A 583 LEU cc_start: 0.3162 (OUTLIER) cc_final: 0.2911 (tp) REVERT: A 627 GLU cc_start: 0.7558 (tm-30) cc_final: 0.5968 (tm-30) REVERT: A 818 PHE cc_start: 0.5889 (t80) cc_final: 0.5686 (t80) REVERT: B 559 ILE cc_start: 0.7406 (mt) cc_final: 0.6815 (mt) REVERT: B 607 ASN cc_start: 0.7576 (m-40) cc_final: 0.7270 (m-40) REVERT: B 627 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7252 (tp30) REVERT: C 580 LYS cc_start: 0.8001 (tttt) cc_final: 0.7281 (mmtt) REVERT: C 792 MET cc_start: 0.8734 (ptp) cc_final: 0.8302 (ptp) REVERT: D 583 LEU cc_start: 0.3124 (OUTLIER) cc_final: 0.2872 (tp) REVERT: D 627 GLU cc_start: 0.7575 (tm-30) cc_final: 0.6017 (tm-30) REVERT: D 651 MET cc_start: 0.9055 (ttt) cc_final: 0.8712 (ttt) REVERT: D 818 PHE cc_start: 0.5867 (t80) cc_final: 0.5623 (t80) REVERT: D 834 ILE cc_start: 0.6974 (mm) cc_final: 0.6678 (mp) REVERT: D 835 ARG cc_start: 0.7498 (ptt-90) cc_final: 0.7282 (ptt-90) REVERT: E 559 ILE cc_start: 0.7436 (mt) cc_final: 0.6825 (mt) REVERT: E 627 GLU cc_start: 0.7589 (tm-30) cc_final: 0.6188 (tm-30) REVERT: F 545 THR cc_start: 0.8104 (m) cc_final: 0.7901 (m) REVERT: F 606 ASP cc_start: 0.6875 (t0) cc_final: 0.6526 (t0) REVERT: F 792 MET cc_start: 0.8726 (ptp) cc_final: 0.8289 (ptp) outliers start: 55 outliers final: 28 residues processed: 282 average time/residue: 0.2991 time to fit residues: 124.2683 Evaluate side-chains 263 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 233 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 712 ASP Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 796 LYS Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain F residue 532 VAL Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 712 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 86 optimal weight: 0.0670 chunk 178 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16932 Z= 0.321 Angle : 0.625 7.384 22986 Z= 0.317 Chirality : 0.047 0.154 2628 Planarity : 0.004 0.052 2988 Dihedral : 5.436 19.919 2370 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.38 % Allowed : 15.64 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.18), residues: 2166 helix: -2.31 (0.36), residues: 162 sheet: -0.92 (0.18), residues: 774 loop : -0.80 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 574 HIS 0.004 0.001 HIS E 558 PHE 0.018 0.002 PHE C 689 TYR 0.016 0.002 TYR A 563 ARG 0.006 0.001 ARG C 536 *********************** 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 292 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 233 time to evaluate : 1.851 Fit side-chains revert: symmetry clash REVERT: A 627 GLU cc_start: 0.7586 (tm-30) cc_final: 0.5989 (tm-30) REVERT: A 818 PHE cc_start: 0.5912 (t80) cc_final: 0.5677 (t80) REVERT: B 607 ASN cc_start: 0.7652 (m-40) cc_final: 0.7355 (m-40) REVERT: B 627 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7160 (tp30) REVERT: C 580 LYS cc_start: 0.7923 (tttt) cc_final: 0.7110 (mmtt) REVERT: C 583 LEU cc_start: 0.4056 (OUTLIER) cc_final: 0.3787 (tp) REVERT: C 792 MET cc_start: 0.8747 (ptp) cc_final: 0.8351 (ptp) REVERT: D 627 GLU cc_start: 0.7598 (tm-30) cc_final: 0.6034 (tm-30) REVERT: D 818 PHE cc_start: 0.5964 (t80) cc_final: 0.5732 (t80) REVERT: D 834 ILE cc_start: 0.7051 (mm) cc_final: 0.6803 (mp) REVERT: E 627 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7128 (tp30) REVERT: F 545 THR cc_start: 0.8031 (m) cc_final: 0.7817 (m) REVERT: F 583 LEU cc_start: 0.4199 (OUTLIER) cc_final: 0.3978 (tp) REVERT: F 792 MET cc_start: 0.8737 (ptp) cc_final: 0.8339 (ptp) outliers start: 59 outliers final: 47 residues processed: 276 average time/residue: 0.2842 time to fit residues: 117.4125 Evaluate side-chains 271 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 222 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 712 ASP Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 870 GLU Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 583 LEU Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 704 SER Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 870 GLU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 704 SER Chi-restraints excluded: chain F residue 712 ASP Chi-restraints excluded: chain F residue 780 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 chunk 51 optimal weight: 0.0060 chunk 208 optimal weight: 1.9990 chunk 173 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 109 optimal weight: 0.0370 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 HIS ** E 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 710 HIS F 607 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16932 Z= 0.173 Angle : 0.555 7.288 22986 Z= 0.283 Chirality : 0.045 0.145 2628 Planarity : 0.004 0.037 2988 Dihedral : 5.082 19.319 2370 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.52 % Allowed : 17.12 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.18), residues: 2166 helix: -1.85 (0.40), residues: 162 sheet: -0.89 (0.18), residues: 786 loop : -0.67 (0.19), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 574 HIS 0.001 0.000 HIS A 857 PHE 0.013 0.002 PHE C 818 TYR 0.020 0.001 TYR B 563 ARG 0.003 0.000 ARG E 835 *********************** 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 284 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 240 time to evaluate : 1.868 Fit side-chains REVERT: A 627 GLU cc_start: 0.7520 (tm-30) cc_final: 0.5953 (tm-30) REVERT: A 818 PHE cc_start: 0.5872 (t80) cc_final: 0.5614 (t80) REVERT: B 627 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7156 (tp30) REVERT: C 536 ARG cc_start: 0.6396 (mmm-85) cc_final: 0.6076 (mmm160) REVERT: C 580 LYS cc_start: 0.7668 (tttt) cc_final: 0.6967 (mmtt) REVERT: C 792 MET cc_start: 0.8706 (ptp) cc_final: 0.8303 (ptp) REVERT: D 627 GLU cc_start: 0.7526 (tm-30) cc_final: 0.5971 (tm-30) REVERT: D 818 PHE cc_start: 0.5836 (t80) cc_final: 0.5584 (t80) REVERT: E 627 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7166 (tp30) REVERT: F 545 THR cc_start: 0.7926 (m) cc_final: 0.7723 (m) REVERT: F 792 MET cc_start: 0.8703 (ptp) cc_final: 0.8329 (ptp) outliers start: 44 outliers final: 33 residues processed: 267 average time/residue: 0.2746 time to fit residues: 110.0075 Evaluate side-chains 255 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 222 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 712 ASP Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 870 GLU Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 712 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 208 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 ASN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN ** E 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16932 Z= 0.429 Angle : 0.673 8.421 22986 Z= 0.341 Chirality : 0.049 0.182 2628 Planarity : 0.005 0.035 2988 Dihedral : 5.543 20.413 2370 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.61 % Allowed : 16.67 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.18), residues: 2166 helix: -1.98 (0.38), residues: 162 sheet: -0.99 (0.17), residues: 798 loop : -0.80 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 574 HIS 0.004 0.001 HIS D 558 PHE 0.025 0.002 PHE C 689 TYR 0.014 0.002 TYR A 718 ARG 0.004 0.001 ARG D 835 *********************** 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 275 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 212 time to evaluate : 1.827 Fit side-chains REVERT: A 627 GLU cc_start: 0.7709 (tm-30) cc_final: 0.6140 (tm-30) REVERT: A 651 MET cc_start: 0.8946 (ttt) cc_final: 0.8374 (ttt) REVERT: A 810 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8540 (tt) REVERT: B 627 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7134 (tp30) REVERT: C 536 ARG cc_start: 0.6495 (mmm-85) cc_final: 0.5937 (mmm-85) REVERT: C 580 LYS cc_start: 0.7966 (tttt) cc_final: 0.7329 (mptt) REVERT: C 792 MET cc_start: 0.8758 (ptp) cc_final: 0.8356 (ptp) REVERT: D 627 GLU cc_start: 0.7692 (tm-30) cc_final: 0.6146 (tm-30) REVERT: D 651 MET cc_start: 0.8941 (ttt) cc_final: 0.8381 (ttt) REVERT: D 810 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8544 (tt) REVERT: E 627 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7141 (tp30) REVERT: F 792 MET cc_start: 0.8741 (ptp) cc_final: 0.8382 (ptp) outliers start: 63 outliers final: 54 residues processed: 257 average time/residue: 0.2753 time to fit residues: 106.0665 Evaluate side-chains 265 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 209 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 796 LYS Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 673 ASN Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 712 ASP Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 870 GLU Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 583 LEU Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 704 SER Chi-restraints excluded: chain E residue 722 GLU Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 870 GLU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 704 SER Chi-restraints excluded: chain F residue 712 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.0670 chunk 83 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 62 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 132 optimal weight: 0.3980 chunk 141 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 chunk 189 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 607 ASN ** E 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16932 Z= 0.173 Angle : 0.578 8.102 22986 Z= 0.294 Chirality : 0.045 0.189 2628 Planarity : 0.004 0.071 2988 Dihedral : 5.164 19.227 2370 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.81 % Allowed : 17.93 % Favored : 79.27 % 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: -1.39 (0.18), residues: 2166 helix: -1.52 (0.42), residues: 162 sheet: -0.98 (0.17), residues: 810 loop : -0.69 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 574 HIS 0.001 0.000 HIS B 800 PHE 0.015 0.002 PHE B 833 TYR 0.025 0.001 TYR C 563 ARG 0.010 0.000 ARG E 536 *********************** 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 270 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 221 time to evaluate : 1.974 Fit side-chains revert: symmetry clash REVERT: A 583 LEU cc_start: 0.3290 (OUTLIER) cc_final: 0.3006 (tp) REVERT: A 627 GLU cc_start: 0.7571 (tm-30) cc_final: 0.5976 (tm-30) REVERT: A 651 MET cc_start: 0.8997 (ttt) cc_final: 0.8426 (ttt) REVERT: A 818 PHE cc_start: 0.6016 (t80) cc_final: 0.5748 (t80) REVERT: B 627 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7187 (tp30) REVERT: C 580 LYS cc_start: 0.7919 (tttt) cc_final: 0.7309 (mptt) REVERT: C 792 MET cc_start: 0.8712 (ptp) cc_final: 0.8347 (ptp) REVERT: D 627 GLU cc_start: 0.7640 (tm-30) cc_final: 0.6092 (tm-30) REVERT: D 651 MET cc_start: 0.8982 (ttt) cc_final: 0.8433 (ttt) REVERT: E 627 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7170 (tp30) REVERT: F 792 MET cc_start: 0.8697 (ptp) cc_final: 0.8333 (ptp) outliers start: 49 outliers final: 45 residues processed: 255 average time/residue: 0.2687 time to fit residues: 104.2587 Evaluate side-chains 260 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 214 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 870 GLU Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 583 LEU Chi-restraints excluded: chain E residue 595 LEU Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 796 LYS Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 870 GLU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 712 ASP Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 807 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 1.9990 chunk 181 optimal weight: 0.1980 chunk 194 optimal weight: 0.6980 chunk 116 optimal weight: 0.0870 chunk 84 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 ASN C 607 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3758 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= 0.191 Angle : 0.576 9.155 22986 Z= 0.290 Chirality : 0.045 0.160 2628 Planarity : 0.004 0.053 2988 Dihedral : 4.979 19.124 2370 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.81 % Allowed : 18.44 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.18), residues: 2166 helix: -1.25 (0.44), residues: 162 sheet: -0.94 (0.17), residues: 810 loop : -0.66 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 809 HIS 0.001 0.000 HIS C 558 PHE 0.014 0.002 PHE B 833 TYR 0.019 0.001 TYR C 563 ARG 0.014 0.000 ARG E 536 *********************** 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 276 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 227 time to evaluate : 1.895 Fit side-chains revert: symmetry clash REVERT: A 627 GLU cc_start: 0.7598 (tm-30) cc_final: 0.6125 (tm-30) REVERT: B 627 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7178 (tp30) REVERT: C 580 LYS cc_start: 0.7912 (tttt) cc_final: 0.7305 (mptt) REVERT: C 792 MET cc_start: 0.8732 (ptp) cc_final: 0.8341 (ptp) REVERT: D 627 GLU cc_start: 0.7588 (tm-30) cc_final: 0.6138 (tm-30) REVERT: E 627 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7166 (tp30) REVERT: F 792 MET cc_start: 0.8705 (ptp) cc_final: 0.8326 (ptp) outliers start: 49 outliers final: 43 residues processed: 261 average time/residue: 0.2764 time to fit residues: 108.1390 Evaluate side-chains 262 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 219 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 870 GLU Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 583 LEU Chi-restraints excluded: chain E residue 595 LEU Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 870 GLU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 712 ASP Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 807 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 142 optimal weight: 0.7980 chunk 215 optimal weight: 0.0970 chunk 198 optimal weight: 0.5980 chunk 171 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 132 optimal weight: 0.0970 chunk 105 optimal weight: 0.0470 chunk 136 optimal weight: 0.5980 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 ASN D 607 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16932 Z= 0.147 Angle : 0.568 9.424 22986 Z= 0.284 Chirality : 0.045 0.154 2628 Planarity : 0.004 0.069 2988 Dihedral : 4.718 18.521 2370 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.12 % Allowed : 19.53 % 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: -1.23 (0.18), residues: 2166 helix: -0.98 (0.46), residues: 162 sheet: -0.82 (0.18), residues: 792 loop : -0.70 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 809 HIS 0.001 0.000 HIS A 558 PHE 0.015 0.001 PHE F 818 TYR 0.022 0.001 TYR C 563 ARG 0.008 0.000 ARG E 536 ********************** 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 290 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 253 time to evaluate : 2.070 Fit side-chains revert: symmetry clash REVERT: A 627 GLU cc_start: 0.7515 (tm-30) cc_final: 0.6061 (tm-30) REVERT: A 651 MET cc_start: 0.8962 (ttt) cc_final: 0.8334 (ttt) REVERT: B 627 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7120 (tp30) REVERT: C 580 LYS cc_start: 0.7916 (tttt) cc_final: 0.7351 (mptt) REVERT: C 792 MET cc_start: 0.8723 (ptp) cc_final: 0.8295 (ptp) REVERT: D 627 GLU cc_start: 0.7506 (tm-30) cc_final: 0.6075 (tm-30) REVERT: D 651 MET cc_start: 0.8943 (ttt) cc_final: 0.8335 (ttt) REVERT: D 798 TYR cc_start: 0.8960 (m-80) cc_final: 0.8706 (m-80) REVERT: E 627 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7134 (tp30) REVERT: F 792 MET cc_start: 0.8712 (ptp) cc_final: 0.8334 (ptp) outliers start: 37 outliers final: 32 residues processed: 279 average time/residue: 0.2617 time to fit residues: 111.5836 Evaluate side-chains 260 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 228 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 870 GLU Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 870 GLU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 712 ASP Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 807 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.147271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.118443 restraints weight = 23286.995| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.53 r_work: 0.3236 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16932 Z= 0.223 Angle : 0.594 9.055 22986 Z= 0.296 Chirality : 0.046 0.159 2628 Planarity : 0.004 0.065 2988 Dihedral : 4.827 18.975 2370 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.23 % Allowed : 19.76 % Favored : 78.01 % 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: -1.24 (0.18), residues: 2166 helix: -0.99 (0.45), residues: 162 sheet: -0.88 (0.19), residues: 714 loop : -0.69 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 809 HIS 0.002 0.000 HIS D 558 PHE 0.016 0.002 PHE C 818 TYR 0.030 0.001 TYR D 563 ARG 0.009 0.000 ARG E 536 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3746.26 seconds wall clock time: 67 minutes 42.85 seconds (4062.85 seconds total)