Starting phenix.real_space_refine on Fri May 16 01:26:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8io5_35608/05_2025/8io5_35608.cif Found real_map, /net/cci-nas-00/data/ceres_data/8io5_35608/05_2025/8io5_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_35608/05_2025/8io5_35608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8io5_35608/05_2025/8io5_35608.map" model { file = "/net/cci-nas-00/data/ceres_data/8io5_35608/05_2025/8io5_35608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8io5_35608/05_2025/8io5_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13736 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 9.37, per 1000 atoms: 0.68 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: 3.31 Conformation dependent library (CDL) restraints added in 1.7 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: 1.36 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: 4.00 Time building geometry restraints manager: 3.88 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: 0.03 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: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.430 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.620 ------------------------------------------------------------------------------- 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= 0.229 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 Details of bonding type rmsd hydrogen bonds : bond 0.14627 ( 810) hydrogen bonds : angle 6.51961 ( 2397) covalent geometry : bond 0.00477 (14096) covalent geometry : angle 0.87505 (19152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.392 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: 0.2550 time to fit residues: 112.7004 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 : 1.530 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.188397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.129629 restraints weight = 29904.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.131768 restraints weight = 19167.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.131991 restraints weight = 12601.577| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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= 0.189 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 Details of bonding type rmsd hydrogen bonds : bond 0.07206 ( 810) hydrogen bonds : angle 5.35219 ( 2397) covalent geometry : bond 0.00403 (14096) covalent geometry : angle 0.73991 (19152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 282 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 TRP cc_start: 0.6581 (m100) cc_final: 0.6213 (m100) REVERT: A 551 PHE cc_start: 0.8341 (t80) cc_final: 0.8103 (t80) REVERT: A 592 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: A 691 ASN cc_start: 0.8496 (t0) cc_final: 0.8285 (t0) REVERT: A 711 ILE cc_start: 0.9076 (mt) cc_final: 0.8647 (mm) REVERT: A 713 MET cc_start: 0.8345 (mmt) cc_final: 0.7829 (mmt) REVERT: A 832 LYS cc_start: 0.7445 (tptp) cc_final: 0.6968 (tptt) REVERT: B 497 TRP cc_start: 0.6592 (m100) cc_final: 0.6240 (m100) REVERT: B 551 PHE cc_start: 0.8405 (t80) cc_final: 0.8164 (t80) REVERT: B 592 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7986 (mp10) REVERT: B 698 GLU cc_start: 0.8781 (mp0) cc_final: 0.8418 (mp0) REVERT: B 832 LYS cc_start: 0.7458 (tptp) cc_final: 0.6980 (tptt) REVERT: C 497 TRP cc_start: 0.6602 (m100) cc_final: 0.6247 (m100) REVERT: C 551 PHE cc_start: 0.8379 (t80) cc_final: 0.8150 (t80) REVERT: C 592 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7994 (mp10) REVERT: C 698 GLU cc_start: 0.8774 (mp0) cc_final: 0.8402 (mp0) REVERT: C 832 LYS cc_start: 0.7443 (tptp) cc_final: 0.6972 (tptt) REVERT: D 497 TRP cc_start: 0.6626 (m100) cc_final: 0.6251 (m100) REVERT: D 551 PHE cc_start: 0.8373 (t80) cc_final: 0.8147 (t80) REVERT: D 592 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7978 (mp10) REVERT: D 682 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7461 (tm-30) REVERT: D 832 LYS cc_start: 0.7469 (tptp) cc_final: 0.6981 (tptt) outliers start: 16 outliers final: 12 residues processed: 292 average time/residue: 0.2194 time to fit residues: 95.4788 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 : 1.356 ------------------------------------------------------------------------------- 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 136 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 162 optimal weight: 0.1980 chunk 40 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 819 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.190539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.133737 restraints weight = 29754.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.135313 restraints weight = 17611.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.134547 restraints weight = 11711.918| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1958 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= 0.152 Angle : 0.712 11.336 19152 Z= 0.355 Chirality : 0.044 0.181 2176 Planarity : 0.004 0.036 2376 Dihedral : 4.688 20.433 1876 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.01 % Favored : 92.52 % Rotamer: Outliers : 1.03 % Allowed : 16.35 % Favored : 82.62 % 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: 0.82 (0.16), residues: 1056 sheet: -2.85 (0.59), residues: 44 loop : -2.74 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 705 HIS 0.005 0.001 HIS B 731 PHE 0.012 0.002 PHE D 557 TYR 0.015 0.001 TYR A 652 ARG 0.003 0.000 ARG D 814 Details of bonding type rmsd hydrogen bonds : bond 0.06480 ( 810) hydrogen bonds : angle 4.97031 ( 2397) covalent geometry : bond 0.00303 (14096) covalent geometry : angle 0.71168 (19152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 251 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 551 PHE cc_start: 0.8316 (t80) cc_final: 0.8066 (t80) REVERT: A 592 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7873 (mp10) REVERT: A 691 ASN cc_start: 0.8512 (t0) cc_final: 0.8260 (t0) REVERT: A 713 MET cc_start: 0.8216 (mmt) cc_final: 0.7661 (mmt) REVERT: A 832 LYS cc_start: 0.7392 (tptp) cc_final: 0.6767 (tptt) REVERT: A 834 HIS cc_start: 0.7889 (m90) cc_final: 0.7065 (m90) REVERT: B 551 PHE cc_start: 0.8340 (t80) cc_final: 0.8107 (t80) REVERT: B 592 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7880 (mp10) REVERT: B 713 MET cc_start: 0.8644 (mmt) cc_final: 0.8433 (mmt) REVERT: B 832 LYS cc_start: 0.7387 (tptp) cc_final: 0.6755 (tptt) REVERT: B 834 HIS cc_start: 0.7884 (m90) cc_final: 0.7043 (m90) REVERT: C 551 PHE cc_start: 0.8315 (t80) cc_final: 0.8093 (t80) REVERT: C 592 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7857 (mp10) REVERT: C 832 LYS cc_start: 0.7378 (tptp) cc_final: 0.6744 (tptt) REVERT: C 834 HIS cc_start: 0.7849 (m90) cc_final: 0.7008 (m90) REVERT: D 551 PHE cc_start: 0.8322 (t80) cc_final: 0.8083 (t80) REVERT: D 592 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: D 682 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7445 (tm-30) REVERT: D 725 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8821 (pt0) REVERT: D 832 LYS cc_start: 0.7396 (tptp) cc_final: 0.6765 (tptt) REVERT: D 834 HIS cc_start: 0.7853 (m90) cc_final: 0.7014 (m90) outliers start: 15 outliers final: 7 residues processed: 260 average time/residue: 0.2489 time to fit residues: 93.5617 Evaluate side-chains 240 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 228 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 GLN 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 592 GLN Chi-restraints excluded: chain D residue 725 GLN Chi-restraints excluded: chain D residue 771 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 72 optimal weight: 0.1980 chunk 34 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 158 optimal weight: 0.5980 chunk 146 optimal weight: 0.1980 chunk 79 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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** B 695 GLN ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 810 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.191364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.136760 restraints weight = 29537.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.136764 restraints weight = 16429.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.136153 restraints weight = 11153.778| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14096 Z= 0.141 Angle : 0.670 10.354 19152 Z= 0.338 Chirality : 0.044 0.182 2176 Planarity : 0.004 0.037 2376 Dihedral : 4.497 18.955 1876 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.59 % Favored : 92.93 % Rotamer: Outliers : 2.40 % Allowed : 18.75 % Favored : 78.85 % 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: -0.47 (0.21), residues: 1684 helix: 0.99 (0.16), residues: 1056 sheet: -2.58 (0.66), residues: 44 loop : -2.65 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 705 HIS 0.004 0.001 HIS C 731 PHE 0.013 0.001 PHE B 557 TYR 0.013 0.001 TYR A 652 ARG 0.004 0.000 ARG B 679 Details of bonding type rmsd hydrogen bonds : bond 0.05969 ( 810) hydrogen bonds : angle 4.71693 ( 2397) covalent geometry : bond 0.00282 (14096) covalent geometry : angle 0.67046 (19152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 265 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 TRP cc_start: 0.6851 (t-100) cc_final: 0.6650 (t-100) REVERT: A 462 MET cc_start: 0.5677 (pmm) cc_final: 0.5367 (pmm) REVERT: A 551 PHE cc_start: 0.8291 (t80) cc_final: 0.7972 (t80) REVERT: A 592 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7855 (mp10) REVERT: A 711 ILE cc_start: 0.9189 (mt) cc_final: 0.8897 (mm) REVERT: A 713 MET cc_start: 0.8143 (mmt) cc_final: 0.7657 (mmt) REVERT: A 725 GLN cc_start: 0.8737 (pt0) cc_final: 0.8332 (pm20) REVERT: A 832 LYS cc_start: 0.7505 (tptp) cc_final: 0.7215 (tptt) REVERT: A 833 ILE cc_start: 0.4331 (OUTLIER) cc_final: 0.3875 (mp) REVERT: B 462 MET cc_start: 0.5681 (pmm) cc_final: 0.5357 (pmm) REVERT: B 551 PHE cc_start: 0.8328 (t80) cc_final: 0.8011 (t80) REVERT: B 592 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7818 (mp10) REVERT: B 713 MET cc_start: 0.8535 (mmt) cc_final: 0.8273 (mmt) REVERT: B 725 GLN cc_start: 0.8781 (pt0) cc_final: 0.8411 (pm20) REVERT: B 832 LYS cc_start: 0.7507 (tptp) cc_final: 0.7225 (tptt) REVERT: B 833 ILE cc_start: 0.4314 (OUTLIER) cc_final: 0.3861 (mp) REVERT: C 462 MET cc_start: 0.5633 (pmm) cc_final: 0.5315 (pmm) REVERT: C 551 PHE cc_start: 0.8315 (t80) cc_final: 0.8011 (t80) REVERT: C 592 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7818 (mp10) REVERT: C 725 GLN cc_start: 0.8762 (pt0) cc_final: 0.8372 (pm20) REVERT: C 832 LYS cc_start: 0.7492 (tptp) cc_final: 0.7205 (tptt) REVERT: C 833 ILE cc_start: 0.4321 (OUTLIER) cc_final: 0.3853 (mp) REVERT: D 462 MET cc_start: 0.5679 (pmm) cc_final: 0.5390 (pmm) REVERT: D 551 PHE cc_start: 0.8306 (t80) cc_final: 0.7997 (t80) REVERT: D 592 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7952 (mp10) REVERT: D 682 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7559 (tm-30) REVERT: D 832 LYS cc_start: 0.7512 (tptp) cc_final: 0.7230 (tptt) REVERT: D 833 ILE cc_start: 0.4341 (OUTLIER) cc_final: 0.3876 (mp) outliers start: 35 outliers final: 13 residues processed: 287 average time/residue: 0.2358 time to fit residues: 99.7758 Evaluate side-chains 262 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 241 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 GLN 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 592 GLN 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 592 GLN 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 833 ILE Chi-restraints excluded: chain D residue 592 GLN Chi-restraints excluded: chain D residue 714 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 133 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 83 optimal weight: 7.9990 chunk 102 optimal weight: 0.5980 chunk 116 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 129 optimal weight: 20.0000 chunk 46 optimal weight: 0.2980 chunk 163 optimal weight: 9.9990 chunk 128 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** B 695 GLN B 819 ASN ** C 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN ** D 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 GLN D 725 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.191657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.129595 restraints weight = 29808.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.132987 restraints weight = 14255.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.135083 restraints weight = 9431.923| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 0.029 14096 Z= 0.143 Angle : 0.662 9.669 19152 Z= 0.336 Chirality : 0.044 0.247 2176 Planarity : 0.003 0.035 2376 Dihedral : 4.391 19.275 1876 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.53 % Favored : 92.99 % Rotamer: Outliers : 2.20 % Allowed : 20.74 % Favored : 77.06 % 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: -0.31 (0.21), residues: 1684 helix: 1.07 (0.16), residues: 1068 sheet: -2.67 (0.65), residues: 44 loop : -2.55 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 705 HIS 0.004 0.001 HIS A 731 PHE 0.020 0.001 PHE C 557 TYR 0.022 0.001 TYR A 700 ARG 0.003 0.000 ARG C 696 Details of bonding type rmsd hydrogen bonds : bond 0.05851 ( 810) hydrogen bonds : angle 4.57518 ( 2397) covalent geometry : bond 0.00290 (14096) covalent geometry : angle 0.66159 (19152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 251 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 PHE cc_start: 0.5585 (OUTLIER) cc_final: 0.5109 (t80) REVERT: A 592 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7841 (mp10) REVERT: A 700 TYR cc_start: 0.8886 (t80) cc_final: 0.8673 (t80) REVERT: A 711 ILE cc_start: 0.9189 (mt) cc_final: 0.8876 (mm) REVERT: A 713 MET cc_start: 0.8035 (mmt) cc_final: 0.7583 (mmt) REVERT: A 725 GLN cc_start: 0.8701 (pt0) cc_final: 0.8301 (pm20) REVERT: A 833 ILE cc_start: 0.4302 (OUTLIER) cc_final: 0.3854 (mp) REVERT: B 471 PHE cc_start: 0.5575 (OUTLIER) cc_final: 0.5102 (t80) REVERT: B 592 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7804 (mp10) REVERT: B 664 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: B 682 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7978 (tm-30) REVERT: B 705 TRP cc_start: 0.8704 (t60) cc_final: 0.8275 (t60) REVERT: B 713 MET cc_start: 0.8424 (mmt) cc_final: 0.8182 (mmt) REVERT: B 725 GLN cc_start: 0.8707 (pt0) cc_final: 0.8340 (pm20) REVERT: B 833 ILE cc_start: 0.4316 (OUTLIER) cc_final: 0.3880 (mp) REVERT: C 471 PHE cc_start: 0.5597 (OUTLIER) cc_final: 0.5126 (t80) REVERT: C 592 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: C 725 GLN cc_start: 0.8709 (pt0) cc_final: 0.8335 (pm20) REVERT: C 833 ILE cc_start: 0.4305 (OUTLIER) cc_final: 0.3857 (mp) REVERT: D 471 PHE cc_start: 0.5611 (OUTLIER) cc_final: 0.5135 (t80) REVERT: D 592 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7956 (mp10) REVERT: D 664 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8137 (tt0) REVERT: D 682 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7640 (tm-30) REVERT: D 751 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8544 (mt) REVERT: D 833 ILE cc_start: 0.4320 (OUTLIER) cc_final: 0.3877 (mp) outliers start: 32 outliers final: 7 residues processed: 274 average time/residue: 0.2311 time to fit residues: 94.2373 Evaluate side-chains 265 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 243 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 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 664 GLN 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 831 HIS Chi-restraints excluded: chain C residue 833 ILE Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 592 GLN 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 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 59 optimal weight: 3.9990 chunk 19 optimal weight: 0.0060 chunk 103 optimal weight: 0.0970 chunk 137 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- 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 664 GLN A 695 GLN ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN B 819 ASN ** C 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 GLN C 695 GLN ** D 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.191140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.129553 restraints weight = 30064.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.133849 restraints weight = 16806.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.134269 restraints weight = 9484.312| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2904 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= 0.156 Angle : 0.712 9.769 19152 Z= 0.357 Chirality : 0.045 0.235 2176 Planarity : 0.004 0.037 2376 Dihedral : 4.344 18.878 1876 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.53 % Favored : 92.99 % Rotamer: Outliers : 2.68 % Allowed : 20.19 % Favored : 77.13 % 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: -0.31 (0.21), residues: 1684 helix: 1.08 (0.16), residues: 1068 sheet: -2.73 (0.66), residues: 44 loop : -2.55 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 705 HIS 0.005 0.001 HIS A 851 PHE 0.021 0.002 PHE A 551 TYR 0.021 0.001 TYR D 700 ARG 0.003 0.000 ARG B 679 Details of bonding type rmsd hydrogen bonds : bond 0.05963 ( 810) hydrogen bonds : angle 4.56160 ( 2397) covalent geometry : bond 0.00333 (14096) covalent geometry : angle 0.71154 (19152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 246 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 PHE cc_start: 0.5420 (OUTLIER) cc_final: 0.4986 (t80) REVERT: A 592 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: A 700 TYR cc_start: 0.9014 (t80) cc_final: 0.8614 (t80) REVERT: A 711 ILE cc_start: 0.9188 (mt) cc_final: 0.8851 (mm) REVERT: A 713 MET cc_start: 0.8136 (mmt) cc_final: 0.7662 (mmt) REVERT: A 722 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8203 (mm-30) REVERT: A 725 GLN cc_start: 0.8755 (pt0) cc_final: 0.8291 (pm20) REVERT: A 751 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8494 (mt) REVERT: A 832 LYS cc_start: 0.7650 (tptt) cc_final: 0.7432 (tptt) REVERT: B 471 PHE cc_start: 0.5353 (OUTLIER) cc_final: 0.4924 (t80) REVERT: B 592 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7782 (mp10) REVERT: B 682 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7749 (tm-30) REVERT: B 705 TRP cc_start: 0.8809 (t60) cc_final: 0.8350 (t60) REVERT: B 713 MET cc_start: 0.8505 (mmt) cc_final: 0.8231 (mmt) REVERT: B 725 GLN cc_start: 0.8769 (pt0) cc_final: 0.8333 (pm20) REVERT: B 751 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8552 (mt) REVERT: B 832 LYS cc_start: 0.7693 (tptt) cc_final: 0.7485 (tptt) REVERT: B 834 HIS cc_start: 0.7869 (m90) cc_final: 0.7644 (m90) REVERT: C 471 PHE cc_start: 0.5370 (OUTLIER) cc_final: 0.4944 (t80) REVERT: C 592 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7766 (mp10) REVERT: C 713 MET cc_start: 0.8169 (mmt) cc_final: 0.7893 (mmt) REVERT: C 725 GLN cc_start: 0.8719 (pt0) cc_final: 0.8321 (pm20) REVERT: C 751 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8550 (mt) REVERT: C 834 HIS cc_start: 0.7909 (m90) cc_final: 0.7688 (m90) REVERT: D 471 PHE cc_start: 0.5365 (OUTLIER) cc_final: 0.4938 (t80) REVERT: D 592 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7965 (mp10) REVERT: D 664 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: D 682 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7725 (tm-30) REVERT: D 700 TYR cc_start: 0.8915 (t80) cc_final: 0.8491 (t80) REVERT: D 725 GLN cc_start: 0.8816 (pt0) cc_final: 0.8405 (pt0) REVERT: D 751 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8438 (mt) REVERT: D 832 LYS cc_start: 0.7702 (tptt) cc_final: 0.7500 (tptt) REVERT: D 834 HIS cc_start: 0.7944 (m90) cc_final: 0.7712 (m90) REVERT: D 839 LEU cc_start: 0.8015 (mt) cc_final: 0.7695 (pp) outliers start: 39 outliers final: 18 residues processed: 276 average time/residue: 0.2235 time to fit residues: 92.1316 Evaluate side-chains 266 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 664 GLN 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 B residue 471 PHE Chi-restraints excluded: chain B residue 592 GLN 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 C residue 471 PHE Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 723 CYS 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 664 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 0.7980 chunk 49 optimal weight: 30.0000 chunk 4 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 31 optimal weight: 0.0980 chunk 159 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 664 GLN A 810 ASN ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN B 819 ASN ** C 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN ** D 402 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 = 0.4558 r_free = 0.4558 target = 0.190506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.131287 restraints weight = 29995.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.132701 restraints weight = 17050.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.132722 restraints weight = 11838.272| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14096 Z= 0.160 Angle : 0.692 8.541 19152 Z= 0.349 Chirality : 0.045 0.197 2176 Planarity : 0.004 0.036 2376 Dihedral : 4.351 19.276 1876 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.53 % Favored : 92.99 % Rotamer: Outliers : 2.82 % Allowed : 20.33 % Favored : 76.85 % 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: -0.30 (0.21), residues: 1684 helix: 1.09 (0.16), residues: 1068 sheet: -2.80 (0.66), residues: 44 loop : -2.54 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 705 HIS 0.006 0.001 HIS C 851 PHE 0.024 0.002 PHE A 551 TYR 0.024 0.001 TYR B 700 ARG 0.002 0.000 ARG A 679 Details of bonding type rmsd hydrogen bonds : bond 0.06000 ( 810) hydrogen bonds : angle 4.54794 ( 2397) covalent geometry : bond 0.00341 (14096) covalent geometry : angle 0.69184 (19152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 240 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 PHE cc_start: 0.5453 (OUTLIER) cc_final: 0.5066 (t80) REVERT: A 592 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7836 (mp10) REVERT: A 700 TYR cc_start: 0.9092 (t80) cc_final: 0.8704 (t80) REVERT: A 711 ILE cc_start: 0.9194 (mt) cc_final: 0.8816 (mm) REVERT: A 713 MET cc_start: 0.8174 (mmt) cc_final: 0.7651 (mmt) REVERT: A 722 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8219 (mm-30) REVERT: A 725 GLN cc_start: 0.8792 (pt0) cc_final: 0.8288 (pm20) REVERT: A 751 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8422 (mt) REVERT: A 832 LYS cc_start: 0.7689 (tptt) cc_final: 0.7394 (tptt) REVERT: B 471 PHE cc_start: 0.5422 (OUTLIER) cc_final: 0.5040 (t80) REVERT: B 592 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7830 (mp10) REVERT: B 664 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8111 (tt0) REVERT: B 682 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7678 (tm-30) REVERT: B 700 TYR cc_start: 0.9043 (t80) cc_final: 0.8771 (t80) REVERT: B 705 TRP cc_start: 0.8849 (t60) cc_final: 0.8373 (t60) REVERT: B 713 MET cc_start: 0.8523 (mmt) cc_final: 0.8235 (mmt) REVERT: B 725 GLN cc_start: 0.8805 (pt0) cc_final: 0.8340 (pm20) REVERT: B 751 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8426 (mt) REVERT: B 832 LYS cc_start: 0.7697 (tptt) cc_final: 0.7411 (tptt) REVERT: C 471 PHE cc_start: 0.5436 (OUTLIER) cc_final: 0.4944 (t80) REVERT: C 592 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7806 (mp10) REVERT: C 713 MET cc_start: 0.8113 (mmt) cc_final: 0.7781 (mmt) REVERT: C 725 GLN cc_start: 0.8754 (pt0) cc_final: 0.8288 (pm20) REVERT: C 751 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8426 (mt) REVERT: C 832 LYS cc_start: 0.7587 (tptt) cc_final: 0.7359 (tptt) REVERT: D 471 PHE cc_start: 0.5434 (OUTLIER) cc_final: 0.4919 (t80) REVERT: D 592 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7971 (mp10) REVERT: D 664 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: D 682 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7707 (tm-30) REVERT: D 700 TYR cc_start: 0.9063 (t80) cc_final: 0.8556 (t80) REVERT: D 713 MET cc_start: 0.8444 (mmt) cc_final: 0.8156 (mmt) REVERT: D 751 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8390 (mt) REVERT: D 832 LYS cc_start: 0.7716 (tptt) cc_final: 0.7387 (tptt) outliers start: 41 outliers final: 23 residues processed: 271 average time/residue: 0.2303 time to fit residues: 93.3838 Evaluate side-chains 272 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 1.367 ------------------------------------------------------------------------------- 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 714 ASN 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 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 664 GLN 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 C residue 471 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 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 664 GLN Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 771 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 51 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 146 optimal weight: 0.1980 chunk 114 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 161 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 664 GLN ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 810 ASN ** C 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 ASN D 402 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.191683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.129153 restraints weight = 29830.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.133228 restraints weight = 13886.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.133842 restraints weight = 9493.033| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14096 Z= 0.146 Angle : 0.736 12.014 19152 Z= 0.367 Chirality : 0.045 0.212 2176 Planarity : 0.003 0.035 2376 Dihedral : 4.310 19.531 1876 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.29 % Favored : 93.23 % Rotamer: Outliers : 3.02 % Allowed : 21.15 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1684 helix: 1.15 (0.16), residues: 1068 sheet: -2.75 (0.65), residues: 44 loop : -2.51 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 705 HIS 0.005 0.001 HIS C 851 PHE 0.024 0.002 PHE A 551 TYR 0.029 0.001 TYR C 700 ARG 0.005 0.000 ARG D 694 Details of bonding type rmsd hydrogen bonds : bond 0.05916 ( 810) hydrogen bonds : angle 4.52057 ( 2397) covalent geometry : bond 0.00299 (14096) covalent geometry : angle 0.73567 (19152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 247 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 PHE cc_start: 0.5370 (OUTLIER) cc_final: 0.4974 (t80) REVERT: A 592 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: A 664 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7337 (tt0) REVERT: A 700 TYR cc_start: 0.9088 (t80) cc_final: 0.8732 (t80) REVERT: A 711 ILE cc_start: 0.9188 (mt) cc_final: 0.8829 (mm) REVERT: A 713 MET cc_start: 0.8218 (mmt) cc_final: 0.7737 (mmt) REVERT: A 722 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8236 (mm-30) REVERT: A 725 GLN cc_start: 0.8783 (pt0) cc_final: 0.8283 (pm20) REVERT: A 751 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8415 (mt) REVERT: A 832 LYS cc_start: 0.7740 (tptt) cc_final: 0.7436 (tptt) REVERT: B 471 PHE cc_start: 0.5376 (OUTLIER) cc_final: 0.4997 (t80) REVERT: B 592 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7811 (mp10) REVERT: B 664 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: B 700 TYR cc_start: 0.9075 (t80) cc_final: 0.8642 (t80) REVERT: B 705 TRP cc_start: 0.8877 (t60) cc_final: 0.8419 (t60) REVERT: B 713 MET cc_start: 0.8513 (mmt) cc_final: 0.8201 (mmt) REVERT: B 725 GLN cc_start: 0.8810 (pt0) cc_final: 0.8346 (pm20) REVERT: B 751 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8440 (mt) REVERT: B 832 LYS cc_start: 0.7740 (tptt) cc_final: 0.7444 (tptt) REVERT: C 471 PHE cc_start: 0.5376 (OUTLIER) cc_final: 0.5076 (t80) REVERT: C 592 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: C 664 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: C 725 GLN cc_start: 0.8741 (pt0) cc_final: 0.8278 (pm20) REVERT: C 751 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8433 (mt) REVERT: D 471 PHE cc_start: 0.5384 (OUTLIER) cc_final: 0.4947 (t80) REVERT: D 592 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7950 (mp10) REVERT: D 664 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: D 682 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7816 (tm-30) REVERT: D 691 ASN cc_start: 0.8506 (t0) cc_final: 0.7940 (t0) REVERT: D 695 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8091 (mm-40) REVERT: D 700 TYR cc_start: 0.9074 (t80) cc_final: 0.8584 (t80) REVERT: D 713 MET cc_start: 0.8412 (mmt) cc_final: 0.8100 (mmt) REVERT: D 751 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8403 (mt) REVERT: D 832 LYS cc_start: 0.7680 (tptt) cc_final: 0.7367 (tptt) outliers start: 44 outliers final: 23 residues processed: 282 average time/residue: 0.2251 time to fit residues: 94.4346 Evaluate side-chains 277 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 237 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 714 ASN 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 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 664 GLN 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 C residue 471 PHE Chi-restraints excluded: chain C residue 556 THR 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 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 556 THR 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 664 GLN Chi-restraints excluded: chain D residue 695 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 35 optimal weight: 0.0970 chunk 54 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 139 optimal weight: 0.4980 chunk 151 optimal weight: 0.6980 chunk 83 optimal weight: 0.0060 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS A 664 GLN B 402 HIS C 402 HIS C 664 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.195017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.136939 restraints weight = 29513.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.136032 restraints weight = 17671.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.137993 restraints weight = 12180.104| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14096 Z= 0.143 Angle : 0.728 11.110 19152 Z= 0.367 Chirality : 0.045 0.206 2176 Planarity : 0.003 0.034 2376 Dihedral : 4.293 19.310 1876 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.41 % Favored : 93.11 % Rotamer: Outliers : 3.37 % Allowed : 20.95 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1684 helix: 1.21 (0.16), residues: 1060 sheet: -2.75 (0.62), residues: 44 loop : -2.41 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 705 HIS 0.005 0.001 HIS B 851 PHE 0.026 0.002 PHE B 498 TYR 0.025 0.001 TYR C 700 ARG 0.003 0.000 ARG D 681 Details of bonding type rmsd hydrogen bonds : bond 0.05696 ( 810) hydrogen bonds : angle 4.42343 ( 2397) covalent geometry : bond 0.00288 (14096) covalent geometry : angle 0.72832 (19152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 239 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 PHE cc_start: 0.5241 (OUTLIER) cc_final: 0.4690 (t80) REVERT: A 498 PHE cc_start: 0.5064 (OUTLIER) cc_final: 0.4388 (m-80) REVERT: A 592 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7837 (mp10) REVERT: A 700 TYR cc_start: 0.9016 (t80) cc_final: 0.8707 (t80) REVERT: A 711 ILE cc_start: 0.9182 (mt) cc_final: 0.8832 (mm) REVERT: A 713 MET cc_start: 0.8165 (mmt) cc_final: 0.7732 (mmt) REVERT: A 722 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8267 (mm-30) REVERT: A 725 GLN cc_start: 0.8759 (pt0) cc_final: 0.8259 (pm20) REVERT: A 751 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8405 (mt) REVERT: A 832 LYS cc_start: 0.7712 (tptt) cc_final: 0.7397 (tptt) REVERT: B 471 PHE cc_start: 0.5309 (OUTLIER) cc_final: 0.4799 (t80) REVERT: B 498 PHE cc_start: 0.4952 (OUTLIER) cc_final: 0.4174 (m-80) REVERT: B 592 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7815 (mp10) REVERT: B 664 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8277 (tt0) REVERT: B 682 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7859 (tm-30) REVERT: B 700 TYR cc_start: 0.9064 (t80) cc_final: 0.8624 (t80) REVERT: B 705 TRP cc_start: 0.8809 (t60) cc_final: 0.8346 (t60) REVERT: B 713 MET cc_start: 0.8484 (mmt) cc_final: 0.8138 (mmt) REVERT: B 725 GLN cc_start: 0.8789 (pt0) cc_final: 0.8302 (pm20) REVERT: B 751 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8400 (mt) REVERT: B 832 LYS cc_start: 0.7712 (tptt) cc_final: 0.7414 (tptt) REVERT: C 471 PHE cc_start: 0.5293 (OUTLIER) cc_final: 0.4965 (t80) REVERT: C 498 PHE cc_start: 0.6527 (t80) cc_final: 0.6219 (m-80) REVERT: C 592 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7793 (mp10) REVERT: C 664 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: C 725 GLN cc_start: 0.8725 (pt0) cc_final: 0.8210 (pm20) REVERT: C 751 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8394 (mt) REVERT: D 471 PHE cc_start: 0.5352 (OUTLIER) cc_final: 0.5067 (t80) REVERT: D 592 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: D 664 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7615 (tt0) REVERT: D 682 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7831 (tm-30) REVERT: D 700 TYR cc_start: 0.9056 (t80) cc_final: 0.8660 (t80) REVERT: D 713 MET cc_start: 0.8360 (mmt) cc_final: 0.8058 (mmt) REVERT: D 722 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7971 (mm-30) REVERT: D 725 GLN cc_start: 0.8858 (pt0) cc_final: 0.8329 (pm20) REVERT: D 751 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8365 (mt) REVERT: D 832 LYS cc_start: 0.7632 (tptt) cc_final: 0.7319 (tptt) outliers start: 49 outliers final: 24 residues processed: 274 average time/residue: 0.2455 time to fit residues: 101.6839 Evaluate side-chains 273 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 695 GLN Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 498 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 695 GLN 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 C residue 471 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 695 GLN 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 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 695 GLN 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 831 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 85 optimal weight: 3.9990 chunk 19 optimal weight: 0.0010 chunk 113 optimal weight: 0.0870 chunk 150 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 overall best weight: 0.6168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN C 664 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.195220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.131117 restraints weight = 29525.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.134754 restraints weight = 13287.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.137062 restraints weight = 8700.829| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14096 Z= 0.145 Angle : 0.745 11.127 19152 Z= 0.371 Chirality : 0.046 0.206 2176 Planarity : 0.003 0.034 2376 Dihedral : 4.274 19.362 1876 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.53 % Favored : 92.99 % Rotamer: Outliers : 3.09 % Allowed : 21.15 % 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: -0.11 (0.21), residues: 1684 helix: 1.25 (0.16), residues: 1044 sheet: -2.57 (0.62), residues: 44 loop : -2.35 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 705 HIS 0.005 0.001 HIS D 851 PHE 0.022 0.002 PHE A 498 TYR 0.021 0.001 TYR C 700 ARG 0.003 0.000 ARG B 681 Details of bonding type rmsd hydrogen bonds : bond 0.05640 ( 810) hydrogen bonds : angle 4.43845 ( 2397) covalent geometry : bond 0.00299 (14096) covalent geometry : angle 0.74475 (19152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 230 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 PHE cc_start: 0.5112 (OUTLIER) cc_final: 0.4599 (t80) REVERT: A 498 PHE cc_start: 0.5079 (OUTLIER) cc_final: 0.4414 (m-80) REVERT: A 592 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7806 (mp10) REVERT: A 664 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: A 700 TYR cc_start: 0.8759 (t80) cc_final: 0.8517 (t80) REVERT: A 711 ILE cc_start: 0.9200 (mt) cc_final: 0.8843 (mm) REVERT: A 713 MET cc_start: 0.8004 (mmt) cc_final: 0.7632 (mmt) REVERT: A 725 GLN cc_start: 0.8720 (pt0) cc_final: 0.8254 (pm20) REVERT: A 751 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8411 (mt) REVERT: A 832 LYS cc_start: 0.7564 (tptt) cc_final: 0.7242 (tptt) REVERT: B 471 PHE cc_start: 0.5214 (OUTLIER) cc_final: 0.4736 (t80) REVERT: B 498 PHE cc_start: 0.5043 (OUTLIER) cc_final: 0.4338 (m-80) REVERT: B 592 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7773 (mp10) REVERT: B 700 TYR cc_start: 0.8801 (t80) cc_final: 0.8365 (t80) REVERT: B 705 TRP cc_start: 0.8741 (t60) cc_final: 0.8375 (t60) REVERT: B 713 MET cc_start: 0.8286 (mmt) cc_final: 0.7958 (mmt) REVERT: B 725 GLN cc_start: 0.8721 (pt0) cc_final: 0.8318 (pm20) REVERT: B 751 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8407 (mt) REVERT: B 832 LYS cc_start: 0.7579 (tptt) cc_final: 0.7261 (tptt) REVERT: C 471 PHE cc_start: 0.5343 (OUTLIER) cc_final: 0.4937 (t80) REVERT: C 498 PHE cc_start: 0.6471 (t80) cc_final: 0.6118 (m-80) REVERT: C 592 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7774 (mp10) REVERT: C 725 GLN cc_start: 0.8693 (pt0) cc_final: 0.8252 (pm20) REVERT: C 751 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8393 (mt) REVERT: C 832 LYS cc_start: 0.7504 (tptt) cc_final: 0.7076 (tptt) REVERT: D 471 PHE cc_start: 0.5326 (OUTLIER) cc_final: 0.4960 (t80) REVERT: D 498 PHE cc_start: 0.6492 (t80) cc_final: 0.6158 (m-80) REVERT: D 592 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7902 (mp10) REVERT: D 664 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: D 682 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7764 (tm-30) REVERT: D 700 TYR cc_start: 0.8834 (t80) cc_final: 0.8499 (t80) REVERT: D 713 MET cc_start: 0.8153 (mmt) cc_final: 0.7901 (mmt) REVERT: D 725 GLN cc_start: 0.8821 (pt0) cc_final: 0.8332 (pm20) REVERT: D 751 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8379 (mt) REVERT: D 832 LYS cc_start: 0.7521 (tptt) cc_final: 0.7214 (tptt) outliers start: 45 outliers final: 28 residues processed: 263 average time/residue: 0.2386 time to fit residues: 93.7818 Evaluate side-chains 274 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 230 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 498 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 695 GLN 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 B residue 471 PHE Chi-restraints excluded: chain B residue 498 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 695 GLN 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 C residue 471 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 695 GLN 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 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 695 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 chunk 56 optimal weight: 0.0040 chunk 12 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 140 optimal weight: 0.0030 overall best weight: 0.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN C 664 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.195361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.132908 restraints weight = 29725.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.137476 restraints weight = 15678.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.138032 restraints weight = 9120.351| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14096 Z= 0.142 Angle : 0.742 11.069 19152 Z= 0.369 Chirality : 0.045 0.205 2176 Planarity : 0.003 0.035 2376 Dihedral : 4.251 19.220 1876 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.83 % Favored : 92.70 % Rotamer: Outliers : 3.37 % Allowed : 21.22 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1684 helix: 1.26 (0.16), residues: 1044 sheet: -2.51 (0.61), residues: 44 loop : -2.35 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 705 HIS 0.005 0.001 HIS D 851 PHE 0.022 0.002 PHE A 551 TYR 0.020 0.001 TYR C 700 ARG 0.003 0.000 ARG A 681 Details of bonding type rmsd hydrogen bonds : bond 0.05567 ( 810) hydrogen bonds : angle 4.42260 ( 2397) covalent geometry : bond 0.00293 (14096) covalent geometry : angle 0.74178 (19152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5072.62 seconds wall clock time: 90 minutes 18.69 seconds (5418.69 seconds total)