Starting phenix.real_space_refine on Mon Apr 8 20:19:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fws_29517/04_2024/8fws_29517_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fws_29517/04_2024/8fws_29517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fws_29517/04_2024/8fws_29517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fws_29517/04_2024/8fws_29517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fws_29517/04_2024/8fws_29517_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fws_29517/04_2024/8fws_29517_updated.pdb" } resolution = 3.23 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= 0.004 sd= 0.085 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: 8 Type Number sf(0) Gaussians P 16 5.49 5 S 80 5.16 5 Cl 2 4.86 5 Na 6 4.78 5 C 9432 2.51 5 N 2190 2.21 5 O 2686 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 503": "NH1" <-> "NH2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A ARG 800": "NH1" <-> "NH2" Residue "B TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 503": "NH1" <-> "NH2" Residue "B PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 713": "NH1" <-> "NH2" Residue "B ARG 800": "NH1" <-> "NH2" Residue "C ARG 503": "NH1" <-> "NH2" Residue "C PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C ARG 800": "NH1" <-> "NH2" Residue "D TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 503": "NH1" <-> "NH2" Residue "D PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 713": "NH1" <-> "NH2" Residue "D ARG 800": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14416 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "B" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "C" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "D" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 362 Unusual residues: {' CL': 1, ' NA': 3, '2J9': 2, 'NAG': 1, 'POV': 6} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 157 Unusual residues: {' NA': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 256 Unusual residues: {' CL': 1, ' NA': 1, '2J9': 2, 'NAG': 1, 'POV': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 157 Unusual residues: {' NA': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.87, per 1000 atoms: 0.55 Number of scatterers: 14416 At special positions: 0 Unit cell: (115.625, 132.275, 136.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 2 17.00 S 80 16.00 P 16 15.00 Na 6 11.00 F 4 9.00 O 2686 8.00 N 2190 7.00 C 9432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS B 595 " distance=2.00 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.02 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.02 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS D 595 " distance=2.06 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.02 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.02 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 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " " BMA I 3 " - " BMA I 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1006 " - " ASN A 751 " " NAG C1006 " - " ASN C 751 " " NAG E 1 " - " ASN A 546 " " NAG F 1 " - " ASN B 546 " " NAG G 1 " - " ASN B 751 " " NAG H 1 " - " ASN C 546 " " NAG I 1 " - " ASN D 546 " " NAG J 1 " - " ASN D 751 " Time building additional restraints: 5.90 Conformation dependent library (CDL) restraints added in 2.4 seconds 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 10 sheets defined 42.3% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 462 through 474 removed outlier: 3.946A pdb=" N ILE A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 521 through 524 No H-bonds generated for 'chain 'A' and resid 521 through 524' Processing helix chain 'A' and resid 561 through 584 removed outlier: 3.516A pdb=" N MET A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 575 " --> pdb=" O CYS A 571 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 632 through 664 removed outlier: 3.575A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 689 through 695 removed outlier: 3.688A pdb=" N PHE A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 711 Processing helix chain 'A' and resid 721 through 730 removed outlier: 3.664A pdb=" N GLN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 787 removed outlier: 3.649A pdb=" N ASP A 776 " --> pdb=" O PRO A 773 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 777 " --> pdb=" O TYR A 774 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 778 " --> pdb=" O ARG A 775 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 779 " --> pdb=" O ASP A 776 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A 782 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 783 " --> pdb=" O ILE A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 793 No H-bonds generated for 'chain 'A' and resid 790 through 793' Processing helix chain 'A' and resid 795 through 798 No H-bonds generated for 'chain 'A' and resid 795 through 798' Processing helix chain 'A' and resid 822 through 849 removed outlier: 3.525A pdb=" N LEU A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 846 " --> pdb=" O PHE A 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 474 removed outlier: 3.517A pdb=" N ILE B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 506 Processing helix chain 'B' and resid 521 through 524 No H-bonds generated for 'chain 'B' and resid 521 through 524' Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 561 through 584 removed outlier: 3.729A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 575 " --> pdb=" O CYS B 571 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 583 " --> pdb=" O PHE B 579 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 588 No H-bonds generated for 'chain 'B' and resid 586 through 588' Processing helix chain 'B' and resid 608 through 619 removed outlier: 3.618A pdb=" N PHE B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 658 removed outlier: 3.570A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 696 removed outlier: 3.648A pdb=" N PHE B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 710 removed outlier: 3.590A pdb=" N PHE B 708 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 730 removed outlier: 3.553A pdb=" N GLN B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 748 removed outlier: 3.704A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 748 " --> pdb=" O PHE B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 788 removed outlier: 3.528A pdb=" N ILE B 778 " --> pdb=" O TYR B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 793 No H-bonds generated for 'chain 'B' and resid 790 through 793' Processing helix chain 'B' and resid 795 through 798 No H-bonds generated for 'chain 'B' and resid 795 through 798' Processing helix chain 'B' and resid 823 through 849 removed outlier: 3.731A pdb=" N VAL B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 844 " --> pdb=" O GLY B 840 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 845 " --> pdb=" O GLU B 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 474 removed outlier: 3.946A pdb=" N ILE C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 506 Processing helix chain 'C' and resid 521 through 524 No H-bonds generated for 'chain 'C' and resid 521 through 524' Processing helix chain 'C' and resid 561 through 584 removed outlier: 3.516A pdb=" N MET C 565 " --> pdb=" O PRO C 561 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL C 580 " --> pdb=" O CYS C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 619 Processing helix chain 'C' and resid 632 through 664 removed outlier: 3.576A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 646 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR C 660 " --> pdb=" O ALA C 656 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 676 Processing helix chain 'C' and resid 689 through 695 removed outlier: 3.688A pdb=" N PHE C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 711 Processing helix chain 'C' and resid 721 through 730 removed outlier: 3.664A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 787 removed outlier: 3.648A pdb=" N ASP C 776 " --> pdb=" O PRO C 773 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS C 777 " --> pdb=" O TYR C 774 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C 778 " --> pdb=" O ARG C 775 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR C 779 " --> pdb=" O ASP C 776 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE C 782 " --> pdb=" O THR C 779 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 783 " --> pdb=" O ILE C 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 793 No H-bonds generated for 'chain 'C' and resid 790 through 793' Processing helix chain 'C' and resid 795 through 798 No H-bonds generated for 'chain 'C' and resid 795 through 798' Processing helix chain 'C' and resid 822 through 849 removed outlier: 3.525A pdb=" N LEU C 833 " --> pdb=" O ALA C 829 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 835 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 846 " --> pdb=" O PHE C 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 474 removed outlier: 3.518A pdb=" N ILE D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 506 Processing helix chain 'D' and resid 521 through 524 No H-bonds generated for 'chain 'D' and resid 521 through 524' Processing helix chain 'D' and resid 554 through 556 No H-bonds generated for 'chain 'D' and resid 554 through 556' Processing helix chain 'D' and resid 561 through 584 removed outlier: 3.729A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 575 " --> pdb=" O CYS D 571 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG D 583 " --> pdb=" O PHE D 579 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 588 No H-bonds generated for 'chain 'D' and resid 586 through 588' Processing helix chain 'D' and resid 608 through 619 removed outlier: 3.618A pdb=" N PHE D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 658 removed outlier: 3.569A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE D 646 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 696 removed outlier: 3.648A pdb=" N PHE D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 710 removed outlier: 3.590A pdb=" N PHE D 708 " --> pdb=" O LYS D 704 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 730 removed outlier: 3.553A pdb=" N GLN D 726 " --> pdb=" O GLU D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 748 removed outlier: 3.703A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG D 748 " --> pdb=" O PHE D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 788 removed outlier: 3.527A pdb=" N ILE D 778 " --> pdb=" O TYR D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 793 No H-bonds generated for 'chain 'D' and resid 790 through 793' Processing helix chain 'D' and resid 795 through 798 No H-bonds generated for 'chain 'D' and resid 795 through 798' Processing helix chain 'D' and resid 823 through 849 removed outlier: 3.731A pdb=" N VAL D 835 " --> pdb=" O LEU D 831 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR D 844 " --> pdb=" O GLY D 840 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS D 845 " --> pdb=" O GLU D 841 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 433 through 437 removed outlier: 3.508A pdb=" N VAL A 435 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR A 437 " --> pdb=" O ARG A 481 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.830A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 752 through 755 removed outlier: 3.995A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG A 543 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N TYR A 733 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU A 681 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU A 736 " --> pdb=" O GLU A 681 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY A 683 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N GLU A 738 " --> pdb=" O GLY A 683 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 534 through 536 removed outlier: 4.058A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 735 through 738 removed outlier: 4.247A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 433 through 437 removed outlier: 3.508A pdb=" N VAL C 435 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR C 437 " --> pdb=" O ARG C 481 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.830A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 752 through 755 removed outlier: 3.994A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG C 543 " --> pdb=" O TYR C 733 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N TYR C 733 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU C 681 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU C 736 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY C 683 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N GLU C 738 " --> pdb=" O GLY C 683 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 534 through 536 removed outlier: 4.058A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 735 through 738 removed outlier: 4.248A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1260 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: 3.94 Time building geometry restraints manager: 6.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2224 1.31 - 1.44: 3912 1.44 - 1.57: 8392 1.57 - 1.70: 48 1.70 - 1.83: 132 Bond restraints: 14708 Sorted by residual: bond pdb=" OAA 2J9 A1001 " pdb=" SAP 2J9 A1001 " ideal model delta sigma weight residual 1.452 1.655 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" OAA 2J9 C1002 " pdb=" SAP 2J9 C1002 " ideal model delta sigma weight residual 1.452 1.655 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" OAA 2J9 A1009 " pdb=" SAP 2J9 A1009 " ideal model delta sigma weight residual 1.452 1.654 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" OAB 2J9 A1009 " pdb=" SAP 2J9 A1009 " ideal model delta sigma weight residual 1.452 1.654 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" OAA 2J9 C1001 " pdb=" SAP 2J9 C1001 " ideal model delta sigma weight residual 1.452 1.654 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 14703 not shown) Histogram of bond angle deviations from ideal: 59.79 - 77.98: 12 77.98 - 96.17: 0 96.17 - 114.36: 9060 114.36 - 132.55: 10664 132.55 - 150.74: 46 Bond angle restraints: 19782 Sorted by residual: angle pdb=" CAH 2J9 A1009 " pdb=" CAN 2J9 A1009 " pdb=" NAO 2J9 A1009 " ideal model delta sigma weight residual 117.67 150.56 -32.89 3.00e+00 1.11e-01 1.20e+02 angle pdb=" CAH 2J9 C1001 " pdb=" CAN 2J9 C1001 " pdb=" NAO 2J9 C1001 " ideal model delta sigma weight residual 117.67 150.26 -32.59 3.00e+00 1.11e-01 1.18e+02 angle pdb=" CAH 2J9 C1002 " pdb=" CAN 2J9 C1002 " pdb=" NAO 2J9 C1002 " ideal model delta sigma weight residual 117.67 149.75 -32.08 3.00e+00 1.11e-01 1.14e+02 angle pdb=" CAG 2J9 A1001 " pdb=" CAN 2J9 A1001 " pdb=" NAO 2J9 A1001 " ideal model delta sigma weight residual 118.82 150.74 -31.92 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CAH 2J9 A1001 " pdb=" CAN 2J9 A1001 " pdb=" NAO 2J9 A1001 " ideal model delta sigma weight residual 117.67 149.24 -31.57 3.00e+00 1.11e-01 1.11e+02 ... (remaining 19777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.61: 8509 28.61 - 57.22: 474 57.22 - 85.82: 114 85.82 - 114.43: 37 114.43 - 143.04: 14 Dihedral angle restraints: 9148 sinusoidal: 4308 harmonic: 4840 Sorted by residual: dihedral pdb=" CA TYR D 478 " pdb=" C TYR D 478 " pdb=" N GLU D 479 " pdb=" CA GLU D 479 " ideal model delta harmonic sigma weight residual -180.00 -129.43 -50.57 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA TYR B 478 " pdb=" C TYR B 478 " pdb=" N GLU B 479 " pdb=" CA GLU B 479 " ideal model delta harmonic sigma weight residual -180.00 -129.48 -50.52 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA VAL B 716 " pdb=" C VAL B 716 " pdb=" N LEU B 717 " pdb=" CA LEU B 717 " ideal model delta harmonic sigma weight residual 180.00 141.31 38.69 0 5.00e+00 4.00e-02 5.99e+01 ... (remaining 9145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.464: 2154 0.464 - 0.927: 0 0.927 - 1.391: 0 1.391 - 1.854: 0 1.854 - 2.318: 4 Chirality restraints: 2158 Sorted by residual: chirality pdb=" CAN 2J9 A1009 " pdb=" CAG 2J9 A1009 " pdb=" CAH 2J9 A1009 " pdb=" NAO 2J9 A1009 " both_signs ideal model delta sigma weight residual True 2.32 -0.00 2.32 2.00e-01 2.50e+01 1.34e+02 chirality pdb=" CAN 2J9 C1001 " pdb=" CAG 2J9 C1001 " pdb=" CAH 2J9 C1001 " pdb=" NAO 2J9 C1001 " both_signs ideal model delta sigma weight residual True 2.32 0.02 2.30 2.00e-01 2.50e+01 1.32e+02 chirality pdb=" CAN 2J9 C1002 " pdb=" CAG 2J9 C1002 " pdb=" CAH 2J9 C1002 " pdb=" NAO 2J9 C1002 " both_signs ideal model delta sigma weight residual True 2.32 -0.02 2.30 2.00e-01 2.50e+01 1.32e+02 ... (remaining 2155 not shown) Planarity restraints: 2398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 716 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C VAL D 716 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL D 716 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU D 717 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 716 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C VAL B 716 " -0.056 2.00e-02 2.50e+03 pdb=" O VAL B 716 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 717 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 515 " -0.039 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO B 516 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 516 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 516 " -0.033 5.00e-02 4.00e+02 ... (remaining 2395 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3240 2.78 - 3.31: 12314 3.31 - 3.84: 22458 3.84 - 4.37: 28092 4.37 - 4.90: 47455 Nonbonded interactions: 113559 Sorted by model distance: nonbonded pdb=" OG SER C 554 " pdb=" O ASN C 819 " model vdw 2.250 2.440 nonbonded pdb=" OG SER A 554 " pdb=" O ASN A 819 " model vdw 2.251 2.440 nonbonded pdb=" OG SER A 834 " pdb=" O SER D 632 " model vdw 2.273 2.440 nonbonded pdb=" O SER C 632 " pdb=" OG SER D 834 " model vdw 2.306 2.440 nonbonded pdb=" OG SER A 585 " pdb=" OE2 GLU B 841 " model vdw 2.307 2.440 ... (remaining 113554 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' and (resid 431 through 850 or resid 1003)) selection = (chain 'B' and (resid 431 through 850 or resid 1003)) selection = (chain 'C' and (resid 431 through 850 or resid 1003)) selection = (chain 'D' and (resid 431 through 850 or resid 1003)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'I' } 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=0.45 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: 3.990 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: 12.530 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 40.130 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.110 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 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 : 0.012 0.203 14708 Z= 0.668 Angle : 1.620 32.889 19782 Z= 0.770 Chirality : 0.116 2.318 2158 Planarity : 0.007 0.058 2390 Dihedral : 19.895 143.040 6034 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.49 % Favored : 91.15 % Rotamer: Outliers : 0.55 % Allowed : 4.28 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -5.96 (0.13), residues: 1672 helix: -4.37 (0.07), residues: 802 sheet: -3.11 (0.38), residues: 134 loop : -3.49 (0.17), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 706 HIS 0.005 0.001 HIS D 593 PHE 0.029 0.003 PHE D 446 TYR 0.028 0.003 TYR B 702 ARG 0.008 0.001 ARG B 713 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 356 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7629 (t70) cc_final: 0.7262 (t0) REVERT: A 468 ARG cc_start: 0.7093 (ttm110) cc_final: 0.6806 (mtm110) REVERT: A 591 ASN cc_start: 0.8028 (t160) cc_final: 0.7782 (t0) REVERT: A 719 LYS cc_start: 0.7853 (pptt) cc_final: 0.7174 (mtpp) REVERT: A 751 ASN cc_start: 0.6673 (m-40) cc_final: 0.5963 (t0) REVERT: A 776 ASP cc_start: 0.7460 (m-30) cc_final: 0.6979 (m-30) REVERT: A 796 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7208 (mt-10) REVERT: A 845 LYS cc_start: 0.6977 (tptt) cc_final: 0.6703 (tppp) REVERT: B 790 LYS cc_start: 0.7862 (mptp) cc_final: 0.7503 (mmmt) REVERT: B 818 GLN cc_start: 0.8085 (pt0) cc_final: 0.7783 (pm20) REVERT: C 468 ARG cc_start: 0.7114 (ttm110) cc_final: 0.6726 (mtm110) REVERT: C 487 LYS cc_start: 0.7416 (mtpp) cc_final: 0.7138 (mtmt) REVERT: C 584 PHE cc_start: 0.6603 (t80) cc_final: 0.6359 (t80) REVERT: C 591 ASN cc_start: 0.8102 (t160) cc_final: 0.7722 (t0) REVERT: C 677 GLN cc_start: 0.6669 (mp-120) cc_final: 0.6240 (mp10) REVERT: C 696 LYS cc_start: 0.7910 (mtpt) cc_final: 0.7452 (mtmt) REVERT: C 719 LYS cc_start: 0.8313 (pptt) cc_final: 0.7641 (mtpp) REVERT: C 726 GLN cc_start: 0.7509 (mm-40) cc_final: 0.7271 (mm-40) REVERT: C 776 ASP cc_start: 0.7331 (m-30) cc_final: 0.6747 (m-30) REVERT: C 796 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6992 (mt-10) REVERT: C 845 LYS cc_start: 0.6933 (tptt) cc_final: 0.6686 (tppt) REVERT: D 492 ASP cc_start: 0.7492 (t70) cc_final: 0.6809 (m-30) REVERT: D 790 LYS cc_start: 0.7758 (mptp) cc_final: 0.7417 (mmmt) outliers start: 8 outliers final: 0 residues processed: 362 average time/residue: 0.3385 time to fit residues: 169.9576 Evaluate side-chains 193 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 70 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 152 optimal weight: 0.5980 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 456 ASN A 591 ASN A 596 ASN A 604 ASN B 456 ASN ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 GLN ** B 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 GLN C 456 ASN C 591 ASN C 593 HIS C 596 ASN C 604 ASN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN D 604 ASN D 754 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14708 Z= 0.228 Angle : 0.708 9.524 19782 Z= 0.352 Chirality : 0.045 0.153 2158 Planarity : 0.005 0.039 2390 Dihedral : 22.590 139.283 2894 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.79 % Favored : 90.73 % Rotamer: Outliers : 2.42 % Allowed : 9.88 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -4.17 (0.16), residues: 1672 helix: -2.43 (0.14), residues: 822 sheet: -2.87 (0.34), residues: 162 loop : -3.02 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 706 HIS 0.003 0.001 HIS D 593 PHE 0.016 0.002 PHE B 735 TYR 0.021 0.002 TYR D 478 ARG 0.007 0.001 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 186 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7679 (t70) cc_final: 0.7187 (t0) REVERT: A 487 LYS cc_start: 0.7539 (mtpp) cc_final: 0.7258 (mtmt) REVERT: A 591 ASN cc_start: 0.7985 (t0) cc_final: 0.7750 (t0) REVERT: A 664 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.8023 (mtm) REVERT: A 715 SER cc_start: 0.7376 (OUTLIER) cc_final: 0.6854 (p) REVERT: A 719 LYS cc_start: 0.8000 (pptt) cc_final: 0.7248 (mtpp) REVERT: A 776 ASP cc_start: 0.7212 (m-30) cc_final: 0.6845 (m-30) REVERT: A 796 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7272 (mt-10) REVERT: B 691 MET cc_start: 0.7304 (ttp) cc_final: 0.7039 (ttt) REVERT: B 790 LYS cc_start: 0.7834 (mptp) cc_final: 0.7424 (mmmt) REVERT: B 825 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7972 (mt) REVERT: C 468 ARG cc_start: 0.6920 (ttm110) cc_final: 0.6590 (mtm110) REVERT: C 487 LYS cc_start: 0.7431 (mtpp) cc_final: 0.7062 (mtmt) REVERT: C 568 LEU cc_start: 0.7607 (tt) cc_final: 0.7335 (mt) REVERT: C 591 ASN cc_start: 0.8122 (t0) cc_final: 0.7915 (t0) REVERT: C 696 LYS cc_start: 0.7908 (mtpt) cc_final: 0.7473 (mtmt) REVERT: C 719 LYS cc_start: 0.8440 (pptt) cc_final: 0.7746 (mtpp) REVERT: C 776 ASP cc_start: 0.7221 (m-30) cc_final: 0.6782 (m-30) REVERT: C 796 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7198 (mt-10) REVERT: C 845 LYS cc_start: 0.6931 (tptt) cc_final: 0.6669 (tppt) REVERT: D 790 LYS cc_start: 0.7802 (mptp) cc_final: 0.7353 (mmmt) REVERT: D 819 ASN cc_start: 0.8141 (m110) cc_final: 0.7921 (m110) REVERT: D 825 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8012 (mt) outliers start: 35 outliers final: 16 residues processed: 211 average time/residue: 0.2794 time to fit residues: 86.0720 Evaluate side-chains 182 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 151 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 GLN B 456 ASN C 677 GLN D 456 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14708 Z= 0.238 Angle : 0.664 9.023 19782 Z= 0.325 Chirality : 0.045 0.212 2158 Planarity : 0.004 0.040 2390 Dihedral : 20.844 140.818 2894 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.25 % Favored : 91.27 % Rotamer: Outliers : 3.11 % Allowed : 12.02 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.14 (0.18), residues: 1672 helix: -1.29 (0.16), residues: 830 sheet: -2.59 (0.35), residues: 162 loop : -2.88 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 706 HIS 0.003 0.001 HIS B 593 PHE 0.017 0.002 PHE D 579 TYR 0.021 0.002 TYR D 844 ARG 0.007 0.001 ARG D 712 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 156 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7740 (t70) cc_final: 0.7250 (t0) REVERT: A 487 LYS cc_start: 0.7574 (mtpp) cc_final: 0.7296 (mtmt) REVERT: A 566 TYR cc_start: 0.7604 (m-10) cc_final: 0.7033 (m-10) REVERT: A 703 ASP cc_start: 0.7611 (t70) cc_final: 0.7075 (t0) REVERT: A 715 SER cc_start: 0.7226 (OUTLIER) cc_final: 0.6737 (p) REVERT: A 719 LYS cc_start: 0.8002 (pptt) cc_final: 0.7322 (mtpp) REVERT: A 776 ASP cc_start: 0.7158 (m-30) cc_final: 0.6764 (m-30) REVERT: A 796 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7283 (mt-10) REVERT: B 691 MET cc_start: 0.7339 (ttp) cc_final: 0.7093 (ttt) REVERT: B 743 GLU cc_start: 0.8224 (mp0) cc_final: 0.7990 (mp0) REVERT: B 790 LYS cc_start: 0.7869 (mptp) cc_final: 0.7462 (mmmt) REVERT: B 825 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8010 (mt) REVERT: C 487 LYS cc_start: 0.7384 (mtpp) cc_final: 0.7074 (mtmt) REVERT: C 584 PHE cc_start: 0.6384 (t80) cc_final: 0.6114 (t80) REVERT: C 591 ASN cc_start: 0.8239 (t0) cc_final: 0.8019 (t0) REVERT: C 696 LYS cc_start: 0.7881 (mtpt) cc_final: 0.7437 (mtmt) REVERT: C 719 LYS cc_start: 0.8461 (pptt) cc_final: 0.7832 (mtpp) REVERT: C 748 ARG cc_start: 0.7215 (mpt-90) cc_final: 0.6901 (mtp-110) REVERT: C 776 ASP cc_start: 0.7219 (m-30) cc_final: 0.6775 (m-30) REVERT: C 796 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7233 (mt-10) REVERT: D 790 LYS cc_start: 0.7897 (mptp) cc_final: 0.7424 (mmmt) REVERT: D 819 ASN cc_start: 0.8232 (m110) cc_final: 0.7997 (m110) REVERT: D 825 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8058 (mt) outliers start: 45 outliers final: 27 residues processed: 189 average time/residue: 0.2660 time to fit residues: 75.0771 Evaluate side-chains 171 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 762 LYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 16 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 145 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 677 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14708 Z= 0.223 Angle : 0.639 9.986 19782 Z= 0.310 Chirality : 0.043 0.201 2158 Planarity : 0.004 0.038 2390 Dihedral : 20.137 140.484 2894 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.01 % Favored : 91.51 % Rotamer: Outliers : 3.31 % Allowed : 13.12 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.56 (0.19), residues: 1672 helix: -0.66 (0.17), residues: 828 sheet: -2.49 (0.36), residues: 162 loop : -2.78 (0.21), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 706 HIS 0.002 0.001 HIS B 593 PHE 0.013 0.001 PHE D 584 TYR 0.020 0.001 TYR D 844 ARG 0.009 0.001 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 152 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7690 (t70) cc_final: 0.7201 (t0) REVERT: A 566 TYR cc_start: 0.7633 (m-10) cc_final: 0.7043 (m-10) REVERT: A 703 ASP cc_start: 0.7608 (t70) cc_final: 0.7090 (t0) REVERT: A 715 SER cc_start: 0.7213 (OUTLIER) cc_final: 0.6715 (p) REVERT: A 719 LYS cc_start: 0.7999 (pptt) cc_final: 0.7343 (mtpp) REVERT: A 776 ASP cc_start: 0.7075 (m-30) cc_final: 0.6680 (m-30) REVERT: A 796 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7348 (mt-10) REVERT: B 669 ASP cc_start: 0.7559 (t70) cc_final: 0.7114 (t70) REVERT: B 691 MET cc_start: 0.7344 (ttp) cc_final: 0.7140 (ttt) REVERT: B 743 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: B 790 LYS cc_start: 0.7864 (mptp) cc_final: 0.7450 (mmmt) REVERT: B 825 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8023 (mt) REVERT: C 457 ASP cc_start: 0.7660 (t0) cc_final: 0.7401 (t0) REVERT: C 487 LYS cc_start: 0.7346 (mtpp) cc_final: 0.7056 (mtmt) REVERT: C 584 PHE cc_start: 0.6354 (t80) cc_final: 0.6077 (t80) REVERT: C 591 ASN cc_start: 0.8221 (t0) cc_final: 0.7997 (t0) REVERT: C 696 LYS cc_start: 0.7821 (mtpt) cc_final: 0.7383 (mtmt) REVERT: C 719 LYS cc_start: 0.8469 (pptt) cc_final: 0.7833 (mtpp) REVERT: C 748 ARG cc_start: 0.7190 (mpt-90) cc_final: 0.6841 (mtp-110) REVERT: C 776 ASP cc_start: 0.7210 (m-30) cc_final: 0.6785 (m-30) REVERT: C 796 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7302 (mt-10) REVERT: D 743 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: D 790 LYS cc_start: 0.7894 (mptp) cc_final: 0.7461 (mmmt) REVERT: D 819 ASN cc_start: 0.8213 (m110) cc_final: 0.7985 (m110) REVERT: D 825 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8032 (mt) outliers start: 48 outliers final: 26 residues processed: 189 average time/residue: 0.2720 time to fit residues: 75.4442 Evaluate side-chains 175 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 120 optimal weight: 0.0980 chunk 67 optimal weight: 4.9990 chunk 138 optimal weight: 0.4980 chunk 112 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 456 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14708 Z= 0.202 Angle : 0.628 9.340 19782 Z= 0.304 Chirality : 0.043 0.184 2158 Planarity : 0.004 0.038 2390 Dihedral : 19.181 140.515 2894 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.95 % Favored : 91.51 % Rotamer: Outliers : 3.87 % Allowed : 13.54 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.09 (0.20), residues: 1672 helix: -0.11 (0.18), residues: 828 sheet: -2.42 (0.35), residues: 166 loop : -2.76 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 706 HIS 0.002 0.000 HIS B 593 PHE 0.012 0.001 PHE D 584 TYR 0.022 0.001 TYR D 844 ARG 0.007 0.001 ARG D 712 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 153 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7692 (t70) cc_final: 0.7221 (t0) REVERT: A 487 LYS cc_start: 0.7501 (mtpp) cc_final: 0.7122 (mtmt) REVERT: A 703 ASP cc_start: 0.7588 (t70) cc_final: 0.7073 (t0) REVERT: A 715 SER cc_start: 0.7228 (OUTLIER) cc_final: 0.6739 (p) REVERT: A 719 LYS cc_start: 0.8030 (pptt) cc_final: 0.7383 (mtpp) REVERT: A 776 ASP cc_start: 0.7068 (m-30) cc_final: 0.6547 (m-30) REVERT: B 669 ASP cc_start: 0.7809 (t70) cc_final: 0.7538 (t70) REVERT: B 677 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.5629 (mp10) REVERT: B 691 MET cc_start: 0.7288 (ttp) cc_final: 0.7081 (ttt) REVERT: B 743 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: B 790 LYS cc_start: 0.7873 (mptp) cc_final: 0.7617 (tppt) REVERT: B 796 GLU cc_start: 0.7159 (tt0) cc_final: 0.6902 (tt0) REVERT: B 825 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.8008 (mt) REVERT: C 487 LYS cc_start: 0.7341 (mtpp) cc_final: 0.7021 (mtmt) REVERT: C 584 PHE cc_start: 0.6328 (t80) cc_final: 0.6043 (t80) REVERT: C 591 ASN cc_start: 0.8182 (t0) cc_final: 0.7933 (t0) REVERT: C 696 LYS cc_start: 0.7815 (mtpt) cc_final: 0.7389 (mtmt) REVERT: C 719 LYS cc_start: 0.8461 (pptt) cc_final: 0.7831 (mtpp) REVERT: C 748 ARG cc_start: 0.7063 (mpt-90) cc_final: 0.6724 (mtp-110) REVERT: C 776 ASP cc_start: 0.7152 (m-30) cc_final: 0.6615 (m-30) REVERT: C 796 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7311 (mt-10) REVERT: C 804 CYS cc_start: 0.3429 (OUTLIER) cc_final: 0.2237 (t) REVERT: D 743 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: D 790 LYS cc_start: 0.7846 (mptp) cc_final: 0.7567 (tppt) REVERT: D 793 MET cc_start: 0.7529 (mmt) cc_final: 0.7177 (mtt) REVERT: D 819 ASN cc_start: 0.8240 (m110) cc_final: 0.8009 (m110) REVERT: D 825 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8018 (mt) outliers start: 56 outliers final: 29 residues processed: 194 average time/residue: 0.2533 time to fit residues: 73.4056 Evaluate side-chains 183 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 147 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 0.0570 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14708 Z= 0.248 Angle : 0.636 8.961 19782 Z= 0.307 Chirality : 0.044 0.192 2158 Planarity : 0.004 0.040 2390 Dihedral : 18.860 140.502 2894 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.95 % Favored : 91.69 % Rotamer: Outliers : 3.25 % Allowed : 14.23 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.91 (0.20), residues: 1672 helix: 0.06 (0.18), residues: 828 sheet: -2.06 (0.38), residues: 138 loop : -2.77 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 706 HIS 0.002 0.001 HIS A 593 PHE 0.013 0.002 PHE D 584 TYR 0.022 0.001 TYR D 844 ARG 0.007 0.001 ARG A 748 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 159 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7634 (t70) cc_final: 0.7142 (t0) REVERT: A 487 LYS cc_start: 0.7493 (mtpp) cc_final: 0.7253 (mtmt) REVERT: A 703 ASP cc_start: 0.7725 (t70) cc_final: 0.7190 (t0) REVERT: A 706 TRP cc_start: 0.7658 (t-100) cc_final: 0.7375 (t-100) REVERT: A 715 SER cc_start: 0.7158 (OUTLIER) cc_final: 0.6682 (p) REVERT: A 719 LYS cc_start: 0.8028 (pptt) cc_final: 0.7357 (mtpp) REVERT: A 776 ASP cc_start: 0.7096 (m-30) cc_final: 0.6661 (m-30) REVERT: B 665 GLU cc_start: 0.6705 (mm-30) cc_final: 0.6362 (mm-30) REVERT: B 669 ASP cc_start: 0.7865 (t70) cc_final: 0.7577 (t70) REVERT: B 677 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.5572 (mp10) REVERT: B 691 MET cc_start: 0.7305 (ttp) cc_final: 0.7101 (ttt) REVERT: B 743 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: B 790 LYS cc_start: 0.7917 (mptp) cc_final: 0.7645 (tppt) REVERT: B 825 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8049 (mt) REVERT: C 487 LYS cc_start: 0.7313 (mtpp) cc_final: 0.6979 (mtmt) REVERT: C 584 PHE cc_start: 0.6340 (t80) cc_final: 0.6036 (t80) REVERT: C 591 ASN cc_start: 0.8185 (t0) cc_final: 0.7940 (t0) REVERT: C 696 LYS cc_start: 0.7801 (mtpt) cc_final: 0.7385 (mtmt) REVERT: C 719 LYS cc_start: 0.8440 (pptt) cc_final: 0.7803 (mtpp) REVERT: C 748 ARG cc_start: 0.7133 (mpt-90) cc_final: 0.6764 (mtt90) REVERT: C 776 ASP cc_start: 0.7210 (m-30) cc_final: 0.6638 (m-30) REVERT: C 796 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7308 (mt-10) REVERT: D 620 MET cc_start: 0.9117 (mmt) cc_final: 0.8874 (mmt) REVERT: D 743 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: D 790 LYS cc_start: 0.7875 (mptp) cc_final: 0.7485 (tppt) REVERT: D 819 ASN cc_start: 0.8274 (m110) cc_final: 0.8025 (m110) REVERT: D 825 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8036 (mt) outliers start: 47 outliers final: 31 residues processed: 195 average time/residue: 0.2906 time to fit residues: 83.7898 Evaluate side-chains 185 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 148 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 136 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 ASN D 593 HIS D 596 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14708 Z= 0.203 Angle : 0.614 9.167 19782 Z= 0.298 Chirality : 0.042 0.210 2158 Planarity : 0.004 0.038 2390 Dihedral : 18.412 140.464 2894 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.89 % Favored : 91.69 % Rotamer: Outliers : 3.25 % Allowed : 14.78 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 (0.20), residues: 1672 helix: 0.35 (0.18), residues: 828 sheet: -2.04 (0.38), residues: 138 loop : -2.67 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 706 HIS 0.001 0.000 HIS B 593 PHE 0.013 0.001 PHE A 553 TYR 0.022 0.001 TYR D 844 ARG 0.007 0.001 ARG A 748 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 158 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7627 (t70) cc_final: 0.7167 (t0) REVERT: A 487 LYS cc_start: 0.7425 (mtpp) cc_final: 0.7153 (mtmt) REVERT: A 703 ASP cc_start: 0.7652 (t70) cc_final: 0.7173 (t0) REVERT: A 706 TRP cc_start: 0.7702 (t-100) cc_final: 0.7437 (t-100) REVERT: A 715 SER cc_start: 0.7157 (OUTLIER) cc_final: 0.6676 (p) REVERT: A 719 LYS cc_start: 0.8048 (pptt) cc_final: 0.7376 (mtpp) REVERT: A 776 ASP cc_start: 0.7025 (m-30) cc_final: 0.6587 (m-30) REVERT: B 677 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.5559 (mp10) REVERT: B 691 MET cc_start: 0.7294 (ttp) cc_final: 0.7091 (ttt) REVERT: B 743 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: B 793 MET cc_start: 0.7469 (mmt) cc_final: 0.7116 (mtt) REVERT: C 487 LYS cc_start: 0.7275 (mtpp) cc_final: 0.6902 (mtmt) REVERT: C 565 MET cc_start: 0.7937 (ttp) cc_final: 0.7705 (ttt) REVERT: C 584 PHE cc_start: 0.6235 (t80) cc_final: 0.5927 (t80) REVERT: C 591 ASN cc_start: 0.8099 (t0) cc_final: 0.7854 (t0) REVERT: C 691 MET cc_start: 0.6776 (ttp) cc_final: 0.6544 (ttp) REVERT: C 696 LYS cc_start: 0.7789 (mtpt) cc_final: 0.7340 (mtmt) REVERT: C 709 MET cc_start: 0.6624 (mtm) cc_final: 0.5880 (mtm) REVERT: C 719 LYS cc_start: 0.8432 (pptt) cc_final: 0.7785 (mtpp) REVERT: C 776 ASP cc_start: 0.7164 (m-30) cc_final: 0.6590 (m-30) REVERT: C 796 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7285 (mt-10) REVERT: D 620 MET cc_start: 0.9123 (mmt) cc_final: 0.8847 (mmt) REVERT: D 743 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: D 790 LYS cc_start: 0.7868 (mptp) cc_final: 0.7554 (tppt) REVERT: D 819 ASN cc_start: 0.8272 (m110) cc_final: 0.8028 (m110) REVERT: D 825 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7991 (mt) outliers start: 47 outliers final: 32 residues processed: 193 average time/residue: 0.2929 time to fit residues: 84.8255 Evaluate side-chains 190 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 153 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 0.0040 chunk 48 optimal weight: 0.0010 chunk 31 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 80 optimal weight: 0.0170 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14708 Z= 0.155 Angle : 0.593 8.990 19782 Z= 0.288 Chirality : 0.041 0.197 2158 Planarity : 0.004 0.060 2390 Dihedral : 18.002 140.638 2894 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.54 % Favored : 92.11 % Rotamer: Outliers : 2.28 % Allowed : 15.95 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.31 (0.20), residues: 1672 helix: 0.68 (0.18), residues: 824 sheet: -2.04 (0.38), residues: 138 loop : -2.58 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 706 HIS 0.003 0.001 HIS D 593 PHE 0.010 0.001 PHE C 555 TYR 0.021 0.001 TYR D 844 ARG 0.007 0.000 ARG A 748 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 160 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7438 (t70) cc_final: 0.7053 (t0) REVERT: A 487 LYS cc_start: 0.7464 (mtpp) cc_final: 0.7211 (mtmt) REVERT: A 703 ASP cc_start: 0.7725 (t70) cc_final: 0.7264 (t0) REVERT: A 706 TRP cc_start: 0.7740 (t-100) cc_final: 0.7489 (t-100) REVERT: A 715 SER cc_start: 0.7168 (OUTLIER) cc_final: 0.6706 (p) REVERT: A 719 LYS cc_start: 0.8035 (pptt) cc_final: 0.7359 (mtpp) REVERT: A 776 ASP cc_start: 0.7043 (m-30) cc_final: 0.6445 (m-30) REVERT: B 677 GLN cc_start: 0.6887 (OUTLIER) cc_final: 0.5632 (mp10) REVERT: B 691 MET cc_start: 0.7271 (ttp) cc_final: 0.7070 (ttt) REVERT: B 743 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: B 790 LYS cc_start: 0.7818 (tppt) cc_final: 0.7359 (mmmt) REVERT: B 793 MET cc_start: 0.7465 (mmt) cc_final: 0.7085 (mtt) REVERT: C 434 ILE cc_start: 0.8746 (mp) cc_final: 0.8524 (mm) REVERT: C 487 LYS cc_start: 0.7258 (mtpp) cc_final: 0.6939 (mtmt) REVERT: C 565 MET cc_start: 0.7915 (ttp) cc_final: 0.7682 (ttt) REVERT: C 584 PHE cc_start: 0.6197 (t80) cc_final: 0.5905 (t80) REVERT: C 591 ASN cc_start: 0.8169 (t0) cc_final: 0.7966 (t0) REVERT: C 691 MET cc_start: 0.6753 (ttp) cc_final: 0.6542 (ttp) REVERT: C 696 LYS cc_start: 0.7834 (mtpt) cc_final: 0.7395 (mtmt) REVERT: C 709 MET cc_start: 0.6612 (mtm) cc_final: 0.5967 (mtm) REVERT: C 719 LYS cc_start: 0.8442 (pptt) cc_final: 0.7788 (mtpp) REVERT: C 776 ASP cc_start: 0.7108 (m-30) cc_final: 0.6568 (m-30) REVERT: C 796 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7272 (mt-10) REVERT: D 620 MET cc_start: 0.9104 (mmt) cc_final: 0.8892 (mmt) REVERT: D 743 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: D 790 LYS cc_start: 0.7854 (mptp) cc_final: 0.7609 (tppt) REVERT: D 793 MET cc_start: 0.7558 (mmt) cc_final: 0.7254 (mtt) REVERT: D 819 ASN cc_start: 0.8269 (m110) cc_final: 0.8024 (m110) outliers start: 33 outliers final: 24 residues processed: 183 average time/residue: 0.2624 time to fit residues: 71.3257 Evaluate side-chains 179 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 150 optimal weight: 0.0050 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 142 optimal weight: 0.0870 chunk 99 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 overall best weight: 0.4572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 549 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14708 Z= 0.172 Angle : 0.599 9.058 19782 Z= 0.291 Chirality : 0.042 0.198 2158 Planarity : 0.004 0.050 2390 Dihedral : 17.691 140.619 2894 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.78 % Favored : 91.81 % Rotamer: Outliers : 2.56 % Allowed : 15.95 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.20), residues: 1672 helix: 0.76 (0.18), residues: 830 sheet: -1.93 (0.39), residues: 138 loop : -2.60 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 798 HIS 0.002 0.000 HIS C 792 PHE 0.010 0.001 PHE D 584 TYR 0.022 0.001 TYR D 844 ARG 0.009 0.001 ARG A 748 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 155 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7407 (t70) cc_final: 0.7034 (t0) REVERT: A 487 LYS cc_start: 0.7445 (mtpp) cc_final: 0.7189 (mtmt) REVERT: A 703 ASP cc_start: 0.7739 (t70) cc_final: 0.7262 (t0) REVERT: A 706 TRP cc_start: 0.7776 (t-100) cc_final: 0.7525 (t-100) REVERT: A 715 SER cc_start: 0.7182 (OUTLIER) cc_final: 0.6748 (p) REVERT: A 719 LYS cc_start: 0.8026 (pptt) cc_final: 0.7357 (mtpp) REVERT: A 776 ASP cc_start: 0.6916 (m-30) cc_final: 0.6389 (m-30) REVERT: B 526 VAL cc_start: 0.7971 (t) cc_final: 0.7734 (m) REVERT: B 677 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.5589 (mp10) REVERT: B 691 MET cc_start: 0.7271 (ttp) cc_final: 0.7066 (ttt) REVERT: B 743 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: B 790 LYS cc_start: 0.7787 (tppt) cc_final: 0.7447 (mmmt) REVERT: B 793 MET cc_start: 0.7482 (mmt) cc_final: 0.7163 (mtt) REVERT: C 434 ILE cc_start: 0.8757 (mp) cc_final: 0.8536 (mm) REVERT: C 487 LYS cc_start: 0.7245 (mtpp) cc_final: 0.6911 (mtmt) REVERT: C 565 MET cc_start: 0.7922 (ttp) cc_final: 0.7692 (ttt) REVERT: C 584 PHE cc_start: 0.6232 (t80) cc_final: 0.5958 (t80) REVERT: C 664 MET cc_start: 0.8172 (mtm) cc_final: 0.7922 (mtt) REVERT: C 691 MET cc_start: 0.6745 (ttp) cc_final: 0.6543 (ttp) REVERT: C 696 LYS cc_start: 0.7850 (mtpt) cc_final: 0.7425 (mtmt) REVERT: C 709 MET cc_start: 0.6610 (mtm) cc_final: 0.6060 (mtm) REVERT: C 719 LYS cc_start: 0.8445 (pptt) cc_final: 0.7789 (mtpp) REVERT: C 776 ASP cc_start: 0.7091 (m-30) cc_final: 0.6539 (m-30) REVERT: C 796 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7244 (mt-10) REVERT: D 743 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: D 790 LYS cc_start: 0.7861 (mptp) cc_final: 0.7589 (tppt) REVERT: D 793 MET cc_start: 0.7592 (mmt) cc_final: 0.7240 (mtt) REVERT: D 825 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7971 (mt) outliers start: 37 outliers final: 27 residues processed: 182 average time/residue: 0.2707 time to fit residues: 73.3638 Evaluate side-chains 179 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 14708 Z= 0.405 Angle : 0.748 9.127 19782 Z= 0.365 Chirality : 0.048 0.222 2158 Planarity : 0.005 0.043 2390 Dihedral : 18.239 140.180 2894 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.97 % Favored : 90.55 % Rotamer: Outliers : 2.56 % Allowed : 16.44 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -1.89 (0.20), residues: 1672 helix: 0.11 (0.18), residues: 828 sheet: -2.13 (0.36), residues: 152 loop : -2.79 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 706 HIS 0.003 0.001 HIS A 593 PHE 0.020 0.002 PHE A 533 TYR 0.024 0.002 TYR D 844 ARG 0.008 0.001 ARG D 712 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 158 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7474 (t70) cc_final: 0.7097 (t0) REVERT: A 703 ASP cc_start: 0.7865 (t70) cc_final: 0.7409 (t0) REVERT: A 706 TRP cc_start: 0.7835 (t-100) cc_final: 0.7572 (t-100) REVERT: A 715 SER cc_start: 0.7179 (OUTLIER) cc_final: 0.6722 (p) REVERT: A 719 LYS cc_start: 0.8078 (pptt) cc_final: 0.7517 (mtpp) REVERT: A 776 ASP cc_start: 0.7168 (m-30) cc_final: 0.6706 (m-30) REVERT: B 677 GLN cc_start: 0.6809 (OUTLIER) cc_final: 0.5453 (mp10) REVERT: B 691 MET cc_start: 0.7330 (ttp) cc_final: 0.7112 (ttt) REVERT: B 743 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: B 790 LYS cc_start: 0.7750 (tppt) cc_final: 0.7267 (mmmt) REVERT: B 825 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8177 (mt) REVERT: C 434 ILE cc_start: 0.8792 (mp) cc_final: 0.8581 (mm) REVERT: C 487 LYS cc_start: 0.7256 (mtpp) cc_final: 0.6917 (mtpt) REVERT: C 664 MET cc_start: 0.8103 (mtm) cc_final: 0.7852 (mtt) REVERT: C 691 MET cc_start: 0.6884 (ttp) cc_final: 0.6663 (ttp) REVERT: C 696 LYS cc_start: 0.7927 (mtpt) cc_final: 0.7543 (mtmm) REVERT: C 709 MET cc_start: 0.6668 (mtm) cc_final: 0.6194 (mtm) REVERT: C 719 LYS cc_start: 0.8452 (pptt) cc_final: 0.7783 (mtpp) REVERT: C 776 ASP cc_start: 0.7279 (m-30) cc_final: 0.6835 (m-30) REVERT: C 796 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7329 (mt-10) REVERT: D 743 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: D 790 LYS cc_start: 0.7817 (mptp) cc_final: 0.7543 (tppt) REVERT: D 825 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8080 (mt) outliers start: 37 outliers final: 27 residues processed: 187 average time/residue: 0.2585 time to fit residues: 72.0882 Evaluate side-chains 180 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 147 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 823 ILE Chi-restraints excluded: chain D residue 825 ILE Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 chunk 19 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 137 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.0370 chunk 117 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 593 HIS B 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.164255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.132776 restraints weight = 16357.714| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.52 r_work: 0.3221 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14708 Z= 0.180 Angle : 0.624 9.164 19782 Z= 0.307 Chirality : 0.042 0.223 2158 Planarity : 0.004 0.039 2390 Dihedral : 17.726 140.462 2894 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.64 % Favored : 93.00 % Rotamer: Outliers : 2.00 % Allowed : 17.06 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -1.38 (0.20), residues: 1672 helix: 0.64 (0.18), residues: 830 sheet: -2.14 (0.39), residues: 138 loop : -2.64 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 706 HIS 0.003 0.001 HIS D 593 PHE 0.020 0.001 PHE C 584 TYR 0.021 0.001 TYR D 844 ARG 0.009 0.001 ARG A 748 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3320.22 seconds wall clock time: 61 minutes 27.10 seconds (3687.10 seconds total)