Starting phenix.real_space_refine on Mon Dec 30 19:39:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8io5_35608/12_2024/8io5_35608.cif Found real_map, /net/cci-nas-00/data/ceres_data/8io5_35608/12_2024/8io5_35608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8io5_35608/12_2024/8io5_35608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8io5_35608/12_2024/8io5_35608.map" model { file = "/net/cci-nas-00/data/ceres_data/8io5_35608/12_2024/8io5_35608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8io5_35608/12_2024/8io5_35608.cif" } resolution = 3.8 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= 0.012 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 42 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13736 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 9.15, per 1000 atoms: 0.67 Number of scatterers: 13736 At special positions: 0 Unit cell: (119.709, 119.709, 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: 3.40 Conformation dependent library (CDL) restraints added in 1.8 seconds 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3232 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 12 sheets defined 64.8% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 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: 3.571A pdb=" N ASP A 460 " --> pdb=" O ASP A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 494 removed outlier: 3.938A pdb=" N ILE A 489 " --> pdb=" O HIS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 505 removed outlier: 3.504A pdb=" N ILE A 500 " --> pdb=" O GLY A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 538 Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 545 through 576 removed outlier: 3.915A pdb=" N VAL A 549 " --> pdb=" O TYR A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 593 removed outlier: 3.649A pdb=" N ASN A 588 " --> pdb=" O GLY A 584 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 623 removed outlier: 4.624A pdb=" N ALA A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 687 removed outlier: 4.519A pdb=" N GLY A 669 " --> pdb=" O ARG A 665 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS A 687 " --> pdb=" O PHE A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 709 removed outlier: 3.923A pdb=" N TYR A 707 " --> pdb=" O HIS A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 720 removed outlier: 4.042A pdb=" N VAL A 716 " --> pdb=" O ASP A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 732 removed outlier: 3.559A pdb=" N GLN A 725 " --> pdb=" O PRO A 721 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 732 " --> pdb=" O ILE A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 745 removed outlier: 3.783A pdb=" N ARG A 744 " --> pdb=" O CYS A 740 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY A 745 " --> pdb=" O LYS A 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 745' Processing helix chain 'A' and resid 747 through 758 removed outlier: 3.643A pdb=" N PHE A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 843 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: 3.571A pdb=" N ASP B 460 " --> pdb=" O ASP B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 494 removed outlier: 3.938A pdb=" N ILE B 489 " --> pdb=" O HIS B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 505 removed outlier: 3.504A pdb=" N ILE B 500 " --> pdb=" O GLY B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 538 Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 545 through 576 removed outlier: 3.915A pdb=" N VAL B 549 " --> pdb=" O TYR B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 593 removed outlier: 3.584A pdb=" N ASN B 588 " --> pdb=" O GLY B 584 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 623 removed outlier: 4.563A pdb=" N ALA B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 687 removed outlier: 4.522A pdb=" N GLY B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 708 removed outlier: 3.978A pdb=" N TYR B 707 " --> pdb=" O HIS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 720 removed outlier: 4.021A pdb=" N VAL B 716 " --> pdb=" O ASP B 712 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 720 " --> pdb=" O VAL B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 732 removed outlier: 3.570A pdb=" N GLN B 725 " --> pdb=" O PRO B 721 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 745 removed outlier: 3.781A pdb=" N ARG B 744 " --> pdb=" O CYS B 740 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY B 745 " --> pdb=" O LYS B 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 740 through 745' Processing helix chain 'B' and resid 747 through 758 removed outlier: 3.667A pdb=" N PHE B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 843 Processing helix chain 'B' and resid 845 through 855 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: 3.571A pdb=" N ASP C 460 " --> pdb=" O ASP C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 494 removed outlier: 3.938A pdb=" N ILE C 489 " --> pdb=" O HIS C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 505 removed outlier: 3.504A pdb=" N ILE C 500 " --> pdb=" O GLY C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 538 Processing helix chain 'C' and resid 538 through 543 Processing helix chain 'C' and resid 545 through 576 removed outlier: 3.915A pdb=" N VAL C 549 " --> pdb=" O TYR C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 593 removed outlier: 3.582A pdb=" N ASN C 588 " --> pdb=" O GLY C 584 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 593 " --> pdb=" O LEU C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 623 removed outlier: 4.562A pdb=" N ALA C 614 " --> pdb=" O LYS C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 687 removed outlier: 4.525A pdb=" N GLY C 669 " --> pdb=" O ARG C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 708 removed outlier: 3.977A pdb=" N TYR C 707 " --> pdb=" O HIS C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 720 removed outlier: 4.029A pdb=" N VAL C 716 " --> pdb=" O ASP C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 732 removed outlier: 3.569A pdb=" N GLN C 725 " --> pdb=" O PRO C 721 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 732 " --> pdb=" O ILE C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 745 removed outlier: 3.782A pdb=" N ARG C 744 " --> pdb=" O CYS C 740 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY C 745 " --> pdb=" O LYS C 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 740 through 745' Processing helix chain 'C' and resid 747 through 758 removed outlier: 3.667A pdb=" N PHE C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 843 Processing helix chain 'C' and resid 845 through 855 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: 3.571A pdb=" N ASP D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 494 removed outlier: 3.942A pdb=" N ILE D 489 " --> pdb=" O HIS D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 505 removed outlier: 3.503A pdb=" N ILE D 500 " --> pdb=" O GLY D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 538 Processing helix chain 'D' and resid 538 through 543 Processing helix chain 'D' and resid 545 through 576 removed outlier: 3.915A pdb=" N VAL D 549 " --> pdb=" O TYR D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 593 removed outlier: 3.591A pdb=" N ASN D 588 " --> pdb=" O GLY D 584 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 593 " --> pdb=" O LEU D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 623 removed outlier: 4.670A pdb=" N ALA D 614 " --> pdb=" O LYS D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 687 removed outlier: 4.517A pdb=" N GLY D 669 " --> pdb=" O ARG D 665 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS D 687 " --> pdb=" O PHE D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 709 removed outlier: 3.923A pdb=" N TYR D 707 " --> pdb=" O HIS D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 720 removed outlier: 4.098A pdb=" N VAL D 716 " --> pdb=" O ASP D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 732 removed outlier: 3.589A pdb=" N GLN D 725 " --> pdb=" O PRO D 721 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU D 732 " --> pdb=" O ILE D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 745 removed outlier: 3.782A pdb=" N ARG D 744 " --> pdb=" O CYS D 740 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY D 745 " --> pdb=" O LYS D 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 740 through 745' Processing helix chain 'D' and resid 747 through 758 removed outlier: 3.659A pdb=" N PHE D 758 " --> pdb=" O LEU D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 836 through 843 Processing helix chain 'D' and resid 845 through 855 Processing sheet with id=AA1, first strand: chain 'A' and resid 759 through 761 Processing sheet with id=AA2, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AA3, first strand: chain 'A' and resid 805 through 806 removed outlier: 3.930A pdb=" N GLY A 806 " --> pdb=" O PHE A 860 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 759 through 761 Processing sheet with id=AA5, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AA6, first strand: chain 'B' and resid 805 through 806 removed outlier: 3.932A pdb=" N GLY B 806 " --> pdb=" O PHE B 860 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 759 through 761 Processing sheet with id=AA8, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AA9, first strand: chain 'C' and resid 805 through 806 removed outlier: 3.957A pdb=" N GLY C 806 " --> pdb=" O PHE C 860 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 759 through 761 Processing sheet with id=AB2, first strand: chain 'D' and resid 789 through 790 removed outlier: 3.534A pdb=" N ILE D 789 " --> pdb=" O VAL D 796 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 805 through 806 removed outlier: 3.903A pdb=" N GLY D 806 " --> pdb=" O PHE D 860 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 810 hydrogen bonds defined for protein. 2397 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.29 Time building geometry restraints manager: 3.92 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: 4243 1.34 - 1.46: 2605 1.46 - 1.58: 7144 1.58 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 14096 Sorted by residual: bond pdb=" CG GLU A 698 " pdb=" CD GLU A 698 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.36e+00 bond pdb=" C LEU B 666 " pdb=" O LEU B 666 " ideal model delta sigma weight residual 1.236 1.259 -0.023 1.28e-02 6.10e+03 3.15e+00 bond pdb=" C LEU C 666 " pdb=" O LEU C 666 " ideal model delta sigma weight residual 1.236 1.258 -0.022 1.28e-02 6.10e+03 3.02e+00 bond pdb=" C LEU D 666 " pdb=" O LEU D 666 " ideal model delta sigma weight residual 1.236 1.258 -0.022 1.28e-02 6.10e+03 3.01e+00 bond pdb=" C LEU A 666 " pdb=" O LEU A 666 " ideal model delta sigma weight residual 1.236 1.258 -0.022 1.28e-02 6.10e+03 2.91e+00 ... (remaining 14091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 18642 2.34 - 4.68: 422 4.68 - 7.01: 70 7.01 - 9.35: 14 9.35 - 11.69: 4 Bond angle restraints: 19152 Sorted by residual: angle pdb=" N GLU A 698 " pdb=" CA GLU A 698 " pdb=" CB GLU A 698 " ideal model delta sigma weight residual 110.28 116.44 -6.16 1.55e+00 4.16e-01 1.58e+01 angle pdb=" CB MET D 462 " pdb=" CG MET D 462 " pdb=" SD MET D 462 " ideal model delta sigma weight residual 112.70 124.39 -11.69 3.00e+00 1.11e-01 1.52e+01 angle pdb=" C ILE D 684 " pdb=" N ARG D 685 " pdb=" CA ARG D 685 " ideal model delta sigma weight residual 122.38 115.34 7.04 1.81e+00 3.05e-01 1.51e+01 angle pdb=" CB MET A 462 " pdb=" CG MET A 462 " pdb=" SD MET A 462 " ideal model delta sigma weight residual 112.70 124.37 -11.67 3.00e+00 1.11e-01 1.51e+01 angle pdb=" CB MET B 462 " pdb=" CG MET B 462 " pdb=" SD MET B 462 " ideal model delta sigma weight residual 112.70 124.36 -11.66 3.00e+00 1.11e-01 1.51e+01 ... (remaining 19147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 7345 16.90 - 33.80: 705 33.80 - 50.70: 128 50.70 - 67.60: 22 67.60 - 84.50: 8 Dihedral angle restraints: 8208 sinusoidal: 3192 harmonic: 5016 Sorted by residual: dihedral pdb=" CA THR C 826 " pdb=" C THR C 826 " pdb=" N TYR C 827 " pdb=" CA TYR C 827 " ideal model delta harmonic sigma weight residual -180.00 -161.35 -18.65 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA THR B 826 " pdb=" C THR B 826 " pdb=" N TYR B 827 " pdb=" CA TYR B 827 " ideal model delta harmonic sigma weight residual 180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA THR D 826 " pdb=" C THR D 826 " pdb=" N TYR D 827 " pdb=" CA TYR D 827 " ideal model delta harmonic sigma weight residual -180.00 -161.40 -18.60 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 8205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1417 0.040 - 0.079: 537 0.079 - 0.119: 158 0.119 - 0.159: 44 0.159 - 0.199: 20 Chirality restraints: 2176 Sorted by residual: chirality pdb=" CA GLU B 722 " pdb=" N GLU B 722 " pdb=" C GLU B 722 " pdb=" CB GLU B 722 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CA GLU D 722 " pdb=" N GLU D 722 " pdb=" C GLU D 722 " pdb=" CB GLU D 722 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.84e-01 chirality pdb=" CA GLU C 722 " pdb=" N GLU C 722 " pdb=" C GLU C 722 " pdb=" CB GLU C 722 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.81e-01 ... (remaining 2173 not shown) Planarity restraints: 2376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 694 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C ARG D 694 " -0.047 2.00e-02 2.50e+03 pdb=" O ARG D 694 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN D 695 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 694 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C ARG B 694 " -0.045 2.00e-02 2.50e+03 pdb=" O ARG B 694 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN B 695 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 694 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.55e+00 pdb=" C ARG C 694 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG C 694 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN C 695 " 0.015 2.00e-02 2.50e+03 ... (remaining 2373 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 337 2.69 - 3.24: 14993 3.24 - 3.79: 22088 3.79 - 4.35: 27835 4.35 - 4.90: 44092 Nonbonded interactions: 109345 Sorted by model distance: nonbonded pdb=" O ILE D 804 " pdb=" OG1 THR D 859 " model vdw 2.135 3.040 nonbonded pdb=" O ILE A 804 " pdb=" OG1 THR A 859 " model vdw 2.136 3.040 nonbonded pdb=" O ILE B 804 " pdb=" OG1 THR B 859 " model vdw 2.138 3.040 nonbonded pdb=" O ILE C 804 " pdb=" OG1 THR C 859 " model vdw 2.138 3.040 nonbonded pdb=" ND2 ASN A 629 " pdb=" O PRO B 632 " model vdw 2.139 3.120 ... (remaining 109340 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 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: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.820 Find NCS groups from input model: 0.460 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.005 0.052 14096 Z= 0.307 Angle : 0.875 11.691 19152 Z= 0.485 Chirality : 0.049 0.199 2176 Planarity : 0.005 0.057 2376 Dihedral : 13.878 84.499 4976 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.19 % Favored : 92.34 % 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: -1.31 (0.20), residues: 1684 helix: 0.27 (0.16), residues: 1048 sheet: -4.13 (0.37), residues: 44 loop : -2.70 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 705 HIS 0.008 0.002 HIS B 731 PHE 0.018 0.003 PHE D 848 TYR 0.026 0.002 TYR B 652 ARG 0.005 0.001 ARG A 835 *********************** 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 300 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.503 Fit side-chains REVERT: A 551 PHE cc_start: 0.8406 (t80) cc_final: 0.8142 (t80) REVERT: A 705 TRP cc_start: 0.8705 (t60) cc_final: 0.8221 (t60) REVERT: A 775 LEU cc_start: 0.8132 (mt) cc_final: 0.7896 (mt) REVERT: A 832 LYS cc_start: 0.7273 (tptp) cc_final: 0.6611 (tptt) REVERT: A 834 HIS cc_start: 0.7998 (m90) cc_final: 0.7029 (m90) REVERT: B 551 PHE cc_start: 0.8451 (t80) cc_final: 0.8183 (t80) REVERT: B 695 GLN cc_start: 0.8915 (mm110) cc_final: 0.8684 (mm110) REVERT: B 705 TRP cc_start: 0.8711 (t60) cc_final: 0.8260 (t60) REVERT: B 775 LEU cc_start: 0.8142 (mt) cc_final: 0.7902 (mt) REVERT: B 832 LYS cc_start: 0.7310 (tptp) cc_final: 0.6634 (tptt) REVERT: B 834 HIS cc_start: 0.8016 (m90) cc_final: 0.7068 (m90) REVERT: C 551 PHE cc_start: 0.8421 (t80) cc_final: 0.8162 (t80) REVERT: C 695 GLN cc_start: 0.8909 (mm110) cc_final: 0.8675 (mm110) REVERT: C 705 TRP cc_start: 0.8717 (t60) cc_final: 0.8267 (t60) REVERT: C 775 LEU cc_start: 0.8140 (mt) cc_final: 0.7901 (mt) REVERT: C 832 LYS cc_start: 0.7264 (tptp) cc_final: 0.6585 (tptt) REVERT: C 834 HIS cc_start: 0.7973 (m90) cc_final: 0.7006 (m90) REVERT: D 551 PHE cc_start: 0.8412 (t80) cc_final: 0.8150 (t80) REVERT: D 695 GLN cc_start: 0.8877 (mm110) cc_final: 0.8626 (mm110) REVERT: D 705 TRP cc_start: 0.8650 (t60) cc_final: 0.8221 (t60) REVERT: D 808 PRO cc_start: 0.6343 (Cg_exo) cc_final: 0.6004 (Cg_endo) REVERT: D 832 LYS cc_start: 0.7284 (tptp) cc_final: 0.6599 (tptt) REVERT: D 834 HIS cc_start: 0.7979 (m90) cc_final: 0.7013 (m90) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2475 time to fit residues: 109.2958 Evaluate side-chains 234 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 1.893 ------------------------------------------------------------------------------- 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: 3.9990 chunk 130 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 134 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 0.0000 chunk 100 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 GLN ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN D 702 GLN ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14096 Z= 0.259 Angle : 0.740 8.675 19152 Z= 0.381 Chirality : 0.046 0.181 2176 Planarity : 0.005 0.043 2376 Dihedral : 4.841 18.955 1876 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.83 % Favored : 92.70 % Rotamer: Outliers : 1.10 % Allowed : 12.16 % Favored : 86.74 % 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: -0.89 (0.21), residues: 1684 helix: 0.66 (0.16), residues: 1056 sheet: -3.44 (0.48), residues: 44 loop : -2.76 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 705 HIS 0.007 0.002 HIS B 731 PHE 0.017 0.002 PHE A 758 TYR 0.020 0.002 TYR C 652 ARG 0.004 0.000 ARG D 814 *********************** 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 298 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 282 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 TRP cc_start: 0.6404 (m100) cc_final: 0.6015 (m100) REVERT: A 551 PHE cc_start: 0.8390 (t80) cc_final: 0.8148 (t80) REVERT: A 592 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8020 (mp10) REVERT: A 691 ASN cc_start: 0.8516 (t0) cc_final: 0.8297 (t0) REVERT: A 711 ILE cc_start: 0.9056 (mt) cc_final: 0.8625 (mm) REVERT: A 713 MET cc_start: 0.8411 (mmt) cc_final: 0.7882 (mmt) REVERT: A 832 LYS cc_start: 0.7438 (tptp) cc_final: 0.6951 (tptt) REVERT: B 497 TRP cc_start: 0.6380 (m100) cc_final: 0.6010 (m100) REVERT: B 551 PHE cc_start: 0.8436 (t80) cc_final: 0.8194 (t80) REVERT: B 592 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8004 (mp10) REVERT: B 698 GLU cc_start: 0.8796 (mp0) cc_final: 0.8424 (mp0) REVERT: B 832 LYS cc_start: 0.7468 (tptp) cc_final: 0.6990 (tptt) REVERT: C 497 TRP cc_start: 0.6403 (m100) cc_final: 0.6028 (m100) REVERT: C 551 PHE cc_start: 0.8405 (t80) cc_final: 0.8174 (t80) REVERT: C 592 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8027 (mp10) REVERT: C 698 GLU cc_start: 0.8770 (mp0) cc_final: 0.8399 (mp0) REVERT: C 832 LYS cc_start: 0.7425 (tptp) cc_final: 0.6942 (tptt) REVERT: D 497 TRP cc_start: 0.6437 (m100) cc_final: 0.6047 (m100) REVERT: D 551 PHE cc_start: 0.8384 (t80) cc_final: 0.8160 (t80) REVERT: D 592 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8043 (mp10) REVERT: D 682 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7524 (tm-30) REVERT: D 832 LYS cc_start: 0.7457 (tptp) cc_final: 0.6948 (tptt) outliers start: 16 outliers final: 12 residues processed: 292 average time/residue: 0.2453 time to fit residues: 106.5920 Evaluate side-chains 248 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 232 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 771 HIS Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 771 HIS Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 592 GLN Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 714 ASN Chi-restraints excluded: chain D residue 771 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 129 optimal weight: 20.0000 chunk 106 optimal weight: 0.7980 chunk 43 optimal weight: 20.0000 chunk 156 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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 819 ASN ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 819 ASN ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 810 ASN D 819 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 14096 Z= 0.457 Angle : 0.878 13.237 19152 Z= 0.444 Chirality : 0.050 0.181 2176 Planarity : 0.005 0.047 2376 Dihedral : 5.085 21.469 1876 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.36 % Favored : 92.16 % Rotamer: Outliers : 2.82 % Allowed : 17.45 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.20), residues: 1684 helix: 0.26 (0.15), residues: 1060 sheet: -2.63 (0.64), residues: 44 loop : -2.93 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 705 HIS 0.007 0.002 HIS A 851 PHE 0.023 0.003 PHE D 557 TYR 0.028 0.002 TYR A 652 ARG 0.004 0.001 ARG A 679 *********************** 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 295 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 254 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 551 PHE cc_start: 0.8391 (t80) cc_final: 0.8182 (t80) REVERT: A 592 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8010 (mp10) REVERT: A 691 ASN cc_start: 0.8603 (t0) cc_final: 0.8322 (t0) REVERT: A 713 MET cc_start: 0.8243 (mmt) cc_final: 0.7501 (mmt) REVERT: A 725 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8865 (pt0) REVERT: A 832 LYS cc_start: 0.7522 (tptp) cc_final: 0.7147 (tptt) REVERT: A 833 ILE cc_start: 0.4500 (OUTLIER) cc_final: 0.4255 (mp) REVERT: B 551 PHE cc_start: 0.8440 (t80) cc_final: 0.8235 (t80) REVERT: B 592 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8002 (mp10) REVERT: B 699 GLU cc_start: 0.8753 (pt0) cc_final: 0.8354 (pt0) REVERT: B 705 TRP cc_start: 0.8943 (t60) cc_final: 0.8463 (t60) REVERT: B 713 MET cc_start: 0.8676 (mmt) cc_final: 0.8395 (mmt) REVERT: B 725 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8889 (pt0) REVERT: B 832 LYS cc_start: 0.7543 (tptp) cc_final: 0.7180 (tptt) REVERT: B 833 ILE cc_start: 0.4450 (OUTLIER) cc_final: 0.4205 (mp) REVERT: C 592 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8022 (mp10) REVERT: C 705 TRP cc_start: 0.8933 (t60) cc_final: 0.8461 (t60) REVERT: C 725 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8899 (pt0) REVERT: C 833 ILE cc_start: 0.4482 (OUTLIER) cc_final: 0.4164 (mp) REVERT: D 551 PHE cc_start: 0.8394 (t80) cc_final: 0.8190 (t80) REVERT: D 592 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8078 (mp10) REVERT: D 682 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7288 (tm-30) REVERT: D 725 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8864 (pt0) REVERT: D 833 ILE cc_start: 0.4501 (OUTLIER) cc_final: 0.4190 (mp) outliers start: 41 outliers final: 19 residues processed: 280 average time/residue: 0.2623 time to fit residues: 106.0564 Evaluate side-chains 255 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 725 GLN Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 725 GLN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 771 HIS Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 725 GLN Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 771 HIS Chi-restraints excluded: chain C residue 833 ILE Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 592 GLN Chi-restraints excluded: chain D residue 621 SER Chi-restraints excluded: chain D residue 714 ASN Chi-restraints excluded: chain D residue 725 GLN Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 771 HIS Chi-restraints excluded: chain D residue 833 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 81 optimal weight: 7.9990 chunk 17 optimal weight: 0.0030 chunk 74 optimal weight: 0.6980 chunk 105 optimal weight: 0.1980 chunk 157 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 148 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 810 ASN A 819 ASN ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 810 ASN B 819 ASN ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 ASN ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 819 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14096 Z= 0.193 Angle : 0.706 10.182 19152 Z= 0.360 Chirality : 0.045 0.184 2176 Planarity : 0.004 0.034 2376 Dihedral : 4.704 19.197 1876 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.83 % Favored : 92.70 % Rotamer: Outliers : 1.99 % Allowed : 20.47 % Favored : 77.54 % 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: -0.69 (0.21), residues: 1684 helix: 0.84 (0.16), residues: 1060 sheet: -2.65 (0.66), residues: 44 loop : -2.81 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 705 HIS 0.005 0.001 HIS B 731 PHE 0.021 0.002 PHE C 557 TYR 0.014 0.001 TYR A 420 ARG 0.008 0.001 ARG D 679 *********************** 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 271 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.5659 (pmm) cc_final: 0.5272 (pmm) REVERT: A 551 PHE cc_start: 0.8368 (t80) cc_final: 0.8109 (t80) REVERT: A 592 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: A 682 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7936 (tm-30) REVERT: A 711 ILE cc_start: 0.9116 (mt) cc_final: 0.8576 (mm) REVERT: A 713 MET cc_start: 0.8207 (mmt) cc_final: 0.7577 (mmt) REVERT: A 751 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8546 (mm) REVERT: A 832 LYS cc_start: 0.7476 (tptp) cc_final: 0.6929 (tptt) REVERT: A 834 HIS cc_start: 0.7854 (m90) cc_final: 0.7262 (m90) REVERT: B 462 MET cc_start: 0.5702 (pmm) cc_final: 0.5304 (pmm) REVERT: B 551 PHE cc_start: 0.8422 (t80) cc_final: 0.8156 (t80) REVERT: B 592 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7892 (mp10) REVERT: B 705 TRP cc_start: 0.8891 (t60) cc_final: 0.8477 (t60) REVERT: B 713 MET cc_start: 0.8605 (mmt) cc_final: 0.8296 (mmt) REVERT: B 751 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8558 (mm) REVERT: B 832 LYS cc_start: 0.7501 (tptp) cc_final: 0.6959 (tptt) REVERT: B 834 HIS cc_start: 0.7899 (m90) cc_final: 0.7310 (m90) REVERT: C 462 MET cc_start: 0.5685 (pmm) cc_final: 0.5283 (pmm) REVERT: C 592 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7888 (mp10) REVERT: C 705 TRP cc_start: 0.8895 (t60) cc_final: 0.8473 (t60) REVERT: C 751 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8551 (mm) REVERT: C 832 LYS cc_start: 0.7663 (tptt) cc_final: 0.7195 (tptt) REVERT: D 462 MET cc_start: 0.5657 (pmm) cc_final: 0.5271 (pmm) REVERT: D 551 PHE cc_start: 0.8374 (t80) cc_final: 0.8115 (t80) REVERT: D 592 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7963 (mp10) REVERT: D 682 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7373 (tm-30) REVERT: D 751 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8539 (mm) REVERT: D 832 LYS cc_start: 0.7673 (tptt) cc_final: 0.7267 (tptt) outliers start: 29 outliers final: 14 residues processed: 261 average time/residue: 0.2557 time to fit residues: 97.9184 Evaluate side-chains 240 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 771 HIS Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 771 HIS Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain D residue 592 GLN Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 771 HIS Chi-restraints excluded: chain D residue 831 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 GLN ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 725 GLN ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14096 Z= 0.201 Angle : 0.691 9.772 19152 Z= 0.352 Chirality : 0.045 0.178 2176 Planarity : 0.004 0.035 2376 Dihedral : 4.593 20.632 1876 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.01 % Favored : 92.46 % Rotamer: Outliers : 3.02 % Allowed : 21.02 % Favored : 75.96 % 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: -0.60 (0.21), residues: 1684 helix: 0.92 (0.16), residues: 1060 sheet: -2.77 (0.67), residues: 44 loop : -2.78 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 705 HIS 0.003 0.001 HIS A 731 PHE 0.022 0.002 PHE C 551 TYR 0.011 0.001 TYR A 700 ARG 0.003 0.000 ARG D 814 *********************** 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 279 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 235 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 PHE cc_start: 0.5344 (OUTLIER) cc_final: 0.5101 (t80) REVERT: A 551 PHE cc_start: 0.8335 (t80) cc_final: 0.8077 (t80) REVERT: A 592 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7896 (mp10) REVERT: A 682 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7925 (tm-30) REVERT: A 711 ILE cc_start: 0.9098 (mt) cc_final: 0.8584 (mm) REVERT: A 713 MET cc_start: 0.8179 (mmt) cc_final: 0.7588 (mmt) REVERT: A 751 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8547 (mm) REVERT: A 832 LYS cc_start: 0.7507 (tptp) cc_final: 0.7035 (tptt) REVERT: A 833 ILE cc_start: 0.4166 (OUTLIER) cc_final: 0.3857 (mp) REVERT: A 834 HIS cc_start: 0.7849 (m90) cc_final: 0.7388 (m90) REVERT: B 471 PHE cc_start: 0.5346 (OUTLIER) cc_final: 0.5095 (t80) REVERT: B 551 PHE cc_start: 0.8378 (t80) cc_final: 0.8118 (t80) REVERT: B 592 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7903 (mp10) REVERT: B 713 MET cc_start: 0.8496 (mmt) cc_final: 0.8181 (mmt) REVERT: B 725 GLN cc_start: 0.8777 (pt0) cc_final: 0.8348 (pm20) REVERT: B 751 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8555 (mm) REVERT: B 832 LYS cc_start: 0.7533 (tptp) cc_final: 0.7063 (tptt) REVERT: B 833 ILE cc_start: 0.4123 (OUTLIER) cc_final: 0.3817 (mp) REVERT: B 834 HIS cc_start: 0.7968 (m90) cc_final: 0.7521 (m90) REVERT: C 471 PHE cc_start: 0.5338 (OUTLIER) cc_final: 0.4869 (t80) REVERT: C 592 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7869 (mp10) REVERT: C 722 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8093 (mm-30) REVERT: C 725 GLN cc_start: 0.8768 (pt0) cc_final: 0.8302 (pm20) REVERT: C 751 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8547 (mm) REVERT: C 832 LYS cc_start: 0.7634 (tptt) cc_final: 0.7419 (tptt) REVERT: D 471 PHE cc_start: 0.5418 (OUTLIER) cc_final: 0.5008 (t80) REVERT: D 551 PHE cc_start: 0.8331 (t80) cc_final: 0.8082 (t80) REVERT: D 592 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7973 (mp10) REVERT: D 682 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7454 (tm-30) REVERT: D 695 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8456 (mm110) REVERT: D 751 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8536 (mm) REVERT: D 832 LYS cc_start: 0.7647 (tptt) cc_final: 0.7283 (tptt) REVERT: D 833 ILE cc_start: 0.4270 (OUTLIER) cc_final: 0.3942 (mp) outliers start: 44 outliers final: 20 residues processed: 268 average time/residue: 0.2412 time to fit residues: 95.7755 Evaluate side-chains 251 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 771 HIS Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 771 HIS Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 592 GLN Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 621 SER Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 771 HIS Chi-restraints excluded: chain D residue 831 HIS Chi-restraints excluded: chain D residue 833 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 ASN ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 819 ASN ** C 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 819 ASN ** D 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14096 Z= 0.264 Angle : 0.738 9.245 19152 Z= 0.377 Chirality : 0.048 0.289 2176 Planarity : 0.004 0.037 2376 Dihedral : 4.571 20.056 1876 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.19 % Favored : 92.28 % Rotamer: Outliers : 3.43 % Allowed : 20.12 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.21), residues: 1684 helix: 0.93 (0.16), residues: 1060 sheet: -2.79 (0.64), residues: 44 loop : -2.82 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 705 HIS 0.004 0.001 HIS D 731 PHE 0.022 0.002 PHE C 551 TYR 0.025 0.002 TYR A 700 ARG 0.003 0.000 ARG D 814 *********************** 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 274 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 224 time to evaluate : 1.536 Fit side-chains REVERT: A 471 PHE cc_start: 0.5552 (OUTLIER) cc_final: 0.5026 (t80) REVERT: A 551 PHE cc_start: 0.8344 (t80) cc_final: 0.8085 (t80) REVERT: A 592 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7944 (mp10) REVERT: A 664 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: A 700 TYR cc_start: 0.9074 (t80) cc_final: 0.8682 (t80) REVERT: A 711 ILE cc_start: 0.9101 (mt) cc_final: 0.8504 (mm) REVERT: A 713 MET cc_start: 0.8192 (mmt) cc_final: 0.7582 (mmt) REVERT: A 725 GLN cc_start: 0.8879 (pt0) cc_final: 0.8418 (pt0) REVERT: A 751 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8489 (mm) REVERT: A 832 LYS cc_start: 0.7541 (tptp) cc_final: 0.6888 (tptp) REVERT: A 833 ILE cc_start: 0.4086 (OUTLIER) cc_final: 0.3418 (mp) REVERT: A 834 HIS cc_start: 0.7902 (m90) cc_final: 0.7464 (m90) REVERT: B 471 PHE cc_start: 0.5615 (OUTLIER) cc_final: 0.5068 (t80) REVERT: B 551 PHE cc_start: 0.8386 (t80) cc_final: 0.8122 (t80) REVERT: B 592 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7950 (mp10) REVERT: B 713 MET cc_start: 0.8416 (mmt) cc_final: 0.8113 (mmt) REVERT: B 725 GLN cc_start: 0.8820 (pt0) cc_final: 0.8345 (pm20) REVERT: B 751 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8499 (mm) REVERT: B 832 LYS cc_start: 0.7555 (tptp) cc_final: 0.6913 (tptp) REVERT: B 833 ILE cc_start: 0.4100 (OUTLIER) cc_final: 0.3443 (mp) REVERT: B 834 HIS cc_start: 0.8011 (m90) cc_final: 0.7575 (m90) REVERT: C 471 PHE cc_start: 0.5410 (OUTLIER) cc_final: 0.4768 (t80) REVERT: C 494 PHE cc_start: 0.2418 (OUTLIER) cc_final: 0.1926 (m-10) REVERT: C 592 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7903 (mp10) REVERT: C 664 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: C 722 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8077 (mm-30) REVERT: C 725 GLN cc_start: 0.8773 (pt0) cc_final: 0.8254 (pm20) REVERT: C 751 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8492 (mm) REVERT: C 832 LYS cc_start: 0.7576 (tptt) cc_final: 0.7103 (tptt) REVERT: D 471 PHE cc_start: 0.5426 (OUTLIER) cc_final: 0.4771 (t80) REVERT: D 494 PHE cc_start: 0.2409 (OUTLIER) cc_final: 0.1923 (m-10) REVERT: D 551 PHE cc_start: 0.8337 (t80) cc_final: 0.8086 (t80) REVERT: D 592 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7995 (mp10) REVERT: D 682 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7474 (tm-30) REVERT: D 725 GLN cc_start: 0.8857 (pt0) cc_final: 0.8456 (pt0) REVERT: D 751 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8476 (mm) REVERT: D 832 LYS cc_start: 0.7620 (tptt) cc_final: 0.7342 (tptt) outliers start: 50 outliers final: 25 residues processed: 265 average time/residue: 0.2625 time to fit residues: 103.6656 Evaluate side-chains 258 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 214 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 771 HIS Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 771 HIS Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 494 PHE Chi-restraints excluded: chain D residue 592 GLN Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 621 SER Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 771 HIS Chi-restraints excluded: chain D residue 782 ILE 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: 0.6980 chunk 94 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 165 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 102 optimal weight: 0.0670 chunk 66 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 ASN ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 819 ASN ** C 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14096 Z= 0.188 Angle : 0.715 11.712 19152 Z= 0.359 Chirality : 0.046 0.301 2176 Planarity : 0.003 0.037 2376 Dihedral : 4.485 19.621 1876 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.41 % Favored : 93.05 % Rotamer: Outliers : 3.23 % Allowed : 21.02 % Favored : 75.76 % 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: -0.42 (0.21), residues: 1684 helix: 1.03 (0.16), residues: 1068 sheet: -2.59 (0.59), residues: 44 loop : -2.71 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 705 HIS 0.005 0.001 HIS C 831 PHE 0.021 0.002 PHE C 551 TYR 0.021 0.001 TYR D 700 ARG 0.003 0.000 ARG B 681 *********************** 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 284 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 237 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 PHE cc_start: 0.5539 (OUTLIER) cc_final: 0.4958 (t80) REVERT: A 494 PHE cc_start: 0.2515 (OUTLIER) cc_final: 0.1999 (m-10) REVERT: A 551 PHE cc_start: 0.8360 (t80) cc_final: 0.8100 (t80) REVERT: A 592 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7902 (mp10) REVERT: A 664 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: A 711 ILE cc_start: 0.9097 (mt) cc_final: 0.8680 (mm) REVERT: A 713 MET cc_start: 0.8186 (mmt) cc_final: 0.7726 (mmt) REVERT: A 751 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8518 (mm) REVERT: A 832 LYS cc_start: 0.7525 (tptp) cc_final: 0.7137 (tptp) REVERT: A 833 ILE cc_start: 0.4088 (OUTLIER) cc_final: 0.3639 (mp) REVERT: A 845 TYR cc_start: 0.8385 (m-80) cc_final: 0.8076 (m-10) REVERT: B 471 PHE cc_start: 0.5556 (OUTLIER) cc_final: 0.4955 (t80) REVERT: B 494 PHE cc_start: 0.2546 (OUTLIER) cc_final: 0.2017 (m-10) REVERT: B 551 PHE cc_start: 0.8403 (t80) cc_final: 0.8130 (t80) REVERT: B 592 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: B 695 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8624 (mm110) REVERT: B 713 MET cc_start: 0.8403 (mmt) cc_final: 0.8090 (mmt) REVERT: B 725 GLN cc_start: 0.8820 (pt0) cc_final: 0.8368 (pm20) REVERT: B 751 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8521 (mm) REVERT: B 832 LYS cc_start: 0.7551 (tptp) cc_final: 0.7169 (tptp) REVERT: B 833 ILE cc_start: 0.4057 (OUTLIER) cc_final: 0.3608 (mp) REVERT: C 471 PHE cc_start: 0.5400 (OUTLIER) cc_final: 0.4906 (t80) REVERT: C 592 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7834 (mp10) REVERT: C 664 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: C 725 GLN cc_start: 0.8704 (pt0) cc_final: 0.8179 (pm20) REVERT: C 751 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8518 (mm) REVERT: C 832 LYS cc_start: 0.7604 (tptt) cc_final: 0.7207 (tptt) REVERT: D 471 PHE cc_start: 0.5377 (OUTLIER) cc_final: 0.4894 (t80) REVERT: D 551 PHE cc_start: 0.8359 (t80) cc_final: 0.8098 (t80) REVERT: D 592 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7950 (mp10) REVERT: D 682 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7738 (tm-30) REVERT: D 722 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8054 (mm-30) REVERT: D 725 GLN cc_start: 0.8828 (pt0) cc_final: 0.8323 (pm20) REVERT: D 751 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8484 (mm) REVERT: D 832 LYS cc_start: 0.7653 (tptt) cc_final: 0.7263 (tptt) outliers start: 47 outliers final: 23 residues processed: 274 average time/residue: 0.2585 time to fit residues: 104.8746 Evaluate side-chains 268 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 226 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 771 HIS Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 771 HIS Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 592 GLN Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 722 GLU Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 771 HIS Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 831 HIS Chi-restraints excluded: chain D residue 841 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 30.0000 chunk 32 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 81 optimal weight: 0.0170 chunk 15 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 144 optimal weight: 0.7980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS A 819 ASN B 402 HIS B 819 ASN ** C 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14096 Z= 0.197 Angle : 0.753 13.447 19152 Z= 0.379 Chirality : 0.047 0.290 2176 Planarity : 0.003 0.034 2376 Dihedral : 4.386 18.793 1876 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.41 % Favored : 93.05 % Rotamer: Outliers : 3.85 % Allowed : 22.05 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1684 helix: 1.07 (0.16), residues: 1064 sheet: -2.15 (0.63), residues: 44 loop : -2.72 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 705 HIS 0.007 0.001 HIS C 851 PHE 0.021 0.001 PHE C 551 TYR 0.021 0.001 TYR A 700 ARG 0.007 0.000 ARG B 696 *********************** 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 291 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 235 time to evaluate : 1.445 Fit side-chains revert: symmetry clash REVERT: A 471 PHE cc_start: 0.5424 (OUTLIER) cc_final: 0.4992 (t80) REVERT: A 494 PHE cc_start: 0.2586 (OUTLIER) cc_final: 0.2045 (m-10) REVERT: A 551 PHE cc_start: 0.8356 (t80) cc_final: 0.8063 (t80) REVERT: A 592 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7897 (mp10) REVERT: A 664 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: A 698 GLU cc_start: 0.8654 (mp0) cc_final: 0.8435 (pm20) REVERT: A 700 TYR cc_start: 0.8981 (t80) cc_final: 0.8764 (t80) REVERT: A 711 ILE cc_start: 0.9089 (mt) cc_final: 0.8685 (mm) REVERT: A 713 MET cc_start: 0.8186 (mmt) cc_final: 0.7729 (mmt) REVERT: A 722 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8122 (pm20) REVERT: A 725 GLN cc_start: 0.8933 (pt0) cc_final: 0.8373 (pm20) REVERT: A 751 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8485 (mm) REVERT: A 832 LYS cc_start: 0.7610 (tptp) cc_final: 0.7265 (tptt) REVERT: B 471 PHE cc_start: 0.5411 (OUTLIER) cc_final: 0.4967 (t80) REVERT: B 494 PHE cc_start: 0.2606 (OUTLIER) cc_final: 0.2057 (m-10) REVERT: B 551 PHE cc_start: 0.8384 (t80) cc_final: 0.8098 (t80) REVERT: B 592 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7907 (mp10) REVERT: B 664 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7636 (tt0) REVERT: B 713 MET cc_start: 0.8362 (mmt) cc_final: 0.8075 (mmt) REVERT: B 725 GLN cc_start: 0.8800 (pt0) cc_final: 0.8277 (pm20) REVERT: B 751 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8500 (mm) REVERT: B 832 LYS cc_start: 0.7636 (tptp) cc_final: 0.7293 (tptt) REVERT: C 471 PHE cc_start: 0.5393 (OUTLIER) cc_final: 0.4861 (t80) REVERT: C 494 PHE cc_start: 0.2387 (OUTLIER) cc_final: 0.1899 (m-10) REVERT: C 592 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7813 (mp10) REVERT: C 664 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: C 725 GLN cc_start: 0.8699 (pt0) cc_final: 0.8136 (pm20) REVERT: C 751 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8496 (mm) REVERT: C 832 LYS cc_start: 0.7601 (tptt) cc_final: 0.7349 (tptt) REVERT: D 471 PHE cc_start: 0.5379 (OUTLIER) cc_final: 0.5111 (t80) REVERT: D 494 PHE cc_start: 0.2370 (OUTLIER) cc_final: 0.1888 (m-10) REVERT: D 551 PHE cc_start: 0.8341 (t80) cc_final: 0.8065 (t80) REVERT: D 592 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7962 (mp10) REVERT: D 664 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: D 682 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7780 (tm-30) REVERT: D 722 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8077 (mm-30) REVERT: D 725 GLN cc_start: 0.8852 (pt0) cc_final: 0.8370 (pm20) REVERT: D 751 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8481 (mm) REVERT: D 832 LYS cc_start: 0.7632 (tptt) cc_final: 0.7245 (tptt) outliers start: 56 outliers final: 31 residues processed: 280 average time/residue: 0.2432 time to fit residues: 101.5943 Evaluate side-chains 280 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 227 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 664 GLN Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 771 HIS Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 771 HIS Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 494 PHE Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 592 GLN Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 722 GLU Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 771 HIS Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 831 HIS Chi-restraints excluded: chain D residue 841 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 121 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 163 optimal weight: 0.0470 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 819 ASN ** C 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 HIS D 695 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14096 Z= 0.200 Angle : 0.752 10.749 19152 Z= 0.380 Chirality : 0.047 0.332 2176 Planarity : 0.003 0.033 2376 Dihedral : 4.344 18.355 1876 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.29 % Favored : 93.17 % Rotamer: Outliers : 3.78 % Allowed : 22.53 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1684 helix: 1.11 (0.16), residues: 1064 sheet: -2.05 (0.63), residues: 44 loop : -2.71 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 705 HIS 0.005 0.001 HIS C 851 PHE 0.024 0.002 PHE C 551 TYR 0.025 0.001 TYR B 700 ARG 0.005 0.000 ARG B 696 *********************** 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 285 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 230 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 PHE cc_start: 0.5418 (OUTLIER) cc_final: 0.4980 (t80) REVERT: A 551 PHE cc_start: 0.8348 (t80) cc_final: 0.8056 (t80) REVERT: A 592 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: A 664 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7117 (tt0) REVERT: A 700 TYR cc_start: 0.8997 (t80) cc_final: 0.8716 (t80) REVERT: A 711 ILE cc_start: 0.9093 (mt) cc_final: 0.8682 (mm) REVERT: A 713 MET cc_start: 0.8140 (mmt) cc_final: 0.7728 (mmt) REVERT: A 722 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8001 (mm-30) REVERT: A 725 GLN cc_start: 0.8934 (pt0) cc_final: 0.8346 (pm20) REVERT: A 751 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8468 (mm) REVERT: A 832 LYS cc_start: 0.7634 (tptp) cc_final: 0.7215 (tptt) REVERT: A 845 TYR cc_start: 0.8283 (m-80) cc_final: 0.7922 (m-10) REVERT: B 471 PHE cc_start: 0.5415 (OUTLIER) cc_final: 0.4954 (t80) REVERT: B 551 PHE cc_start: 0.8384 (t80) cc_final: 0.8088 (t80) REVERT: B 592 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: B 664 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7072 (tt0) REVERT: B 713 MET cc_start: 0.8322 (mmt) cc_final: 0.8069 (mmt) REVERT: B 725 GLN cc_start: 0.8798 (pt0) cc_final: 0.8260 (pm20) REVERT: B 751 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8493 (mm) REVERT: B 832 LYS cc_start: 0.7653 (tptp) cc_final: 0.7240 (tptt) REVERT: C 471 PHE cc_start: 0.5350 (OUTLIER) cc_final: 0.4814 (t80) REVERT: C 494 PHE cc_start: 0.2463 (OUTLIER) cc_final: 0.1972 (m-10) REVERT: C 592 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7810 (mp10) REVERT: C 664 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7132 (tt0) REVERT: C 725 GLN cc_start: 0.8716 (pt0) cc_final: 0.8196 (pm20) REVERT: C 751 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8485 (mm) REVERT: C 832 LYS cc_start: 0.7527 (tptt) cc_final: 0.7055 (tptt) REVERT: D 471 PHE cc_start: 0.5547 (OUTLIER) cc_final: 0.4937 (t80) REVERT: D 494 PHE cc_start: 0.2519 (OUTLIER) cc_final: 0.2002 (m-10) REVERT: D 551 PHE cc_start: 0.8338 (t80) cc_final: 0.8053 (t80) REVERT: D 592 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7980 (mp10) REVERT: D 664 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7091 (tt0) REVERT: D 682 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7818 (tm-30) REVERT: D 725 GLN cc_start: 0.8896 (pt0) cc_final: 0.8389 (pm20) REVERT: D 751 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8464 (mm) REVERT: D 832 LYS cc_start: 0.7623 (tptt) cc_final: 0.7247 (tptt) outliers start: 55 outliers final: 31 residues processed: 272 average time/residue: 0.2386 time to fit residues: 96.4736 Evaluate side-chains 276 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 226 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 651 MET Chi-restraints excluded: chain B residue 664 GLN Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 771 HIS Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 771 HIS Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 494 PHE Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 592 GLN Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 651 MET Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 771 HIS Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 831 HIS Chi-restraints excluded: chain D residue 841 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN A 695 GLN B 664 GLN ** C 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 GLN D 664 GLN ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14096 Z= 0.206 Angle : 0.769 12.006 19152 Z= 0.386 Chirality : 0.047 0.326 2176 Planarity : 0.004 0.035 2376 Dihedral : 4.298 18.013 1876 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.35 % Favored : 93.05 % Rotamer: Outliers : 3.71 % Allowed : 22.80 % Favored : 73.49 % 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: -0.34 (0.21), residues: 1684 helix: 1.09 (0.16), residues: 1064 sheet: -2.12 (0.60), residues: 44 loop : -2.70 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 705 HIS 0.004 0.001 HIS D 851 PHE 0.024 0.002 PHE C 551 TYR 0.024 0.001 TYR C 700 ARG 0.006 0.000 ARG B 696 ********************** 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 288 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 234 time to evaluate : 1.492 Fit side-chains REVERT: A 471 PHE cc_start: 0.5415 (OUTLIER) cc_final: 0.4914 (t80) REVERT: A 551 PHE cc_start: 0.8365 (t80) cc_final: 0.8060 (t80) REVERT: A 592 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: A 664 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: A 700 TYR cc_start: 0.8999 (t80) cc_final: 0.8721 (t80) REVERT: A 711 ILE cc_start: 0.9110 (mt) cc_final: 0.8707 (mm) REVERT: A 713 MET cc_start: 0.8132 (mmt) cc_final: 0.7759 (mmt) REVERT: A 722 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8000 (mm-30) REVERT: A 725 GLN cc_start: 0.8961 (pt0) cc_final: 0.8390 (pm20) REVERT: A 751 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8245 (mt) REVERT: A 832 LYS cc_start: 0.7661 (tptp) cc_final: 0.7233 (tptt) REVERT: B 471 PHE cc_start: 0.5424 (OUTLIER) cc_final: 0.4907 (t80) REVERT: B 592 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7926 (mp10) REVERT: B 664 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7130 (tt0) REVERT: B 713 MET cc_start: 0.8264 (mmt) cc_final: 0.8017 (mmt) REVERT: B 725 GLN cc_start: 0.8840 (pt0) cc_final: 0.8308 (pm20) REVERT: B 751 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8494 (mm) REVERT: B 832 LYS cc_start: 0.7663 (tptp) cc_final: 0.7253 (tptt) REVERT: C 471 PHE cc_start: 0.5385 (OUTLIER) cc_final: 0.4830 (t80) REVERT: C 494 PHE cc_start: 0.2505 (OUTLIER) cc_final: 0.1980 (m-10) REVERT: C 592 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7824 (mp10) REVERT: C 664 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7158 (tt0) REVERT: C 722 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7953 (mm-30) REVERT: C 725 GLN cc_start: 0.8760 (pt0) cc_final: 0.8213 (pm20) REVERT: C 751 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8467 (mm) REVERT: C 832 LYS cc_start: 0.7513 (tptt) cc_final: 0.7261 (tptt) REVERT: D 471 PHE cc_start: 0.5411 (OUTLIER) cc_final: 0.4887 (t80) REVERT: D 551 PHE cc_start: 0.8345 (t80) cc_final: 0.8063 (t80) REVERT: D 592 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7992 (mp10) REVERT: D 664 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7170 (tt0) REVERT: D 682 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7872 (tm-30) REVERT: D 725 GLN cc_start: 0.8931 (pt0) cc_final: 0.8393 (pm20) REVERT: D 751 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8463 (mm) REVERT: D 832 LYS cc_start: 0.7598 (tptt) cc_final: 0.7227 (tptt) outliers start: 54 outliers final: 32 residues processed: 272 average time/residue: 0.2391 time to fit residues: 97.0059 Evaluate side-chains 285 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 234 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 651 MET Chi-restraints excluded: chain B residue 664 GLN Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 771 HIS Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 695 GLN Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 771 HIS Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 592 GLN Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 651 MET Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 695 GLN Chi-restraints excluded: chain D residue 722 GLU Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 771 HIS Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 831 HIS Chi-restraints excluded: chain D residue 841 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 37 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN B 664 GLN B 691 ASN ** C 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 GLN ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 GLN ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.190462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.126041 restraints weight = 29689.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.129524 restraints weight = 14059.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.131724 restraints weight = 9300.285| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14096 Z= 0.232 Angle : 0.780 11.701 19152 Z= 0.392 Chirality : 0.048 0.319 2176 Planarity : 0.004 0.032 2376 Dihedral : 4.345 17.722 1876 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.83 % Favored : 92.58 % Rotamer: Outliers : 3.85 % Allowed : 22.73 % Favored : 73.42 % 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: -0.36 (0.21), residues: 1684 helix: 1.09 (0.16), residues: 1048 sheet: -2.20 (0.58), residues: 44 loop : -2.61 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 497 HIS 0.006 0.001 HIS D 851 PHE 0.023 0.002 PHE C 551 TYR 0.034 0.002 TYR A 845 ARG 0.005 0.000 ARG B 696 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2928.14 seconds wall clock time: 55 minutes 1.60 seconds (3301.60 seconds total)