Starting phenix.real_space_refine on Thu Jul 31 21:47:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iob_35614/07_2025/8iob_35614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iob_35614/07_2025/8iob_35614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iob_35614/07_2025/8iob_35614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iob_35614/07_2025/8iob_35614.map" model { file = "/net/cci-nas-00/data/ceres_data/8iob_35614/07_2025/8iob_35614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iob_35614/07_2025/8iob_35614.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 9008 2.51 5 N 2324 2.21 5 O 2336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13736 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 10.11, per 1000 atoms: 0.74 Number of scatterers: 13736 At special positions: 0 Unit cell: (116.313, 116.313, 125.652, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2336 8.00 N 2324 7.00 C 9008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.95 Conformation dependent library (CDL) restraints added in 2.1 seconds 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3232 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 10 sheets defined 64.6% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 404 through 431 Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 451 through 473 removed outlier: 3.642A pdb=" N ASP A 460 " --> pdb=" O ASP A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 494 removed outlier: 3.825A pdb=" N ILE A 489 " --> pdb=" O HIS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 506 removed outlier: 3.562A pdb=" N ILE A 500 " --> pdb=" O GLY A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 537 removed outlier: 4.333A pdb=" N LEU A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 545 through 576 removed outlier: 3.899A pdb=" N VAL A 549 " --> pdb=" O TYR A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 593 Processing helix chain 'A' and resid 608 through 621 removed outlier: 4.318A pdb=" N ALA A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 687 removed outlier: 5.002A pdb=" N GLY A 669 " --> pdb=" O ARG A 665 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N THR A 670 " --> pdb=" O LEU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 708 removed outlier: 3.711A pdb=" N TYR A 707 " --> pdb=" O HIS A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 720 removed outlier: 4.056A pdb=" N VAL A 716 " --> pdb=" O ASP A 712 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 731 removed outlier: 3.540A pdb=" N LEU A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS A 731 " --> pdb=" O ASP A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 746 Processing helix chain 'A' and resid 747 through 757 Processing helix chain 'A' and resid 834 through 843 removed outlier: 3.584A pdb=" N LEU A 839 " --> pdb=" O ARG A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 855 Processing helix chain 'B' and resid 404 through 431 Proline residue: B 426 - end of helix Processing helix chain 'B' and resid 451 through 473 removed outlier: 3.591A pdb=" N ASP B 460 " --> pdb=" O ASP B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 494 removed outlier: 3.875A pdb=" N ILE B 489 " --> pdb=" O HIS B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 506 Processing helix chain 'B' and resid 525 through 538 removed outlier: 4.160A pdb=" N LEU B 529 " --> pdb=" O LYS B 525 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 532 " --> pdb=" O ARG B 528 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 535 " --> pdb=" O ARG B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 545 through 576 removed outlier: 3.930A pdb=" N VAL B 549 " --> pdb=" O TYR B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 593 Processing helix chain 'B' and resid 608 through 621 removed outlier: 4.269A pdb=" N ALA B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 687 removed outlier: 5.013A pdb=" N GLY B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N THR B 670 " --> pdb=" O LEU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 708 removed outlier: 3.581A pdb=" N TYR B 707 " --> pdb=" O HIS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 720 removed outlier: 4.019A pdb=" N VAL B 716 " --> pdb=" O ASP B 712 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B 720 " --> pdb=" O VAL B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 731 removed outlier: 3.546A pdb=" N LEU B 730 " --> pdb=" O ALA B 726 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS B 731 " --> pdb=" O ASP B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 746 removed outlier: 3.518A pdb=" N ARG B 744 " --> pdb=" O LYS B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 757 Processing helix chain 'B' and resid 834 through 844 removed outlier: 3.693A pdb=" N MET B 844 " --> pdb=" O GLU B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 855 removed outlier: 3.619A pdb=" N SER B 849 " --> pdb=" O TYR B 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 431 Proline residue: C 426 - end of helix Processing helix chain 'C' and resid 451 through 473 removed outlier: 3.607A pdb=" N ASP C 460 " --> pdb=" O ASP C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 494 removed outlier: 3.870A pdb=" N ILE C 489 " --> pdb=" O HIS C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 506 Processing helix chain 'C' and resid 525 through 538 removed outlier: 4.168A pdb=" N LEU C 529 " --> pdb=" O LYS C 525 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 532 " --> pdb=" O ARG C 528 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL C 533 " --> pdb=" O LEU C 529 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG C 534 " --> pdb=" O LEU C 530 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 535 " --> pdb=" O ARG C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 Processing helix chain 'C' and resid 545 through 576 removed outlier: 3.907A pdb=" N VAL C 549 " --> pdb=" O TYR C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 593 Processing helix chain 'C' and resid 608 through 621 removed outlier: 4.285A pdb=" N ALA C 614 " --> pdb=" O LYS C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 687 removed outlier: 4.945A pdb=" N GLY C 669 " --> pdb=" O ARG C 665 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N THR C 670 " --> pdb=" O LEU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 708 removed outlier: 3.594A pdb=" N TYR C 707 " --> pdb=" O HIS C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 720 removed outlier: 4.000A pdb=" N VAL C 716 " --> pdb=" O ASP C 712 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE C 720 " --> pdb=" O VAL C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 731 removed outlier: 3.566A pdb=" N LEU C 730 " --> pdb=" O ALA C 726 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS C 731 " --> pdb=" O ASP C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 746 Processing helix chain 'C' and resid 747 through 757 Processing helix chain 'C' and resid 834 through 844 removed outlier: 3.698A pdb=" N MET C 844 " --> pdb=" O GLU C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 855 removed outlier: 3.613A pdb=" N SER C 849 " --> pdb=" O TYR C 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 431 Proline residue: D 426 - end of helix Processing helix chain 'D' and resid 451 through 473 removed outlier: 3.609A pdb=" N ASP D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 494 removed outlier: 3.797A pdb=" N ILE D 489 " --> pdb=" O HIS D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 506 Processing helix chain 'D' and resid 525 through 538 removed outlier: 4.211A pdb=" N LEU D 529 " --> pdb=" O LYS D 525 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 532 " --> pdb=" O ARG D 528 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL D 533 " --> pdb=" O LEU D 529 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG D 534 " --> pdb=" O LEU D 530 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 535 " --> pdb=" O ARG D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 543 Processing helix chain 'D' and resid 545 through 576 removed outlier: 3.897A pdb=" N VAL D 549 " --> pdb=" O TYR D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 593 Processing helix chain 'D' and resid 608 through 621 removed outlier: 4.343A pdb=" N ALA D 614 " --> pdb=" O LYS D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 687 removed outlier: 4.939A pdb=" N GLY D 669 " --> pdb=" O ARG D 665 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N THR D 670 " --> pdb=" O LEU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 708 removed outlier: 3.832A pdb=" N TYR D 707 " --> pdb=" O HIS D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 720 removed outlier: 4.012A pdb=" N VAL D 716 " --> pdb=" O ASP D 712 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE D 720 " --> pdb=" O VAL D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 731 removed outlier: 3.571A pdb=" N LEU D 730 " --> pdb=" O ALA D 726 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS D 731 " --> pdb=" O ASP D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 746 Processing helix chain 'D' and resid 747 through 757 Processing helix chain 'D' and resid 834 through 844 removed outlier: 3.773A pdb=" N MET D 844 " --> pdb=" O GLU D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 855 Processing sheet with id=AA1, first strand: chain 'A' and resid 762 through 763 removed outlier: 7.437A pdb=" N ASP A 829 " --> pdb=" O SER A 783 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 795 through 796 removed outlier: 3.799A pdb=" N GLU A 788 " --> pdb=" O ARG A 823 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 759 through 763 removed outlier: 7.468A pdb=" N ASP B 829 " --> pdb=" O SER B 783 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 795 through 796 removed outlier: 3.806A pdb=" N GLU B 788 " --> pdb=" O ARG B 823 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 762 through 763 removed outlier: 7.417A pdb=" N ASP C 829 " --> pdb=" O SER C 783 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 795 through 796 removed outlier: 3.804A pdb=" N GLU C 788 " --> pdb=" O ARG C 823 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 805 through 806 removed outlier: 4.214A pdb=" N GLY C 806 " --> pdb=" O PHE C 860 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 762 through 763 removed outlier: 7.355A pdb=" N ASP D 829 " --> pdb=" O SER D 783 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 795 through 796 removed outlier: 3.803A pdb=" N GLU D 788 " --> pdb=" O ARG D 823 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 805 through 806 removed outlier: 4.227A pdb=" N GLY D 806 " --> pdb=" O PHE D 860 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 800 hydrogen bonds defined for protein. 2352 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.73 Time building geometry restraints manager: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4255 1.34 - 1.46: 2719 1.46 - 1.58: 7017 1.58 - 1.70: 1 1.70 - 1.82: 104 Bond restraints: 14096 Sorted by residual: bond pdb=" CB PRO C 808 " pdb=" CG PRO C 808 " ideal model delta sigma weight residual 1.492 1.607 -0.115 5.00e-02 4.00e+02 5.33e+00 bond pdb=" CG GLN B 676 " pdb=" CD GLN B 676 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.15e+00 bond pdb=" CB LYS A 718 " pdb=" CG LYS A 718 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.13e+00 bond pdb=" CB LYS C 718 " pdb=" CG LYS C 718 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" CG GLN C 676 " pdb=" CD GLN C 676 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.11e+00 ... (remaining 14091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 18364 1.67 - 3.34: 618 3.34 - 5.01: 130 5.01 - 6.68: 26 6.68 - 8.35: 14 Bond angle restraints: 19152 Sorted by residual: angle pdb=" CA PRO C 808 " pdb=" N PRO C 808 " pdb=" CD PRO C 808 " ideal model delta sigma weight residual 112.00 105.27 6.73 1.40e+00 5.10e-01 2.31e+01 angle pdb=" N GLY C 806 " pdb=" CA GLY C 806 " pdb=" C GLY C 806 " ideal model delta sigma weight residual 110.29 115.37 -5.08 1.28e+00 6.10e-01 1.58e+01 angle pdb=" N PRO C 808 " pdb=" CD PRO C 808 " pdb=" CG PRO C 808 " ideal model delta sigma weight residual 103.20 97.92 5.28 1.50e+00 4.44e-01 1.24e+01 angle pdb=" N GLY D 806 " pdb=" CA GLY D 806 " pdb=" C GLY D 806 " ideal model delta sigma weight residual 110.29 114.78 -4.49 1.28e+00 6.10e-01 1.23e+01 angle pdb=" C VAL B 491 " pdb=" N HIS B 492 " pdb=" CA HIS B 492 " ideal model delta sigma weight residual 120.68 114.75 5.93 1.70e+00 3.46e-01 1.22e+01 ... (remaining 19147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 7313 16.06 - 32.13: 733 32.13 - 48.19: 137 48.19 - 64.26: 17 64.26 - 80.32: 8 Dihedral angle restraints: 8208 sinusoidal: 3192 harmonic: 5016 Sorted by residual: dihedral pdb=" CA LYS C 757 " pdb=" C LYS C 757 " pdb=" N PHE C 758 " pdb=" CA PHE C 758 " ideal model delta harmonic sigma weight residual 180.00 156.64 23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA LYS B 757 " pdb=" C LYS B 757 " pdb=" N PHE B 758 " pdb=" CA PHE B 758 " ideal model delta harmonic sigma weight residual 180.00 158.99 21.01 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA TYR C 780 " pdb=" C TYR C 780 " pdb=" N PHE C 781 " pdb=" CA PHE C 781 " ideal model delta harmonic sigma weight residual 180.00 160.99 19.01 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 8205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1380 0.034 - 0.069: 533 0.069 - 0.103: 176 0.103 - 0.138: 69 0.138 - 0.172: 18 Chirality restraints: 2176 Sorted by residual: chirality pdb=" CB ILE D 521 " pdb=" CA ILE D 521 " pdb=" CG1 ILE D 521 " pdb=" CG2 ILE D 521 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CB ILE B 521 " pdb=" CA ILE B 521 " pdb=" CG1 ILE B 521 " pdb=" CG2 ILE B 521 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CB ILE A 521 " pdb=" CA ILE A 521 " pdb=" CG1 ILE A 521 " pdb=" CG2 ILE A 521 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 2173 not shown) Planarity restraints: 2376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 652 " 0.022 2.00e-02 2.50e+03 1.49e-02 4.45e+00 pdb=" CG TYR B 652 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR B 652 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 652 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 652 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 652 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 652 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 652 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 720 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO A 721 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 721 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 721 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 720 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO B 721 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 721 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 721 " -0.025 5.00e-02 4.00e+02 ... (remaining 2373 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 238 2.68 - 3.23: 14387 3.23 - 3.79: 22425 3.79 - 4.34: 28236 4.34 - 4.90: 45123 Nonbonded interactions: 110409 Sorted by model distance: nonbonded pdb=" O ARG B 672 " pdb=" OG1 THR B 675 " model vdw 2.123 3.040 nonbonded pdb=" O ARG C 672 " pdb=" OG1 THR C 675 " model vdw 2.124 3.040 nonbonded pdb=" OG SER B 735 " pdb=" OD1 ASN B 802 " model vdw 2.127 3.040 nonbonded pdb=" OG SER C 735 " pdb=" OD1 ASN C 802 " model vdw 2.128 3.040 nonbonded pdb=" OG SER A 735 " pdb=" OD1 ASN A 802 " model vdw 2.129 3.040 ... (remaining 110404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 40.140 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.140 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:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 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 : 0.003 0.115 14096 Z= 0.155 Angle : 0.757 8.346 19152 Z= 0.428 Chirality : 0.045 0.172 2176 Planarity : 0.004 0.045 2376 Dihedral : 13.275 80.323 4976 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.77 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1684 helix: 1.38 (0.16), residues: 1048 sheet: -3.71 (0.48), residues: 68 loop : -2.52 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 410 HIS 0.006 0.001 HIS D 703 PHE 0.025 0.002 PHE B 656 TYR 0.035 0.002 TYR B 652 ARG 0.010 0.001 ARG C 679 Details of bonding type rmsd hydrogen bonds : bond 0.14031 ( 800) hydrogen bonds : angle 5.91064 ( 2352) covalent geometry : bond 0.00311 (14096) covalent geometry : angle 0.75711 (19152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 ARG cc_start: 0.7946 (mtp85) cc_final: 0.7191 (ttm170) REVERT: A 586 LEU cc_start: 0.9051 (mt) cc_final: 0.8840 (mt) REVERT: A 698 GLU cc_start: 0.8990 (pp20) cc_final: 0.8688 (pp20) REVERT: A 728 ILE cc_start: 0.9364 (tp) cc_final: 0.9100 (tp) REVERT: A 729 CYS cc_start: 0.8943 (m) cc_final: 0.8678 (p) REVERT: A 731 HIS cc_start: 0.8320 (m-70) cc_final: 0.7878 (m-70) REVERT: A 756 MET cc_start: 0.8917 (ttp) cc_final: 0.8600 (ttp) REVERT: B 678 LEU cc_start: 0.9328 (mt) cc_final: 0.8829 (mt) REVERT: B 705 TRP cc_start: 0.8753 (t-100) cc_final: 0.8534 (t-100) REVERT: B 728 ILE cc_start: 0.9369 (tp) cc_final: 0.9109 (tp) REVERT: B 729 CYS cc_start: 0.9031 (m) cc_final: 0.8755 (p) REVERT: B 731 HIS cc_start: 0.8318 (m-70) cc_final: 0.7896 (m-70) REVERT: B 759 LYS cc_start: 0.9110 (mptt) cc_final: 0.8895 (mmtm) REVERT: C 562 HIS cc_start: 0.8624 (t-90) cc_final: 0.8415 (t-170) REVERT: C 586 LEU cc_start: 0.9041 (mt) cc_final: 0.8837 (mt) REVERT: C 678 LEU cc_start: 0.9329 (mt) cc_final: 0.8826 (mt) REVERT: C 728 ILE cc_start: 0.9345 (tp) cc_final: 0.9070 (tp) REVERT: C 729 CYS cc_start: 0.8995 (m) cc_final: 0.8722 (p) REVERT: C 731 HIS cc_start: 0.8326 (m-70) cc_final: 0.7917 (m-70) REVERT: C 759 LYS cc_start: 0.9084 (mptt) cc_final: 0.8853 (mmtm) REVERT: C 780 TYR cc_start: 0.7669 (m-10) cc_final: 0.7462 (m-10) REVERT: C 819 ASN cc_start: 0.5623 (t0) cc_final: 0.5403 (t0) REVERT: D 586 LEU cc_start: 0.9057 (mt) cc_final: 0.8844 (mt) REVERT: D 676 GLN cc_start: 0.9403 (mt0) cc_final: 0.8888 (mt0) REVERT: D 728 ILE cc_start: 0.9349 (tp) cc_final: 0.9095 (tp) REVERT: D 729 CYS cc_start: 0.9009 (m) cc_final: 0.8672 (p) REVERT: D 731 HIS cc_start: 0.8338 (m-70) cc_final: 0.7926 (m-70) REVERT: D 756 MET cc_start: 0.8898 (ttp) cc_final: 0.8605 (ptm) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.3108 time to fit residues: 162.3421 Evaluate side-chains 276 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.0980 chunk 130 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 HIS A 633 ASN A 714 ASN ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 HIS ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 762 HIS B 810 ASN B 831 HIS C 633 ASN ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 762 HIS C 810 ASN D 633 ASN ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 831 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.154207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.112065 restraints weight = 42157.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.115802 restraints weight = 18276.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.117809 restraints weight = 11028.281| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14096 Z= 0.172 Angle : 0.710 9.392 19152 Z= 0.365 Chirality : 0.046 0.183 2176 Planarity : 0.005 0.049 2376 Dihedral : 4.422 21.502 1876 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.78 % Favored : 91.98 % Rotamer: Outliers : 2.13 % Allowed : 12.71 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1684 helix: 1.44 (0.16), residues: 1076 sheet: -4.01 (0.45), residues: 68 loop : -2.64 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 705 HIS 0.010 0.001 HIS A 674 PHE 0.024 0.002 PHE D 758 TYR 0.018 0.002 TYR C 827 ARG 0.008 0.001 ARG A 531 Details of bonding type rmsd hydrogen bonds : bond 0.05134 ( 800) hydrogen bonds : angle 5.25883 ( 2352) covalent geometry : bond 0.00369 (14096) covalent geometry : angle 0.71028 (19152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 304 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 GLN cc_start: 0.9319 (mt0) cc_final: 0.9093 (mp10) REVERT: A 728 ILE cc_start: 0.9366 (tp) cc_final: 0.9107 (tp) REVERT: A 731 HIS cc_start: 0.8340 (m-70) cc_final: 0.7918 (m-70) REVERT: A 748 LYS cc_start: 0.9053 (mmmm) cc_final: 0.8596 (pttm) REVERT: B 541 ARG cc_start: 0.7831 (tpt90) cc_final: 0.7448 (tpt90) REVERT: B 678 LEU cc_start: 0.9380 (mt) cc_final: 0.9138 (mt) REVERT: B 705 TRP cc_start: 0.8671 (t-100) cc_final: 0.8453 (t-100) REVERT: B 728 ILE cc_start: 0.9344 (tp) cc_final: 0.9093 (tp) REVERT: B 731 HIS cc_start: 0.8366 (m-70) cc_final: 0.7953 (m-70) REVERT: B 841 VAL cc_start: 0.9112 (p) cc_final: 0.8817 (p) REVERT: B 844 MET cc_start: 0.7685 (tmm) cc_final: 0.6901 (tmm) REVERT: B 853 TRP cc_start: 0.7703 (m100) cc_final: 0.7499 (m100) REVERT: C 678 LEU cc_start: 0.9381 (mt) cc_final: 0.9138 (mt) REVERT: C 705 TRP cc_start: 0.8659 (t-100) cc_final: 0.8272 (t-100) REVERT: C 728 ILE cc_start: 0.9344 (tp) cc_final: 0.9047 (tp) REVERT: C 729 CYS cc_start: 0.9139 (m) cc_final: 0.8792 (p) REVERT: C 731 HIS cc_start: 0.8331 (m-70) cc_final: 0.7912 (m-70) REVERT: C 756 MET cc_start: 0.8970 (ptp) cc_final: 0.8713 (ptt) REVERT: C 831 HIS cc_start: 0.8693 (OUTLIER) cc_final: 0.8388 (m-70) REVERT: C 844 MET cc_start: 0.7735 (tmm) cc_final: 0.7047 (tmm) REVERT: D 541 ARG cc_start: 0.7823 (tpt90) cc_final: 0.7456 (tpt90) REVERT: D 728 ILE cc_start: 0.9362 (tp) cc_final: 0.9069 (tp) REVERT: D 729 CYS cc_start: 0.9106 (m) cc_final: 0.8619 (p) REVERT: D 731 HIS cc_start: 0.8355 (m-70) cc_final: 0.7932 (m-70) REVERT: D 756 MET cc_start: 0.8943 (ttp) cc_final: 0.8680 (ttp) REVERT: D 759 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8554 (mmtm) outliers start: 31 outliers final: 25 residues processed: 317 average time/residue: 0.2405 time to fit residues: 112.6700 Evaluate side-chains 299 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 273 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 831 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 136 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 162 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 124 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS A 810 ASN ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS B 831 HIS ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 HIS C 831 HIS D 676 GLN D 702 GLN ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.154099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.112458 restraints weight = 41785.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.116266 restraints weight = 17922.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.118306 restraints weight = 10678.881| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14096 Z= 0.152 Angle : 0.672 10.311 19152 Z= 0.344 Chirality : 0.045 0.168 2176 Planarity : 0.004 0.034 2376 Dihedral : 4.332 19.698 1876 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.84 % Favored : 91.92 % Rotamer: Outliers : 2.61 % Allowed : 15.80 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.21), residues: 1684 helix: 1.43 (0.16), residues: 1052 sheet: -4.00 (0.48), residues: 68 loop : -2.57 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 705 HIS 0.008 0.001 HIS A 674 PHE 0.029 0.002 PHE C 758 TYR 0.019 0.002 TYR A 673 ARG 0.007 0.001 ARG D 531 Details of bonding type rmsd hydrogen bonds : bond 0.04888 ( 800) hydrogen bonds : angle 5.00741 ( 2352) covalent geometry : bond 0.00327 (14096) covalent geometry : angle 0.67202 (19152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 297 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.6712 (m100) cc_final: 0.6461 (m100) REVERT: A 629 ASN cc_start: 0.8377 (t0) cc_final: 0.8125 (t0) REVERT: A 673 TYR cc_start: 0.9350 (t80) cc_final: 0.9055 (t80) REVERT: A 676 GLN cc_start: 0.9369 (mt0) cc_final: 0.9053 (mp10) REVERT: A 698 GLU cc_start: 0.9063 (pp20) cc_final: 0.8744 (pp20) REVERT: A 728 ILE cc_start: 0.9397 (tp) cc_final: 0.9071 (tp) REVERT: A 729 CYS cc_start: 0.9185 (m) cc_final: 0.8758 (p) REVERT: A 731 HIS cc_start: 0.8355 (m-70) cc_final: 0.7937 (m-70) REVERT: A 748 LYS cc_start: 0.9000 (mmmm) cc_final: 0.8584 (pttm) REVERT: A 759 LYS cc_start: 0.8929 (mmtt) cc_final: 0.8559 (mmtm) REVERT: A 831 HIS cc_start: 0.8668 (OUTLIER) cc_final: 0.8057 (m-70) REVERT: A 853 TRP cc_start: 0.7663 (m100) cc_final: 0.7445 (m100) REVERT: B 415 LEU cc_start: 0.8380 (mt) cc_final: 0.8113 (mt) REVERT: B 541 ARG cc_start: 0.7699 (tpt90) cc_final: 0.7345 (tpt90) REVERT: B 676 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8196 (mp10) REVERT: B 728 ILE cc_start: 0.9408 (tp) cc_final: 0.9093 (tp) REVERT: B 729 CYS cc_start: 0.9179 (m) cc_final: 0.8772 (p) REVERT: B 731 HIS cc_start: 0.8358 (m-70) cc_final: 0.7975 (m-70) REVERT: B 756 MET cc_start: 0.9140 (ptt) cc_final: 0.8789 (ptt) REVERT: B 759 LYS cc_start: 0.9090 (mptt) cc_final: 0.8875 (mmtt) REVERT: B 831 HIS cc_start: 0.8439 (OUTLIER) cc_final: 0.7899 (m90) REVERT: C 415 LEU cc_start: 0.8406 (tp) cc_final: 0.8169 (mt) REVERT: C 541 ARG cc_start: 0.7689 (tpt90) cc_final: 0.7321 (tpt90) REVERT: C 705 TRP cc_start: 0.8615 (t-100) cc_final: 0.8303 (t-100) REVERT: C 728 ILE cc_start: 0.9319 (tp) cc_final: 0.9066 (tp) REVERT: C 731 HIS cc_start: 0.8307 (m-70) cc_final: 0.7883 (m-70) REVERT: C 759 LYS cc_start: 0.9111 (mptt) cc_final: 0.8834 (mmtm) REVERT: D 415 LEU cc_start: 0.8400 (mt) cc_final: 0.8128 (mt) REVERT: D 541 ARG cc_start: 0.7776 (tpt90) cc_final: 0.7368 (tpt90) REVERT: D 676 GLN cc_start: 0.9211 (mt0) cc_final: 0.8930 (mt0) REVERT: D 702 GLN cc_start: 0.9334 (mm110) cc_final: 0.9053 (pp30) REVERT: D 705 TRP cc_start: 0.8719 (t-100) cc_final: 0.8040 (t-100) REVERT: D 728 ILE cc_start: 0.9339 (tp) cc_final: 0.9049 (tp) REVERT: D 729 CYS cc_start: 0.9071 (m) cc_final: 0.8626 (p) REVERT: D 731 HIS cc_start: 0.8332 (m-70) cc_final: 0.7918 (m-70) REVERT: D 748 LYS cc_start: 0.9144 (mmmm) cc_final: 0.8596 (pttm) REVERT: D 756 MET cc_start: 0.8941 (ttp) cc_final: 0.8721 (ttp) REVERT: D 758 PHE cc_start: 0.7953 (m-80) cc_final: 0.7509 (m-80) REVERT: D 759 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8538 (mmtm) REVERT: D 823 ARG cc_start: 0.8193 (mmt180) cc_final: 0.7924 (mmt-90) REVERT: D 831 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.7950 (m-70) outliers start: 38 outliers final: 29 residues processed: 317 average time/residue: 0.2927 time to fit residues: 136.0463 Evaluate side-chains 303 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 270 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 676 GLN Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 831 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 34 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 158 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS A 831 HIS ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 HIS ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.154589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.112760 restraints weight = 41871.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.116661 restraints weight = 17414.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.118806 restraints weight = 10179.277| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14096 Z= 0.142 Angle : 0.688 14.965 19152 Z= 0.342 Chirality : 0.044 0.170 2176 Planarity : 0.004 0.049 2376 Dihedral : 4.293 18.902 1876 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.02 % Favored : 91.75 % Rotamer: Outliers : 2.61 % Allowed : 19.02 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1684 helix: 1.43 (0.16), residues: 1044 sheet: -4.33 (0.43), residues: 44 loop : -2.57 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 705 HIS 0.007 0.001 HIS A 674 PHE 0.029 0.002 PHE D 848 TYR 0.022 0.002 TYR B 700 ARG 0.005 0.000 ARG D 531 Details of bonding type rmsd hydrogen bonds : bond 0.04752 ( 800) hydrogen bonds : angle 4.90323 ( 2352) covalent geometry : bond 0.00306 (14096) covalent geometry : angle 0.68772 (19152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 294 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.6836 (m100) cc_final: 0.6594 (m100) REVERT: A 534 ARG cc_start: 0.8384 (mtp85) cc_final: 0.7633 (ttm170) REVERT: A 541 ARG cc_start: 0.7757 (tpt90) cc_final: 0.7505 (tpt90) REVERT: A 629 ASN cc_start: 0.8469 (t0) cc_final: 0.8159 (t0) REVERT: A 729 CYS cc_start: 0.9150 (m) cc_final: 0.8778 (p) REVERT: A 748 LYS cc_start: 0.9020 (mmmm) cc_final: 0.8607 (pttm) REVERT: A 759 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8546 (mmtm) REVERT: A 831 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.8085 (m90) REVERT: B 415 LEU cc_start: 0.8369 (mt) cc_final: 0.8109 (mt) REVERT: B 541 ARG cc_start: 0.7668 (tpt90) cc_final: 0.7326 (tpt90) REVERT: B 629 ASN cc_start: 0.8333 (t0) cc_final: 0.8119 (t0) REVERT: B 729 CYS cc_start: 0.9150 (m) cc_final: 0.8726 (p) REVERT: B 756 MET cc_start: 0.9132 (ptt) cc_final: 0.8737 (ptt) REVERT: B 831 HIS cc_start: 0.8400 (OUTLIER) cc_final: 0.7828 (m-70) REVERT: C 415 LEU cc_start: 0.8395 (tp) cc_final: 0.8170 (mt) REVERT: C 705 TRP cc_start: 0.8579 (t-100) cc_final: 0.8330 (t-100) REVERT: C 729 CYS cc_start: 0.9172 (m) cc_final: 0.8713 (p) REVERT: C 756 MET cc_start: 0.9054 (ptt) cc_final: 0.8649 (ptp) REVERT: C 831 HIS cc_start: 0.8566 (OUTLIER) cc_final: 0.7984 (m-70) REVERT: D 415 LEU cc_start: 0.8394 (mt) cc_final: 0.8126 (mt) REVERT: D 541 ARG cc_start: 0.7738 (tpt90) cc_final: 0.7352 (tpt90) REVERT: D 586 LEU cc_start: 0.9045 (mt) cc_final: 0.8800 (mt) REVERT: D 645 MET cc_start: 0.8640 (mtm) cc_final: 0.8410 (mtm) REVERT: D 676 GLN cc_start: 0.9293 (mt0) cc_final: 0.9052 (mt0) REVERT: D 702 GLN cc_start: 0.9343 (mm110) cc_final: 0.9032 (pp30) REVERT: D 705 TRP cc_start: 0.8671 (t-100) cc_final: 0.8074 (t-100) REVERT: D 729 CYS cc_start: 0.9026 (m) cc_final: 0.8567 (p) REVERT: D 758 PHE cc_start: 0.7957 (m-80) cc_final: 0.7670 (m-80) REVERT: D 759 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8612 (mmtm) REVERT: D 780 TYR cc_start: 0.7580 (m-80) cc_final: 0.7309 (m-10) REVERT: D 831 HIS cc_start: 0.8560 (OUTLIER) cc_final: 0.8260 (m-70) outliers start: 38 outliers final: 29 residues processed: 316 average time/residue: 0.3305 time to fit residues: 153.5148 Evaluate side-chains 304 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 271 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain D residue 492 HIS Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 651 MET Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 831 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 133 optimal weight: 4.9990 chunk 36 optimal weight: 0.0980 chunk 83 optimal weight: 0.6980 chunk 102 optimal weight: 0.0370 chunk 116 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 HIS ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS A 831 HIS ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS B 831 HIS C 762 HIS C 831 HIS C 834 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.155503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.114288 restraints weight = 41826.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.118109 restraints weight = 17952.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.120216 restraints weight = 10602.664| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14096 Z= 0.134 Angle : 0.679 12.233 19152 Z= 0.336 Chirality : 0.044 0.161 2176 Planarity : 0.004 0.037 2376 Dihedral : 4.254 19.318 1876 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.54 % Favored : 92.22 % Rotamer: Outliers : 3.30 % Allowed : 21.29 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1684 helix: 1.39 (0.16), residues: 1056 sheet: -4.47 (0.39), residues: 44 loop : -2.45 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 705 HIS 0.010 0.001 HIS A 831 PHE 0.027 0.002 PHE C 758 TYR 0.023 0.002 TYR A 673 ARG 0.005 0.000 ARG D 823 Details of bonding type rmsd hydrogen bonds : bond 0.04621 ( 800) hydrogen bonds : angle 4.77217 ( 2352) covalent geometry : bond 0.00289 (14096) covalent geometry : angle 0.67908 (19152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 291 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.6901 (m100) cc_final: 0.6620 (m100) REVERT: A 534 ARG cc_start: 0.8406 (mtp85) cc_final: 0.8112 (ttm-80) REVERT: A 541 ARG cc_start: 0.7743 (tpt90) cc_final: 0.7522 (tpt90) REVERT: A 629 ASN cc_start: 0.8612 (t0) cc_final: 0.8336 (t0) REVERT: A 729 CYS cc_start: 0.9176 (m) cc_final: 0.8792 (p) REVERT: A 748 LYS cc_start: 0.9032 (mmmm) cc_final: 0.8636 (pttm) REVERT: A 756 MET cc_start: 0.8936 (ptm) cc_final: 0.8463 (ptt) REVERT: A 759 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8731 (mmtm) REVERT: B 415 LEU cc_start: 0.8399 (mt) cc_final: 0.8147 (mt) REVERT: B 541 ARG cc_start: 0.7632 (tpt90) cc_final: 0.7298 (tpt90) REVERT: B 729 CYS cc_start: 0.9152 (m) cc_final: 0.8730 (p) REVERT: B 756 MET cc_start: 0.9073 (ptt) cc_final: 0.8681 (ptt) REVERT: B 759 LYS cc_start: 0.9033 (mptt) cc_final: 0.8720 (mmtm) REVERT: B 831 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.7890 (m90) REVERT: B 832 LYS cc_start: 0.8863 (tmtt) cc_final: 0.8490 (tmtt) REVERT: C 415 LEU cc_start: 0.8400 (tp) cc_final: 0.8176 (mt) REVERT: C 541 ARG cc_start: 0.7646 (tpt90) cc_final: 0.7312 (tpt90) REVERT: C 559 LEU cc_start: 0.9367 (mm) cc_final: 0.9166 (tp) REVERT: C 645 MET cc_start: 0.8618 (mtm) cc_final: 0.8326 (mtm) REVERT: C 676 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.7888 (mp10) REVERT: C 729 CYS cc_start: 0.9168 (m) cc_final: 0.8723 (p) REVERT: C 759 LYS cc_start: 0.9133 (mptt) cc_final: 0.8877 (mmtm) REVERT: C 831 HIS cc_start: 0.8596 (OUTLIER) cc_final: 0.8125 (m90) REVERT: C 857 GLU cc_start: 0.8104 (mp0) cc_final: 0.7486 (pm20) REVERT: D 415 LEU cc_start: 0.8393 (mt) cc_final: 0.8132 (mt) REVERT: D 541 ARG cc_start: 0.7766 (tpt90) cc_final: 0.7399 (tpt90) REVERT: D 586 LEU cc_start: 0.9072 (mt) cc_final: 0.8856 (mt) REVERT: D 645 MET cc_start: 0.8663 (mtm) cc_final: 0.8339 (mtm) REVERT: D 676 GLN cc_start: 0.9343 (mt0) cc_final: 0.9051 (mp10) REVERT: D 705 TRP cc_start: 0.8628 (t-100) cc_final: 0.8211 (t-100) REVERT: D 748 LYS cc_start: 0.9030 (mmmm) cc_final: 0.8509 (pttm) REVERT: D 758 PHE cc_start: 0.7937 (m-80) cc_final: 0.7634 (m-80) REVERT: D 831 HIS cc_start: 0.8642 (OUTLIER) cc_final: 0.8261 (m-70) outliers start: 48 outliers final: 30 residues processed: 318 average time/residue: 0.3095 time to fit residues: 145.3747 Evaluate side-chains 313 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 278 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 759 LYS Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain C residue 834 HIS Chi-restraints excluded: chain D residue 492 HIS Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 831 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 59 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 103 optimal weight: 0.4980 chunk 137 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 HIS A 676 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS A 831 HIS ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS B 831 HIS B 834 HIS C 687 HIS C 762 HIS C 831 HIS C 834 HIS D 664 GLN D 702 GLN ** D 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.155221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.116017 restraints weight = 42614.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.119269 restraints weight = 20639.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.120504 restraints weight = 10869.193| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14096 Z= 0.142 Angle : 0.695 12.876 19152 Z= 0.345 Chirality : 0.045 0.163 2176 Planarity : 0.004 0.032 2376 Dihedral : 4.226 19.141 1876 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.66 % Favored : 92.10 % Rotamer: Outliers : 3.02 % Allowed : 22.66 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1684 helix: 1.29 (0.16), residues: 1064 sheet: -4.52 (0.40), residues: 44 loop : -2.37 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 705 HIS 0.008 0.001 HIS B 687 PHE 0.037 0.002 PHE B 758 TYR 0.029 0.002 TYR A 673 ARG 0.004 0.000 ARG D 531 Details of bonding type rmsd hydrogen bonds : bond 0.04567 ( 800) hydrogen bonds : angle 4.68997 ( 2352) covalent geometry : bond 0.00317 (14096) covalent geometry : angle 0.69473 (19152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 286 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.7032 (m100) cc_final: 0.6707 (m100) REVERT: A 534 ARG cc_start: 0.8318 (mtp85) cc_final: 0.8043 (ttm-80) REVERT: A 541 ARG cc_start: 0.7859 (tpt90) cc_final: 0.7599 (tpt90) REVERT: A 629 ASN cc_start: 0.8619 (t0) cc_final: 0.8394 (t0) REVERT: A 673 TYR cc_start: 0.9110 (t80) cc_final: 0.8683 (t80) REVERT: A 729 CYS cc_start: 0.9226 (m) cc_final: 0.8814 (p) REVERT: A 748 LYS cc_start: 0.8976 (mmmm) cc_final: 0.8554 (pttm) REVERT: A 756 MET cc_start: 0.8870 (ptm) cc_final: 0.8371 (ptt) REVERT: A 759 LYS cc_start: 0.9086 (mmtt) cc_final: 0.8839 (mmtm) REVERT: B 415 LEU cc_start: 0.8301 (mt) cc_final: 0.8056 (mt) REVERT: B 541 ARG cc_start: 0.7653 (tpt90) cc_final: 0.7326 (tpt90) REVERT: B 729 CYS cc_start: 0.9173 (m) cc_final: 0.8732 (p) REVERT: B 832 LYS cc_start: 0.8816 (tmtt) cc_final: 0.8446 (tptp) REVERT: B 833 ILE cc_start: 0.5662 (OUTLIER) cc_final: 0.4477 (pt) REVERT: B 834 HIS cc_start: 0.9232 (OUTLIER) cc_final: 0.8655 (m170) REVERT: C 415 LEU cc_start: 0.8342 (tp) cc_final: 0.8116 (mt) REVERT: C 541 ARG cc_start: 0.7678 (tpt90) cc_final: 0.7343 (tpt90) REVERT: C 645 MET cc_start: 0.8461 (mtm) cc_final: 0.8200 (mtm) REVERT: C 729 CYS cc_start: 0.9151 (m) cc_final: 0.8714 (p) REVERT: C 756 MET cc_start: 0.9014 (ptt) cc_final: 0.8544 (ptp) REVERT: C 759 LYS cc_start: 0.9236 (mptt) cc_final: 0.8991 (mmtm) REVERT: D 415 LEU cc_start: 0.8329 (mt) cc_final: 0.8097 (mt) REVERT: D 541 ARG cc_start: 0.7806 (tpt90) cc_final: 0.7436 (tpt90) REVERT: D 586 LEU cc_start: 0.9003 (mt) cc_final: 0.8799 (mt) REVERT: D 645 MET cc_start: 0.8608 (mtm) cc_final: 0.8265 (mtm) REVERT: D 676 GLN cc_start: 0.9365 (mt0) cc_final: 0.9065 (mp10) REVERT: D 702 GLN cc_start: 0.9394 (mm110) cc_final: 0.9190 (mm-40) REVERT: D 705 TRP cc_start: 0.8601 (t-100) cc_final: 0.8197 (t-100) REVERT: D 729 CYS cc_start: 0.9096 (m) cc_final: 0.8507 (p) REVERT: D 748 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8446 (pttm) REVERT: D 758 PHE cc_start: 0.8189 (m-80) cc_final: 0.7828 (m-80) REVERT: D 759 LYS cc_start: 0.9365 (mptt) cc_final: 0.9137 (mmtt) REVERT: D 831 HIS cc_start: 0.8731 (OUTLIER) cc_final: 0.8406 (m-70) outliers start: 44 outliers final: 28 residues processed: 310 average time/residue: 0.2410 time to fit residues: 110.0029 Evaluate side-chains 292 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 261 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain B residue 834 HIS Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain C residue 834 HIS Chi-restraints excluded: chain D residue 492 HIS Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 831 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.0060 chunk 4 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 167 optimal weight: 0.4980 chunk 114 optimal weight: 0.5980 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 GLN A 688 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS B 676 GLN B 762 HIS ** C 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 HIS C 831 HIS C 834 HIS ** D 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.155914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.114456 restraints weight = 42155.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.118323 restraints weight = 17999.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.120487 restraints weight = 10712.644| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14096 Z= 0.146 Angle : 0.724 15.384 19152 Z= 0.357 Chirality : 0.045 0.191 2176 Planarity : 0.004 0.032 2376 Dihedral : 4.183 20.534 1876 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.48 % Favored : 92.28 % Rotamer: Outliers : 2.61 % Allowed : 23.28 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1684 helix: 1.26 (0.16), residues: 1064 sheet: -4.05 (0.49), residues: 44 loop : -2.32 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 705 HIS 0.007 0.001 HIS A 674 PHE 0.030 0.002 PHE C 758 TYR 0.026 0.002 TYR B 700 ARG 0.004 0.000 ARG D 531 Details of bonding type rmsd hydrogen bonds : bond 0.04549 ( 800) hydrogen bonds : angle 4.64364 ( 2352) covalent geometry : bond 0.00325 (14096) covalent geometry : angle 0.72373 (19152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 270 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.6949 (m100) cc_final: 0.6659 (m100) REVERT: A 534 ARG cc_start: 0.8523 (mtp85) cc_final: 0.8136 (ttm-80) REVERT: A 629 ASN cc_start: 0.8702 (t0) cc_final: 0.8450 (t0) REVERT: A 677 MET cc_start: 0.8462 (mtm) cc_final: 0.8053 (mtm) REVERT: A 729 CYS cc_start: 0.9172 (m) cc_final: 0.8810 (p) REVERT: A 748 LYS cc_start: 0.8947 (mmmm) cc_final: 0.8538 (pttm) REVERT: A 756 MET cc_start: 0.8942 (ptm) cc_final: 0.8545 (ptt) REVERT: A 758 PHE cc_start: 0.7091 (m-80) cc_final: 0.6889 (m-80) REVERT: A 759 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8681 (mmtm) REVERT: B 415 LEU cc_start: 0.8368 (mt) cc_final: 0.8113 (mt) REVERT: B 541 ARG cc_start: 0.7609 (tpt90) cc_final: 0.7297 (tpt90) REVERT: B 729 CYS cc_start: 0.9129 (m) cc_final: 0.8715 (p) REVERT: B 756 MET cc_start: 0.8991 (ptt) cc_final: 0.8510 (ptt) REVERT: B 831 HIS cc_start: 0.8334 (OUTLIER) cc_final: 0.7903 (m-70) REVERT: B 832 LYS cc_start: 0.8966 (tmtt) cc_final: 0.8521 (tptp) REVERT: B 834 HIS cc_start: 0.9136 (m-70) cc_final: 0.8522 (m-70) REVERT: C 415 LEU cc_start: 0.8405 (tp) cc_final: 0.8155 (mt) REVERT: C 541 ARG cc_start: 0.7616 (tpt90) cc_final: 0.7291 (tpt90) REVERT: C 645 MET cc_start: 0.8642 (mtm) cc_final: 0.8257 (mtm) REVERT: C 729 CYS cc_start: 0.9131 (m) cc_final: 0.8716 (p) REVERT: C 759 LYS cc_start: 0.9115 (mptt) cc_final: 0.8823 (mmtm) REVERT: C 831 HIS cc_start: 0.8487 (OUTLIER) cc_final: 0.7990 (m90) REVERT: C 857 GLU cc_start: 0.8140 (mp0) cc_final: 0.7595 (pm20) REVERT: D 415 LEU cc_start: 0.8394 (mt) cc_final: 0.8128 (mt) REVERT: D 541 ARG cc_start: 0.7768 (tpt90) cc_final: 0.7420 (tpt90) REVERT: D 645 MET cc_start: 0.8701 (mtm) cc_final: 0.8340 (mtp) REVERT: D 676 GLN cc_start: 0.9374 (mt0) cc_final: 0.9059 (mp10) REVERT: D 702 GLN cc_start: 0.9352 (mm110) cc_final: 0.9120 (mm-40) REVERT: D 705 TRP cc_start: 0.8584 (t-100) cc_final: 0.8196 (t-100) REVERT: D 729 CYS cc_start: 0.9035 (m) cc_final: 0.8517 (p) REVERT: D 748 LYS cc_start: 0.8970 (mmmm) cc_final: 0.8498 (pttm) REVERT: D 758 PHE cc_start: 0.8076 (m-80) cc_final: 0.7780 (m-80) REVERT: D 759 LYS cc_start: 0.9244 (mptt) cc_final: 0.8920 (mmtm) REVERT: D 831 HIS cc_start: 0.8650 (OUTLIER) cc_final: 0.8323 (m-70) REVERT: D 832 LYS cc_start: 0.9132 (tmtt) cc_final: 0.8550 (tptp) REVERT: D 834 HIS cc_start: 0.8959 (OUTLIER) cc_final: 0.8134 (m90) outliers start: 38 outliers final: 26 residues processed: 293 average time/residue: 0.2545 time to fit residues: 109.4987 Evaluate side-chains 284 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 254 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain C residue 834 HIS Chi-restraints excluded: chain D residue 492 HIS Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 831 HIS Chi-restraints excluded: chain D residue 834 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 51 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 171 optimal weight: 20.0000 chunk 146 optimal weight: 0.9990 chunk 114 optimal weight: 0.0470 chunk 69 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS A 810 ASN B 688 GLN B 762 HIS B 810 ASN B 831 HIS B 834 HIS ** C 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 GLN C 762 HIS C 810 ASN C 831 HIS C 834 HIS ** D 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 810 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.156087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.114221 restraints weight = 42680.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.118106 restraints weight = 18043.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.120173 restraints weight = 10704.244| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14096 Z= 0.144 Angle : 0.752 15.956 19152 Z= 0.367 Chirality : 0.046 0.219 2176 Planarity : 0.004 0.030 2376 Dihedral : 4.186 22.675 1876 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.60 % Favored : 92.10 % Rotamer: Outliers : 2.40 % Allowed : 23.97 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1684 helix: 1.30 (0.16), residues: 1056 sheet: -3.98 (0.51), residues: 44 loop : -2.31 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 705 HIS 0.007 0.001 HIS C 703 PHE 0.027 0.002 PHE B 758 TYR 0.018 0.002 TYR C 700 ARG 0.004 0.000 ARG D 823 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 800) hydrogen bonds : angle 4.61757 ( 2352) covalent geometry : bond 0.00325 (14096) covalent geometry : angle 0.75207 (19152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 271 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.7014 (m100) cc_final: 0.6756 (m100) REVERT: A 534 ARG cc_start: 0.8488 (mtp85) cc_final: 0.8110 (ttm-80) REVERT: A 629 ASN cc_start: 0.8773 (t0) cc_final: 0.8525 (t0) REVERT: A 645 MET cc_start: 0.8645 (mtm) cc_final: 0.8255 (mtm) REVERT: A 729 CYS cc_start: 0.9174 (m) cc_final: 0.8810 (p) REVERT: A 748 LYS cc_start: 0.8951 (mmmm) cc_final: 0.8552 (pttm) REVERT: A 756 MET cc_start: 0.8902 (ptm) cc_final: 0.8444 (ptt) REVERT: A 758 PHE cc_start: 0.7122 (m-80) cc_final: 0.6872 (m-80) REVERT: A 759 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8657 (mmtm) REVERT: B 415 LEU cc_start: 0.8342 (mt) cc_final: 0.8088 (mt) REVERT: B 541 ARG cc_start: 0.7630 (tpt90) cc_final: 0.7305 (tpt90) REVERT: B 729 CYS cc_start: 0.9142 (m) cc_final: 0.8718 (p) REVERT: B 756 MET cc_start: 0.8947 (ptt) cc_final: 0.8449 (ptt) REVERT: B 759 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8440 (mmtm) REVERT: B 831 HIS cc_start: 0.8308 (OUTLIER) cc_final: 0.7946 (m90) REVERT: B 832 LYS cc_start: 0.8896 (tmtt) cc_final: 0.8394 (tptp) REVERT: B 834 HIS cc_start: 0.9198 (OUTLIER) cc_final: 0.8500 (m90) REVERT: C 410 TRP cc_start: 0.6808 (t-100) cc_final: 0.6541 (t-100) REVERT: C 541 ARG cc_start: 0.7649 (tpt90) cc_final: 0.7314 (tpt90) REVERT: C 729 CYS cc_start: 0.9151 (m) cc_final: 0.8730 (p) REVERT: C 756 MET cc_start: 0.8959 (ptt) cc_final: 0.8504 (ptp) REVERT: C 759 LYS cc_start: 0.9115 (mptt) cc_final: 0.8902 (mmtm) REVERT: C 834 HIS cc_start: 0.8938 (OUTLIER) cc_final: 0.8390 (t70) REVERT: C 857 GLU cc_start: 0.8116 (mp0) cc_final: 0.7616 (pm20) REVERT: D 415 LEU cc_start: 0.8373 (mt) cc_final: 0.8122 (mt) REVERT: D 541 ARG cc_start: 0.7795 (tpt90) cc_final: 0.7423 (tpt90) REVERT: D 645 MET cc_start: 0.8709 (mtm) cc_final: 0.8332 (mtp) REVERT: D 676 GLN cc_start: 0.9380 (mt0) cc_final: 0.9052 (mp10) REVERT: D 702 GLN cc_start: 0.9364 (mm110) cc_final: 0.9130 (mm-40) REVERT: D 705 TRP cc_start: 0.8588 (t-100) cc_final: 0.8188 (t-100) REVERT: D 729 CYS cc_start: 0.9064 (m) cc_final: 0.8586 (p) REVERT: D 735 SER cc_start: 0.7475 (OUTLIER) cc_final: 0.6637 (p) REVERT: D 748 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8435 (pttp) REVERT: D 758 PHE cc_start: 0.8112 (m-80) cc_final: 0.7855 (m-80) REVERT: D 831 HIS cc_start: 0.8525 (OUTLIER) cc_final: 0.8233 (m-70) REVERT: D 832 LYS cc_start: 0.9108 (tmtt) cc_final: 0.8689 (tptp) REVERT: D 834 HIS cc_start: 0.9005 (m-70) cc_final: 0.8276 (m-70) outliers start: 35 outliers final: 25 residues processed: 291 average time/residue: 0.2553 time to fit residues: 110.0571 Evaluate side-chains 283 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 492 HIS Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain B residue 834 HIS Chi-restraints excluded: chain C residue 492 HIS Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain C residue 834 HIS Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 831 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 35 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS A 834 HIS B 762 HIS B 831 HIS C 592 GLN ** C 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 HIS C 831 HIS C 834 HIS D 592 GLN ** D 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.154251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.112418 restraints weight = 42352.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.116226 restraints weight = 17980.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.118319 restraints weight = 10717.234| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14096 Z= 0.177 Angle : 0.768 15.244 19152 Z= 0.380 Chirality : 0.047 0.268 2176 Planarity : 0.004 0.041 2376 Dihedral : 4.223 23.441 1876 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.42 % Favored : 92.22 % Rotamer: Outliers : 2.34 % Allowed : 24.66 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.21), residues: 1684 helix: 1.28 (0.16), residues: 1052 sheet: -3.96 (0.47), residues: 68 loop : -2.23 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 705 HIS 0.010 0.001 HIS B 834 PHE 0.039 0.002 PHE C 758 TYR 0.025 0.002 TYR C 700 ARG 0.008 0.000 ARG B 835 Details of bonding type rmsd hydrogen bonds : bond 0.04535 ( 800) hydrogen bonds : angle 4.73835 ( 2352) covalent geometry : bond 0.00402 (14096) covalent geometry : angle 0.76820 (19152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.7061 (m100) cc_final: 0.6815 (m100) REVERT: A 534 ARG cc_start: 0.8537 (mtp85) cc_final: 0.8124 (ttm-80) REVERT: A 645 MET cc_start: 0.8763 (mtm) cc_final: 0.8365 (mtm) REVERT: A 651 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8223 (ppp) REVERT: A 729 CYS cc_start: 0.9177 (m) cc_final: 0.8817 (p) REVERT: A 748 LYS cc_start: 0.8937 (mmmm) cc_final: 0.8528 (pttp) REVERT: A 756 MET cc_start: 0.8901 (ptm) cc_final: 0.8431 (ptt) REVERT: A 759 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8751 (mmtm) REVERT: B 415 LEU cc_start: 0.8375 (mt) cc_final: 0.8123 (mt) REVERT: B 541 ARG cc_start: 0.7672 (tpt90) cc_final: 0.7338 (tpt90) REVERT: B 729 CYS cc_start: 0.9161 (m) cc_final: 0.8738 (p) REVERT: B 756 MET cc_start: 0.8958 (ptt) cc_final: 0.8455 (ptt) REVERT: B 759 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8688 (mmtm) REVERT: B 832 LYS cc_start: 0.8853 (tmtt) cc_final: 0.8469 (tptp) REVERT: B 834 HIS cc_start: 0.9157 (m-70) cc_final: 0.8503 (m-70) REVERT: C 410 TRP cc_start: 0.6910 (t-100) cc_final: 0.6651 (t-100) REVERT: C 415 LEU cc_start: 0.8346 (tp) cc_final: 0.8084 (mt) REVERT: C 541 ARG cc_start: 0.7679 (tpt90) cc_final: 0.7338 (tpt90) REVERT: C 729 CYS cc_start: 0.9178 (m) cc_final: 0.8783 (p) REVERT: C 756 MET cc_start: 0.8984 (ptt) cc_final: 0.8551 (ptp) REVERT: C 831 HIS cc_start: 0.8530 (OUTLIER) cc_final: 0.8017 (m90) REVERT: C 834 HIS cc_start: 0.8970 (OUTLIER) cc_final: 0.8415 (t70) REVERT: C 857 GLU cc_start: 0.8202 (mp0) cc_final: 0.7637 (pm20) REVERT: D 415 LEU cc_start: 0.8398 (mt) cc_final: 0.8141 (mt) REVERT: D 541 ARG cc_start: 0.7814 (tpt90) cc_final: 0.7434 (tpt90) REVERT: D 629 ASN cc_start: 0.8612 (t0) cc_final: 0.8356 (t0) REVERT: D 645 MET cc_start: 0.8764 (mtm) cc_final: 0.8426 (mtp) REVERT: D 676 GLN cc_start: 0.9389 (mt0) cc_final: 0.9051 (mp10) REVERT: D 677 MET cc_start: 0.8580 (tmm) cc_final: 0.8152 (tmm) REVERT: D 702 GLN cc_start: 0.9338 (mm110) cc_final: 0.9072 (mm-40) REVERT: D 705 TRP cc_start: 0.8660 (t-100) cc_final: 0.8235 (t-100) REVERT: D 729 CYS cc_start: 0.9075 (m) cc_final: 0.8636 (p) REVERT: D 731 HIS cc_start: 0.8805 (m-70) cc_final: 0.8385 (m-70) REVERT: D 748 LYS cc_start: 0.8880 (mmmm) cc_final: 0.8412 (pttp) REVERT: D 758 PHE cc_start: 0.8129 (m-80) cc_final: 0.7810 (m-80) REVERT: D 759 LYS cc_start: 0.9282 (mptt) cc_final: 0.8987 (mmtm) REVERT: D 831 HIS cc_start: 0.8455 (OUTLIER) cc_final: 0.8234 (m-70) REVERT: D 832 LYS cc_start: 0.9166 (tmtt) cc_final: 0.8677 (tptp) REVERT: D 834 HIS cc_start: 0.9039 (m90) cc_final: 0.8203 (m90) outliers start: 34 outliers final: 27 residues processed: 279 average time/residue: 0.2368 time to fit residues: 97.7289 Evaluate side-chains 279 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain B residue 492 HIS Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain C residue 834 HIS Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 831 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 85 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 83 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 HIS ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS B 831 HIS B 834 HIS ** C 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 HIS C 831 HIS C 834 HIS D 688 GLN ** D 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.155712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.113779 restraints weight = 42125.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.117829 restraints weight = 17407.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.119945 restraints weight = 10162.259| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14096 Z= 0.146 Angle : 0.771 14.856 19152 Z= 0.377 Chirality : 0.047 0.263 2176 Planarity : 0.004 0.043 2376 Dihedral : 4.247 25.066 1876 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.42 % Favored : 92.16 % Rotamer: Outliers : 2.34 % Allowed : 25.27 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1684 helix: 1.26 (0.16), residues: 1052 sheet: -3.74 (0.48), residues: 68 loop : -2.21 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 705 HIS 0.007 0.001 HIS A 674 PHE 0.032 0.002 PHE B 758 TYR 0.020 0.002 TYR C 700 ARG 0.008 0.000 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 800) hydrogen bonds : angle 4.64588 ( 2352) covalent geometry : bond 0.00331 (14096) covalent geometry : angle 0.77069 (19152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 253 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.7074 (m100) cc_final: 0.6819 (m100) REVERT: A 534 ARG cc_start: 0.8537 (mtp85) cc_final: 0.8127 (ttm-80) REVERT: A 645 MET cc_start: 0.8729 (mtm) cc_final: 0.8491 (mtp) REVERT: A 651 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8202 (ppp) REVERT: A 677 MET cc_start: 0.8536 (mtm) cc_final: 0.8182 (mtm) REVERT: A 729 CYS cc_start: 0.9122 (m) cc_final: 0.8793 (p) REVERT: A 748 LYS cc_start: 0.8921 (mmmm) cc_final: 0.8507 (pttp) REVERT: A 756 MET cc_start: 0.8915 (ptm) cc_final: 0.8453 (ptt) REVERT: A 759 LYS cc_start: 0.9003 (mmtt) cc_final: 0.8731 (mmtm) REVERT: B 415 LEU cc_start: 0.8369 (mt) cc_final: 0.8115 (mt) REVERT: B 541 ARG cc_start: 0.7684 (tpt90) cc_final: 0.7314 (tpt90) REVERT: B 729 CYS cc_start: 0.9150 (m) cc_final: 0.8784 (p) REVERT: B 735 SER cc_start: 0.7177 (OUTLIER) cc_final: 0.6048 (t) REVERT: B 756 MET cc_start: 0.8945 (ptt) cc_final: 0.8433 (ptt) REVERT: B 759 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8504 (mmtm) REVERT: B 831 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.7909 (m90) REVERT: B 832 LYS cc_start: 0.8887 (tmtt) cc_final: 0.8360 (tptp) REVERT: B 834 HIS cc_start: 0.9148 (m90) cc_final: 0.8433 (m-70) REVERT: C 415 LEU cc_start: 0.8328 (tp) cc_final: 0.8071 (mt) REVERT: C 541 ARG cc_start: 0.7686 (tpt90) cc_final: 0.7307 (tpt90) REVERT: C 729 CYS cc_start: 0.9146 (m) cc_final: 0.8755 (p) REVERT: C 735 SER cc_start: 0.7223 (OUTLIER) cc_final: 0.6121 (t) REVERT: C 756 MET cc_start: 0.8965 (ptt) cc_final: 0.8484 (ptp) REVERT: C 759 LYS cc_start: 0.9149 (mptt) cc_final: 0.8917 (mmtm) REVERT: C 834 HIS cc_start: 0.8941 (OUTLIER) cc_final: 0.8314 (t70) REVERT: C 857 GLU cc_start: 0.8189 (mp0) cc_final: 0.7639 (pm20) REVERT: D 410 TRP cc_start: 0.6977 (t-100) cc_final: 0.6715 (t-100) REVERT: D 415 LEU cc_start: 0.8396 (mt) cc_final: 0.8140 (mt) REVERT: D 541 ARG cc_start: 0.7804 (tpt90) cc_final: 0.7397 (tpt90) REVERT: D 629 ASN cc_start: 0.8602 (t0) cc_final: 0.8330 (t0) REVERT: D 645 MET cc_start: 0.8762 (mtm) cc_final: 0.8401 (mtp) REVERT: D 676 GLN cc_start: 0.9385 (mt0) cc_final: 0.9054 (mp10) REVERT: D 677 MET cc_start: 0.8525 (tmm) cc_final: 0.8088 (tmm) REVERT: D 702 GLN cc_start: 0.9326 (mm110) cc_final: 0.9062 (mm-40) REVERT: D 705 TRP cc_start: 0.8594 (t-100) cc_final: 0.8182 (t-100) REVERT: D 729 CYS cc_start: 0.9035 (m) cc_final: 0.8587 (p) REVERT: D 731 HIS cc_start: 0.8823 (m-70) cc_final: 0.8352 (m-70) REVERT: D 735 SER cc_start: 0.7526 (OUTLIER) cc_final: 0.6736 (p) REVERT: D 748 LYS cc_start: 0.8861 (mmmm) cc_final: 0.8432 (pttp) REVERT: D 758 PHE cc_start: 0.8150 (m-80) cc_final: 0.7824 (m-80) REVERT: D 759 LYS cc_start: 0.9273 (mptt) cc_final: 0.8986 (mmtm) REVERT: D 832 LYS cc_start: 0.9144 (tmtt) cc_final: 0.8635 (tptp) REVERT: D 834 HIS cc_start: 0.9031 (m90) cc_final: 0.8143 (m90) outliers start: 34 outliers final: 24 residues processed: 271 average time/residue: 0.2332 time to fit residues: 93.2104 Evaluate side-chains 275 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain B residue 492 HIS Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain C residue 834 HIS Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 830 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 96 optimal weight: 0.0070 chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 162 optimal weight: 10.0000 chunk 100 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 HIS A 676 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 831 HIS B 834 HIS ** C 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 HIS C 831 HIS C 834 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.160264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.113808 restraints weight = 43575.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.117736 restraints weight = 18699.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.119911 restraints weight = 11106.405| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14096 Z= 0.142 Angle : 0.767 14.795 19152 Z= 0.375 Chirality : 0.047 0.253 2176 Planarity : 0.004 0.040 2376 Dihedral : 4.255 26.564 1876 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.24 % Favored : 92.28 % Rotamer: Outliers : 2.06 % Allowed : 25.62 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1684 helix: 1.27 (0.16), residues: 1056 sheet: -3.55 (0.49), residues: 68 loop : -2.18 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 705 HIS 0.007 0.001 HIS A 703 PHE 0.035 0.002 PHE B 640 TYR 0.017 0.002 TYR C 700 ARG 0.007 0.000 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.04437 ( 800) hydrogen bonds : angle 4.60407 ( 2352) covalent geometry : bond 0.00321 (14096) covalent geometry : angle 0.76655 (19152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6607.91 seconds wall clock time: 121 minutes 49.27 seconds (7309.27 seconds total)