Starting phenix.real_space_refine on Sat Aug 23 18:10:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8io5_35608/08_2025/8io5_35608.cif Found real_map, /net/cci-nas-00/data/ceres_data/8io5_35608/08_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_35608/08_2025/8io5_35608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8io5_35608/08_2025/8io5_35608.map" model { file = "/net/cci-nas-00/data/ceres_data/8io5_35608/08_2025/8io5_35608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8io5_35608/08_2025/8io5_35608.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'TRP:plan': 1, 'GLU:plan': 2, '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: {'TRP:plan': 1, 'GLU:plan': 2, '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: {'TRP:plan': 1, 'GLU:plan': 2, '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: {'TRP:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 3.53, per 1000 atoms: 0.26 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: 1.23 Conformation dependent library (CDL) restraints added in 628.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.45 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: 2.26 Time building geometry restraints manager: 1.63 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.170 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.670 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG A 835 TYR 0.026 0.002 TYR B 652 PHE 0.018 0.003 PHE D 848 TRP 0.027 0.002 TRP A 705 HIS 0.008 0.002 HIS B 731 Details of bonding type rmsd covalent geometry : bond 0.00477 (14096) covalent geometry : angle 0.87505 (19152) hydrogen bonds : bond 0.14627 ( 810) hydrogen bonds : angle 6.51961 ( 2397) *********************** 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 : 0.525 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: 0.7898 (mt) REVERT: A 832 LYS cc_start: 0.7273 (tptp) cc_final: 0.6613 (tptt) REVERT: A 834 HIS cc_start: 0.7998 (m90) cc_final: 0.7033 (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: 0.7903 (mt) REVERT: B 832 LYS cc_start: 0.7310 (tptp) cc_final: 0.6636 (tptt) REVERT: B 834 HIS cc_start: 0.8016 (m90) cc_final: 0.7072 (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: 0.7902 (mt) REVERT: C 832 LYS cc_start: 0.7264 (tptp) cc_final: 0.6587 (tptt) REVERT: C 834 HIS cc_start: 0.7973 (m90) cc_final: 0.7010 (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: 0.6600 (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: 0.1141 time to fit residues: 51.1495 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 : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.0050 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.7796 ------------------------------------------------------------------------------- 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** D 819 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.189977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.137154 restraints weight = 29896.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.133871 restraints weight = 18070.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.135386 restraints weight = 14071.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.136174 restraints weight = 11784.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.136352 restraints weight = 10328.610| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1500 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= 0.164 Angle : 0.717 8.710 19152 Z= 0.368 Chirality : 0.046 0.184 2176 Planarity : 0.005 0.041 2376 Dihedral : 4.776 19.721 1876 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.77 % Favored : 92.76 % Rotamer: Outliers : 0.96 % Allowed : 10.92 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.21), residues: 1684 helix: 0.77 (0.16), residues: 1052 sheet: -3.34 (0.50), residues: 44 loop : -2.76 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 814 TYR 0.018 0.002 TYR C 652 PHE 0.015 0.002 PHE A 471 TRP 0.012 0.002 TRP B 705 HIS 0.007 0.001 HIS D 731 Details of bonding type rmsd covalent geometry : bond 0.00332 (14096) covalent geometry : angle 0.71698 (19152) hydrogen bonds : bond 0.06881 ( 810) hydrogen bonds : angle 5.23019 ( 2397) *********************** 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 293 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 279 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 TRP cc_start: 0.6747 (m100) cc_final: 0.6376 (m100) REVERT: A 551 PHE cc_start: 0.8310 (t80) cc_final: 0.8065 (t80) REVERT: A 592 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7986 (mp10) REVERT: A 691 ASN cc_start: 0.8420 (t0) cc_final: 0.8216 (t0) REVERT: A 698 GLU cc_start: 0.8389 (mp0) cc_final: 0.8044 (mp0) REVERT: A 711 ILE cc_start: 0.9048 (mt) cc_final: 0.8646 (mm) REVERT: A 713 MET cc_start: 0.8246 (mmt) cc_final: 0.7756 (mmt) REVERT: A 832 LYS cc_start: 0.7373 (tptp) cc_final: 0.6856 (tptt) REVERT: B 497 TRP cc_start: 0.6759 (m100) cc_final: 0.6395 (m100) REVERT: B 551 PHE cc_start: 0.8364 (t80) cc_final: 0.8119 (t80) REVERT: B 592 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7939 (mp10) REVERT: B 698 GLU cc_start: 0.8690 (mp0) cc_final: 0.8382 (mp0) REVERT: B 832 LYS cc_start: 0.7393 (tptp) cc_final: 0.6871 (tptt) REVERT: C 497 TRP cc_start: 0.6762 (m100) cc_final: 0.6392 (m100) REVERT: C 551 PHE cc_start: 0.8324 (t80) cc_final: 0.8090 (t80) REVERT: C 592 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7936 (mp10) REVERT: C 698 GLU cc_start: 0.8681 (mp0) cc_final: 0.8372 (mp0) REVERT: C 832 LYS cc_start: 0.7381 (tptp) cc_final: 0.6862 (tptt) REVERT: D 497 TRP cc_start: 0.6771 (m100) cc_final: 0.6404 (m100) REVERT: D 551 PHE cc_start: 0.8313 (t80) cc_final: 0.8079 (t80) REVERT: D 592 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8008 (mp10) REVERT: D 682 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7389 (tm-30) REVERT: D 698 GLU cc_start: 0.8473 (mp0) cc_final: 0.8108 (mp0) REVERT: D 832 LYS cc_start: 0.7412 (tptp) cc_final: 0.6888 (tptt) outliers start: 14 outliers final: 10 residues processed: 288 average time/residue: 0.1031 time to fit residues: 45.0778 Evaluate side-chains 252 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 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 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 169 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 135 optimal weight: 30.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 819 ASN ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 810 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.186297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.121978 restraints weight = 30105.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.125308 restraints weight = 15336.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.126449 restraints weight = 10663.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.126803 restraints weight = 8104.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.127052 restraints weight = 8361.129| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14096 Z= 0.241 Angle : 0.802 12.576 19152 Z= 0.400 Chirality : 0.047 0.181 2176 Planarity : 0.005 0.040 2376 Dihedral : 4.826 21.181 1876 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.83 % Favored : 92.70 % Rotamer: Outliers : 1.85 % Allowed : 16.90 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.20), residues: 1684 helix: 0.55 (0.15), residues: 1060 sheet: -2.66 (0.63), residues: 44 loop : -2.75 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 814 TYR 0.022 0.002 TYR D 652 PHE 0.018 0.002 PHE A 557 TRP 0.016 0.002 TRP B 705 HIS 0.007 0.002 HIS A 851 Details of bonding type rmsd covalent geometry : bond 0.00534 (14096) covalent geometry : angle 0.80178 (19152) hydrogen bonds : bond 0.07148 ( 810) hydrogen bonds : angle 5.22645 ( 2397) *********************** 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: 27 poor density : 240 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 551 PHE cc_start: 0.8310 (t80) cc_final: 0.8081 (t80) REVERT: A 592 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7974 (mp10) REVERT: A 682 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7984 (tm-30) REVERT: A 691 ASN cc_start: 0.8530 (t0) cc_final: 0.8216 (t0) REVERT: A 713 MET cc_start: 0.8184 (mmt) cc_final: 0.7516 (mmt) REVERT: A 725 GLN cc_start: 0.8900 (pt0) cc_final: 0.8370 (pm20) REVERT: A 832 LYS cc_start: 0.7494 (tptp) cc_final: 0.7116 (tptt) REVERT: B 551 PHE cc_start: 0.8322 (t80) cc_final: 0.8099 (t80) REVERT: B 592 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7936 (mp10) REVERT: B 713 MET cc_start: 0.8576 (mmt) cc_final: 0.8294 (mmt) REVERT: B 725 GLN cc_start: 0.8890 (pt0) cc_final: 0.8418 (pm20) REVERT: B 832 LYS cc_start: 0.7501 (tptp) cc_final: 0.7123 (tptt) REVERT: C 551 PHE cc_start: 0.8312 (t80) cc_final: 0.8092 (t80) REVERT: C 592 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7940 (mp10) REVERT: C 705 TRP cc_start: 0.8907 (t60) cc_final: 0.8437 (t60) REVERT: C 722 GLU cc_start: 0.8240 (pm20) cc_final: 0.8002 (mm-30) REVERT: C 725 GLN cc_start: 0.8944 (pt0) cc_final: 0.8403 (pm20) REVERT: C 832 LYS cc_start: 0.7493 (tptp) cc_final: 0.7109 (tptt) REVERT: D 551 PHE cc_start: 0.8303 (t80) cc_final: 0.8078 (t80) REVERT: D 592 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8020 (mp10) REVERT: D 682 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7240 (tm-30) REVERT: D 695 GLN cc_start: 0.8658 (mm110) cc_final: 0.8446 (mm110) REVERT: D 725 GLN cc_start: 0.8920 (pt0) cc_final: 0.8402 (pm20) REVERT: D 832 LYS cc_start: 0.7497 (tptp) cc_final: 0.7096 (tptt) outliers start: 27 outliers final: 19 residues processed: 257 average time/residue: 0.1120 time to fit residues: 41.8283 Evaluate side-chains 253 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 771 HIS Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 670 THR 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 556 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 136 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 chunk 150 optimal weight: 0.6980 chunk 168 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 58 optimal weight: 0.1980 chunk 170 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN ** 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 810 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.190781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.130728 restraints weight = 29760.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.135292 restraints weight = 15371.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.135530 restraints weight = 9293.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.135276 restraints weight = 8091.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.135526 restraints weight = 8306.256| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2412 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= 0.141 Angle : 0.670 9.855 19152 Z= 0.337 Chirality : 0.043 0.181 2176 Planarity : 0.004 0.033 2376 Dihedral : 4.579 19.040 1876 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.59 % Favored : 92.93 % Rotamer: Outliers : 1.85 % Allowed : 19.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.21), residues: 1684 helix: 0.96 (0.16), residues: 1060 sheet: -2.66 (0.67), residues: 44 loop : -2.70 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 679 TYR 0.014 0.001 TYR A 420 PHE 0.025 0.002 PHE C 557 TRP 0.021 0.002 TRP B 705 HIS 0.004 0.001 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00280 (14096) covalent geometry : angle 0.67038 (19152) hydrogen bonds : bond 0.06230 ( 810) hydrogen bonds : angle 4.72428 ( 2397) *********************** 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 282 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 255 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.5606 (pmm) cc_final: 0.5176 (pmm) REVERT: A 551 PHE cc_start: 0.8331 (t80) cc_final: 0.8043 (t80) REVERT: A 592 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7887 (mp10) REVERT: A 711 ILE cc_start: 0.8947 (mt) cc_final: 0.8641 (mm) REVERT: A 713 MET cc_start: 0.8278 (mmt) cc_final: 0.7694 (mmt) REVERT: A 833 ILE cc_start: 0.4177 (OUTLIER) cc_final: 0.3730 (mp) REVERT: B 462 MET cc_start: 0.5662 (pmm) cc_final: 0.5212 (pmm) REVERT: B 551 PHE cc_start: 0.8361 (t80) cc_final: 0.8040 (t80) REVERT: B 592 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7843 (mp10) REVERT: B 713 MET cc_start: 0.8608 (mmt) cc_final: 0.8328 (mmt) REVERT: B 725 GLN cc_start: 0.8781 (pt0) cc_final: 0.8351 (pm20) REVERT: B 833 ILE cc_start: 0.4149 (OUTLIER) cc_final: 0.3723 (mp) REVERT: C 462 MET cc_start: 0.5647 (pmm) cc_final: 0.5187 (pmm) REVERT: C 551 PHE cc_start: 0.8356 (t80) cc_final: 0.8040 (t80) REVERT: C 592 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7850 (mp10) REVERT: C 682 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7787 (tm-30) REVERT: C 705 TRP cc_start: 0.8920 (t60) cc_final: 0.8491 (t60) REVERT: C 725 GLN cc_start: 0.8834 (pt0) cc_final: 0.8308 (pm20) REVERT: C 833 ILE cc_start: 0.4151 (OUTLIER) cc_final: 0.3728 (mp) REVERT: D 462 MET cc_start: 0.5629 (pmm) cc_final: 0.5187 (pmm) REVERT: D 551 PHE cc_start: 0.8334 (t80) cc_final: 0.8035 (t80) REVERT: D 592 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7914 (mp10) REVERT: D 682 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7447 (tm-30) REVERT: D 695 GLN cc_start: 0.8734 (mm110) cc_final: 0.8506 (mm110) REVERT: D 713 MET cc_start: 0.8382 (mmt) cc_final: 0.8106 (mmt) REVERT: D 725 GLN cc_start: 0.8779 (pt0) cc_final: 0.8296 (pm20) REVERT: D 833 ILE cc_start: 0.4161 (OUTLIER) cc_final: 0.3707 (mp) outliers start: 27 outliers final: 13 residues processed: 278 average time/residue: 0.0965 time to fit residues: 39.8374 Evaluate side-chains 265 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 714 ASN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 771 HIS Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 771 HIS Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain C residue 833 ILE Chi-restraints excluded: chain D residue 592 GLN Chi-restraints excluded: chain D residue 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 141 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 81 optimal weight: 0.0570 chunk 90 optimal weight: 0.8980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 819 ASN ** C 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 ASN ** D 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.190419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.132253 restraints weight = 30027.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.132517 restraints weight = 19399.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.133458 restraints weight = 12395.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.134454 restraints weight = 10995.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.134496 restraints weight = 9549.143| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2718 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 : 0.658 9.266 19152 Z= 0.332 Chirality : 0.044 0.178 2176 Planarity : 0.004 0.032 2376 Dihedral : 4.454 18.400 1876 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.59 % Favored : 92.93 % Rotamer: Outliers : 3.30 % Allowed : 19.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.21), residues: 1684 helix: 1.01 (0.16), residues: 1060 sheet: -2.59 (0.70), residues: 44 loop : -2.69 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 679 TYR 0.026 0.001 TYR A 700 PHE 0.017 0.002 PHE A 557 TRP 0.026 0.001 TRP B 705 HIS 0.004 0.001 HIS C 731 Details of bonding type rmsd covalent geometry : bond 0.00297 (14096) covalent geometry : angle 0.65826 (19152) hydrogen bonds : bond 0.06023 ( 810) hydrogen bonds : angle 4.60290 ( 2397) *********************** 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 306 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 258 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 PHE cc_start: 0.5524 (OUTLIER) cc_final: 0.5027 (t80) REVERT: A 551 PHE cc_start: 0.8293 (t80) cc_final: 0.7988 (t80) REVERT: A 592 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7874 (mp10) REVERT: A 664 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: A 700 TYR cc_start: 0.9128 (t80) cc_final: 0.8865 (t80) REVERT: A 711 ILE cc_start: 0.8978 (mt) cc_final: 0.8743 (mm) REVERT: A 713 MET cc_start: 0.8199 (mmt) cc_final: 0.7643 (mmt) REVERT: A 725 GLN cc_start: 0.8769 (pt0) cc_final: 0.8336 (pm20) REVERT: A 751 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8475 (mt) REVERT: B 471 PHE cc_start: 0.5307 (OUTLIER) cc_final: 0.4962 (t80) REVERT: B 551 PHE cc_start: 0.8323 (t80) cc_final: 0.8010 (t80) REVERT: B 592 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7785 (mp10) REVERT: B 664 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: B 713 MET cc_start: 0.8555 (mmt) cc_final: 0.8285 (mmt) REVERT: B 725 GLN cc_start: 0.8770 (pt0) cc_final: 0.8319 (pm20) REVERT: B 751 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8510 (mt) REVERT: C 471 PHE cc_start: 0.5263 (OUTLIER) cc_final: 0.4853 (t80) REVERT: C 551 PHE cc_start: 0.8321 (t80) cc_final: 0.8016 (t80) REVERT: C 592 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7805 (mp10) REVERT: C 664 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: C 705 TRP cc_start: 0.8851 (t60) cc_final: 0.8464 (t60) REVERT: C 725 GLN cc_start: 0.8806 (pt0) cc_final: 0.8331 (pm20) REVERT: C 751 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8505 (mt) REVERT: D 471 PHE cc_start: 0.5277 (OUTLIER) cc_final: 0.4855 (t80) REVERT: D 551 PHE cc_start: 0.8307 (t80) cc_final: 0.7994 (t80) REVERT: D 592 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7902 (mp10) REVERT: D 664 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7929 (tt0) REVERT: D 676 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8299 (mm-40) REVERT: D 682 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7607 (tm-30) REVERT: D 713 MET cc_start: 0.8239 (mmt) cc_final: 0.8034 (mmt) REVERT: D 725 GLN cc_start: 0.8787 (pt0) cc_final: 0.8288 (pm20) REVERT: D 751 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8503 (mt) outliers start: 48 outliers final: 22 residues processed: 293 average time/residue: 0.1026 time to fit residues: 44.9219 Evaluate side-chains 274 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 621 SER Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 664 GLN Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 771 HIS Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 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 419 ILE Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 592 GLN Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 621 SER Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 714 ASN 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 163 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 695 GLN ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.190020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.131329 restraints weight = 29535.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.132572 restraints weight = 19019.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.133455 restraints weight = 11764.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.133872 restraints weight = 9668.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.134057 restraints weight = 8903.905| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14096 Z= 0.145 Angle : 0.710 9.771 19152 Z= 0.356 Chirality : 0.045 0.281 2176 Planarity : 0.004 0.031 2376 Dihedral : 4.420 20.351 1876 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.71 % Favored : 92.81 % Rotamer: Outliers : 3.23 % Allowed : 19.71 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.21), residues: 1684 helix: 1.04 (0.16), residues: 1064 sheet: -2.83 (0.68), residues: 44 loop : -2.64 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 679 TYR 0.018 0.001 TYR A 700 PHE 0.017 0.001 PHE B 557 TRP 0.025 0.001 TRP B 705 HIS 0.003 0.001 HIS B 851 Details of bonding type rmsd covalent geometry : bond 0.00301 (14096) covalent geometry : angle 0.71043 (19152) hydrogen bonds : bond 0.05971 ( 810) hydrogen bonds : angle 4.60975 ( 2397) *********************** 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 297 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 250 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 PHE cc_start: 0.5384 (OUTLIER) cc_final: 0.5037 (t80) REVERT: A 551 PHE cc_start: 0.8323 (t80) cc_final: 0.8029 (t80) REVERT: A 592 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7894 (mp10) REVERT: A 664 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: A 700 TYR cc_start: 0.9039 (t80) cc_final: 0.8695 (t80) REVERT: A 711 ILE cc_start: 0.9150 (mt) cc_final: 0.8757 (mm) REVERT: A 713 MET cc_start: 0.8168 (mmt) cc_final: 0.7695 (mmt) REVERT: A 725 GLN cc_start: 0.8766 (pt0) cc_final: 0.8345 (pm20) REVERT: A 751 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8515 (mt) REVERT: A 832 LYS cc_start: 0.7475 (tptt) cc_final: 0.7135 (tptt) REVERT: B 471 PHE cc_start: 0.5308 (OUTLIER) cc_final: 0.4902 (t80) REVERT: B 551 PHE cc_start: 0.8321 (t80) cc_final: 0.8030 (t80) REVERT: B 592 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: B 664 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: B 695 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8390 (mm110) REVERT: B 713 MET cc_start: 0.8475 (mmt) cc_final: 0.8186 (mmt) REVERT: B 725 GLN cc_start: 0.8791 (pt0) cc_final: 0.8343 (pm20) REVERT: B 751 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8534 (mt) REVERT: B 832 LYS cc_start: 0.7482 (tptt) cc_final: 0.7142 (tptt) REVERT: C 471 PHE cc_start: 0.5242 (OUTLIER) cc_final: 0.4841 (t80) REVERT: C 551 PHE cc_start: 0.8328 (t80) cc_final: 0.8048 (t80) REVERT: C 592 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7808 (mp10) REVERT: C 664 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: C 682 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7720 (tm-30) REVERT: C 725 GLN cc_start: 0.8765 (pt0) cc_final: 0.8353 (pm20) REVERT: C 751 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8536 (mt) REVERT: C 832 LYS cc_start: 0.7489 (tptt) cc_final: 0.7151 (tptt) REVERT: D 551 PHE cc_start: 0.8310 (t80) cc_final: 0.8027 (t80) REVERT: D 592 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7881 (mp10) REVERT: D 664 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: D 682 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7637 (tm-30) REVERT: D 713 MET cc_start: 0.8178 (mmt) cc_final: 0.7801 (mmt) REVERT: D 725 GLN cc_start: 0.8736 (pt0) cc_final: 0.8292 (pm20) REVERT: D 751 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8459 (mt) REVERT: D 832 LYS cc_start: 0.7482 (tptt) cc_final: 0.7139 (tptt) outliers start: 47 outliers final: 25 residues processed: 286 average time/residue: 0.1131 time to fit residues: 47.7801 Evaluate side-chains 278 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 238 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 556 THR 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 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 419 ILE Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 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 419 ILE Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 723 CYS Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 771 HIS Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain D residue 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 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 135 optimal weight: 20.0000 chunk 167 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 695 GLN ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 819 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.187285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.129803 restraints weight = 29518.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.131339 restraints weight = 18775.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.130983 restraints weight = 13283.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.131187 restraints weight = 11794.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.131278 restraints weight = 10567.778| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14096 Z= 0.192 Angle : 0.750 14.158 19152 Z= 0.374 Chirality : 0.046 0.237 2176 Planarity : 0.004 0.036 2376 Dihedral : 4.455 19.871 1876 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.89 % Favored : 92.64 % Rotamer: Outliers : 3.85 % Allowed : 19.92 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.21), residues: 1684 helix: 1.04 (0.16), residues: 1060 sheet: -2.89 (0.63), residues: 44 loop : -2.68 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 679 TYR 0.026 0.002 TYR D 700 PHE 0.018 0.002 PHE D 557 TRP 0.027 0.002 TRP B 705 HIS 0.006 0.001 HIS D 851 Details of bonding type rmsd covalent geometry : bond 0.00425 (14096) covalent geometry : angle 0.75017 (19152) hydrogen bonds : bond 0.06410 ( 810) hydrogen bonds : angle 4.69287 ( 2397) *********************** 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 296 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 240 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 471 PHE cc_start: 0.5156 (OUTLIER) cc_final: 0.4784 (t80) REVERT: A 551 PHE cc_start: 0.8330 (t80) cc_final: 0.8043 (t80) REVERT: A 592 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7941 (mp10) REVERT: A 664 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: A 700 TYR cc_start: 0.8900 (t80) cc_final: 0.8571 (t80) REVERT: A 711 ILE cc_start: 0.9165 (mt) cc_final: 0.8703 (mm) REVERT: A 713 MET cc_start: 0.8030 (mmt) cc_final: 0.7502 (mmt) REVERT: A 725 GLN cc_start: 0.8801 (pt0) cc_final: 0.8345 (pm20) REVERT: A 751 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8499 (mt) REVERT: A 832 LYS cc_start: 0.7376 (tptt) cc_final: 0.6999 (tptt) REVERT: B 471 PHE cc_start: 0.5019 (OUTLIER) cc_final: 0.4659 (t80) REVERT: B 551 PHE cc_start: 0.8322 (t80) cc_final: 0.8061 (t80) REVERT: B 592 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7855 (mp10) REVERT: B 713 MET cc_start: 0.8223 (mmt) cc_final: 0.7942 (mmt) REVERT: B 722 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8199 (mm-30) REVERT: B 725 GLN cc_start: 0.8803 (pt0) cc_final: 0.8359 (pm20) REVERT: B 751 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8590 (mt) REVERT: B 832 LYS cc_start: 0.7403 (tptt) cc_final: 0.7035 (tptt) REVERT: C 471 PHE cc_start: 0.4976 (OUTLIER) cc_final: 0.4634 (t80) REVERT: C 551 PHE cc_start: 0.8320 (t80) cc_final: 0.8073 (t80) REVERT: C 592 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7875 (mp10) REVERT: C 664 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: C 725 GLN cc_start: 0.8776 (pt0) cc_final: 0.8367 (pm20) REVERT: C 751 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8584 (mt) REVERT: C 832 LYS cc_start: 0.7400 (tptt) cc_final: 0.7024 (tptt) REVERT: D 551 PHE cc_start: 0.8316 (t80) cc_final: 0.8077 (t80) REVERT: D 592 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7917 (mp10) REVERT: D 682 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7552 (tm-30) REVERT: D 700 TYR cc_start: 0.8971 (t80) cc_final: 0.8696 (t80) REVERT: D 725 GLN cc_start: 0.8749 (pt0) cc_final: 0.8378 (pm20) REVERT: D 751 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8629 (mm) REVERT: D 832 LYS cc_start: 0.7420 (tptt) cc_final: 0.7059 (tptt) outliers start: 56 outliers final: 29 residues processed: 278 average time/residue: 0.1154 time to fit residues: 47.6838 Evaluate side-chains 265 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 556 THR 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 722 GLU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 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 C residue 419 ILE Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 723 CYS Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 771 HIS Chi-restraints excluded: chain D residue 419 ILE 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 714 ASN Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 771 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 91 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 129 optimal weight: 20.0000 chunk 31 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 695 GLN ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 GLN D 819 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.189884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.131917 restraints weight = 29710.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.129578 restraints weight = 18758.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.131769 restraints weight = 14905.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.132522 restraints weight = 10252.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.132667 restraints weight = 9905.429| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3156 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= 0.162 Angle : 0.775 13.690 19152 Z= 0.384 Chirality : 0.046 0.232 2176 Planarity : 0.004 0.037 2376 Dihedral : 4.467 19.270 1876 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.89 % Favored : 92.64 % Rotamer: Outliers : 3.09 % Allowed : 20.54 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.21), residues: 1684 helix: 1.05 (0.16), residues: 1064 sheet: -2.32 (0.62), residues: 44 loop : -2.61 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 679 TYR 0.026 0.001 TYR B 700 PHE 0.019 0.002 PHE A 557 TRP 0.023 0.001 TRP B 705 HIS 0.005 0.001 HIS B 731 Details of bonding type rmsd covalent geometry : bond 0.00343 (14096) covalent geometry : angle 0.77513 (19152) hydrogen bonds : bond 0.06295 ( 810) hydrogen bonds : angle 4.59798 ( 2397) *********************** 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 282 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 237 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 PHE cc_start: 0.5420 (OUTLIER) cc_final: 0.4842 (t80) REVERT: A 551 PHE cc_start: 0.8334 (t80) cc_final: 0.8091 (t80) REVERT: A 592 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7944 (mp10) REVERT: A 664 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: A 700 TYR cc_start: 0.9011 (t80) cc_final: 0.8653 (t80) REVERT: A 711 ILE cc_start: 0.9095 (mt) cc_final: 0.8704 (mm) REVERT: A 713 MET cc_start: 0.8088 (mmt) cc_final: 0.7660 (mmt) REVERT: A 725 GLN cc_start: 0.8845 (pt0) cc_final: 0.8360 (pm20) REVERT: A 751 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8481 (mt) REVERT: A 832 LYS cc_start: 0.7420 (tptt) cc_final: 0.7148 (tptt) REVERT: B 471 PHE cc_start: 0.5220 (OUTLIER) cc_final: 0.4726 (t80) REVERT: B 551 PHE cc_start: 0.8371 (t80) cc_final: 0.8091 (t80) REVERT: B 592 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7843 (mp10) REVERT: B 664 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: B 700 TYR cc_start: 0.8997 (t80) cc_final: 0.8754 (t80) REVERT: B 713 MET cc_start: 0.8273 (mmt) cc_final: 0.8016 (mmt) REVERT: B 722 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8316 (mm-30) REVERT: B 725 GLN cc_start: 0.8826 (pt0) cc_final: 0.8329 (pm20) REVERT: B 751 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8420 (mt) REVERT: B 832 LYS cc_start: 0.7428 (tptt) cc_final: 0.7152 (tptt) REVERT: C 471 PHE cc_start: 0.5205 (OUTLIER) cc_final: 0.4718 (t80) REVERT: C 551 PHE cc_start: 0.8361 (t80) cc_final: 0.8088 (t80) REVERT: C 592 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7847 (mp10) REVERT: C 664 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: C 725 GLN cc_start: 0.8758 (pt0) cc_final: 0.8290 (pm20) REVERT: C 730 LEU cc_start: 0.9175 (pp) cc_final: 0.8946 (tt) REVERT: C 751 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8438 (mt) REVERT: C 832 LYS cc_start: 0.7430 (tptt) cc_final: 0.7162 (tptt) REVERT: D 551 PHE cc_start: 0.8358 (t80) cc_final: 0.8084 (t80) REVERT: D 592 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7885 (mp10) REVERT: D 664 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: D 682 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7724 (tm-30) REVERT: D 700 TYR cc_start: 0.9060 (t80) cc_final: 0.8833 (t80) REVERT: D 725 GLN cc_start: 0.8798 (pt0) cc_final: 0.8359 (pm20) REVERT: D 751 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8532 (mm) REVERT: D 832 LYS cc_start: 0.7434 (tptt) cc_final: 0.7156 (tptt) outliers start: 45 outliers final: 29 residues processed: 276 average time/residue: 0.1008 time to fit residues: 41.8967 Evaluate side-chains 272 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 556 THR 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 722 GLU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 664 GLN Chi-restraints excluded: chain B residue 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 471 PHE Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 723 CYS Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 771 HIS Chi-restraints excluded: chain C residue 831 HIS Chi-restraints excluded: chain D residue 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 722 GLU Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 771 HIS Chi-restraints excluded: chain D residue 831 HIS Chi-restraints excluded: chain D residue 841 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 151 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 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 402 HIS B 402 HIS B 695 GLN ** C 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.190962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.128075 restraints weight = 29863.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.133451 restraints weight = 15528.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.133485 restraints weight = 8595.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.133314 restraints weight = 8363.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.133457 restraints weight = 8426.812| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14096 Z= 0.151 Angle : 0.760 12.331 19152 Z= 0.377 Chirality : 0.046 0.354 2176 Planarity : 0.004 0.078 2376 Dihedral : 4.343 18.509 1876 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.89 % Favored : 92.64 % Rotamer: Outliers : 3.30 % Allowed : 20.74 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.21), residues: 1684 helix: 1.17 (0.16), residues: 1068 sheet: -1.69 (0.72), residues: 44 loop : -2.57 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 679 TYR 0.021 0.001 TYR B 700 PHE 0.018 0.001 PHE A 557 TRP 0.029 0.001 TRP B 705 HIS 0.005 0.001 HIS B 851 Details of bonding type rmsd covalent geometry : bond 0.00315 (14096) covalent geometry : angle 0.76035 (19152) hydrogen bonds : bond 0.06095 ( 810) hydrogen bonds : angle 4.52683 ( 2397) *********************** 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 281 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 233 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 PHE cc_start: 0.5264 (OUTLIER) cc_final: 0.4784 (t80) REVERT: A 551 PHE cc_start: 0.8356 (t80) cc_final: 0.8037 (t80) REVERT: A 592 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: A 664 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: A 700 TYR cc_start: 0.8949 (t80) cc_final: 0.8612 (t80) REVERT: A 711 ILE cc_start: 0.9113 (mt) cc_final: 0.8745 (mm) REVERT: A 713 MET cc_start: 0.8048 (mmt) cc_final: 0.7571 (mmt) REVERT: A 725 GLN cc_start: 0.8840 (pt0) cc_final: 0.8361 (pm20) REVERT: A 751 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8555 (mm) REVERT: A 832 LYS cc_start: 0.7369 (tptt) cc_final: 0.7112 (tptt) REVERT: B 471 PHE cc_start: 0.5184 (OUTLIER) cc_final: 0.4744 (t80) REVERT: B 551 PHE cc_start: 0.8350 (t80) cc_final: 0.8052 (t80) REVERT: B 592 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7807 (mp10) REVERT: B 664 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: B 700 TYR cc_start: 0.8935 (t80) cc_final: 0.8589 (t80) REVERT: B 713 MET cc_start: 0.8199 (mmt) cc_final: 0.7941 (mmt) REVERT: B 725 GLN cc_start: 0.8827 (pt0) cc_final: 0.8361 (pm20) REVERT: B 751 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8561 (mm) REVERT: B 832 LYS cc_start: 0.7373 (tptt) cc_final: 0.7118 (tptt) REVERT: C 471 PHE cc_start: 0.5148 (OUTLIER) cc_final: 0.4730 (t80) REVERT: C 551 PHE cc_start: 0.8305 (t80) cc_final: 0.8019 (t80) REVERT: C 592 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7844 (mp10) REVERT: C 664 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: C 725 GLN cc_start: 0.8774 (pt0) cc_final: 0.8261 (pm20) REVERT: C 751 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8481 (mt) REVERT: C 832 LYS cc_start: 0.7355 (tptt) cc_final: 0.7096 (tptt) REVERT: D 551 PHE cc_start: 0.8341 (t80) cc_final: 0.8050 (t80) REVERT: D 592 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7866 (mp10) REVERT: D 664 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: D 682 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7779 (tm-30) REVERT: D 691 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8235 (t0) REVERT: D 700 TYR cc_start: 0.8976 (t80) cc_final: 0.8699 (t80) REVERT: D 725 GLN cc_start: 0.8736 (pt0) cc_final: 0.8340 (pm20) REVERT: D 751 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8569 (mm) REVERT: D 832 LYS cc_start: 0.7380 (tptt) cc_final: 0.7103 (tptt) outliers start: 48 outliers final: 31 residues processed: 270 average time/residue: 0.0960 time to fit residues: 38.9682 Evaluate side-chains 276 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 229 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 556 THR 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 651 MET Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 651 MET Chi-restraints excluded: chain B residue 664 GLN Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 771 HIS Chi-restraints excluded: chain B residue 831 HIS Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 651 MET 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 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 691 ASN Chi-restraints excluded: chain D residue 722 GLU Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 771 HIS Chi-restraints excluded: chain D residue 831 HIS Chi-restraints excluded: chain D residue 841 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 149 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 145 optimal weight: 0.1980 chunk 105 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 691 ASN ** C 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.191168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.128530 restraints weight = 29696.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.131831 restraints weight = 14313.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.132659 restraints weight = 10207.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.132668 restraints weight = 8194.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.132884 restraints weight = 8549.618| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3453 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= 0.149 Angle : 0.754 12.569 19152 Z= 0.375 Chirality : 0.046 0.338 2176 Planarity : 0.004 0.036 2376 Dihedral : 4.294 18.158 1876 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.65 % Favored : 92.87 % Rotamer: Outliers : 3.16 % Allowed : 21.09 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.21), residues: 1684 helix: 1.18 (0.16), residues: 1068 sheet: -2.43 (0.66), residues: 52 loop : -2.67 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 679 TYR 0.019 0.001 TYR B 700 PHE 0.016 0.001 PHE A 557 TRP 0.058 0.002 TRP B 705 HIS 0.005 0.001 HIS B 851 Details of bonding type rmsd covalent geometry : bond 0.00311 (14096) covalent geometry : angle 0.75430 (19152) hydrogen bonds : bond 0.05999 ( 810) hydrogen bonds : angle 4.48470 ( 2397) ********************** 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 281 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 PHE cc_start: 0.5306 (OUTLIER) cc_final: 0.4790 (t80) REVERT: A 551 PHE cc_start: 0.8302 (t80) cc_final: 0.7993 (t80) REVERT: A 592 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7906 (mp10) REVERT: A 664 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: A 700 TYR cc_start: 0.8923 (t80) cc_final: 0.8566 (t80) REVERT: A 711 ILE cc_start: 0.9100 (mt) cc_final: 0.8717 (mm) REVERT: A 713 MET cc_start: 0.8100 (mmt) cc_final: 0.7615 (mmt) REVERT: A 725 GLN cc_start: 0.8844 (pt0) cc_final: 0.8354 (pm20) REVERT: A 751 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8552 (mm) REVERT: A 832 LYS cc_start: 0.7318 (tptt) cc_final: 0.7062 (tptt) REVERT: B 471 PHE cc_start: 0.5224 (OUTLIER) cc_final: 0.4763 (t80) REVERT: B 551 PHE cc_start: 0.8324 (t80) cc_final: 0.8027 (t80) REVERT: B 592 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7798 (mp10) REVERT: B 664 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7514 (tt0) REVERT: B 691 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8315 (t0) REVERT: B 700 TYR cc_start: 0.8944 (t80) cc_final: 0.8571 (t80) REVERT: B 713 MET cc_start: 0.8155 (mmt) cc_final: 0.7928 (mmt) REVERT: B 725 GLN cc_start: 0.8827 (pt0) cc_final: 0.8386 (pm20) REVERT: B 751 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8555 (mm) REVERT: B 832 LYS cc_start: 0.7313 (tptt) cc_final: 0.7053 (tptt) REVERT: C 471 PHE cc_start: 0.5251 (OUTLIER) cc_final: 0.4790 (t80) REVERT: C 551 PHE cc_start: 0.8286 (t80) cc_final: 0.7988 (t80) REVERT: C 592 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7829 (mp10) REVERT: C 664 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: C 725 GLN cc_start: 0.8762 (pt0) cc_final: 0.8268 (pm20) REVERT: C 751 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8353 (mt) REVERT: C 832 LYS cc_start: 0.7296 (tptt) cc_final: 0.7056 (tptt) REVERT: D 551 PHE cc_start: 0.8311 (t80) cc_final: 0.8014 (t80) REVERT: D 592 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7874 (mp10) REVERT: D 664 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: D 682 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7765 (tm-30) REVERT: D 700 TYR cc_start: 0.8930 (t80) cc_final: 0.8708 (t80) REVERT: D 725 GLN cc_start: 0.8744 (pt0) cc_final: 0.8320 (pm20) REVERT: D 751 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8390 (mt) REVERT: D 832 LYS cc_start: 0.7332 (tptt) cc_final: 0.7071 (tptt) outliers start: 46 outliers final: 27 residues processed: 271 average time/residue: 0.1027 time to fit residues: 41.3851 Evaluate side-chains 273 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 230 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 556 THR 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 722 GLU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 831 HIS Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 651 MET Chi-restraints excluded: chain B residue 664 GLN Chi-restraints excluded: chain B residue 691 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 471 PHE Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 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 751 LEU Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 771 HIS Chi-restraints excluded: chain D residue 831 HIS Chi-restraints excluded: chain D residue 841 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 122 optimal weight: 0.4980 chunk 155 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 145 optimal weight: 0.4980 chunk 151 optimal weight: 0.8980 chunk 135 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 0.7980 chunk 160 optimal weight: 0.7980 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 695 GLN C 402 HIS D 691 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.191543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.129583 restraints weight = 29905.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.134329 restraints weight = 16498.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.134503 restraints weight = 9572.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.134234 restraints weight = 8720.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.134586 restraints weight = 8672.902| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3539 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= 0.148 Angle : 0.757 12.379 19152 Z= 0.377 Chirality : 0.046 0.328 2176 Planarity : 0.003 0.034 2376 Dihedral : 4.256 17.962 1876 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.16 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.21), residues: 1684 helix: 1.24 (0.16), residues: 1052 sheet: -2.37 (0.66), residues: 52 loop : -2.58 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 679 TYR 0.026 0.001 TYR C 700 PHE 0.016 0.001 PHE D 557 TRP 0.025 0.002 TRP A 497 HIS 0.005 0.001 HIS B 851 Details of bonding type rmsd covalent geometry : bond 0.00309 (14096) covalent geometry : angle 0.75659 (19152) hydrogen bonds : bond 0.05921 ( 810) hydrogen bonds : angle 4.45956 ( 2397) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2631.64 seconds wall clock time: 46 minutes 14.33 seconds (2774.33 seconds total)