Starting phenix.real_space_refine on Fri May 16 01:59:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iob_35614/05_2025/8iob_35614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iob_35614/05_2025/8iob_35614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iob_35614/05_2025/8iob_35614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iob_35614/05_2025/8iob_35614.map" model { file = "/net/cci-nas-00/data/ceres_data/8iob_35614/05_2025/8iob_35614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iob_35614/05_2025/8iob_35614.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 9008 2.51 5 N 2324 2.21 5 O 2336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.62, per 1000 atoms: 0.70 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: 3.68 Conformation dependent library (CDL) restraints added in 1.9 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: 1.54 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: 3.84 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4255 1.34 - 1.46: 2719 1.46 - 1.58: 7017 1.58 - 1.70: 1 1.70 - 1.82: 104 Bond restraints: 14096 Sorted by residual: bond pdb=" CB PRO C 808 " pdb=" CG PRO C 808 " ideal model delta sigma weight residual 1.492 1.607 -0.115 5.00e-02 4.00e+02 5.33e+00 bond pdb=" CG GLN B 676 " pdb=" CD GLN B 676 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.15e+00 bond pdb=" CB LYS A 718 " pdb=" CG LYS A 718 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.13e+00 bond pdb=" CB LYS C 718 " pdb=" CG LYS C 718 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" CG GLN C 676 " pdb=" CD GLN C 676 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.11e+00 ... (remaining 14091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 18364 1.67 - 3.34: 618 3.34 - 5.01: 130 5.01 - 6.68: 26 6.68 - 8.35: 14 Bond angle restraints: 19152 Sorted by residual: angle pdb=" CA PRO C 808 " pdb=" N PRO C 808 " pdb=" CD PRO C 808 " ideal model delta sigma weight residual 112.00 105.27 6.73 1.40e+00 5.10e-01 2.31e+01 angle pdb=" N GLY C 806 " pdb=" CA GLY C 806 " pdb=" C GLY C 806 " ideal model delta sigma weight residual 110.29 115.37 -5.08 1.28e+00 6.10e-01 1.58e+01 angle pdb=" N PRO C 808 " pdb=" CD PRO C 808 " pdb=" CG PRO C 808 " ideal model delta sigma weight residual 103.20 97.92 5.28 1.50e+00 4.44e-01 1.24e+01 angle pdb=" N GLY D 806 " pdb=" CA GLY D 806 " pdb=" C GLY D 806 " ideal model delta sigma weight residual 110.29 114.78 -4.49 1.28e+00 6.10e-01 1.23e+01 angle pdb=" C VAL B 491 " pdb=" N HIS B 492 " pdb=" CA HIS B 492 " ideal model delta sigma weight residual 120.68 114.75 5.93 1.70e+00 3.46e-01 1.22e+01 ... (remaining 19147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 7313 16.06 - 32.13: 733 32.13 - 48.19: 137 48.19 - 64.26: 17 64.26 - 80.32: 8 Dihedral angle restraints: 8208 sinusoidal: 3192 harmonic: 5016 Sorted by residual: dihedral pdb=" CA LYS C 757 " pdb=" C LYS C 757 " pdb=" N PHE C 758 " pdb=" CA PHE C 758 " ideal model delta harmonic sigma weight residual 180.00 156.64 23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA LYS B 757 " pdb=" C LYS B 757 " pdb=" N PHE B 758 " pdb=" CA PHE B 758 " ideal model delta harmonic sigma weight residual 180.00 158.99 21.01 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA TYR C 780 " pdb=" C TYR C 780 " pdb=" N PHE C 781 " pdb=" CA PHE C 781 " ideal model delta harmonic sigma weight residual 180.00 160.99 19.01 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 8205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1380 0.034 - 0.069: 533 0.069 - 0.103: 176 0.103 - 0.138: 69 0.138 - 0.172: 18 Chirality restraints: 2176 Sorted by residual: chirality pdb=" CB ILE D 521 " pdb=" CA ILE D 521 " pdb=" CG1 ILE D 521 " pdb=" CG2 ILE D 521 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CB ILE B 521 " pdb=" CA ILE B 521 " pdb=" CG1 ILE B 521 " pdb=" CG2 ILE B 521 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CB ILE A 521 " pdb=" CA ILE A 521 " pdb=" CG1 ILE A 521 " pdb=" CG2 ILE A 521 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 2173 not shown) Planarity restraints: 2376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 652 " 0.022 2.00e-02 2.50e+03 1.49e-02 4.45e+00 pdb=" CG TYR B 652 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR B 652 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 652 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 652 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 652 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 652 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 652 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 720 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO A 721 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 721 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 721 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 720 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO B 721 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 721 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 721 " -0.025 5.00e-02 4.00e+02 ... (remaining 2373 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 238 2.68 - 3.23: 14387 3.23 - 3.79: 22425 3.79 - 4.34: 28236 4.34 - 4.90: 45123 Nonbonded interactions: 110409 Sorted by model distance: nonbonded pdb=" O ARG B 672 " pdb=" OG1 THR B 675 " model vdw 2.123 3.040 nonbonded pdb=" O ARG C 672 " pdb=" OG1 THR C 675 " model vdw 2.124 3.040 nonbonded pdb=" OG SER B 735 " pdb=" OD1 ASN B 802 " model vdw 2.127 3.040 nonbonded pdb=" OG SER C 735 " pdb=" OD1 ASN C 802 " model vdw 2.128 3.040 nonbonded pdb=" OG SER A 735 " pdb=" OD1 ASN A 802 " model vdw 2.129 3.040 ... (remaining 110404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 34.190 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 14096 Z= 0.155 Angle : 0.757 8.346 19152 Z= 0.428 Chirality : 0.045 0.172 2176 Planarity : 0.004 0.045 2376 Dihedral : 13.275 80.323 4976 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.77 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1684 helix: 1.38 (0.16), residues: 1048 sheet: -3.71 (0.48), residues: 68 loop : -2.52 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 410 HIS 0.006 0.001 HIS D 703 PHE 0.025 0.002 PHE B 656 TYR 0.035 0.002 TYR B 652 ARG 0.010 0.001 ARG C 679 Details of bonding type rmsd hydrogen bonds : bond 0.14031 ( 800) hydrogen bonds : angle 5.91064 ( 2352) covalent geometry : bond 0.00311 (14096) covalent geometry : angle 0.75711 (19152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 1.484 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: 0.2356 time to fit residues: 120.5126 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 : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.0980 chunk 130 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 HIS A 633 ASN A 714 ASN ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 HIS ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 762 HIS B 810 ASN B 831 HIS C 633 ASN ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 762 HIS C 810 ASN D 633 ASN ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 831 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.154207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.112061 restraints weight = 42157.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.115802 restraints weight = 18254.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.117824 restraints weight = 11017.791| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14096 Z= 0.172 Angle : 0.710 9.392 19152 Z= 0.365 Chirality : 0.046 0.183 2176 Planarity : 0.005 0.049 2376 Dihedral : 4.422 21.502 1876 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.78 % Favored : 91.98 % Rotamer: Outliers : 2.13 % Allowed : 12.71 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1684 helix: 1.44 (0.16), residues: 1076 sheet: -4.01 (0.45), residues: 68 loop : -2.64 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 705 HIS 0.010 0.001 HIS A 674 PHE 0.024 0.002 PHE D 758 TYR 0.018 0.002 TYR C 827 ARG 0.008 0.001 ARG A 531 Details of bonding type rmsd hydrogen bonds : bond 0.05134 ( 800) hydrogen bonds : angle 5.25883 ( 2352) covalent geometry : bond 0.00369 (14096) covalent geometry : angle 0.71028 (19152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 304 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 GLN cc_start: 0.9319 (mt0) cc_final: 0.9093 (mp10) REVERT: A 728 ILE cc_start: 0.9366 (tp) cc_final: 0.9107 (tp) REVERT: A 731 HIS cc_start: 0.8339 (m-70) cc_final: 0.7918 (m-70) REVERT: A 748 LYS cc_start: 0.9053 (mmmm) cc_final: 0.8596 (pttm) REVERT: B 541 ARG cc_start: 0.7831 (tpt90) cc_final: 0.7448 (tpt90) REVERT: B 678 LEU cc_start: 0.9380 (mt) cc_final: 0.9138 (mt) REVERT: B 705 TRP cc_start: 0.8672 (t-100) cc_final: 0.8453 (t-100) REVERT: B 728 ILE cc_start: 0.9344 (tp) cc_final: 0.9094 (tp) REVERT: B 731 HIS cc_start: 0.8366 (m-70) cc_final: 0.7953 (m-70) REVERT: B 841 VAL cc_start: 0.9112 (p) cc_final: 0.8817 (p) REVERT: B 844 MET cc_start: 0.7685 (tmm) cc_final: 0.6901 (tmm) REVERT: B 853 TRP cc_start: 0.7704 (m100) cc_final: 0.7499 (m100) REVERT: C 678 LEU cc_start: 0.9381 (mt) cc_final: 0.9138 (mt) REVERT: C 705 TRP cc_start: 0.8659 (t-100) cc_final: 0.8272 (t-100) REVERT: C 728 ILE cc_start: 0.9344 (tp) cc_final: 0.9047 (tp) REVERT: C 729 CYS cc_start: 0.9139 (m) cc_final: 0.8792 (p) REVERT: C 731 HIS cc_start: 0.8331 (m-70) cc_final: 0.7911 (m-70) REVERT: C 756 MET cc_start: 0.8970 (ptp) cc_final: 0.8713 (ptt) REVERT: C 831 HIS cc_start: 0.8692 (OUTLIER) cc_final: 0.8387 (m-70) REVERT: C 844 MET cc_start: 0.7734 (tmm) cc_final: 0.7046 (tmm) REVERT: D 541 ARG cc_start: 0.7823 (tpt90) cc_final: 0.7456 (tpt90) REVERT: D 728 ILE cc_start: 0.9362 (tp) cc_final: 0.9069 (tp) REVERT: D 729 CYS cc_start: 0.9107 (m) cc_final: 0.8619 (p) REVERT: D 731 HIS cc_start: 0.8355 (m-70) cc_final: 0.7931 (m-70) REVERT: D 756 MET cc_start: 0.8943 (ttp) cc_final: 0.8680 (ttp) REVERT: D 759 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8555 (mmtm) outliers start: 31 outliers final: 25 residues processed: 317 average time/residue: 0.2384 time to fit residues: 110.9919 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 : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 831 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 136 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 140 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 162 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 124 optimal weight: 30.0000 chunk 2 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.153264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.111416 restraints weight = 41910.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.115223 restraints weight = 17977.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.117228 restraints weight = 10707.245| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2105 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= 0.171 Angle : 0.681 10.639 19152 Z= 0.350 Chirality : 0.045 0.171 2176 Planarity : 0.004 0.033 2376 Dihedral : 4.345 19.376 1876 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.72 % Favored : 92.04 % Rotamer: Outliers : 2.68 % Allowed : 16.14 % Favored : 81.18 % 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: 1.40 (0.16), residues: 1048 sheet: -4.05 (0.47), residues: 68 loop : -2.59 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 705 HIS 0.009 0.001 HIS A 674 PHE 0.029 0.002 PHE C 758 TYR 0.016 0.002 TYR A 493 ARG 0.007 0.001 ARG D 531 Details of bonding type rmsd hydrogen bonds : bond 0.04950 ( 800) hydrogen bonds : angle 5.07692 ( 2352) covalent geometry : bond 0.00372 (14096) covalent geometry : angle 0.68145 (19152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 293 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.6674 (m100) cc_final: 0.6331 (m100) REVERT: A 534 ARG cc_start: 0.8351 (mtp85) cc_final: 0.7577 (ttm170) REVERT: A 541 ARG cc_start: 0.7807 (tpt90) cc_final: 0.7598 (tpt90) REVERT: A 673 TYR cc_start: 0.9352 (t80) cc_final: 0.9036 (t80) REVERT: A 676 GLN cc_start: 0.9373 (mt0) cc_final: 0.9056 (mp10) REVERT: A 698 GLU cc_start: 0.9096 (pp20) cc_final: 0.8767 (pp20) REVERT: A 728 ILE cc_start: 0.9388 (tp) cc_final: 0.9059 (tp) REVERT: A 729 CYS cc_start: 0.9183 (m) cc_final: 0.8784 (p) REVERT: A 731 HIS cc_start: 0.8343 (m-70) cc_final: 0.7930 (m-70) REVERT: A 748 LYS cc_start: 0.9024 (mmmm) cc_final: 0.8590 (pttm) REVERT: A 756 MET cc_start: 0.8774 (ttp) cc_final: 0.8428 (ttp) REVERT: A 759 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8575 (mmtm) REVERT: A 831 HIS cc_start: 0.8617 (OUTLIER) cc_final: 0.8009 (m-70) REVERT: B 415 LEU cc_start: 0.8386 (mt) cc_final: 0.8146 (mm) REVERT: B 559 LEU cc_start: 0.9364 (mm) cc_final: 0.9151 (tp) REVERT: B 676 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.7728 (mp10) REVERT: B 729 CYS cc_start: 0.9164 (m) cc_final: 0.8757 (p) REVERT: B 756 MET cc_start: 0.9163 (ptt) cc_final: 0.8825 (ptt) REVERT: B 759 LYS cc_start: 0.9096 (mptt) cc_final: 0.8884 (mmtt) REVERT: B 831 HIS cc_start: 0.8432 (OUTLIER) cc_final: 0.7901 (m90) REVERT: C 415 LEU cc_start: 0.8443 (tp) cc_final: 0.8205 (mt) REVERT: C 541 ARG cc_start: 0.7725 (tpt90) cc_final: 0.7363 (tpt90) REVERT: C 705 TRP cc_start: 0.8658 (t-100) cc_final: 0.8343 (t-100) REVERT: C 759 LYS cc_start: 0.9103 (mptt) cc_final: 0.8837 (mmtm) REVERT: D 415 LEU cc_start: 0.8397 (mt) cc_final: 0.8131 (mt) REVERT: D 541 ARG cc_start: 0.7749 (tpt90) cc_final: 0.7340 (tpt90) REVERT: D 676 GLN cc_start: 0.9215 (mt0) cc_final: 0.8914 (mt0) REVERT: D 702 GLN cc_start: 0.9324 (mm110) cc_final: 0.9052 (pp30) REVERT: D 705 TRP cc_start: 0.8757 (t-100) cc_final: 0.8051 (t-100) REVERT: D 729 CYS cc_start: 0.9075 (m) cc_final: 0.8610 (p) REVERT: D 748 LYS cc_start: 0.9146 (mmmm) cc_final: 0.8610 (pttm) REVERT: D 756 MET cc_start: 0.8908 (ttp) cc_final: 0.8698 (ttp) REVERT: D 758 PHE cc_start: 0.7950 (m-80) cc_final: 0.7503 (m-80) REVERT: D 759 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8544 (mmtm) REVERT: D 831 HIS cc_start: 0.8506 (OUTLIER) cc_final: 0.7942 (m-70) outliers start: 39 outliers final: 33 residues processed: 313 average time/residue: 0.2407 time to fit residues: 110.8753 Evaluate side-chains 307 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 270 time to evaluate : 1.595 ------------------------------------------------------------------------------- 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 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 646 LEU Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 676 GLN Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain D residue 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 103 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 34 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 158 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS A 831 HIS ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.154424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.112563 restraints weight = 42098.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.116409 restraints weight = 17774.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.118465 restraints weight = 10562.697| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14096 Z= 0.142 Angle : 0.677 14.531 19152 Z= 0.339 Chirality : 0.044 0.168 2176 Planarity : 0.004 0.051 2376 Dihedral : 4.296 19.438 1876 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.90 % Favored : 91.86 % Rotamer: Outliers : 2.82 % Allowed : 19.37 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1684 helix: 1.42 (0.16), residues: 1044 sheet: -4.45 (0.41), residues: 44 loop : -2.57 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 705 HIS 0.008 0.001 HIS A 674 PHE 0.022 0.002 PHE B 758 TYR 0.020 0.002 TYR B 700 ARG 0.006 0.000 ARG D 531 Details of bonding type rmsd hydrogen bonds : bond 0.04772 ( 800) hydrogen bonds : angle 4.89058 ( 2352) covalent geometry : bond 0.00306 (14096) covalent geometry : angle 0.67726 (19152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 292 time to evaluate : 1.529 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: symmetry clash REVERT: A 534 ARG cc_start: 0.8361 (mtp85) cc_final: 0.7600 (ttm170) REVERT: A 729 CYS cc_start: 0.9172 (m) cc_final: 0.8785 (p) REVERT: A 748 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8579 (pttm) REVERT: A 831 HIS cc_start: 0.8645 (OUTLIER) cc_final: 0.8109 (m90) REVERT: B 415 LEU cc_start: 0.8345 (mt) cc_final: 0.8101 (mt) REVERT: B 541 ARG cc_start: 0.7713 (tpt90) cc_final: 0.7354 (tpt90) REVERT: B 729 CYS cc_start: 0.9152 (m) cc_final: 0.8713 (p) REVERT: B 756 MET cc_start: 0.9122 (ptt) cc_final: 0.8731 (ptt) REVERT: B 831 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7801 (m-70) REVERT: C 415 LEU cc_start: 0.8386 (tp) cc_final: 0.8166 (mt) REVERT: C 645 MET cc_start: 0.8681 (mtm) cc_final: 0.8388 (mtm) REVERT: C 705 TRP cc_start: 0.8597 (t-100) cc_final: 0.8331 (t-100) REVERT: C 729 CYS cc_start: 0.9177 (m) cc_final: 0.8735 (p) REVERT: C 823 ARG cc_start: 0.8136 (mmt180) cc_final: 0.7932 (mmt-90) REVERT: C 831 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.8096 (m90) REVERT: D 415 LEU cc_start: 0.8398 (mt) cc_final: 0.8136 (mt) REVERT: D 541 ARG cc_start: 0.7739 (tpt90) cc_final: 0.7362 (tpt90) REVERT: D 645 MET cc_start: 0.8684 (mtm) cc_final: 0.8460 (mtm) REVERT: D 676 GLN cc_start: 0.9323 (mt0) cc_final: 0.9005 (mp10) REVERT: D 702 GLN cc_start: 0.9362 (mm110) cc_final: 0.9047 (pp30) REVERT: D 705 TRP cc_start: 0.8703 (t-100) cc_final: 0.8215 (t-100) REVERT: D 729 CYS cc_start: 0.9052 (m) cc_final: 0.8440 (p) REVERT: D 756 MET cc_start: 0.8903 (ttp) cc_final: 0.8646 (ttp) REVERT: D 758 PHE cc_start: 0.7961 (m-80) cc_final: 0.7676 (m-80) REVERT: D 759 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8645 (mmtm) REVERT: D 780 TYR cc_start: 0.7612 (m-80) cc_final: 0.7339 (m-10) REVERT: D 831 HIS cc_start: 0.8592 (OUTLIER) cc_final: 0.8296 (m-70) outliers start: 41 outliers final: 30 residues processed: 312 average time/residue: 0.2453 time to fit residues: 112.1937 Evaluate side-chains 313 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 279 time to evaluate : 1.714 ------------------------------------------------------------------------------- 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 736 LEU 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 676 GLN Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 651 MET Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 831 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 133 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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** A 762 HIS A 831 HIS ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS B 831 HIS B 834 HIS C 762 HIS C 831 HIS D 664 GLN ** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.160122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.115242 restraints weight = 42217.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.119205 restraints weight = 17429.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.121384 restraints weight = 10265.855| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14096 Z= 0.165 Angle : 0.686 10.820 19152 Z= 0.344 Chirality : 0.045 0.164 2176 Planarity : 0.004 0.036 2376 Dihedral : 4.285 19.081 1876 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.66 % Favored : 92.10 % Rotamer: Outliers : 3.57 % Allowed : 21.70 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1684 helix: 1.32 (0.16), residues: 1056 sheet: -4.60 (0.38), residues: 44 loop : -2.36 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 705 HIS 0.007 0.001 HIS A 674 PHE 0.025 0.002 PHE C 758 TYR 0.020 0.002 TYR A 700 ARG 0.005 0.000 ARG D 531 Details of bonding type rmsd hydrogen bonds : bond 0.04749 ( 800) hydrogen bonds : angle 4.88503 ( 2352) covalent geometry : bond 0.00364 (14096) covalent geometry : angle 0.68604 (19152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 289 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.6782 (m100) cc_final: 0.6463 (m100) REVERT: A 534 ARG cc_start: 0.8451 (mtp85) cc_final: 0.8047 (ttm-80) REVERT: A 559 LEU cc_start: 0.9386 (mm) cc_final: 0.9168 (tp) REVERT: A 645 MET cc_start: 0.8751 (mtm) cc_final: 0.8344 (mtm) REVERT: A 676 GLN cc_start: 0.9375 (mt0) cc_final: 0.9140 (mp10) REVERT: A 687 HIS cc_start: 0.8779 (OUTLIER) cc_final: 0.8501 (m170) REVERT: A 729 CYS cc_start: 0.9222 (m) cc_final: 0.8805 (p) REVERT: A 748 LYS cc_start: 0.8980 (mmmm) cc_final: 0.8581 (pttm) REVERT: A 756 MET cc_start: 0.8669 (ttp) cc_final: 0.8468 (ptm) REVERT: B 415 LEU cc_start: 0.8377 (mt) cc_final: 0.8127 (mt) REVERT: B 541 ARG cc_start: 0.7708 (tpt90) cc_final: 0.7361 (tpt90) REVERT: B 645 MET cc_start: 0.8756 (mtm) cc_final: 0.8512 (mtm) REVERT: B 729 CYS cc_start: 0.9220 (m) cc_final: 0.8771 (p) REVERT: B 756 MET cc_start: 0.9046 (ptt) cc_final: 0.8658 (ptt) REVERT: B 759 LYS cc_start: 0.9117 (mptt) cc_final: 0.8863 (mmtm) REVERT: C 415 LEU cc_start: 0.8405 (tp) cc_final: 0.8181 (mt) REVERT: C 541 ARG cc_start: 0.7711 (tpt90) cc_final: 0.7350 (tpt90) REVERT: C 559 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9175 (tp) REVERT: C 645 MET cc_start: 0.8747 (mtm) cc_final: 0.8456 (mtm) REVERT: C 687 HIS cc_start: 0.8805 (OUTLIER) cc_final: 0.8549 (m170) REVERT: C 705 TRP cc_start: 0.8617 (t-100) cc_final: 0.8358 (t-100) REVERT: C 729 CYS cc_start: 0.9212 (m) cc_final: 0.8756 (p) REVERT: C 759 LYS cc_start: 0.9215 (mptt) cc_final: 0.8962 (mmtm) REVERT: C 823 ARG cc_start: 0.8178 (mmt180) cc_final: 0.7957 (mmt-90) REVERT: D 415 LEU cc_start: 0.8429 (mt) cc_final: 0.8181 (mt) REVERT: D 541 ARG cc_start: 0.7770 (tpt90) cc_final: 0.7405 (tpt90) REVERT: D 559 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9202 (tp) REVERT: D 645 MET cc_start: 0.8713 (mtm) cc_final: 0.8414 (mtm) REVERT: D 676 GLN cc_start: 0.9378 (mt0) cc_final: 0.9051 (mp10) REVERT: D 705 TRP cc_start: 0.8709 (t-100) cc_final: 0.8218 (t-100) REVERT: D 758 PHE cc_start: 0.8042 (m-80) cc_final: 0.7707 (m-80) REVERT: D 759 LYS cc_start: 0.9186 (mmtt) cc_final: 0.8818 (mmtm) REVERT: D 831 HIS cc_start: 0.8779 (OUTLIER) cc_final: 0.8400 (m-70) outliers start: 52 outliers final: 38 residues processed: 316 average time/residue: 0.2306 time to fit residues: 106.4752 Evaluate side-chains 308 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 265 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 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 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 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 559 LEU Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 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 C residue 845 TYR 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 651 MET 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 59 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 43 optimal weight: 10.0000 chunk 38 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 HIS ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS A 831 HIS ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS C 762 HIS C 831 HIS ** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.154783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.112732 restraints weight = 42275.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.116607 restraints weight = 17898.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.118707 restraints weight = 10643.038| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14096 Z= 0.140 Angle : 0.697 12.935 19152 Z= 0.345 Chirality : 0.045 0.162 2176 Planarity : 0.004 0.031 2376 Dihedral : 4.280 21.246 1876 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.54 % Favored : 92.22 % Rotamer: Outliers : 3.43 % Allowed : 22.66 % Favored : 73.90 % 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: 1.28 (0.16), residues: 1068 sheet: -4.74 (0.37), residues: 44 loop : -2.47 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 705 HIS 0.015 0.001 HIS B 834 PHE 0.029 0.002 PHE B 758 TYR 0.032 0.002 TYR A 673 ARG 0.004 0.000 ARG D 823 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 800) hydrogen bonds : angle 4.71276 ( 2352) covalent geometry : bond 0.00302 (14096) covalent geometry : angle 0.69731 (19152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 281 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.6968 (m100) cc_final: 0.6662 (m100) REVERT: A 534 ARG cc_start: 0.8470 (mtp85) cc_final: 0.8085 (ttm-80) REVERT: A 541 ARG cc_start: 0.7819 (tpt90) cc_final: 0.7535 (tpt90) REVERT: A 645 MET cc_start: 0.8767 (mtm) cc_final: 0.8354 (mtm) REVERT: A 676 GLN cc_start: 0.9306 (mt0) cc_final: 0.9074 (mp10) REVERT: A 687 HIS cc_start: 0.8740 (OUTLIER) cc_final: 0.8489 (m170) REVERT: A 729 CYS cc_start: 0.9138 (m) cc_final: 0.8750 (p) REVERT: A 748 LYS cc_start: 0.8954 (mmmm) cc_final: 0.8563 (pttm) REVERT: A 758 PHE cc_start: 0.7456 (m-80) cc_final: 0.7180 (m-80) REVERT: A 759 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8822 (mmtm) REVERT: B 415 LEU cc_start: 0.8363 (mt) cc_final: 0.8108 (mt) REVERT: B 541 ARG cc_start: 0.7685 (tpt90) cc_final: 0.7347 (tpt90) REVERT: B 645 MET cc_start: 0.8805 (mtm) cc_final: 0.8539 (mtm) REVERT: B 729 CYS cc_start: 0.9173 (m) cc_final: 0.8762 (p) REVERT: C 415 LEU cc_start: 0.8387 (tp) cc_final: 0.8169 (mt) REVERT: C 677 MET cc_start: 0.8585 (tmm) cc_final: 0.8299 (tmm) REVERT: C 687 HIS cc_start: 0.8750 (OUTLIER) cc_final: 0.8490 (m170) REVERT: C 705 TRP cc_start: 0.8558 (t-100) cc_final: 0.8289 (t-100) REVERT: C 729 CYS cc_start: 0.9147 (m) cc_final: 0.8723 (p) REVERT: C 756 MET cc_start: 0.9023 (ptt) cc_final: 0.8621 (ptt) REVERT: C 759 LYS cc_start: 0.9171 (mptt) cc_final: 0.8933 (mmtm) REVERT: C 857 GLU cc_start: 0.8204 (mp0) cc_final: 0.7371 (pm20) REVERT: D 415 LEU cc_start: 0.8381 (mt) cc_final: 0.8140 (mt) REVERT: D 541 ARG cc_start: 0.7770 (tpt90) cc_final: 0.7408 (tpt90) REVERT: D 559 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9198 (tp) REVERT: D 645 MET cc_start: 0.8750 (mtm) cc_final: 0.8411 (mtm) REVERT: D 676 GLN cc_start: 0.9379 (mt0) cc_final: 0.9056 (mp10) REVERT: D 705 TRP cc_start: 0.8610 (t-100) cc_final: 0.8185 (t-100) REVERT: D 729 CYS cc_start: 0.9083 (m) cc_final: 0.8575 (p) REVERT: D 758 PHE cc_start: 0.7996 (m-80) cc_final: 0.7784 (m-80) REVERT: D 831 HIS cc_start: 0.8668 (OUTLIER) cc_final: 0.8328 (m-70) outliers start: 50 outliers final: 31 residues processed: 311 average time/residue: 0.2460 time to fit residues: 112.9420 Evaluate side-chains 301 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 266 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 830 LEU 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 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 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 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 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 735 SER Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 831 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.0770 chunk 4 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 167 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 HIS A 688 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS A 810 ASN ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 HIS B 762 HIS ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS C 762 HIS C 810 ASN ** D 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 810 ASN D 834 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.162566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.116507 restraints weight = 42160.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.120598 restraints weight = 17454.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.122876 restraints weight = 10321.988| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14096 Z= 0.143 Angle : 0.713 13.804 19152 Z= 0.351 Chirality : 0.045 0.160 2176 Planarity : 0.004 0.030 2376 Dihedral : 4.223 19.337 1876 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.24 % Favored : 92.52 % Rotamer: Outliers : 2.75 % Allowed : 23.70 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1684 helix: 1.27 (0.16), residues: 1064 sheet: -4.58 (0.39), residues: 44 loop : -2.33 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 705 HIS 0.011 0.001 HIS D 687 PHE 0.028 0.002 PHE C 758 TYR 0.032 0.002 TYR A 673 ARG 0.004 0.000 ARG D 531 Details of bonding type rmsd hydrogen bonds : bond 0.04611 ( 800) hydrogen bonds : angle 4.64716 ( 2352) covalent geometry : bond 0.00322 (14096) covalent geometry : angle 0.71339 (19152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 276 time to evaluate : 1.642 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: 0.7030 (m100) cc_final: 0.6662 (m100) REVERT: A 534 ARG cc_start: 0.8479 (mtp85) cc_final: 0.8102 (ttm-80) REVERT: A 541 ARG cc_start: 0.7922 (tpt90) cc_final: 0.7651 (tpt90) REVERT: A 645 MET cc_start: 0.8762 (mtm) cc_final: 0.8310 (mtm) REVERT: A 673 TYR cc_start: 0.9026 (t80) cc_final: 0.8804 (t80) REVERT: A 676 GLN cc_start: 0.9310 (mt0) cc_final: 0.9067 (mp10) REVERT: A 698 GLU cc_start: 0.9317 (tp30) cc_final: 0.9080 (tp30) REVERT: A 729 CYS cc_start: 0.9223 (m) cc_final: 0.8821 (p) REVERT: A 748 LYS cc_start: 0.8915 (mmmm) cc_final: 0.8519 (pttm) REVERT: A 759 LYS cc_start: 0.9131 (mmtt) cc_final: 0.8862 (mmtm) REVERT: B 415 LEU cc_start: 0.8337 (mt) cc_final: 0.8087 (mt) REVERT: B 541 ARG cc_start: 0.7676 (tpt90) cc_final: 0.7341 (tpt90) REVERT: B 729 CYS cc_start: 0.9217 (m) cc_final: 0.8768 (p) REVERT: B 756 MET cc_start: 0.8969 (ptt) cc_final: 0.8458 (ptt) REVERT: B 759 LYS cc_start: 0.9043 (mmtt) cc_final: 0.8802 (mmtm) REVERT: C 410 TRP cc_start: 0.6918 (t-100) cc_final: 0.6657 (t-100) REVERT: C 415 LEU cc_start: 0.8383 (tp) cc_final: 0.8143 (mt) REVERT: C 541 ARG cc_start: 0.7643 (tpt90) cc_final: 0.7304 (tpt90) REVERT: C 645 MET cc_start: 0.8247 (mtp) cc_final: 0.7937 (mtm) REVERT: C 676 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.7905 (mp10) REVERT: C 687 HIS cc_start: 0.8758 (OUTLIER) cc_final: 0.8496 (m170) REVERT: C 729 CYS cc_start: 0.9184 (m) cc_final: 0.8737 (p) REVERT: D 415 LEU cc_start: 0.8358 (mt) cc_final: 0.8114 (mt) REVERT: D 541 ARG cc_start: 0.7781 (tpt90) cc_final: 0.7427 (tpt90) REVERT: D 645 MET cc_start: 0.8723 (mtm) cc_final: 0.8374 (mtp) REVERT: D 676 GLN cc_start: 0.9391 (mt0) cc_final: 0.9053 (mp10) REVERT: D 705 TRP cc_start: 0.8609 (t-100) cc_final: 0.8173 (t-100) REVERT: D 729 CYS cc_start: 0.9186 (m) cc_final: 0.8725 (p) REVERT: D 758 PHE cc_start: 0.8172 (m-80) cc_final: 0.7914 (m-80) REVERT: D 759 LYS cc_start: 0.9317 (mptt) cc_final: 0.8997 (mmtm) REVERT: D 831 HIS cc_start: 0.8781 (OUTLIER) cc_final: 0.8439 (m-70) REVERT: D 832 LYS cc_start: 0.9129 (tmtt) cc_final: 0.8520 (tptp) REVERT: D 834 HIS cc_start: 0.9047 (OUTLIER) cc_final: 0.8260 (m90) outliers start: 40 outliers final: 27 residues processed: 300 average time/residue: 0.2491 time to fit residues: 109.7151 Evaluate side-chains 294 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 263 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 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 B residue 845 TYR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 51 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 171 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 HIS A 687 HIS ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS A 834 HIS ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS B 831 HIS B 834 HIS C 592 GLN ** C 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 HIS ** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.155402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.113942 restraints weight = 42180.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.117823 restraints weight = 17786.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.119925 restraints weight = 10573.681| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14096 Z= 0.143 Angle : 0.719 13.515 19152 Z= 0.354 Chirality : 0.045 0.171 2176 Planarity : 0.004 0.032 2376 Dihedral : 4.206 20.587 1876 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.36 % Favored : 92.34 % Rotamer: Outliers : 2.47 % Allowed : 24.38 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.21), residues: 1684 helix: 1.22 (0.16), residues: 1064 sheet: -4.32 (0.46), residues: 44 loop : -2.30 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 705 HIS 0.012 0.001 HIS B 834 PHE 0.037 0.002 PHE B 758 TYR 0.029 0.002 TYR C 700 ARG 0.004 0.000 ARG D 823 Details of bonding type rmsd hydrogen bonds : bond 0.04546 ( 800) hydrogen bonds : angle 4.61919 ( 2352) covalent geometry : bond 0.00321 (14096) covalent geometry : angle 0.71924 (19152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 275 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.7013 (m100) cc_final: 0.6651 (m100) REVERT: A 534 ARG cc_start: 0.8523 (mtp85) cc_final: 0.8124 (ttm-80) REVERT: A 541 ARG cc_start: 0.7854 (tpt90) cc_final: 0.7587 (tpt90) REVERT: A 645 MET cc_start: 0.8754 (mtm) cc_final: 0.8491 (mtp) REVERT: A 673 TYR cc_start: 0.8982 (t80) cc_final: 0.8699 (t80) REVERT: A 676 GLN cc_start: 0.9287 (mt0) cc_final: 0.9049 (mp10) REVERT: A 729 CYS cc_start: 0.9200 (m) cc_final: 0.8872 (p) REVERT: A 748 LYS cc_start: 0.8955 (mmmm) cc_final: 0.8554 (pttm) REVERT: A 756 MET cc_start: 0.8858 (ptm) cc_final: 0.8406 (ptt) REVERT: A 759 LYS cc_start: 0.9073 (mmtt) cc_final: 0.8776 (mmtm) REVERT: B 415 LEU cc_start: 0.8358 (mt) cc_final: 0.8105 (mt) REVERT: B 541 ARG cc_start: 0.7666 (tpt90) cc_final: 0.7332 (tpt90) REVERT: B 645 MET cc_start: 0.8329 (mtp) cc_final: 0.8051 (mtm) REVERT: B 729 CYS cc_start: 0.9170 (m) cc_final: 0.8774 (p) REVERT: B 756 MET cc_start: 0.9012 (ptt) cc_final: 0.8516 (ptt) REVERT: B 759 LYS cc_start: 0.8972 (mmtt) cc_final: 0.8696 (mmtm) REVERT: C 541 ARG cc_start: 0.7642 (tpt90) cc_final: 0.7301 (tpt90) REVERT: C 729 CYS cc_start: 0.9134 (m) cc_final: 0.8730 (p) REVERT: C 756 MET cc_start: 0.8969 (ptt) cc_final: 0.8608 (ptp) REVERT: C 857 GLU cc_start: 0.8139 (mp0) cc_final: 0.7553 (pm20) REVERT: D 415 LEU cc_start: 0.8366 (mt) cc_final: 0.8118 (mt) REVERT: D 541 ARG cc_start: 0.7797 (tpt90) cc_final: 0.7422 (tpt90) REVERT: D 645 MET cc_start: 0.8767 (mtm) cc_final: 0.8412 (mtp) REVERT: D 676 GLN cc_start: 0.9382 (mt0) cc_final: 0.9049 (mp10) REVERT: D 677 MET cc_start: 0.8569 (tmm) cc_final: 0.8152 (tmm) REVERT: D 705 TRP cc_start: 0.8612 (t-100) cc_final: 0.8192 (t-100) REVERT: D 729 CYS cc_start: 0.9192 (m) cc_final: 0.8773 (p) REVERT: D 748 LYS cc_start: 0.8964 (mmmm) cc_final: 0.8450 (pttm) REVERT: D 758 PHE cc_start: 0.8117 (m-80) cc_final: 0.7860 (m-80) REVERT: D 831 HIS cc_start: 0.8657 (OUTLIER) cc_final: 0.8303 (m-70) REVERT: D 832 LYS cc_start: 0.9060 (tmtt) cc_final: 0.8603 (tptp) REVERT: D 834 HIS cc_start: 0.8999 (m-70) cc_final: 0.8239 (m90) outliers start: 36 outliers final: 29 residues processed: 297 average time/residue: 0.2381 time to fit residues: 103.8132 Evaluate side-chains 283 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain 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 B residue 845 TYR Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain D residue 492 HIS Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 831 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 35 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS B 676 GLN B 688 GLN ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS B 810 ASN B 831 HIS B 834 HIS ** C 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 687 HIS C 762 HIS D 688 GLN ** D 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.154129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.116756 restraints weight = 42434.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.116793 restraints weight = 24576.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.117247 restraints weight = 13198.871| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14096 Z= 0.162 Angle : 0.762 15.413 19152 Z= 0.375 Chirality : 0.047 0.245 2176 Planarity : 0.004 0.040 2376 Dihedral : 4.239 23.875 1876 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.30 % Favored : 92.40 % Rotamer: Outliers : 2.40 % Allowed : 25.27 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1684 helix: 1.18 (0.16), residues: 1064 sheet: -4.11 (0.47), residues: 44 loop : -2.28 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 705 HIS 0.013 0.001 HIS B 831 PHE 0.037 0.002 PHE C 758 TYR 0.026 0.002 TYR A 673 ARG 0.004 0.000 ARG D 823 Details of bonding type rmsd hydrogen bonds : bond 0.04617 ( 800) hydrogen bonds : angle 4.66992 ( 2352) covalent geometry : bond 0.00367 (14096) covalent geometry : angle 0.76242 (19152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 261 time to evaluate : 1.480 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: 0.7055 (m100) cc_final: 0.6743 (m100) REVERT: A 534 ARG cc_start: 0.8542 (mtp85) cc_final: 0.8144 (ttm-80) REVERT: A 645 MET cc_start: 0.8767 (mtm) cc_final: 0.8538 (mtp) REVERT: A 676 GLN cc_start: 0.9309 (mt0) cc_final: 0.8276 (mp10) REVERT: A 729 CYS cc_start: 0.9166 (m) cc_final: 0.8839 (p) REVERT: A 748 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8509 (pttp) REVERT: A 756 MET cc_start: 0.8932 (ptm) cc_final: 0.8450 (ptt) REVERT: A 759 LYS cc_start: 0.9089 (mmtt) cc_final: 0.8815 (mmtm) REVERT: B 415 LEU cc_start: 0.8376 (mt) cc_final: 0.8119 (mt) REVERT: B 541 ARG cc_start: 0.7679 (tpt90) cc_final: 0.7340 (tpt90) REVERT: B 645 MET cc_start: 0.8296 (mtp) cc_final: 0.8013 (mtm) REVERT: B 729 CYS cc_start: 0.9155 (m) cc_final: 0.8765 (p) REVERT: B 756 MET cc_start: 0.9005 (ptt) cc_final: 0.8496 (ptt) REVERT: B 759 LYS cc_start: 0.9018 (mmtt) cc_final: 0.8730 (mmtm) REVERT: C 415 LEU cc_start: 0.8327 (tp) cc_final: 0.8067 (mt) REVERT: C 541 ARG cc_start: 0.7694 (tpt90) cc_final: 0.7341 (tpt90) REVERT: C 645 MET cc_start: 0.8658 (mtm) cc_final: 0.8360 (mtm) REVERT: C 729 CYS cc_start: 0.9119 (m) cc_final: 0.8763 (p) REVERT: C 857 GLU cc_start: 0.8261 (mp0) cc_final: 0.7667 (pm20) REVERT: D 410 TRP cc_start: 0.6919 (t-100) cc_final: 0.6658 (t-100) REVERT: D 415 LEU cc_start: 0.8350 (mt) cc_final: 0.8085 (mt) REVERT: D 541 ARG cc_start: 0.7806 (tpt90) cc_final: 0.7419 (tpt90) REVERT: D 676 GLN cc_start: 0.9395 (mt0) cc_final: 0.9071 (mp10) REVERT: D 705 TRP cc_start: 0.8638 (t-100) cc_final: 0.8201 (t-100) REVERT: D 729 CYS cc_start: 0.9229 (m) cc_final: 0.8816 (p) REVERT: D 748 LYS cc_start: 0.8942 (mmmm) cc_final: 0.8443 (pttm) REVERT: D 758 PHE cc_start: 0.8193 (m-80) cc_final: 0.7895 (m-80) REVERT: D 759 LYS cc_start: 0.9312 (mptt) cc_final: 0.9016 (mmtm) REVERT: D 831 HIS cc_start: 0.8493 (OUTLIER) cc_final: 0.8228 (m-70) REVERT: D 832 LYS cc_start: 0.9135 (tmtt) cc_final: 0.8615 (tptp) REVERT: D 834 HIS cc_start: 0.9061 (OUTLIER) cc_final: 0.8208 (m90) outliers start: 35 outliers final: 30 residues processed: 279 average time/residue: 0.2349 time to fit residues: 96.6516 Evaluate side-chains 285 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain 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 676 GLN 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 B residue 845 TYR Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 85 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 113 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 10 optimal weight: 0.0570 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS B 676 GLN ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS ** C 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 HIS ** D 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.155093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.112888 restraints weight = 42603.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.116878 restraints weight = 17376.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.119000 restraints weight = 10223.792| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14096 Z= 0.150 Angle : 0.804 17.409 19152 Z= 0.391 Chirality : 0.047 0.246 2176 Planarity : 0.004 0.079 2376 Dihedral : 4.270 25.605 1876 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.36 % Favored : 92.34 % Rotamer: Outliers : 2.13 % Allowed : 26.10 % 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: -0.13 (0.21), residues: 1684 helix: 1.22 (0.16), residues: 1056 sheet: -3.98 (0.49), residues: 44 loop : -2.29 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP A 705 HIS 0.018 0.001 HIS A 674 PHE 0.035 0.002 PHE A 758 TYR 0.022 0.002 TYR B 700 ARG 0.012 0.000 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.04693 ( 800) hydrogen bonds : angle 4.65901 ( 2352) covalent geometry : bond 0.00339 (14096) covalent geometry : angle 0.80368 (19152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 261 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.7106 (m100) cc_final: 0.6752 (m100) REVERT: A 534 ARG cc_start: 0.8531 (mtp85) cc_final: 0.8127 (ttm-80) REVERT: A 677 MET cc_start: 0.8620 (mtm) cc_final: 0.8253 (mtm) REVERT: A 729 CYS cc_start: 0.9154 (m) cc_final: 0.8846 (p) REVERT: A 748 LYS cc_start: 0.8901 (mmmm) cc_final: 0.8485 (pttp) REVERT: A 756 MET cc_start: 0.8948 (ptm) cc_final: 0.8528 (ptt) REVERT: A 759 LYS cc_start: 0.9089 (mmtt) cc_final: 0.8816 (mmtm) REVERT: B 415 LEU cc_start: 0.8376 (mt) cc_final: 0.8125 (mt) REVERT: B 541 ARG cc_start: 0.7681 (tpt90) cc_final: 0.7310 (tpt90) REVERT: B 645 MET cc_start: 0.8329 (mtp) cc_final: 0.8037 (mtm) REVERT: B 729 CYS cc_start: 0.9181 (m) cc_final: 0.8799 (p) REVERT: B 756 MET cc_start: 0.8971 (ptt) cc_final: 0.8474 (ptt) REVERT: B 759 LYS cc_start: 0.8990 (mmtt) cc_final: 0.8710 (mmtm) REVERT: C 410 TRP cc_start: 0.6990 (t-100) cc_final: 0.6715 (t-100) REVERT: C 415 LEU cc_start: 0.8331 (tp) cc_final: 0.8067 (mt) REVERT: C 541 ARG cc_start: 0.7699 (tpt90) cc_final: 0.7314 (tpt90) REVERT: C 645 MET cc_start: 0.8696 (mtm) cc_final: 0.8342 (mtm) REVERT: C 677 MET cc_start: 0.8610 (tmm) cc_final: 0.8251 (tmm) REVERT: C 729 CYS cc_start: 0.9140 (m) cc_final: 0.8752 (p) REVERT: C 857 GLU cc_start: 0.8057 (mp0) cc_final: 0.7499 (pm20) REVERT: D 410 TRP cc_start: 0.6927 (t-100) cc_final: 0.6660 (t-100) REVERT: D 415 LEU cc_start: 0.8368 (mt) cc_final: 0.8116 (mt) REVERT: D 541 ARG cc_start: 0.7808 (tpt90) cc_final: 0.7402 (tpt90) REVERT: D 676 GLN cc_start: 0.9384 (mt0) cc_final: 0.9052 (mp10) REVERT: D 677 MET cc_start: 0.8545 (tmm) cc_final: 0.8165 (tmm) REVERT: D 705 TRP cc_start: 0.8635 (t-100) cc_final: 0.8198 (t-100) REVERT: D 729 CYS cc_start: 0.9187 (m) cc_final: 0.8815 (p) REVERT: D 735 SER cc_start: 0.7538 (OUTLIER) cc_final: 0.6737 (p) REVERT: D 748 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8458 (pttm) REVERT: D 758 PHE cc_start: 0.8158 (m-80) cc_final: 0.7863 (m-80) REVERT: D 759 LYS cc_start: 0.9283 (mptt) cc_final: 0.9006 (mmtm) REVERT: D 831 HIS cc_start: 0.8410 (OUTLIER) cc_final: 0.8204 (m-70) REVERT: D 832 LYS cc_start: 0.9200 (tmtt) cc_final: 0.8785 (tptp) REVERT: D 834 HIS cc_start: 0.8985 (m-70) cc_final: 0.8195 (m-70) outliers start: 31 outliers final: 25 residues processed: 278 average time/residue: 0.2371 time to fit residues: 97.1123 Evaluate side-chains 274 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain 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 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 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 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 49 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 162 optimal weight: 0.0370 chunk 100 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN B 762 HIS B 831 HIS B 834 HIS ** C 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 HIS ** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.151678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.107353 restraints weight = 42626.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.111240 restraints weight = 17953.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.113239 restraints weight = 10702.716| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14096 Z= 0.147 Angle : 0.801 15.758 19152 Z= 0.389 Chirality : 0.048 0.249 2176 Planarity : 0.004 0.066 2376 Dihedral : 4.253 27.027 1876 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.24 % Favored : 92.46 % Rotamer: Outliers : 2.20 % Allowed : 26.65 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1684 helix: 1.19 (0.16), residues: 1064 sheet: -3.67 (0.54), residues: 44 loop : -2.25 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 705 HIS 0.016 0.001 HIS A 674 PHE 0.029 0.002 PHE B 758 TYR 0.019 0.002 TYR C 700 ARG 0.012 0.000 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.04604 ( 800) hydrogen bonds : angle 4.66809 ( 2352) covalent geometry : bond 0.00333 (14096) covalent geometry : angle 0.80059 (19152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5865.89 seconds wall clock time: 103 minutes 20.00 seconds (6200.00 seconds total)