Starting phenix.real_space_refine on Thu Jul 31 21:00:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8io5_35608/07_2025/8io5_35608.cif Found real_map, /net/cci-nas-00/data/ceres_data/8io5_35608/07_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_35608/07_2025/8io5_35608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8io5_35608/07_2025/8io5_35608.map" model { file = "/net/cci-nas-00/data/ceres_data/8io5_35608/07_2025/8io5_35608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8io5_35608/07_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-5711/modules/chem_data/mon_lib" Total number of atoms: 13736 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 9.56, per 1000 atoms: 0.70 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: 3.27 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: 1.34 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: 3.72 Time building geometry restraints manager: 3.87 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: 5.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.660 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.630 ------------------------------------------------------------------------------- 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 : 1.379 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: 0.2375 time to fit residues: 105.1070 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 : 1.513 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.127511 restraints weight = 29904.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.131040 restraints weight = 17546.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.131412 restraints weight = 11308.574| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 TRP cc_start: 0.6397 (m100) cc_final: 0.6020 (m100) REVERT: A 551 PHE cc_start: 0.8414 (t80) cc_final: 0.8161 (t80) REVERT: A 592 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8022 (mp10) REVERT: A 691 ASN cc_start: 0.8519 (t0) cc_final: 0.8301 (t0) REVERT: A 711 ILE cc_start: 0.9037 (mt) cc_final: 0.8597 (mm) REVERT: A 713 MET cc_start: 0.8431 (mmt) cc_final: 0.7891 (mmt) REVERT: A 832 LYS cc_start: 0.7499 (tptp) cc_final: 0.7046 (tptt) REVERT: B 497 TRP cc_start: 0.6421 (m100) cc_final: 0.6057 (m100) REVERT: B 551 PHE cc_start: 0.8430 (t80) cc_final: 0.8183 (t80) REVERT: B 592 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8002 (mp10) REVERT: B 698 GLU cc_start: 0.8820 (mp0) cc_final: 0.8431 (mp0) REVERT: B 832 LYS cc_start: 0.7509 (tptp) cc_final: 0.7052 (tptt) REVERT: C 497 TRP cc_start: 0.6425 (m100) cc_final: 0.6057 (m100) REVERT: C 551 PHE cc_start: 0.8423 (t80) cc_final: 0.8184 (t80) REVERT: C 592 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7993 (mp10) REVERT: C 698 GLU cc_start: 0.8802 (mp0) cc_final: 0.8410 (mp0) REVERT: C 832 LYS cc_start: 0.7493 (tptp) cc_final: 0.7046 (tptt) REVERT: D 497 TRP cc_start: 0.6450 (m100) cc_final: 0.6065 (m100) REVERT: D 551 PHE cc_start: 0.8405 (t80) cc_final: 0.8172 (t80) REVERT: D 592 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8004 (mp10) REVERT: D 682 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7492 (tm-30) REVERT: D 832 LYS cc_start: 0.7518 (tptp) cc_final: 0.7053 (tptt) outliers start: 16 outliers final: 12 residues processed: 292 average time/residue: 0.2256 time to fit residues: 98.3548 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 : 1.369 ------------------------------------------------------------------------------- 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: 0.9990 chunk 141 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4555 r_free = 0.4555 target = 0.190021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.135293 restraints weight = 29727.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.134730 restraints weight = 16710.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.134329 restraints weight = 12499.072| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1967 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 : 0.717 11.718 19152 Z= 0.357 Chirality : 0.045 0.181 2176 Planarity : 0.004 0.037 2376 Dihedral : 4.695 20.859 1876 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.01 % Favored : 92.52 % Rotamer: Outliers : 1.10 % Allowed : 16.41 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.21), residues: 1684 helix: 0.81 (0.16), residues: 1056 sheet: -2.81 (0.60), residues: 44 loop : -2.73 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 705 HIS 0.005 0.001 HIS B 731 PHE 0.013 0.002 PHE D 557 TYR 0.015 0.002 TYR A 652 ARG 0.004 0.000 ARG D 814 Details of bonding type rmsd hydrogen bonds : bond 0.06500 ( 810) hydrogen bonds : angle 4.96297 ( 2397) covalent geometry : bond 0.00319 (14096) covalent geometry : angle 0.71670 (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 267 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 251 time to evaluate : 1.488 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 551 PHE cc_start: 0.8321 (t80) cc_final: 0.8080 (t80) REVERT: A 592 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: A 691 ASN cc_start: 0.8530 (t0) cc_final: 0.8266 (t0) REVERT: A 713 MET cc_start: 0.8204 (mmt) cc_final: 0.7649 (mmt) REVERT: A 832 LYS cc_start: 0.7391 (tptp) cc_final: 0.6758 (tptt) REVERT: A 834 HIS cc_start: 0.7918 (m90) cc_final: 0.7138 (m90) REVERT: B 551 PHE cc_start: 0.8350 (t80) cc_final: 0.8114 (t80) REVERT: B 592 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7858 (mp10) REVERT: B 713 MET cc_start: 0.8616 (mmt) cc_final: 0.8385 (mmt) REVERT: B 832 LYS cc_start: 0.7406 (tptp) cc_final: 0.6774 (tptt) REVERT: B 834 HIS cc_start: 0.7895 (m90) cc_final: 0.7076 (m90) REVERT: C 551 PHE cc_start: 0.8309 (t80) cc_final: 0.8093 (t80) REVERT: C 592 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7863 (mp10) REVERT: C 832 LYS cc_start: 0.7401 (tptp) cc_final: 0.6769 (tptt) REVERT: C 834 HIS cc_start: 0.7874 (m90) cc_final: 0.7058 (m90) REVERT: D 551 PHE cc_start: 0.8331 (t80) cc_final: 0.8097 (t80) REVERT: D 592 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7891 (mp10) REVERT: D 682 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7457 (tm-30) REVERT: D 725 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8820 (pt0) REVERT: D 832 LYS cc_start: 0.7414 (tptp) cc_final: 0.6788 (tptt) REVERT: D 834 HIS cc_start: 0.7896 (m90) cc_final: 0.7087 (m90) outliers start: 16 outliers final: 7 residues processed: 261 average time/residue: 0.2516 time to fit residues: 94.7765 Evaluate side-chains 236 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 224 time to evaluate : 1.407 ------------------------------------------------------------------------------- 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: 0.0670 chunk 132 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 155 optimal weight: 0.5980 overall best weight: 0.8922 ------------------------------------------------------------------------------- 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 ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4558 r_free = 0.4558 target = 0.190223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.126817 restraints weight = 29562.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.130396 restraints weight = 13577.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.132440 restraints weight = 8905.761| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2370 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= 0.151 Angle : 0.682 10.154 19152 Z= 0.345 Chirality : 0.045 0.181 2176 Planarity : 0.004 0.059 2376 Dihedral : 4.533 18.992 1876 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.77 % Favored : 92.76 % Rotamer: Outliers : 2.47 % Allowed : 18.82 % Favored : 78.71 % 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: -0.50 (0.21), residues: 1684 helix: 0.92 (0.16), residues: 1060 sheet: -2.48 (0.68), residues: 44 loop : -2.60 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 705 HIS 0.004 0.001 HIS B 731 PHE 0.018 0.002 PHE A 557 TYR 0.014 0.001 TYR A 652 ARG 0.005 0.000 ARG B 679 Details of bonding type rmsd hydrogen bonds : bond 0.06156 ( 810) hydrogen bonds : angle 4.75592 ( 2397) covalent geometry : bond 0.00313 (14096) covalent geometry : angle 0.68249 (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 285 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 249 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 TRP cc_start: 0.6808 (t-100) cc_final: 0.6594 (t-100) REVERT: A 462 MET cc_start: 0.5683 (pmm) cc_final: 0.5412 (pmm) REVERT: A 551 PHE cc_start: 0.8223 (t80) cc_final: 0.7930 (t80) REVERT: A 592 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: A 711 ILE cc_start: 0.9193 (mt) cc_final: 0.8884 (mm) REVERT: A 713 MET cc_start: 0.8015 (mmt) cc_final: 0.7539 (mmt) REVERT: A 725 GLN cc_start: 0.8742 (pt0) cc_final: 0.8387 (pm20) REVERT: A 832 LYS cc_start: 0.7448 (tptp) cc_final: 0.7186 (tptt) REVERT: A 833 ILE cc_start: 0.4319 (OUTLIER) cc_final: 0.3837 (mp) REVERT: B 462 MET cc_start: 0.5655 (pmm) cc_final: 0.5373 (pmm) REVERT: B 551 PHE cc_start: 0.8221 (t80) cc_final: 0.7933 (t80) REVERT: B 592 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7847 (mp10) REVERT: B 713 MET cc_start: 0.8424 (mmt) cc_final: 0.8137 (mmt) REVERT: B 725 GLN cc_start: 0.8736 (pt0) cc_final: 0.8404 (pm20) REVERT: B 832 LYS cc_start: 0.7443 (tptp) cc_final: 0.7186 (tptt) REVERT: B 833 ILE cc_start: 0.4310 (OUTLIER) cc_final: 0.3821 (mp) REVERT: C 462 MET cc_start: 0.5632 (pmm) cc_final: 0.5350 (pmm) REVERT: C 551 PHE cc_start: 0.8206 (t80) cc_final: 0.7924 (t80) REVERT: C 592 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7830 (mp10) REVERT: C 725 GLN cc_start: 0.8746 (pt0) cc_final: 0.8397 (pm20) REVERT: C 832 LYS cc_start: 0.7449 (tptp) cc_final: 0.7181 (tptt) REVERT: C 833 ILE cc_start: 0.4296 (OUTLIER) cc_final: 0.3803 (mp) REVERT: D 462 MET cc_start: 0.5633 (pmm) cc_final: 0.5353 (pmm) REVERT: D 551 PHE cc_start: 0.8208 (t80) cc_final: 0.7925 (t80) REVERT: D 592 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: D 682 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7508 (tm-30) REVERT: D 832 LYS cc_start: 0.7463 (tptp) cc_final: 0.7203 (tptt) REVERT: D 833 ILE cc_start: 0.4285 (OUTLIER) cc_final: 0.3794 (mp) outliers start: 36 outliers final: 15 residues processed: 271 average time/residue: 0.2448 time to fit residues: 98.3850 Evaluate side-chains 257 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 1.509 ------------------------------------------------------------------------------- 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 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 670 THR 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: 0.0060 chunk 83 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 129 optimal weight: 20.0000 chunk 46 optimal weight: 0.6980 chunk 163 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 ASN B 695 GLN ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 819 ASN C 695 GLN C 810 ASN D 695 GLN D 725 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 = 0.191159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.135407 restraints weight = 29891.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.135399 restraints weight = 17273.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.134777 restraints weight = 11948.064| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2697 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 : 0.661 9.483 19152 Z= 0.337 Chirality : 0.045 0.249 2176 Planarity : 0.004 0.037 2376 Dihedral : 4.412 19.638 1876 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.83 % Favored : 92.70 % Rotamer: Outliers : 2.75 % Allowed : 19.78 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.21), residues: 1684 helix: 0.99 (0.16), residues: 1064 sheet: -2.63 (0.68), residues: 44 loop : -2.57 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 705 HIS 0.004 0.001 HIS D 731 PHE 0.022 0.002 PHE C 557 TYR 0.025 0.001 TYR A 700 ARG 0.004 0.000 ARG B 679 Details of bonding type rmsd hydrogen bonds : bond 0.05989 ( 810) hydrogen bonds : angle 4.61817 ( 2397) covalent geometry : bond 0.00293 (14096) covalent geometry : angle 0.66057 (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 297 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 257 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 PHE cc_start: 0.5426 (OUTLIER) cc_final: 0.5045 (t80) REVERT: A 551 PHE cc_start: 0.8270 (t80) cc_final: 0.7963 (t80) REVERT: A 592 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7880 (mp10) REVERT: A 700 TYR cc_start: 0.9032 (t80) cc_final: 0.8765 (t80) REVERT: A 711 ILE cc_start: 0.9183 (mt) cc_final: 0.8844 (mm) REVERT: A 713 MET cc_start: 0.8121 (mmt) cc_final: 0.7643 (mmt) REVERT: A 725 GLN cc_start: 0.8732 (pt0) cc_final: 0.8299 (pm20) REVERT: A 751 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8546 (mt) REVERT: A 832 LYS cc_start: 0.7655 (tptp) cc_final: 0.7266 (tptt) REVERT: B 551 PHE cc_start: 0.8347 (t80) cc_final: 0.8049 (t80) REVERT: B 592 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7865 (mp10) REVERT: B 664 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: B 682 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7656 (tm-30) REVERT: B 713 MET cc_start: 0.8503 (mmt) cc_final: 0.8235 (mmt) REVERT: B 725 GLN cc_start: 0.8741 (pt0) cc_final: 0.8336 (pm20) REVERT: B 751 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8539 (mt) REVERT: B 832 LYS cc_start: 0.7672 (tptp) cc_final: 0.7284 (tptt) REVERT: C 471 PHE cc_start: 0.5254 (OUTLIER) cc_final: 0.5008 (t80) REVERT: C 551 PHE cc_start: 0.8335 (t80) cc_final: 0.8053 (t80) REVERT: C 592 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7832 (mp10) REVERT: C 682 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7787 (tm-30) REVERT: C 713 MET cc_start: 0.8271 (mmt) cc_final: 0.7973 (mmt) REVERT: C 725 GLN cc_start: 0.8739 (pt0) cc_final: 0.8343 (pm20) REVERT: C 751 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8528 (mt) REVERT: C 832 LYS cc_start: 0.7657 (tptp) cc_final: 0.7294 (tptt) REVERT: D 471 PHE cc_start: 0.5281 (OUTLIER) cc_final: 0.4993 (t80) REVERT: D 551 PHE cc_start: 0.8321 (t80) cc_final: 0.8026 (t80) REVERT: D 592 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7900 (mp10) REVERT: D 664 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: D 682 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7648 (tm-30) REVERT: D 700 TYR cc_start: 0.9035 (t80) cc_final: 0.8814 (t80) REVERT: D 713 MET cc_start: 0.8177 (mmt) cc_final: 0.7950 (mmt) REVERT: D 751 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8517 (mt) REVERT: D 832 LYS cc_start: 0.7667 (tptp) cc_final: 0.7274 (tptt) outliers start: 40 outliers final: 15 residues processed: 288 average time/residue: 0.2527 time to fit residues: 108.3217 Evaluate side-chains 265 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 1.458 ------------------------------------------------------------------------------- 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 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 592 GLN 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 592 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 Chi-restraints excluded: chain D residue 831 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 59 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 151 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 38 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN B 810 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.192015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.131822 restraints weight = 30041.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.135945 restraints weight = 16040.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.136095 restraints weight = 9102.834| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14096 Z= 0.138 Angle : 0.684 10.413 19152 Z= 0.344 Chirality : 0.045 0.248 2176 Planarity : 0.003 0.036 2376 Dihedral : 4.383 20.564 1876 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.59 % Favored : 92.93 % Rotamer: Outliers : 2.40 % Allowed : 20.67 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.21), residues: 1684 helix: 1.07 (0.16), residues: 1064 sheet: -2.70 (0.64), residues: 44 loop : -2.58 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 705 HIS 0.005 0.001 HIS A 851 PHE 0.016 0.001 PHE D 557 TYR 0.018 0.001 TYR D 700 ARG 0.003 0.000 ARG D 681 Details of bonding type rmsd hydrogen bonds : bond 0.05781 ( 810) hydrogen bonds : angle 4.52033 ( 2397) covalent geometry : bond 0.00280 (14096) covalent geometry : angle 0.68395 (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 286 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 PHE cc_start: 0.5323 (OUTLIER) cc_final: 0.5000 (t80) REVERT: A 551 PHE cc_start: 0.8340 (t80) cc_final: 0.8137 (t80) REVERT: A 592 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7856 (mp10) REVERT: A 700 TYR cc_start: 0.9006 (t80) cc_final: 0.8654 (t80) REVERT: A 711 ILE cc_start: 0.9206 (mt) cc_final: 0.8895 (mm) REVERT: A 713 MET cc_start: 0.8144 (mmt) cc_final: 0.7695 (mmt) REVERT: A 725 GLN cc_start: 0.8712 (pt0) cc_final: 0.8272 (pm20) REVERT: A 751 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8452 (mt) REVERT: A 832 LYS cc_start: 0.7711 (tptp) cc_final: 0.7439 (tptt) REVERT: B 592 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7849 (mp10) REVERT: B 664 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: B 713 MET cc_start: 0.8496 (mmt) cc_final: 0.8220 (mmt) REVERT: B 725 GLN cc_start: 0.8748 (pt0) cc_final: 0.8297 (pm20) REVERT: B 751 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8457 (mt) REVERT: B 832 LYS cc_start: 0.7704 (tptp) cc_final: 0.7335 (tptt) REVERT: C 471 PHE cc_start: 0.5172 (OUTLIER) cc_final: 0.4829 (t80) REVERT: C 592 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7791 (mp10) REVERT: C 682 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7735 (tm-30) REVERT: C 725 GLN cc_start: 0.8683 (pt0) cc_final: 0.8257 (pm20) REVERT: C 751 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8453 (mt) REVERT: C 832 LYS cc_start: 0.7705 (tptp) cc_final: 0.7332 (tptt) REVERT: D 592 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7852 (mp10) REVERT: D 664 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: D 682 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7746 (tm-30) REVERT: D 700 TYR cc_start: 0.9006 (t80) cc_final: 0.8687 (t80) REVERT: D 725 GLN cc_start: 0.8800 (pt0) cc_final: 0.8359 (pt0) REVERT: D 751 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8446 (mt) REVERT: D 832 LYS cc_start: 0.7698 (tptp) cc_final: 0.7314 (tptt) outliers start: 35 outliers final: 18 residues processed: 276 average time/residue: 0.2800 time to fit residues: 114.3217 Evaluate side-chains 269 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 239 time to evaluate : 1.856 ------------------------------------------------------------------------------- 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 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 592 GLN Chi-restraints excluded: chain B residue 593 ILE 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 592 GLN 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 592 GLN Chi-restraints excluded: chain D residue 593 ILE 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: 0.2980 chunk 49 optimal weight: 20.0000 chunk 4 optimal weight: 0.6980 chunk 84 optimal weight: 0.0050 chunk 31 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 167 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 B 695 GLN ** C 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 GLN 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 = 0.4581 r_free = 0.4581 target = 0.192770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.138362 restraints weight = 30034.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.135069 restraints weight = 17408.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.136952 restraints weight = 13319.611| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3189 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= 0.136 Angle : 0.665 8.885 19152 Z= 0.337 Chirality : 0.044 0.215 2176 Planarity : 0.003 0.034 2376 Dihedral : 4.297 18.685 1876 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.41 % Favored : 93.11 % Rotamer: Outliers : 2.68 % Allowed : 20.74 % Favored : 76.58 % 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: -0.23 (0.21), residues: 1684 helix: 1.15 (0.16), residues: 1064 sheet: -2.80 (0.61), residues: 44 loop : -2.52 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 705 HIS 0.004 0.001 HIS C 851 PHE 0.021 0.002 PHE C 551 TYR 0.027 0.001 TYR B 700 ARG 0.006 0.000 ARG D 694 Details of bonding type rmsd hydrogen bonds : bond 0.05622 ( 810) hydrogen bonds : angle 4.45780 ( 2397) covalent geometry : bond 0.00277 (14096) covalent geometry : angle 0.66506 (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 288 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 249 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 592 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7878 (mp10) REVERT: A 664 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: A 700 TYR cc_start: 0.8979 (t80) cc_final: 0.8690 (t80) REVERT: A 711 ILE cc_start: 0.9216 (mt) cc_final: 0.8891 (mm) REVERT: A 713 MET cc_start: 0.8085 (mmt) cc_final: 0.7686 (mmt) REVERT: A 725 GLN cc_start: 0.8704 (pt0) cc_final: 0.8222 (pm20) REVERT: A 751 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8428 (mt) REVERT: A 832 LYS cc_start: 0.7719 (tptp) cc_final: 0.7283 (tptt) REVERT: B 592 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7843 (mp10) REVERT: B 664 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7194 (tt0) REVERT: B 700 TYR cc_start: 0.8983 (t80) cc_final: 0.8733 (t80) REVERT: B 713 MET cc_start: 0.8445 (mmt) cc_final: 0.8191 (mmt) REVERT: B 722 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8313 (mm-30) REVERT: B 725 GLN cc_start: 0.8732 (pt0) cc_final: 0.8274 (pm20) REVERT: B 751 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8456 (mt) REVERT: B 832 LYS cc_start: 0.7738 (tptp) cc_final: 0.7345 (tptt) REVERT: C 471 PHE cc_start: 0.5141 (OUTLIER) cc_final: 0.4844 (t80) REVERT: C 592 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7771 (mp10) REVERT: C 664 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: C 682 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7870 (tm-30) REVERT: C 725 GLN cc_start: 0.8650 (pt0) cc_final: 0.8215 (pm20) REVERT: C 751 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8475 (mt) REVERT: C 832 LYS cc_start: 0.7708 (tptp) cc_final: 0.7337 (tptt) REVERT: D 592 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7905 (mp10) REVERT: D 664 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: D 682 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7751 (tm-30) REVERT: D 695 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8183 (mm110) REVERT: D 700 TYR cc_start: 0.8952 (t80) cc_final: 0.8649 (t80) REVERT: D 722 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8291 (mm-30) REVERT: D 725 GLN cc_start: 0.8784 (pt0) cc_final: 0.8349 (pm20) REVERT: D 751 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8458 (mt) REVERT: D 832 LYS cc_start: 0.7720 (tptp) cc_final: 0.7266 (tptt) outliers start: 39 outliers final: 17 residues processed: 278 average time/residue: 0.2894 time to fit residues: 119.1013 Evaluate side-chains 272 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 751 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 831 HIS 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 592 GLN Chi-restraints excluded: chain C residue 621 SER 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 831 HIS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 51 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 146 optimal weight: 0.1980 chunk 114 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 819 ASN C 402 HIS C 664 GLN D 402 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.192431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.131471 restraints weight = 29950.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.135013 restraints weight = 15593.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.135813 restraints weight = 9647.800| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14096 Z= 0.147 Angle : 0.691 9.994 19152 Z= 0.351 Chirality : 0.045 0.210 2176 Planarity : 0.003 0.034 2376 Dihedral : 4.275 18.119 1876 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.65 % Favored : 92.87 % Rotamer: Outliers : 2.61 % Allowed : 21.50 % Favored : 75.89 % 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: -0.14 (0.21), residues: 1684 helix: 1.22 (0.16), residues: 1056 sheet: -2.97 (0.57), residues: 44 loop : -2.40 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 705 HIS 0.006 0.001 HIS B 851 PHE 0.023 0.002 PHE C 551 TYR 0.024 0.001 TYR C 700 ARG 0.003 0.000 ARG B 679 Details of bonding type rmsd hydrogen bonds : bond 0.05682 ( 810) hydrogen bonds : angle 4.47841 ( 2397) covalent geometry : bond 0.00309 (14096) covalent geometry : angle 0.69140 (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 285 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 247 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 PHE cc_start: 0.5059 (OUTLIER) cc_final: 0.4685 (m-80) REVERT: A 592 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7863 (mp10) REVERT: A 698 GLU cc_start: 0.8801 (mp0) cc_final: 0.8567 (mp0) REVERT: A 700 TYR cc_start: 0.9130 (t80) cc_final: 0.8775 (t80) REVERT: A 711 ILE cc_start: 0.9185 (mt) cc_final: 0.8857 (mm) REVERT: A 713 MET cc_start: 0.8201 (mmt) cc_final: 0.7735 (mmt) REVERT: A 725 GLN cc_start: 0.8762 (pt0) cc_final: 0.8253 (pm20) REVERT: A 751 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8369 (mt) REVERT: A 832 LYS cc_start: 0.7795 (tptp) cc_final: 0.7358 (tptt) REVERT: B 592 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7855 (mp10) REVERT: B 664 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: B 700 TYR cc_start: 0.9089 (t80) cc_final: 0.8645 (t80) REVERT: B 713 MET cc_start: 0.8540 (mmt) cc_final: 0.8203 (mmt) REVERT: B 725 GLN cc_start: 0.8785 (pt0) cc_final: 0.8286 (pm20) REVERT: B 751 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8354 (mt) REVERT: B 832 LYS cc_start: 0.7779 (tptp) cc_final: 0.7338 (tptt) REVERT: C 592 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7763 (mp10) REVERT: C 682 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7906 (tm-30) REVERT: C 700 TYR cc_start: 0.9060 (t80) cc_final: 0.8840 (t80) REVERT: C 725 GLN cc_start: 0.8727 (pt0) cc_final: 0.8233 (pm20) REVERT: C 751 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8373 (mt) REVERT: C 832 LYS cc_start: 0.7768 (tptp) cc_final: 0.7330 (tptt) REVERT: D 592 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7876 (mp10) REVERT: D 664 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: D 682 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7874 (tm-30) REVERT: D 691 ASN cc_start: 0.8470 (t0) cc_final: 0.8001 (t0) REVERT: D 695 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8126 (mm-40) REVERT: D 700 TYR cc_start: 0.9042 (t80) cc_final: 0.8743 (t80) REVERT: D 722 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8261 (mm-30) REVERT: D 725 GLN cc_start: 0.8841 (pt0) cc_final: 0.8346 (pm20) REVERT: D 751 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8346 (mt) REVERT: D 832 LYS cc_start: 0.7780 (tptp) cc_final: 0.7342 (tptt) outliers start: 38 outliers final: 21 residues processed: 274 average time/residue: 0.2318 time to fit residues: 94.4640 Evaluate side-chains 276 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 243 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 664 GLN Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain B residue 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 771 HIS Chi-restraints excluded: chain B residue 831 HIS 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 771 HIS Chi-restraints excluded: chain C residue 831 HIS 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 831 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 35 optimal weight: 0.2980 chunk 54 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 83 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN B 819 ASN C 470 ASN C 664 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.192704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.133933 restraints weight = 29842.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.135623 restraints weight = 18050.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.136138 restraints weight = 11076.285| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3478 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= 0.144 Angle : 0.704 10.901 19152 Z= 0.353 Chirality : 0.045 0.208 2176 Planarity : 0.003 0.034 2376 Dihedral : 4.249 18.629 1876 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.71 % Favored : 92.81 % Rotamer: Outliers : 3.16 % Allowed : 20.74 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1684 helix: 1.29 (0.16), residues: 1040 sheet: -3.00 (0.53), residues: 44 loop : -2.33 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 705 HIS 0.005 0.001 HIS D 851 PHE 0.024 0.002 PHE A 551 TYR 0.022 0.001 TYR C 700 ARG 0.003 0.000 ARG B 679 Details of bonding type rmsd hydrogen bonds : bond 0.05645 ( 810) hydrogen bonds : angle 4.41155 ( 2397) covalent geometry : bond 0.00300 (14096) covalent geometry : angle 0.70381 (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 283 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 237 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: A 498 PHE cc_start: 0.5085 (OUTLIER) cc_final: 0.4756 (m-80) REVERT: A 592 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7882 (mp10) REVERT: A 700 TYR cc_start: 0.9075 (t80) cc_final: 0.8781 (t80) REVERT: A 711 ILE cc_start: 0.9187 (mt) cc_final: 0.8835 (mm) REVERT: A 713 MET cc_start: 0.8154 (mmt) cc_final: 0.7724 (mmt) REVERT: A 725 GLN cc_start: 0.8765 (pt0) cc_final: 0.8280 (pm20) REVERT: A 751 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8359 (mt) REVERT: A 832 LYS cc_start: 0.7792 (tptp) cc_final: 0.7262 (tptt) REVERT: B 498 PHE cc_start: 0.6290 (t80) cc_final: 0.6069 (m-80) REVERT: B 592 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7871 (mp10) REVERT: B 664 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: B 700 TYR cc_start: 0.9104 (t80) cc_final: 0.8629 (t80) REVERT: B 713 MET cc_start: 0.8547 (mmt) cc_final: 0.8181 (mmt) REVERT: B 725 GLN cc_start: 0.8764 (pt0) cc_final: 0.8270 (pm20) REVERT: B 751 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8381 (mt) REVERT: B 832 LYS cc_start: 0.7776 (tptp) cc_final: 0.7356 (tptt) REVERT: C 592 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: C 682 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7885 (tm-30) REVERT: C 700 TYR cc_start: 0.9060 (t80) cc_final: 0.8696 (t80) REVERT: C 725 GLN cc_start: 0.8726 (pt0) cc_final: 0.8230 (pm20) REVERT: C 751 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8398 (mt) REVERT: C 832 LYS cc_start: 0.7779 (tptp) cc_final: 0.7267 (tptt) REVERT: D 592 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7889 (mp10) REVERT: D 664 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: D 682 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7867 (tm-30) REVERT: D 700 TYR cc_start: 0.9034 (t80) cc_final: 0.8745 (t80) REVERT: D 722 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8299 (mm-30) REVERT: D 725 GLN cc_start: 0.8885 (pt0) cc_final: 0.8386 (pm20) REVERT: D 751 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8350 (mt) REVERT: D 832 LYS cc_start: 0.7769 (tptp) cc_final: 0.7339 (tptt) outliers start: 46 outliers final: 35 residues processed: 268 average time/residue: 0.3116 time to fit residues: 123.9487 Evaluate side-chains 281 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 714 ASN 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 470 ASN Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 695 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 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 651 MET 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 85 optimal weight: 4.9990 chunk 19 optimal weight: 0.0970 chunk 113 optimal weight: 0.9990 chunk 150 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 31 optimal weight: 0.0370 chunk 13 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN A 691 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 GLN ** C 676 GLN ** 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 = 0.4585 r_free = 0.4585 target = 0.193450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.133672 restraints weight = 29887.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.137709 restraints weight = 16539.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.137113 restraints weight = 9304.496| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14096 Z= 0.141 Angle : 0.710 10.729 19152 Z= 0.357 Chirality : 0.045 0.205 2176 Planarity : 0.003 0.034 2376 Dihedral : 4.249 19.065 1876 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.53 % Favored : 92.99 % Rotamer: Outliers : 3.16 % Allowed : 21.29 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1684 helix: 1.27 (0.16), residues: 1044 sheet: -3.00 (0.53), residues: 44 loop : -2.29 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 705 HIS 0.005 0.001 HIS B 851 PHE 0.023 0.002 PHE A 551 TYR 0.024 0.001 TYR C 700 ARG 0.003 0.000 ARG B 679 Details of bonding type rmsd hydrogen bonds : bond 0.05564 ( 810) hydrogen bonds : angle 4.41347 ( 2397) covalent geometry : bond 0.00287 (14096) covalent geometry : angle 0.70958 (19152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 241 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 PHE cc_start: 0.5117 (OUTLIER) cc_final: 0.4843 (m-80) REVERT: A 592 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: A 664 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: A 700 TYR cc_start: 0.9095 (t80) cc_final: 0.8786 (t80) REVERT: A 702 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8405 (mp10) REVERT: A 711 ILE cc_start: 0.9177 (mt) cc_final: 0.8823 (mm) REVERT: A 713 MET cc_start: 0.8187 (mmt) cc_final: 0.7748 (mmt) REVERT: A 725 GLN cc_start: 0.8727 (pt0) cc_final: 0.8249 (pm20) REVERT: A 751 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8350 (mt) REVERT: A 832 LYS cc_start: 0.7766 (tptp) cc_final: 0.7261 (tptt) REVERT: B 498 PHE cc_start: 0.6342 (t80) cc_final: 0.6126 (m-80) REVERT: B 592 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7864 (mp10) REVERT: B 664 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: B 691 ASN cc_start: 0.8515 (t0) cc_final: 0.8082 (t0) REVERT: B 700 TYR cc_start: 0.9098 (t80) cc_final: 0.8699 (t80) REVERT: B 713 MET cc_start: 0.8532 (mmt) cc_final: 0.8167 (mmt) REVERT: B 725 GLN cc_start: 0.8765 (pt0) cc_final: 0.8264 (pm20) REVERT: B 751 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8347 (mt) REVERT: B 832 LYS cc_start: 0.7788 (tptp) cc_final: 0.7282 (tptt) REVERT: C 592 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7778 (mp10) REVERT: C 664 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: C 682 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7948 (tm-30) REVERT: C 700 TYR cc_start: 0.9045 (t80) cc_final: 0.8662 (t80) REVERT: C 725 GLN cc_start: 0.8721 (pt0) cc_final: 0.8215 (pm20) REVERT: C 751 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8327 (mt) REVERT: C 814 ARG cc_start: 0.2005 (mmm160) cc_final: 0.1625 (mmm160) REVERT: C 832 LYS cc_start: 0.7783 (tptp) cc_final: 0.7280 (tptt) REVERT: D 592 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7865 (mp10) REVERT: D 664 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8082 (tt0) REVERT: D 682 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7905 (tm-30) REVERT: D 700 TYR cc_start: 0.9041 (t80) cc_final: 0.8754 (t80) REVERT: D 722 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8290 (mm-30) REVERT: D 725 GLN cc_start: 0.8883 (pt0) cc_final: 0.8367 (pm20) REVERT: D 751 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8312 (mt) REVERT: D 832 LYS cc_start: 0.7778 (tptp) cc_final: 0.7268 (tptt) outliers start: 46 outliers final: 28 residues processed: 272 average time/residue: 0.2549 time to fit residues: 104.3606 Evaluate side-chains 280 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 714 ASN Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 589 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 49 optimal weight: 30.0000 chunk 17 optimal weight: 0.5980 chunk 96 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 162 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN A 691 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 GLN ** C 676 GLN ** 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 = 0.4572 r_free = 0.4572 target = 0.192109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.131177 restraints weight = 30135.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.134398 restraints weight = 16567.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.135171 restraints weight = 10245.160| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14096 Z= 0.157 Angle : 0.734 12.158 19152 Z= 0.366 Chirality : 0.045 0.204 2176 Planarity : 0.003 0.035 2376 Dihedral : 4.251 19.066 1876 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.95 % Favored : 92.58 % Rotamer: Outliers : 3.09 % Allowed : 21.50 % 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: 1.28 (0.16), residues: 1040 sheet: -3.03 (0.50), residues: 44 loop : -2.33 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 705 HIS 0.006 0.001 HIS B 851 PHE 0.024 0.002 PHE A 551 TYR 0.021 0.001 TYR C 700 ARG 0.003 0.000 ARG A 681 Details of bonding type rmsd hydrogen bonds : bond 0.05709 ( 810) hydrogen bonds : angle 4.45636 ( 2397) covalent geometry : bond 0.00339 (14096) covalent geometry : angle 0.73393 (19152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5880.08 seconds wall clock time: 109 minutes 38.49 seconds (6578.49 seconds total)