Starting phenix.real_space_refine on Mon Dec 30 19:59:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iob_35614/12_2024/8iob_35614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iob_35614/12_2024/8iob_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_35614/12_2024/8iob_35614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iob_35614/12_2024/8iob_35614.map" model { file = "/net/cci-nas-00/data/ceres_data/8iob_35614/12_2024/8iob_35614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iob_35614/12_2024/8iob_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 9.27, per 1000 atoms: 0.67 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: 3.84 Conformation dependent library (CDL) restraints added in 1.8 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: 1.56 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: 4.59 Time building geometry restraints manager: 4.33 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: 0.00 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: 4.380 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: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 33.970 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.090 ------------------------------------------------------------------------------- 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= 0.202 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 *********************** 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 : 1.504 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: 0.2432 time to fit residues: 124.5593 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 : 1.866 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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= 0.238 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 *********************** 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 : 1.764 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: 0.9302 (mt0) cc_final: 0.9085 (mp10) REVERT: A 728 ILE cc_start: 0.9372 (tp) cc_final: 0.9125 (tp) REVERT: A 731 HIS cc_start: 0.8401 (m-70) cc_final: 0.7975 (m-70) REVERT: A 748 LYS cc_start: 0.9013 (mmmm) cc_final: 0.8575 (pttm) REVERT: B 541 ARG cc_start: 0.7824 (tpt90) cc_final: 0.7446 (tpt90) REVERT: B 678 LEU cc_start: 0.9378 (mt) cc_final: 0.9132 (mt) REVERT: B 705 TRP cc_start: 0.8665 (t-100) cc_final: 0.8459 (t-100) REVERT: B 728 ILE cc_start: 0.9361 (tp) cc_final: 0.9125 (tp) REVERT: B 731 HIS cc_start: 0.8448 (m-70) cc_final: 0.8022 (m-70) REVERT: B 841 VAL cc_start: 0.9108 (p) cc_final: 0.8817 (p) REVERT: B 844 MET cc_start: 0.7660 (tmm) cc_final: 0.6869 (tmm) REVERT: B 853 TRP cc_start: 0.7727 (m100) cc_final: 0.7524 (m100) REVERT: C 678 LEU cc_start: 0.9382 (mt) cc_final: 0.9137 (mt) REVERT: C 705 TRP cc_start: 0.8659 (t-100) cc_final: 0.8276 (t-100) REVERT: C 728 ILE cc_start: 0.9349 (tp) cc_final: 0.9067 (tp) REVERT: C 729 CYS cc_start: 0.9141 (m) cc_final: 0.8784 (p) REVERT: C 731 HIS cc_start: 0.8398 (m-70) cc_final: 0.7974 (m-70) REVERT: C 756 MET cc_start: 0.8989 (ptp) cc_final: 0.8737 (ptt) REVERT: C 831 HIS cc_start: 0.8733 (OUTLIER) cc_final: 0.8428 (m-70) REVERT: C 844 MET cc_start: 0.7723 (tmm) cc_final: 0.7020 (tmm) REVERT: D 541 ARG cc_start: 0.7813 (tpt90) cc_final: 0.7445 (tpt90) REVERT: D 728 ILE cc_start: 0.9345 (tp) cc_final: 0.9066 (tp) REVERT: D 729 CYS cc_start: 0.9089 (m) cc_final: 0.8604 (p) REVERT: D 731 HIS cc_start: 0.8401 (m-70) cc_final: 0.7977 (m-70) REVERT: D 756 MET cc_start: 0.8952 (ttp) cc_final: 0.8683 (ttp) REVERT: D 759 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8581 (mmtm) outliers start: 31 outliers final: 25 residues processed: 317 average time/residue: 0.2578 time to fit residues: 120.8651 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 : 1.598 ------------------------------------------------------------------------------- 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 86 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 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** ** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14096 Z= 0.333 Angle : 0.726 11.380 19152 Z= 0.377 Chirality : 0.046 0.182 2176 Planarity : 0.004 0.030 2376 Dihedral : 4.427 18.490 1876 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.90 % Favored : 91.86 % Rotamer: Outliers : 3.02 % Allowed : 16.07 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1684 helix: 1.21 (0.16), residues: 1052 sheet: -4.10 (0.47), residues: 68 loop : -2.54 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 705 HIS 0.010 0.002 HIS A 674 PHE 0.029 0.002 PHE C 758 TYR 0.023 0.002 TYR A 673 ARG 0.007 0.001 ARG D 531 *********************** 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 334 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 290 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.6632 (m100) cc_final: 0.6303 (m100) REVERT: A 534 ARG cc_start: 0.8436 (mtp85) cc_final: 0.8031 (ttm-80) REVERT: A 541 ARG cc_start: 0.7816 (tpt90) cc_final: 0.7612 (tpt90) REVERT: A 645 MET cc_start: 0.8733 (mtm) cc_final: 0.8349 (mtm) REVERT: A 673 TYR cc_start: 0.9369 (t80) cc_final: 0.9122 (t80) REVERT: A 676 GLN cc_start: 0.9395 (mt0) cc_final: 0.9076 (mp10) REVERT: A 698 GLU cc_start: 0.9104 (pp20) cc_final: 0.8867 (pp20) REVERT: A 728 ILE cc_start: 0.9429 (tp) cc_final: 0.9120 (tp) REVERT: A 729 CYS cc_start: 0.9210 (m) cc_final: 0.8768 (p) REVERT: A 731 HIS cc_start: 0.8463 (m-70) cc_final: 0.8045 (m-70) REVERT: A 748 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8566 (pttm) REVERT: A 756 MET cc_start: 0.8815 (ttp) cc_final: 0.8490 (ttp) REVERT: A 759 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8633 (mmtm) REVERT: A 831 HIS cc_start: 0.8757 (OUTLIER) cc_final: 0.8159 (m-70) REVERT: B 415 LEU cc_start: 0.8462 (mt) cc_final: 0.8202 (mm) REVERT: B 541 ARG cc_start: 0.7727 (tpt90) cc_final: 0.7377 (tpt90) REVERT: B 559 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9164 (tp) REVERT: B 673 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.8757 (t80) REVERT: B 729 CYS cc_start: 0.9214 (m) cc_final: 0.8744 (p) REVERT: B 756 MET cc_start: 0.9170 (ptt) cc_final: 0.8856 (ptt) REVERT: B 759 LYS cc_start: 0.9116 (mptt) cc_final: 0.8902 (mmtt) REVERT: B 831 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.8019 (m90) REVERT: C 415 LEU cc_start: 0.8462 (tp) cc_final: 0.8227 (mt) REVERT: C 541 ARG cc_start: 0.7749 (tpt90) cc_final: 0.7377 (tpt90) REVERT: C 559 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9155 (tp) REVERT: C 759 LYS cc_start: 0.9159 (mptt) cc_final: 0.8888 (mmtm) REVERT: D 415 LEU cc_start: 0.8453 (mt) cc_final: 0.8188 (mm) REVERT: D 541 ARG cc_start: 0.7804 (tpt90) cc_final: 0.7379 (tpt90) REVERT: D 559 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9183 (tp) REVERT: D 676 GLN cc_start: 0.9254 (mt0) cc_final: 0.8915 (mt0) REVERT: D 702 GLN cc_start: 0.9379 (mm110) cc_final: 0.9136 (pp30) REVERT: D 748 LYS cc_start: 0.9117 (mmmm) cc_final: 0.8588 (pttm) REVERT: D 758 PHE cc_start: 0.8024 (m-80) cc_final: 0.7680 (m-80) REVERT: D 759 LYS cc_start: 0.9051 (mmtt) cc_final: 0.8647 (mmtm) REVERT: D 831 HIS cc_start: 0.8696 (OUTLIER) cc_final: 0.8134 (m-70) outliers start: 44 outliers final: 32 residues processed: 315 average time/residue: 0.2446 time to fit residues: 113.4860 Evaluate side-chains 306 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 267 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 559 LEU 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 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 559 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 673 TYR 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 559 LEU 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 735 SER 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 559 LEU 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 154 optimal weight: 0.2980 chunk 117 optimal weight: 0.3980 chunk 81 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 157 optimal weight: 7.9990 chunk 166 optimal weight: 0.5980 chunk 82 optimal weight: 9.9990 chunk 148 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 762 HIS B 831 HIS C 762 HIS C 831 HIS ** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2446 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= 0.198 Angle : 0.687 16.253 19152 Z= 0.345 Chirality : 0.045 0.173 2176 Planarity : 0.004 0.054 2376 Dihedral : 4.349 19.075 1876 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.90 % Favored : 91.86 % Rotamer: Outliers : 2.82 % Allowed : 18.96 % Favored : 78.23 % 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: -0.15 (0.21), residues: 1684 helix: 1.33 (0.16), residues: 1052 sheet: -4.41 (0.42), residues: 44 loop : -2.51 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 705 HIS 0.008 0.001 HIS A 674 PHE 0.023 0.002 PHE B 758 TYR 0.022 0.002 TYR B 700 ARG 0.006 0.000 ARG D 531 *********************** 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 331 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 290 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 ARG cc_start: 0.8435 (mtp85) cc_final: 0.7675 (ttm170) REVERT: A 645 MET cc_start: 0.8738 (mtm) cc_final: 0.8335 (mtm) REVERT: A 729 CYS cc_start: 0.9167 (m) cc_final: 0.8755 (p) REVERT: A 748 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8571 (pttm) REVERT: A 759 LYS cc_start: 0.9020 (mmtt) cc_final: 0.8657 (mmtm) REVERT: A 831 HIS cc_start: 0.8678 (OUTLIER) cc_final: 0.8172 (m90) REVERT: B 415 LEU cc_start: 0.8429 (mt) cc_final: 0.8170 (mt) REVERT: B 541 ARG cc_start: 0.7716 (tpt90) cc_final: 0.7367 (tpt90) REVERT: B 729 CYS cc_start: 0.9130 (m) cc_final: 0.8702 (p) REVERT: B 756 MET cc_start: 0.9105 (ptt) cc_final: 0.8734 (ptt) REVERT: B 831 HIS cc_start: 0.8303 (OUTLIER) cc_final: 0.7767 (m-70) REVERT: C 415 LEU cc_start: 0.8455 (tp) cc_final: 0.8205 (mt) REVERT: C 541 ARG cc_start: 0.7707 (tpt90) cc_final: 0.7349 (tpt90) REVERT: C 645 MET cc_start: 0.8706 (mtm) cc_final: 0.8433 (mtm) REVERT: C 729 CYS cc_start: 0.9167 (m) cc_final: 0.8715 (p) REVERT: C 831 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.8044 (m90) REVERT: D 415 LEU cc_start: 0.8456 (mt) cc_final: 0.8190 (mm) REVERT: D 541 ARG cc_start: 0.7713 (tpt90) cc_final: 0.7324 (tpt90) REVERT: D 645 MET cc_start: 0.8684 (mtm) cc_final: 0.8433 (mtm) REVERT: D 676 GLN cc_start: 0.9345 (mt0) cc_final: 0.9002 (mp10) REVERT: D 698 GLU cc_start: 0.8994 (pp20) cc_final: 0.8608 (pp20) REVERT: D 702 GLN cc_start: 0.9366 (mm110) cc_final: 0.9068 (pp30) REVERT: D 705 TRP cc_start: 0.8747 (t-100) cc_final: 0.8269 (t-100) REVERT: D 729 CYS cc_start: 0.9086 (m) cc_final: 0.8598 (p) REVERT: D 748 LYS cc_start: 0.9089 (mmmm) cc_final: 0.8570 (pttm) REVERT: D 758 PHE cc_start: 0.7983 (m-80) cc_final: 0.7651 (m-80) REVERT: D 759 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8709 (mmtm) REVERT: D 823 ARG cc_start: 0.8126 (mmt180) cc_final: 0.7862 (mmt-90) REVERT: D 831 HIS cc_start: 0.8671 (OUTLIER) cc_final: 0.8317 (m-70) outliers start: 41 outliers final: 27 residues processed: 307 average time/residue: 0.2500 time to fit residues: 112.6191 Evaluate side-chains 302 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 271 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 LEU 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 830 LEU Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain B residue 845 TYR 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 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 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 138 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 831 HIS B 762 HIS B 831 HIS C 762 HIS C 831 HIS D 664 GLN ** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14096 Z= 0.215 Angle : 0.682 11.394 19152 Z= 0.341 Chirality : 0.045 0.167 2176 Planarity : 0.004 0.034 2376 Dihedral : 4.295 19.247 1876 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.60 % Favored : 92.16 % Rotamer: Outliers : 3.50 % Allowed : 21.57 % Favored : 74.93 % 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: -0.16 (0.21), residues: 1684 helix: 1.31 (0.16), residues: 1060 sheet: -4.48 (0.40), residues: 44 loop : -2.52 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 705 HIS 0.005 0.001 HIS D 674 PHE 0.025 0.002 PHE C 758 TYR 0.024 0.002 TYR A 673 ARG 0.005 0.000 ARG D 531 *********************** 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: 51 poor density : 288 time to evaluate : 1.770 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: 0.6758 (m100) cc_final: 0.6400 (m100) REVERT: A 534 ARG cc_start: 0.8502 (mtp85) cc_final: 0.8091 (ttm-80) REVERT: A 645 MET cc_start: 0.8757 (mtm) cc_final: 0.8350 (mtm) REVERT: A 676 GLN cc_start: 0.9352 (mt0) cc_final: 0.9131 (mp10) REVERT: A 687 HIS cc_start: 0.8730 (OUTLIER) cc_final: 0.8460 (m170) REVERT: A 729 CYS cc_start: 0.9159 (m) cc_final: 0.8786 (p) REVERT: A 748 LYS cc_start: 0.8985 (mmmm) cc_final: 0.8575 (pttm) REVERT: A 756 MET cc_start: 0.8698 (ttp) cc_final: 0.8467 (ptm) REVERT: A 759 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8824 (mmtm) REVERT: B 415 LEU cc_start: 0.8433 (mt) cc_final: 0.8171 (mt) REVERT: B 541 ARG cc_start: 0.7678 (tpt90) cc_final: 0.7341 (tpt90) REVERT: B 645 MET cc_start: 0.8806 (mtm) cc_final: 0.8562 (mtm) REVERT: B 729 CYS cc_start: 0.9174 (m) cc_final: 0.8728 (p) REVERT: B 759 LYS cc_start: 0.9023 (mptt) cc_final: 0.8682 (mmtm) REVERT: B 831 HIS cc_start: 0.8279 (OUTLIER) cc_final: 0.7787 (m90) REVERT: C 415 LEU cc_start: 0.8441 (tp) cc_final: 0.8207 (mt) REVERT: C 541 ARG cc_start: 0.7699 (tpt90) cc_final: 0.7344 (tpt90) REVERT: C 559 LEU cc_start: 0.9400 (mm) cc_final: 0.9154 (tp) REVERT: C 645 MET cc_start: 0.8754 (mtm) cc_final: 0.8451 (mtm) REVERT: C 687 HIS cc_start: 0.8728 (OUTLIER) cc_final: 0.8505 (m170) REVERT: C 729 CYS cc_start: 0.9157 (m) cc_final: 0.8702 (p) REVERT: C 759 LYS cc_start: 0.9149 (mptt) cc_final: 0.8845 (mmtm) REVERT: C 831 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.8076 (m90) REVERT: D 415 LEU cc_start: 0.8442 (mt) cc_final: 0.8185 (mt) REVERT: D 541 ARG cc_start: 0.7745 (tpt90) cc_final: 0.7386 (tpt90) REVERT: D 559 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9185 (tp) REVERT: D 645 MET cc_start: 0.8721 (mtm) cc_final: 0.8413 (mtm) REVERT: D 676 GLN cc_start: 0.9366 (mt0) cc_final: 0.9050 (mp10) REVERT: D 705 TRP cc_start: 0.8677 (t-100) cc_final: 0.8228 (t-100) REVERT: D 729 CYS cc_start: 0.9091 (m) cc_final: 0.8691 (p) REVERT: D 748 LYS cc_start: 0.9069 (mmmm) cc_final: 0.8589 (pttm) REVERT: D 780 TYR cc_start: 0.7679 (m-80) cc_final: 0.7458 (m-10) REVERT: D 823 ARG cc_start: 0.8159 (mmt180) cc_final: 0.7898 (mmt-90) REVERT: D 831 HIS cc_start: 0.8709 (OUTLIER) cc_final: 0.8480 (m-70) outliers start: 51 outliers final: 32 residues processed: 313 average time/residue: 0.2584 time to fit residues: 117.9988 Evaluate side-chains 302 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 263 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 LEU 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 687 HIS Chi-restraints excluded: chain A residue 735 SER 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 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 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 845 TYR 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 678 LEU Chi-restraints excluded: chain C residue 687 HIS 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 492 HIS Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain D residue 559 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 0.0980 chunk 149 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 138 optimal weight: 0.0470 chunk 77 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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 831 HIS B 762 HIS B 831 HIS B 834 HIS C 762 HIS C 831 HIS ** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 831 HIS D 834 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2840 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= 0.206 Angle : 0.699 12.683 19152 Z= 0.347 Chirality : 0.044 0.163 2176 Planarity : 0.004 0.030 2376 Dihedral : 4.260 18.932 1876 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.72 % Favored : 92.04 % Rotamer: Outliers : 3.64 % Allowed : 22.25 % 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: -0.19 (0.21), residues: 1684 helix: 1.24 (0.16), residues: 1068 sheet: -4.39 (0.42), residues: 44 loop : -2.49 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 705 HIS 0.008 0.001 HIS D 687 PHE 0.028 0.002 PHE B 758 TYR 0.028 0.002 TYR A 673 ARG 0.005 0.000 ARG D 665 *********************** 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 337 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 284 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.6823 (m100) cc_final: 0.6531 (m100) REVERT: A 534 ARG cc_start: 0.8556 (mtp85) cc_final: 0.8161 (ttm-80) REVERT: A 645 MET cc_start: 0.8752 (mtm) cc_final: 0.8480 (mtp) REVERT: A 676 GLN cc_start: 0.9283 (mt0) cc_final: 0.9058 (mp10) REVERT: A 687 HIS cc_start: 0.8699 (OUTLIER) cc_final: 0.8431 (m170) REVERT: A 729 CYS cc_start: 0.9138 (m) cc_final: 0.8729 (p) REVERT: A 748 LYS cc_start: 0.8928 (mmmm) cc_final: 0.8546 (pttm) REVERT: A 756 MET cc_start: 0.8838 (ttp) cc_final: 0.8523 (ptm) REVERT: A 759 LYS cc_start: 0.9084 (mmtt) cc_final: 0.8832 (mmtm) REVERT: B 415 LEU cc_start: 0.8424 (mt) cc_final: 0.8158 (mt) REVERT: B 541 ARG cc_start: 0.7661 (tpt90) cc_final: 0.7337 (tpt90) REVERT: B 645 MET cc_start: 0.8828 (mtm) cc_final: 0.8537 (mtm) REVERT: B 687 HIS cc_start: 0.8716 (OUTLIER) cc_final: 0.8461 (m170) REVERT: B 729 CYS cc_start: 0.9143 (m) cc_final: 0.8717 (p) REVERT: B 831 HIS cc_start: 0.8282 (OUTLIER) cc_final: 0.7801 (m-70) REVERT: C 415 LEU cc_start: 0.8437 (tp) cc_final: 0.8195 (mt) REVERT: C 541 ARG cc_start: 0.7634 (tpt90) cc_final: 0.7301 (tpt90) REVERT: C 559 LEU cc_start: 0.9380 (mm) cc_final: 0.9165 (tp) REVERT: C 687 HIS cc_start: 0.8717 (OUTLIER) cc_final: 0.8487 (m170) REVERT: C 729 CYS cc_start: 0.9147 (m) cc_final: 0.8698 (p) REVERT: C 756 MET cc_start: 0.9040 (ptt) cc_final: 0.8631 (ptt) REVERT: C 759 LYS cc_start: 0.9135 (mptt) cc_final: 0.8849 (mmtm) REVERT: C 831 HIS cc_start: 0.8584 (OUTLIER) cc_final: 0.7978 (m90) REVERT: C 857 GLU cc_start: 0.8266 (mp0) cc_final: 0.7419 (pm20) REVERT: D 415 LEU cc_start: 0.8425 (mt) cc_final: 0.8170 (mt) REVERT: D 541 ARG cc_start: 0.7754 (tpt90) cc_final: 0.7396 (tpt90) REVERT: D 559 LEU cc_start: 0.9404 (mm) cc_final: 0.9170 (tp) REVERT: D 676 GLN cc_start: 0.9372 (mt0) cc_final: 0.9052 (mp10) REVERT: D 705 TRP cc_start: 0.8605 (t-100) cc_final: 0.8180 (t-100) REVERT: D 729 CYS cc_start: 0.9089 (m) cc_final: 0.8685 (p) REVERT: D 758 PHE cc_start: 0.8024 (m-80) cc_final: 0.7640 (m-80) REVERT: D 759 LYS cc_start: 0.9284 (mptt) cc_final: 0.9032 (mmtm) REVERT: D 831 HIS cc_start: 0.8779 (OUTLIER) cc_final: 0.8280 (m90) REVERT: D 832 LYS cc_start: 0.9018 (tmtt) cc_final: 0.8359 (tptp) REVERT: D 834 HIS cc_start: 0.9024 (OUTLIER) cc_final: 0.8188 (m90) outliers start: 53 outliers final: 33 residues processed: 315 average time/residue: 0.2542 time to fit residues: 117.2126 Evaluate side-chains 303 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 263 time to evaluate : 1.787 ------------------------------------------------------------------------------- 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 556 THR Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 687 HIS 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 844 MET Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 556 THR 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 687 HIS 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 B residue 845 TYR 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 619 PHE Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 687 HIS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 140 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 103 optimal weight: 0.0370 chunk 101 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 102 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 overall best weight: 1.0060 ------------------------------------------------------------------------------- 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 834 HIS B 762 HIS B 831 HIS B 834 HIS C 592 GLN C 762 HIS C 831 HIS ** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 810 ASN ** D 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3012 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= 0.219 Angle : 0.730 16.189 19152 Z= 0.358 Chirality : 0.045 0.199 2176 Planarity : 0.004 0.038 2376 Dihedral : 4.282 19.615 1876 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.13 % Favored : 92.64 % Rotamer: Outliers : 3.02 % Allowed : 24.18 % Favored : 72.80 % 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: -0.15 (0.21), residues: 1684 helix: 1.25 (0.16), residues: 1064 sheet: -4.52 (0.43), residues: 44 loop : -2.39 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 705 HIS 0.013 0.001 HIS B 834 PHE 0.027 0.002 PHE C 758 TYR 0.031 0.002 TYR A 673 ARG 0.005 0.000 ARG A 541 *********************** 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 315 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 271 time to evaluate : 1.599 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: 0.7002 (m100) cc_final: 0.6692 (m100) REVERT: A 534 ARG cc_start: 0.8574 (mtp85) cc_final: 0.8171 (ttm-80) REVERT: A 673 TYR cc_start: 0.8978 (t80) cc_final: 0.8739 (t80) REVERT: A 676 GLN cc_start: 0.9282 (mt0) cc_final: 0.9040 (mp10) REVERT: A 687 HIS cc_start: 0.8665 (OUTLIER) cc_final: 0.8393 (m170) REVERT: A 698 GLU cc_start: 0.9267 (tp30) cc_final: 0.9039 (tp30) REVERT: A 729 CYS cc_start: 0.9135 (m) cc_final: 0.8739 (p) REVERT: A 748 LYS cc_start: 0.8905 (mmmm) cc_final: 0.8492 (pttm) REVERT: A 756 MET cc_start: 0.8833 (ttp) cc_final: 0.8561 (ptm) REVERT: A 758 PHE cc_start: 0.7476 (m-80) cc_final: 0.7207 (m-80) REVERT: A 759 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8806 (mmtm) REVERT: B 415 LEU cc_start: 0.8430 (mt) cc_final: 0.8162 (mt) REVERT: B 541 ARG cc_start: 0.7663 (tpt90) cc_final: 0.7342 (tpt90) REVERT: B 687 HIS cc_start: 0.8700 (OUTLIER) cc_final: 0.8436 (m170) REVERT: B 705 TRP cc_start: 0.8525 (t-100) cc_final: 0.8155 (t-100) REVERT: B 729 CYS cc_start: 0.9141 (m) cc_final: 0.8725 (p) REVERT: C 541 ARG cc_start: 0.7642 (tpt90) cc_final: 0.7306 (tpt90) REVERT: C 645 MET cc_start: 0.8280 (mtp) cc_final: 0.7982 (mtm) REVERT: C 687 HIS cc_start: 0.8696 (OUTLIER) cc_final: 0.8462 (m170) REVERT: C 729 CYS cc_start: 0.9145 (m) cc_final: 0.8717 (p) REVERT: D 415 LEU cc_start: 0.8424 (mt) cc_final: 0.8171 (mt) REVERT: D 541 ARG cc_start: 0.7767 (tpt90) cc_final: 0.7416 (tpt90) REVERT: D 559 LEU cc_start: 0.9404 (mm) cc_final: 0.9181 (tp) REVERT: D 645 MET cc_start: 0.8262 (mtp) cc_final: 0.7956 (mtm) REVERT: D 676 GLN cc_start: 0.9376 (mt0) cc_final: 0.9047 (mp10) REVERT: D 705 TRP cc_start: 0.8623 (t-100) cc_final: 0.8183 (t-100) REVERT: D 729 CYS cc_start: 0.9097 (m) cc_final: 0.8709 (p) REVERT: D 759 LYS cc_start: 0.9290 (mptt) cc_final: 0.9051 (mmtm) REVERT: D 832 LYS cc_start: 0.9135 (tmtt) cc_final: 0.8626 (tptp) REVERT: D 834 HIS cc_start: 0.9053 (m-70) cc_final: 0.8283 (m90) outliers start: 44 outliers final: 33 residues processed: 297 average time/residue: 0.2701 time to fit residues: 119.3511 Evaluate side-chains 294 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 258 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 687 HIS 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 619 PHE Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 687 HIS 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 B residue 845 TYR 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 676 GLN Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 687 HIS Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 777 THR 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 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 782 ILE Chi-restraints excluded: chain D residue 830 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 0.0050 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 HIS ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 ASN B 688 GLN ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS B 831 HIS B 834 HIS C 762 HIS C 810 ASN C 831 HIS D 688 GLN ** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 831 HIS D 834 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14096 Z= 0.202 Angle : 0.739 15.823 19152 Z= 0.359 Chirality : 0.045 0.221 2176 Planarity : 0.004 0.041 2376 Dihedral : 4.234 20.712 1876 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.42 % Favored : 92.34 % Rotamer: Outliers : 3.09 % Allowed : 24.38 % Favored : 72.53 % 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: 1.27 (0.16), residues: 1064 sheet: -4.26 (0.46), residues: 44 loop : -2.34 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 705 HIS 0.009 0.001 HIS B 834 PHE 0.033 0.002 PHE B 758 TYR 0.031 0.002 TYR A 673 ARG 0.005 0.000 ARG A 541 *********************** 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 316 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 271 time to evaluate : 1.386 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: 0.6996 (m100) cc_final: 0.6717 (m100) REVERT: A 534 ARG cc_start: 0.8566 (mtp85) cc_final: 0.8159 (ttm-80) REVERT: A 673 TYR cc_start: 0.8960 (t80) cc_final: 0.8653 (t80) REVERT: A 676 GLN cc_start: 0.9273 (mt0) cc_final: 0.9037 (mp10) REVERT: A 687 HIS cc_start: 0.8657 (OUTLIER) cc_final: 0.8413 (m170) REVERT: A 729 CYS cc_start: 0.9167 (m) cc_final: 0.8805 (p) REVERT: A 748 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8477 (pttp) REVERT: A 756 MET cc_start: 0.8836 (ttp) cc_final: 0.8602 (ptm) REVERT: A 758 PHE cc_start: 0.7542 (m-80) cc_final: 0.7248 (m-80) REVERT: A 759 LYS cc_start: 0.9090 (mmtt) cc_final: 0.8800 (mmtm) REVERT: B 415 LEU cc_start: 0.8437 (mt) cc_final: 0.8174 (mt) REVERT: B 541 ARG cc_start: 0.7643 (tpt90) cc_final: 0.7319 (tpt90) REVERT: B 645 MET cc_start: 0.8345 (mtp) cc_final: 0.8009 (mtm) REVERT: B 677 MET cc_start: 0.8556 (tmm) cc_final: 0.8240 (tmm) REVERT: B 705 TRP cc_start: 0.8592 (t-100) cc_final: 0.8235 (t-100) REVERT: B 729 CYS cc_start: 0.9131 (m) cc_final: 0.8734 (p) REVERT: B 759 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8555 (mmtm) REVERT: B 831 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7943 (m90) REVERT: C 410 TRP cc_start: 0.7012 (t-100) cc_final: 0.6735 (t-100) REVERT: C 415 LEU cc_start: 0.8325 (mt) cc_final: 0.8037 (mt) REVERT: C 541 ARG cc_start: 0.7677 (tpt90) cc_final: 0.7337 (tpt90) REVERT: C 645 MET cc_start: 0.8278 (mtp) cc_final: 0.7980 (mtm) REVERT: C 677 MET cc_start: 0.8648 (tmm) cc_final: 0.8306 (tmm) REVERT: C 687 HIS cc_start: 0.8654 (OUTLIER) cc_final: 0.8415 (m170) REVERT: C 729 CYS cc_start: 0.9147 (m) cc_final: 0.8720 (p) REVERT: C 756 MET cc_start: 0.9003 (ptt) cc_final: 0.8625 (ptp) REVERT: C 759 LYS cc_start: 0.9172 (mptt) cc_final: 0.8883 (mmtm) REVERT: C 831 HIS cc_start: 0.8563 (OUTLIER) cc_final: 0.8053 (m90) REVERT: C 857 GLU cc_start: 0.8232 (mp0) cc_final: 0.7663 (pm20) REVERT: D 410 TRP cc_start: 0.7086 (t-100) cc_final: 0.6811 (t-100) REVERT: D 415 LEU cc_start: 0.8436 (mt) cc_final: 0.8181 (mt) REVERT: D 541 ARG cc_start: 0.7766 (tpt90) cc_final: 0.7387 (tpt90) REVERT: D 676 GLN cc_start: 0.9377 (mt0) cc_final: 0.9062 (mp10) REVERT: D 705 TRP cc_start: 0.8604 (t-100) cc_final: 0.8176 (t-100) REVERT: D 729 CYS cc_start: 0.9105 (m) cc_final: 0.8722 (p) REVERT: D 748 LYS cc_start: 0.8980 (mmmm) cc_final: 0.8459 (pttm) REVERT: D 758 PHE cc_start: 0.8011 (m-80) cc_final: 0.7809 (m-80) REVERT: D 759 LYS cc_start: 0.9275 (mptt) cc_final: 0.9047 (mmtm) REVERT: D 832 LYS cc_start: 0.9028 (tmtt) cc_final: 0.8499 (tptp) REVERT: D 834 HIS cc_start: 0.9032 (OUTLIER) cc_final: 0.8103 (m90) outliers start: 45 outliers final: 31 residues processed: 299 average time/residue: 0.2502 time to fit residues: 110.2963 Evaluate side-chains 292 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 256 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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 687 HIS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 782 ILE 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 B residue 834 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 676 GLN Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 687 HIS 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 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 782 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 92 optimal weight: 0.2980 chunk 67 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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** B 687 HIS ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS B 810 ASN B 831 HIS B 834 HIS C 762 HIS ** D 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 831 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14096 Z= 0.230 Angle : 0.778 15.374 19152 Z= 0.378 Chirality : 0.046 0.249 2176 Planarity : 0.004 0.054 2376 Dihedral : 4.257 21.512 1876 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.19 % Favored : 92.52 % Rotamer: Outliers : 2.68 % Allowed : 25.41 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1684 helix: 1.25 (0.16), residues: 1064 sheet: -3.99 (0.47), residues: 44 loop : -2.31 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 705 HIS 0.010 0.001 HIS D 834 PHE 0.037 0.002 PHE C 758 TYR 0.028 0.002 TYR A 673 ARG 0.008 0.000 ARG A 541 *********************** 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 301 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 262 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.7023 (m100) cc_final: 0.6764 (m100) REVERT: A 459 VAL cc_start: 0.8335 (t) cc_final: 0.8069 (t) REVERT: A 497 TRP cc_start: 0.7689 (m-90) cc_final: 0.7104 (m-10) REVERT: A 534 ARG cc_start: 0.8636 (mtp85) cc_final: 0.8117 (ttm-80) REVERT: A 676 GLN cc_start: 0.9270 (mt0) cc_final: 0.8275 (mp10) REVERT: A 729 CYS cc_start: 0.9159 (m) cc_final: 0.8803 (p) REVERT: A 748 LYS cc_start: 0.8870 (mmmm) cc_final: 0.8453 (pttp) REVERT: A 759 LYS cc_start: 0.9131 (mmtt) cc_final: 0.8898 (mmtm) REVERT: B 410 TRP cc_start: 0.7087 (t-100) cc_final: 0.6815 (t-100) REVERT: B 415 LEU cc_start: 0.8442 (mt) cc_final: 0.8173 (mt) REVERT: B 541 ARG cc_start: 0.7671 (tpt90) cc_final: 0.7306 (tpt90) REVERT: B 645 MET cc_start: 0.8445 (mtp) cc_final: 0.8107 (mtm) REVERT: B 677 MET cc_start: 0.8581 (tmm) cc_final: 0.8264 (tmm) REVERT: B 705 TRP cc_start: 0.8637 (t-100) cc_final: 0.8282 (t-100) REVERT: B 729 CYS cc_start: 0.9158 (m) cc_final: 0.8746 (p) REVERT: B 759 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8700 (mmtm) REVERT: C 410 TRP cc_start: 0.7063 (t-100) cc_final: 0.6793 (t-100) REVERT: C 415 LEU cc_start: 0.8329 (mt) cc_final: 0.8043 (mt) REVERT: C 541 ARG cc_start: 0.7693 (tpt90) cc_final: 0.7338 (tpt90) REVERT: C 645 MET cc_start: 0.8342 (mtp) cc_final: 0.8000 (mtm) REVERT: C 687 HIS cc_start: 0.8670 (OUTLIER) cc_final: 0.8441 (m170) REVERT: C 729 CYS cc_start: 0.9160 (m) cc_final: 0.8733 (p) REVERT: C 756 MET cc_start: 0.9021 (ptt) cc_final: 0.8635 (ptp) REVERT: C 759 LYS cc_start: 0.9193 (mptt) cc_final: 0.8880 (mmtm) REVERT: C 831 HIS cc_start: 0.8655 (OUTLIER) cc_final: 0.7996 (m-70) REVERT: C 857 GLU cc_start: 0.8227 (mp0) cc_final: 0.7639 (pm20) REVERT: D 415 LEU cc_start: 0.8441 (mt) cc_final: 0.8181 (mt) REVERT: D 541 ARG cc_start: 0.7802 (tpt90) cc_final: 0.7392 (tpt90) REVERT: D 645 MET cc_start: 0.8727 (mtm) cc_final: 0.8395 (mtm) REVERT: D 676 GLN cc_start: 0.9394 (mt0) cc_final: 0.9058 (mp10) REVERT: D 677 MET cc_start: 0.8574 (tmm) cc_final: 0.8163 (tmm) REVERT: D 705 TRP cc_start: 0.8653 (t-100) cc_final: 0.8190 (t-100) REVERT: D 729 CYS cc_start: 0.9104 (m) cc_final: 0.8736 (p) REVERT: D 735 SER cc_start: 0.7502 (OUTLIER) cc_final: 0.6735 (p) REVERT: D 748 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8458 (pttm) REVERT: D 758 PHE cc_start: 0.8145 (m-80) cc_final: 0.7918 (m-80) REVERT: D 759 LYS cc_start: 0.9279 (mptt) cc_final: 0.8973 (mmtm) REVERT: D 832 LYS cc_start: 0.9145 (tmtt) cc_final: 0.8641 (tmtt) REVERT: D 834 HIS cc_start: 0.9063 (m-70) cc_final: 0.8278 (m-70) outliers start: 39 outliers final: 31 residues processed: 285 average time/residue: 0.2597 time to fit residues: 109.2729 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 : 1.618 ------------------------------------------------------------------------------- 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 782 ILE 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 834 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 676 GLN Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 687 HIS Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 777 THR 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 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 99 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 chunk 113 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 chunk 157 optimal weight: 0.2980 chunk 136 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 145 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS C 762 HIS C 831 HIS ** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14096 Z= 0.214 Angle : 0.786 17.010 19152 Z= 0.382 Chirality : 0.047 0.254 2176 Planarity : 0.004 0.056 2376 Dihedral : 4.273 23.760 1876 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.54 % Favored : 92.10 % Rotamer: Outliers : 2.34 % Allowed : 25.89 % Favored : 71.77 % 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: -0.08 (0.21), residues: 1684 helix: 1.29 (0.16), residues: 1056 sheet: -4.01 (0.50), residues: 44 loop : -2.33 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP A 705 HIS 0.020 0.001 HIS A 674 PHE 0.032 0.002 PHE B 758 TYR 0.021 0.002 TYR C 700 ARG 0.009 0.000 ARG A 541 ********************** 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 297 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 263 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.7022 (m100) cc_final: 0.6778 (m100) REVERT: A 497 TRP cc_start: 0.7674 (m-90) cc_final: 0.7105 (m-10) REVERT: A 534 ARG cc_start: 0.8608 (mtp85) cc_final: 0.8102 (ttm-80) REVERT: A 677 MET cc_start: 0.8628 (mtm) cc_final: 0.8277 (mtm) REVERT: A 729 CYS cc_start: 0.9162 (m) cc_final: 0.8856 (p) REVERT: A 748 LYS cc_start: 0.8843 (mmmm) cc_final: 0.8451 (pttp) REVERT: A 758 PHE cc_start: 0.7465 (m-80) cc_final: 0.7241 (m-80) REVERT: A 759 LYS cc_start: 0.9151 (mmtt) cc_final: 0.8881 (mmtm) REVERT: B 410 TRP cc_start: 0.7004 (t-100) cc_final: 0.6803 (t-100) REVERT: B 415 LEU cc_start: 0.8421 (mt) cc_final: 0.8157 (mt) REVERT: B 541 ARG cc_start: 0.7672 (tpt90) cc_final: 0.7312 (tpt90) REVERT: B 645 MET cc_start: 0.8386 (mtp) cc_final: 0.8091 (mtm) REVERT: B 677 MET cc_start: 0.8525 (tmm) cc_final: 0.8196 (tmm) REVERT: B 705 TRP cc_start: 0.8608 (t-100) cc_final: 0.8258 (t-100) REVERT: B 729 CYS cc_start: 0.9158 (m) cc_final: 0.8791 (p) REVERT: B 735 SER cc_start: 0.7149 (OUTLIER) cc_final: 0.6086 (t) REVERT: C 410 TRP cc_start: 0.6983 (t-100) cc_final: 0.6721 (t-100) REVERT: C 415 LEU cc_start: 0.8316 (mt) cc_final: 0.8035 (mt) REVERT: C 541 ARG cc_start: 0.7723 (tpt90) cc_final: 0.7347 (tpt90) REVERT: C 645 MET cc_start: 0.8310 (mtp) cc_final: 0.7997 (mtm) REVERT: C 687 HIS cc_start: 0.8679 (OUTLIER) cc_final: 0.8441 (m170) REVERT: C 705 TRP cc_start: 0.8592 (t-100) cc_final: 0.8229 (t-100) REVERT: C 729 CYS cc_start: 0.9169 (m) cc_final: 0.8751 (p) REVERT: C 735 SER cc_start: 0.7076 (OUTLIER) cc_final: 0.5996 (t) REVERT: C 756 MET cc_start: 0.9009 (ptt) cc_final: 0.8602 (ptp) REVERT: C 758 PHE cc_start: 0.7122 (m-80) cc_final: 0.6896 (m-80) REVERT: C 759 LYS cc_start: 0.9166 (mptt) cc_final: 0.8858 (mmtm) REVERT: C 831 HIS cc_start: 0.8674 (OUTLIER) cc_final: 0.8164 (m90) REVERT: C 857 GLU cc_start: 0.8226 (mp0) cc_final: 0.7652 (pm20) REVERT: D 410 TRP cc_start: 0.7066 (t-100) cc_final: 0.6816 (t-100) REVERT: D 415 LEU cc_start: 0.8427 (mt) cc_final: 0.8163 (mt) REVERT: D 541 ARG cc_start: 0.7788 (tpt90) cc_final: 0.7383 (tpt90) REVERT: D 645 MET cc_start: 0.8714 (mtm) cc_final: 0.8371 (mtm) REVERT: D 676 GLN cc_start: 0.9392 (mt0) cc_final: 0.9061 (mp10) REVERT: D 677 MET cc_start: 0.8549 (tmm) cc_final: 0.8125 (tmm) REVERT: D 705 TRP cc_start: 0.8608 (t-100) cc_final: 0.8176 (t-100) REVERT: D 729 CYS cc_start: 0.9098 (m) cc_final: 0.8719 (p) REVERT: D 735 SER cc_start: 0.7428 (OUTLIER) cc_final: 0.6672 (p) REVERT: D 748 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8471 (pttm) REVERT: D 758 PHE cc_start: 0.8141 (m-80) cc_final: 0.7940 (m-80) REVERT: D 832 LYS cc_start: 0.9113 (tmtt) cc_final: 0.8678 (tptp) REVERT: D 834 HIS cc_start: 0.9069 (m90) cc_final: 0.8171 (m90) outliers start: 34 outliers final: 26 residues processed: 282 average time/residue: 0.2618 time to fit residues: 108.1878 Evaluate side-chains 290 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 259 time to evaluate : 1.668 ------------------------------------------------------------------------------- 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 782 ILE 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 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 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 676 GLN Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 687 HIS 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 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 41 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 0.0670 chunk 136 optimal weight: 9.9990 chunk 57 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 7 optimal weight: 0.0000 overall best weight: 0.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS C 762 HIS C 831 HIS ** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.152178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.108232 restraints weight = 41867.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.112091 restraints weight = 17668.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.114203 restraints weight = 10529.966| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14096 Z= 0.204 Angle : 0.772 14.725 19152 Z= 0.377 Chirality : 0.047 0.288 2176 Planarity : 0.004 0.053 2376 Dihedral : 4.270 24.869 1876 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.19 % Favored : 92.46 % Rotamer: Outliers : 2.13 % Allowed : 26.17 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1684 helix: 1.37 (0.16), residues: 1052 sheet: -3.83 (0.53), residues: 44 loop : -2.35 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 705 HIS 0.027 0.001 HIS B 834 PHE 0.030 0.002 PHE B 758 TYR 0.019 0.002 TYR D 700 ARG 0.009 0.000 ARG A 541 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3326.71 seconds wall clock time: 61 minutes 49.27 seconds (3709.27 seconds total)