Starting phenix.real_space_refine on Thu Jan 15 20:40:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ajb_15476/01_2026/8ajb_15476.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ajb_15476/01_2026/8ajb_15476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ajb_15476/01_2026/8ajb_15476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ajb_15476/01_2026/8ajb_15476.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ajb_15476/01_2026/8ajb_15476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ajb_15476/01_2026/8ajb_15476.map" } resolution = 4.3 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= 0.006 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 18156 2.51 5 N 5852 2.21 5 O 6012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30088 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1876 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 2, 'TRANS': 242} Chain: "B" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1828 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 2, 'TRANS': 235} Chain: "C" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1793 Classifications: {'peptide': 234} Link IDs: {'TRANS': 233} Chain: "D" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1793 Classifications: {'peptide': 234} Link IDs: {'TRANS': 233} Chain: "E" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "F" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 861 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Chain: "G" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1203 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "H" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1264 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain: "I" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'TRANS': 119} Chain: "J" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'TRANS': 119} Chain: "K" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 820 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain breaks: 1 Chain: "M" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1876 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 2, 'TRANS': 242} Chain: "N" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1828 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 2, 'TRANS': 235} Chain: "O" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1793 Classifications: {'peptide': 234} Link IDs: {'TRANS': 233} Chain: "P" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1793 Classifications: {'peptide': 234} Link IDs: {'TRANS': 233} Chain: "Q" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "R" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 861 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Chain: "S" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1203 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "T" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1264 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain: "U" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'TRANS': 119} Chain: "V" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'TRANS': 119} Chain: "W" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "X" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 820 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain breaks: 1 Time building chain proxies: 7.07, per 1000 atoms: 0.23 Number of scatterers: 30088 At special positions: 0 Unit cell: (151.05, 570.81, 90.63, 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 6012 8.00 N 5852 7.00 C 18156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 795 " - pdb=" SG CYS E 868 " distance=2.03 Simple disulfide: pdb=" SG CYS F 795 " - pdb=" SG CYS F 868 " distance=2.06 Simple disulfide: pdb=" SG CYS K 795 " - pdb=" SG CYS K 868 " distance=2.03 Simple disulfide: pdb=" SG CYS L 795 " - pdb=" SG CYS L 868 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 795 " - pdb=" SG CYS Q 868 " distance=2.03 Simple disulfide: pdb=" SG CYS R 795 " - pdb=" SG CYS R 868 " distance=2.06 Simple disulfide: pdb=" SG CYS W 795 " - pdb=" SG CYS W 868 " distance=2.03 Simple disulfide: pdb=" SG CYS X 795 " - pdb=" SG CYS X 868 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.4 seconds 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7360 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 22 sheets defined 78.2% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 35 through 61 removed outlier: 3.937A pdb=" N ALA A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 69 Processing helix chain 'A' and resid 70 through 83 removed outlier: 4.468A pdb=" N ARG A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 277 Processing helix chain 'B' and resid 41 through 277 Proline residue: B 64 - end of helix Proline residue: B 72 - end of helix removed outlier: 3.987A pdb=" N ARG B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 446 removed outlier: 4.258A pdb=" N ARG C 357 " --> pdb=" O VAL C 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 446 Processing helix chain 'E' and resid 859 through 863 Processing helix chain 'F' and resid 859 through 863 Processing helix chain 'G' and resid 40 through 193 Proline residue: G 64 - end of helix Proline residue: G 72 - end of helix removed outlier: 4.018A pdb=" N ALA G 92 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN G 93 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 193 Proline residue: H 64 - end of helix Proline residue: H 72 - end of helix removed outlier: 4.104A pdb=" N ALA H 89 " --> pdb=" O ALA H 85 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL H 90 " --> pdb=" O GLU H 86 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG H 91 " --> pdb=" O LEU H 87 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA H 92 " --> pdb=" O ILE H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 328 through 446 removed outlier: 3.687A pdb=" N GLY I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL I 353 " --> pdb=" O ARG I 349 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR I 355 " --> pdb=" O ALA I 351 " (cutoff:3.500A) Processing helix chain 'J' and resid 328 through 446 Processing helix chain 'K' and resid 833 through 837 removed outlier: 3.580A pdb=" N LYS K 837 " --> pdb=" O ASP K 834 " (cutoff:3.500A) Processing helix chain 'K' and resid 859 through 863 Processing helix chain 'L' and resid 859 through 863 Processing helix chain 'M' and resid 35 through 61 removed outlier: 3.938A pdb=" N ALA M 61 " --> pdb=" O GLU M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 69 Processing helix chain 'M' and resid 70 through 83 removed outlier: 4.467A pdb=" N ARG M 81 " --> pdb=" O PHE M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 277 Processing helix chain 'N' and resid 41 through 277 Proline residue: N 64 - end of helix Proline residue: N 72 - end of helix removed outlier: 3.987A pdb=" N ARG N 91 " --> pdb=" O LEU N 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 214 through 446 removed outlier: 4.258A pdb=" N ARG O 357 " --> pdb=" O VAL O 353 " (cutoff:3.500A) Processing helix chain 'P' and resid 214 through 446 Processing helix chain 'Q' and resid 859 through 863 Processing helix chain 'R' and resid 859 through 863 Processing helix chain 'S' and resid 40 through 193 Proline residue: S 64 - end of helix Proline residue: S 72 - end of helix removed outlier: 4.019A pdb=" N ALA S 92 " --> pdb=" O ILE S 88 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN S 93 " --> pdb=" O ALA S 89 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 193 Proline residue: T 64 - end of helix Proline residue: T 72 - end of helix removed outlier: 4.104A pdb=" N ALA T 89 " --> pdb=" O ALA T 85 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL T 90 " --> pdb=" O GLU T 86 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG T 91 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA T 92 " --> pdb=" O ILE T 88 " (cutoff:3.500A) Processing helix chain 'U' and resid 328 through 446 removed outlier: 3.687A pdb=" N GLY U 352 " --> pdb=" O GLN U 348 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL U 353 " --> pdb=" O ARG U 349 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR U 355 " --> pdb=" O ALA U 351 " (cutoff:3.500A) Processing helix chain 'V' and resid 328 through 446 Processing helix chain 'W' and resid 833 through 837 removed outlier: 3.581A pdb=" N LYS W 837 " --> pdb=" O ASP W 834 " (cutoff:3.500A) Processing helix chain 'W' and resid 859 through 863 Processing helix chain 'X' and resid 859 through 863 Processing sheet with id=AA1, first strand: chain 'E' and resid 791 through 793 removed outlier: 4.132A pdb=" N ASP E 845 " --> pdb=" O THR E 850 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 830 through 832 removed outlier: 3.572A pdb=" N ASN E 831 " --> pdb=" O VAL E 823 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N TRP E 809 " --> pdb=" O VAL E 821 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL E 823 " --> pdb=" O MET E 807 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N MET E 807 " --> pdb=" O VAL E 823 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 869 through 872 removed outlier: 3.773A pdb=" N ALA E 870 " --> pdb=" O TYR E 877 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.916A pdb=" N GLN F 5 " --> pdb=" O ALA F 796 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER F 794 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 820 through 824 removed outlier: 5.030A pdb=" N MET F 820 " --> pdb=" O ARG F 811 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ARG F 811 " --> pdb=" O MET F 820 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA F 822 " --> pdb=" O TRP F 809 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 842 through 845 Processing sheet with id=AA7, first strand: chain 'K' and resid 4 through 5 removed outlier: 3.995A pdb=" N CYS K 795 " --> pdb=" O VAL K 851 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL K 851 " --> pdb=" O CYS K 795 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 818 through 824 removed outlier: 6.977A pdb=" N TRP K 809 " --> pdb=" O VAL K 821 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL K 823 " --> pdb=" O MET K 807 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N MET K 807 " --> pdb=" O VAL K 823 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE K 806 " --> pdb=" O ILE K 871 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 818 through 824 removed outlier: 6.977A pdb=" N TRP K 809 " --> pdb=" O VAL K 821 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL K 823 " --> pdb=" O MET K 807 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N MET K 807 " --> pdb=" O VAL K 823 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE K 806 " --> pdb=" O ILE K 871 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA K 864 " --> pdb=" O VAL K 884 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL K 884 " --> pdb=" O ALA K 864 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.862A pdb=" N THR L 850 " --> pdb=" O ASP L 845 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP L 845 " --> pdb=" O THR L 850 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE L 841 " --> pdb=" O GLN L 854 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 830 through 832 removed outlier: 6.570A pdb=" N TRP L 809 " --> pdb=" O VAL L 821 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL L 823 " --> pdb=" O MET L 807 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N MET L 807 " --> pdb=" O VAL L 823 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 791 through 793 removed outlier: 4.133A pdb=" N ASP Q 845 " --> pdb=" O THR Q 850 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 830 through 832 removed outlier: 3.571A pdb=" N ASN Q 831 " --> pdb=" O VAL Q 823 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N TRP Q 809 " --> pdb=" O VAL Q 821 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL Q 823 " --> pdb=" O MET Q 807 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N MET Q 807 " --> pdb=" O VAL Q 823 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 869 through 872 removed outlier: 3.772A pdb=" N ALA Q 870 " --> pdb=" O TYR Q 877 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 4 through 7 removed outlier: 3.916A pdb=" N GLN R 5 " --> pdb=" O ALA R 796 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER R 794 " --> pdb=" O SER R 7 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 820 through 824 removed outlier: 5.030A pdb=" N MET R 820 " --> pdb=" O ARG R 811 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ARG R 811 " --> pdb=" O MET R 820 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA R 822 " --> pdb=" O TRP R 809 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 842 through 845 Processing sheet with id=AB9, first strand: chain 'W' and resid 4 through 5 removed outlier: 3.995A pdb=" N CYS W 795 " --> pdb=" O VAL W 851 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL W 851 " --> pdb=" O CYS W 795 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'W' and resid 818 through 824 removed outlier: 6.976A pdb=" N TRP W 809 " --> pdb=" O VAL W 821 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL W 823 " --> pdb=" O MET W 807 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N MET W 807 " --> pdb=" O VAL W 823 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE W 806 " --> pdb=" O ILE W 871 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'W' and resid 818 through 824 removed outlier: 6.976A pdb=" N TRP W 809 " --> pdb=" O VAL W 821 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL W 823 " --> pdb=" O MET W 807 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N MET W 807 " --> pdb=" O VAL W 823 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE W 806 " --> pdb=" O ILE W 871 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA W 864 " --> pdb=" O VAL W 884 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL W 884 " --> pdb=" O ALA W 864 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'X' and resid 5 through 6 removed outlier: 3.863A pdb=" N THR X 850 " --> pdb=" O ASP X 845 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP X 845 " --> pdb=" O THR X 850 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE X 841 " --> pdb=" O GLN X 854 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'X' and resid 830 through 832 removed outlier: 6.569A pdb=" N TRP X 809 " --> pdb=" O VAL X 821 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL X 823 " --> pdb=" O MET X 807 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N MET X 807 " --> pdb=" O VAL X 823 " (cutoff:3.500A) 3044 hydrogen bonds defined for protein. 9000 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: 6.29 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11132 1.34 - 1.46: 5670 1.46 - 1.59: 13348 1.59 - 1.72: 0 1.72 - 1.84: 120 Bond restraints: 30270 Sorted by residual: bond pdb=" N ILE K 804 " pdb=" CA ILE K 804 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.99e+00 bond pdb=" N ILE W 804 " pdb=" CA ILE W 804 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.85e+00 bond pdb=" N ARG I 349 " pdb=" CA ARG I 349 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.33e-02 5.65e+03 6.34e+00 bond pdb=" N HIS I 350 " pdb=" CA HIS I 350 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.28e-02 6.10e+03 6.30e+00 bond pdb=" N HIS U 350 " pdb=" CA HIS U 350 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.28e-02 6.10e+03 6.26e+00 ... (remaining 30265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 39905 3.15 - 6.30: 713 6.30 - 9.46: 90 9.46 - 12.61: 12 12.61 - 15.76: 6 Bond angle restraints: 40726 Sorted by residual: angle pdb=" C TYR H 42 " pdb=" N GLU H 43 " pdb=" CA GLU H 43 " ideal model delta sigma weight residual 120.28 112.63 7.65 1.34e+00 5.57e-01 3.26e+01 angle pdb=" C TYR T 42 " pdb=" N GLU T 43 " pdb=" CA GLU T 43 " ideal model delta sigma weight residual 120.28 112.64 7.64 1.34e+00 5.57e-01 3.25e+01 angle pdb=" N THR R 885 " pdb=" CA THR R 885 " pdb=" C THR R 885 " ideal model delta sigma weight residual 108.07 115.90 -7.83 1.38e+00 5.25e-01 3.22e+01 angle pdb=" N THR F 885 " pdb=" CA THR F 885 " pdb=" C THR F 885 " ideal model delta sigma weight residual 108.07 115.88 -7.81 1.38e+00 5.25e-01 3.20e+01 angle pdb=" CA GLU B 76 " pdb=" CB GLU B 76 " pdb=" CG GLU B 76 " ideal model delta sigma weight residual 114.10 103.53 10.57 2.00e+00 2.50e-01 2.79e+01 ... (remaining 40721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16808 17.95 - 35.89: 1820 35.89 - 53.84: 252 53.84 - 71.78: 78 71.78 - 89.73: 64 Dihedral angle restraints: 19022 sinusoidal: 7734 harmonic: 11288 Sorted by residual: dihedral pdb=" CB CYS R 795 " pdb=" SG CYS R 795 " pdb=" SG CYS R 868 " pdb=" CB CYS R 868 " ideal model delta sinusoidal sigma weight residual -86.00 -32.68 -53.32 1 1.00e+01 1.00e-02 3.87e+01 dihedral pdb=" CB CYS F 795 " pdb=" SG CYS F 795 " pdb=" SG CYS F 868 " pdb=" CB CYS F 868 " ideal model delta sinusoidal sigma weight residual -86.00 -32.71 -53.29 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CA ARG H 80 " pdb=" C ARG H 80 " pdb=" N ARG H 81 " pdb=" CA ARG H 81 " ideal model delta harmonic sigma weight residual 180.00 150.46 29.54 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 19019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4002 0.074 - 0.149: 565 0.149 - 0.223: 62 0.223 - 0.298: 11 0.298 - 0.372: 6 Chirality restraints: 4646 Sorted by residual: chirality pdb=" CB VAL A 73 " pdb=" CA VAL A 73 " pdb=" CG1 VAL A 73 " pdb=" CG2 VAL A 73 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CB VAL M 73 " pdb=" CA VAL M 73 " pdb=" CG1 VAL M 73 " pdb=" CG2 VAL M 73 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CA GLU B 76 " pdb=" N GLU B 76 " pdb=" C GLU B 76 " pdb=" CB GLU B 76 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 4643 not shown) Planarity restraints: 5518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA X 813 " -0.057 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO X 814 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO X 814 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO X 814 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 813 " 0.057 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO L 814 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO L 814 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO L 814 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 809 " -0.037 2.00e-02 2.50e+03 2.14e-02 1.15e+01 pdb=" CG TRP R 809 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP R 809 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP R 809 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP R 809 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 809 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 809 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 809 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 809 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP R 809 " -0.022 2.00e-02 2.50e+03 ... (remaining 5515 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 313 2.46 - 3.07: 23230 3.07 - 3.68: 52736 3.68 - 4.29: 67697 4.29 - 4.90: 106012 Nonbonded interactions: 249988 Sorted by model distance: nonbonded pdb=" CB ILE K 804 " pdb=" CE1 TYR K 872 " model vdw 1.847 3.770 nonbonded pdb=" CB ILE W 804 " pdb=" CE1 TYR W 872 " model vdw 1.847 3.770 nonbonded pdb=" O GLY W 803 " pdb=" CD1 TYR W 872 " model vdw 1.881 3.340 nonbonded pdb=" O GLY K 803 " pdb=" CD1 TYR K 872 " model vdw 1.882 3.340 nonbonded pdb=" O ALA D 282 " pdb=" OG1 THR D 285 " model vdw 1.995 3.040 ... (remaining 249983 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 277) selection = chain 'B' selection = (chain 'M' and resid 40 through 277) selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'O' selection = chain 'P' } ncs_group { reference = (chain 'E' and (resid 1 through 8 or resid 791 through 887)) selection = (chain 'F' and (resid 1 through 8 or resid 791 through 887)) selection = (chain 'K' and (resid 1 through 8 or resid 791 through 887)) selection = chain 'L' selection = (chain 'Q' and (resid 1 through 8 or resid 791 through 887)) selection = (chain 'R' and (resid 1 through 8 or resid 791 through 887)) selection = (chain 'W' and (resid 1 through 8 or resid 791 through 887)) selection = chain 'X' } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 39 through 193) selection = chain 'S' selection = (chain 'T' and resid 39 through 193) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'U' selection = chain 'V' } 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: 15.330 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: 0.050 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 28.390 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5309 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 : 0.007 0.174 30280 Z= 0.342 Angle : 1.037 15.759 40742 Z= 0.591 Chirality : 0.053 0.372 4646 Planarity : 0.005 0.085 5518 Dihedral : 15.630 89.725 11638 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 31.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.07 % Allowed : 0.73 % Favored : 99.21 % 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 are not related in a simple way. whole: 0.79 (0.13), residues: 3834 helix: 1.42 (0.09), residues: 2898 sheet: -2.73 (0.27), residues: 302 loop : -1.82 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG P 267 TYR 0.035 0.003 TYR G 42 PHE 0.055 0.007 PHE A 77 TRP 0.049 0.005 TRP R 809 HIS 0.014 0.002 HIS N 58 Details of bonding type rmsd covalent geometry : bond 0.00644 (30270) covalent geometry : angle 1.03449 (40726) SS BOND : bond 0.01583 ( 8) SS BOND : angle 3.53332 ( 16) hydrogen bonds : bond 0.10368 ( 3024) hydrogen bonds : angle 5.94392 ( 9000) Misc. bond : bond 0.12701 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1136 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.6657 (p) cc_final: 0.6402 (p) REVERT: A 63 GLU cc_start: 0.6899 (tm-30) cc_final: 0.6600 (tm-30) REVERT: A 126 ASP cc_start: 0.5591 (t0) cc_final: 0.5226 (t0) REVERT: A 151 LEU cc_start: 0.6467 (mt) cc_final: 0.6033 (mt) REVERT: A 152 GLN cc_start: 0.6532 (pp30) cc_final: 0.6085 (pp30) REVERT: B 86 GLU cc_start: 0.6218 (mm-30) cc_final: 0.5904 (mp0) REVERT: B 91 ARG cc_start: 0.6257 (mtt90) cc_final: 0.5878 (mpt-90) REVERT: B 108 GLU cc_start: 0.6183 (tp30) cc_final: 0.5562 (mm-30) REVERT: B 126 ASP cc_start: 0.6707 (t70) cc_final: 0.5999 (t0) REVERT: B 161 ASP cc_start: 0.6548 (t70) cc_final: 0.5975 (t70) REVERT: C 314 GLN cc_start: 0.6368 (mm110) cc_final: 0.6055 (mm110) REVERT: C 321 ARG cc_start: 0.6549 (tmm-80) cc_final: 0.6234 (mtm-85) REVERT: C 325 LEU cc_start: 0.7221 (mt) cc_final: 0.6828 (mm) REVERT: C 334 ASP cc_start: 0.5885 (m-30) cc_final: 0.5186 (m-30) REVERT: C 392 LEU cc_start: 0.6696 (mm) cc_final: 0.6436 (mt) REVERT: C 393 ASP cc_start: 0.5710 (m-30) cc_final: 0.5475 (m-30) REVERT: C 404 ARG cc_start: 0.6740 (ptt90) cc_final: 0.6259 (mtm110) REVERT: D 380 ARG cc_start: 0.6865 (mtp180) cc_final: 0.6375 (ttm110) REVERT: D 434 LEU cc_start: 0.5416 (mp) cc_final: 0.4860 (mp) REVERT: E 834 ASP cc_start: 0.7257 (p0) cc_final: 0.7037 (p0) REVERT: E 865 VAL cc_start: 0.8456 (p) cc_final: 0.7643 (p) REVERT: E 876 GLU cc_start: 0.6335 (tp30) cc_final: 0.6071 (tp30) REVERT: F 837 LYS cc_start: 0.7950 (mppt) cc_final: 0.7505 (mtmt) REVERT: F 849 ASP cc_start: 0.3527 (t0) cc_final: 0.3099 (t70) REVERT: F 867 SER cc_start: 0.7865 (t) cc_final: 0.6821 (p) REVERT: F 873 ARG cc_start: 0.7363 (mpt-90) cc_final: 0.6455 (mmt90) REVERT: G 104 ILE cc_start: 0.8992 (mm) cc_final: 0.8299 (mm) REVERT: G 168 THR cc_start: 0.3836 (p) cc_final: 0.3307 (p) REVERT: H 101 ILE cc_start: 0.8502 (mt) cc_final: 0.7199 (mt) REVERT: I 341 GLU cc_start: 0.7874 (pt0) cc_final: 0.7267 (pt0) REVERT: I 400 ASP cc_start: 0.6907 (m-30) cc_final: 0.6528 (m-30) REVERT: I 412 LYS cc_start: 0.7525 (tppt) cc_final: 0.7075 (tptt) REVERT: I 429 LEU cc_start: 0.8490 (tt) cc_final: 0.8155 (mt) REVERT: I 434 LEU cc_start: 0.6503 (mt) cc_final: 0.6209 (mt) REVERT: J 367 LEU cc_start: 0.7686 (mt) cc_final: 0.6467 (mt) REVERT: J 399 GLN cc_start: 0.7416 (tp40) cc_final: 0.7204 (mm-40) REVERT: J 405 ASP cc_start: 0.6746 (m-30) cc_final: 0.6324 (m-30) REVERT: J 413 ILE cc_start: 0.8500 (tt) cc_final: 0.7166 (tp) REVERT: J 426 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6554 (tt0) REVERT: K 7 SER cc_start: 0.8248 (p) cc_final: 0.7860 (m) REVERT: K 820 MET cc_start: 0.6910 (tmm) cc_final: 0.6681 (ttp) REVERT: K 842 ILE cc_start: 0.7611 (tp) cc_final: 0.7342 (tt) REVERT: K 880 GLN cc_start: 0.6921 (mm110) cc_final: 0.6070 (mp10) REVERT: M 42 TYR cc_start: 0.5740 (m-10) cc_final: 0.5274 (m-10) REVERT: M 148 ASN cc_start: 0.8148 (m-40) cc_final: 0.7680 (m110) REVERT: M 151 LEU cc_start: 0.7351 (mt) cc_final: 0.6850 (mt) REVERT: M 152 GLN cc_start: 0.7097 (pp30) cc_final: 0.6787 (pp30) REVERT: M 154 ASP cc_start: 0.6638 (t70) cc_final: 0.6269 (t0) REVERT: M 160 LEU cc_start: 0.6945 (tp) cc_final: 0.6732 (tp) REVERT: M 165 ARG cc_start: 0.6363 (mtp85) cc_final: 0.6147 (ttm110) REVERT: M 172 GLU cc_start: 0.6226 (pm20) cc_final: 0.5760 (pm20) REVERT: N 62 ILE cc_start: 0.7291 (mp) cc_final: 0.6864 (mm) REVERT: N 66 ILE cc_start: 0.7735 (mt) cc_final: 0.7415 (tt) REVERT: N 109 ARG cc_start: 0.7366 (mmm-85) cc_final: 0.6737 (mmm-85) REVERT: N 122 LEU cc_start: 0.6663 (mt) cc_final: 0.6315 (tt) REVERT: N 126 ASP cc_start: 0.6817 (t70) cc_final: 0.6154 (t0) REVERT: O 300 MET cc_start: 0.6711 (tmm) cc_final: 0.6294 (tmm) REVERT: O 389 ARG cc_start: 0.6540 (ttp-110) cc_final: 0.6031 (mtm-85) REVERT: O 392 LEU cc_start: 0.6363 (mm) cc_final: 0.5983 (tp) REVERT: O 393 ASP cc_start: 0.6210 (m-30) cc_final: 0.5657 (m-30) REVERT: O 404 ARG cc_start: 0.7142 (ptt90) cc_final: 0.6852 (ptt-90) REVERT: O 434 LEU cc_start: 0.5461 (tp) cc_final: 0.5173 (tp) REVERT: P 344 ASP cc_start: 0.6820 (t0) cc_final: 0.6476 (t70) REVERT: P 380 ARG cc_start: 0.7361 (mtp180) cc_final: 0.5911 (ttp80) REVERT: P 391 ARG cc_start: 0.7307 (tmm-80) cc_final: 0.7020 (ttm-80) REVERT: P 416 LEU cc_start: 0.7683 (mp) cc_final: 0.7297 (mm) REVERT: R 794 SER cc_start: 0.6558 (m) cc_final: 0.6232 (t) REVERT: R 834 ASP cc_start: 0.6646 (m-30) cc_final: 0.6286 (m-30) REVERT: S 98 GLN cc_start: 0.6215 (pp30) cc_final: 0.5667 (pp30) REVERT: T 101 ILE cc_start: 0.7196 (mt) cc_final: 0.6581 (mt) REVERT: T 143 ILE cc_start: 0.4234 (tp) cc_final: 0.3699 (tp) REVERT: U 412 LYS cc_start: 0.7711 (tppt) cc_final: 0.7100 (tptt) REVERT: U 434 LEU cc_start: 0.6835 (mt) cc_final: 0.6253 (mt) REVERT: U 443 ARG cc_start: 0.5829 (ttp-170) cc_final: 0.5562 (ttp-110) REVERT: V 359 THR cc_start: 0.7583 (t) cc_final: 0.6828 (t) REVERT: W 2 VAL cc_start: 0.7106 (t) cc_final: 0.6517 (t) REVERT: W 820 MET cc_start: 0.6810 (tmm) cc_final: 0.6248 (ttp) REVERT: W 842 ILE cc_start: 0.8495 (tp) cc_final: 0.8093 (tt) REVERT: W 873 ARG cc_start: 0.6365 (mtm-85) cc_final: 0.6163 (mpp-170) REVERT: X 806 ILE cc_start: 0.8231 (tp) cc_final: 0.7913 (tt) REVERT: X 859 LYS cc_start: 0.6825 (mptt) cc_final: 0.6617 (mptt) outliers start: 2 outliers final: 0 residues processed: 1136 average time/residue: 0.2505 time to fit residues: 415.5847 Evaluate side-chains 936 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 936 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 HIS A 58 HIS A 276 ASN B 259 GLN C 240 GLN C 249 GLN C 253 ASN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN G 139 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN H 132 GLN I 386 GLN I 387 GLN I 445 GLN J 374 GLN K 805 ASN ** K 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 817 GLN L 856 ASN ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 176 GLN M 249 GLN ** M 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 100 GLN ** N 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 259 GLN ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 5 GLN R 812 GLN R 831 ASN ** R 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 HIS S 100 GLN ** S 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 ASN ** T 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 386 GLN U 445 GLN ** V 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 401 GLN ** W 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 817 GLN X 812 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.185522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.173973 restraints weight = 53518.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.173380 restraints weight = 67908.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.173569 restraints weight = 56273.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.173253 restraints weight = 48656.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.173310 restraints weight = 43363.317| |-----------------------------------------------------------------------------| r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5726 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 30280 Z= 0.290 Angle : 0.851 16.391 40742 Z= 0.456 Chirality : 0.048 0.279 4646 Planarity : 0.006 0.076 5518 Dihedral : 5.255 28.211 4368 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.06 % Allowed : 9.66 % Favored : 89.28 % 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 are not related in a simple way. whole: 1.48 (0.13), residues: 3834 helix: 1.97 (0.09), residues: 2876 sheet: -2.53 (0.26), residues: 330 loop : -1.67 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 80 TYR 0.030 0.003 TYR G 42 PHE 0.044 0.006 PHE B 77 TRP 0.052 0.005 TRP Q 809 HIS 0.021 0.002 HIS N 58 Details of bonding type rmsd covalent geometry : bond 0.00595 (30270) covalent geometry : angle 0.84765 (40726) SS BOND : bond 0.01260 ( 8) SS BOND : angle 3.85306 ( 16) hydrogen bonds : bond 0.06039 ( 3024) hydrogen bonds : angle 4.85041 ( 9000) Misc. bond : bond 0.00608 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 1014 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.6401 (m-10) cc_final: 0.5316 (m-10) REVERT: A 63 GLU cc_start: 0.7011 (tm-30) cc_final: 0.6670 (tm-30) REVERT: A 151 LEU cc_start: 0.6836 (mt) cc_final: 0.6562 (mt) REVERT: A 152 GLN cc_start: 0.6386 (pp30) cc_final: 0.5999 (pp30) REVERT: B 56 MET cc_start: 0.4884 (mpp) cc_final: 0.4573 (mpp) REVERT: B 76 GLU cc_start: 0.5573 (mt-10) cc_final: 0.5192 (mt-10) REVERT: B 80 ARG cc_start: 0.5583 (mtm-85) cc_final: 0.2809 (mtm-85) REVERT: B 91 ARG cc_start: 0.6002 (mtt90) cc_final: 0.4879 (tpp-160) REVERT: B 126 ASP cc_start: 0.6136 (t70) cc_final: 0.5800 (t0) REVERT: B 138 ASP cc_start: 0.6403 (m-30) cc_final: 0.5268 (m-30) REVERT: B 155 LEU cc_start: 0.7075 (tt) cc_final: 0.6821 (tp) REVERT: B 170 ARG cc_start: 0.6847 (ttm-80) cc_final: 0.6499 (ttt-90) REVERT: B 172 GLU cc_start: 0.5884 (tp30) cc_final: 0.5678 (tp30) REVERT: B 255 LEU cc_start: 0.7179 (tp) cc_final: 0.6813 (mt) REVERT: C 245 ARG cc_start: 0.5120 (ttp80) cc_final: 0.4841 (ttp80) REVERT: C 325 LEU cc_start: 0.7576 (mt) cc_final: 0.7048 (mm) REVERT: C 392 LEU cc_start: 0.7102 (mm) cc_final: 0.6837 (mt) REVERT: C 404 ARG cc_start: 0.6836 (ptt90) cc_final: 0.6591 (mtm110) REVERT: C 426 GLU cc_start: 0.6702 (pp20) cc_final: 0.6208 (tm-30) REVERT: C 431 GLU cc_start: 0.6669 (pp20) cc_final: 0.6441 (tm-30) REVERT: C 434 LEU cc_start: 0.6441 (tp) cc_final: 0.5630 (tp) REVERT: D 300 MET cc_start: 0.5837 (pmm) cc_final: 0.5548 (pmm) REVERT: D 372 VAL cc_start: 0.7526 (t) cc_final: 0.7245 (p) REVERT: D 380 ARG cc_start: 0.7296 (mtp180) cc_final: 0.7053 (ttm170) REVERT: D 415 GLU cc_start: 0.5656 (tp30) cc_final: 0.5419 (tp30) REVERT: E 794 SER cc_start: 0.7829 (p) cc_final: 0.7303 (m) REVERT: E 849 ASP cc_start: 0.7645 (m-30) cc_final: 0.7396 (t0) REVERT: E 862 ASP cc_start: 0.6557 (m-30) cc_final: 0.6075 (m-30) REVERT: E 866 TYR cc_start: 0.7237 (m-10) cc_final: 0.5943 (m-80) REVERT: E 876 GLU cc_start: 0.6913 (tp30) cc_final: 0.5909 (tp30) REVERT: E 883 GLN cc_start: 0.6895 (mm110) cc_final: 0.6600 (mm110) REVERT: F 800 SER cc_start: 0.8961 (m) cc_final: 0.8740 (p) REVERT: F 841 ILE cc_start: 0.6380 (tp) cc_final: 0.6086 (mm) REVERT: F 867 SER cc_start: 0.7939 (t) cc_final: 0.7531 (p) REVERT: F 873 ARG cc_start: 0.6945 (mpt-90) cc_final: 0.6607 (mmt90) REVERT: G 100 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7471 (pp30) REVERT: G 115 LEU cc_start: 0.8045 (tp) cc_final: 0.6131 (tp) REVERT: G 157 VAL cc_start: 0.6566 (t) cc_final: 0.6181 (t) REVERT: H 40 GLN cc_start: 0.6756 (pp30) cc_final: 0.6388 (pp30) REVERT: H 94 LEU cc_start: 0.7731 (tp) cc_final: 0.5704 (tp) REVERT: I 387 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6865 (pp30) REVERT: I 406 SER cc_start: 0.7758 (t) cc_final: 0.7239 (t) REVERT: I 416 LEU cc_start: 0.7570 (tt) cc_final: 0.7346 (tp) REVERT: I 421 GLU cc_start: 0.5707 (mm-30) cc_final: 0.5466 (mm-30) REVERT: I 426 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6527 (mt-10) REVERT: J 367 LEU cc_start: 0.8061 (mt) cc_final: 0.7137 (tp) REVERT: J 391 ARG cc_start: 0.5902 (ttm-80) cc_final: 0.5656 (ttm-80) REVERT: J 405 ASP cc_start: 0.6343 (m-30) cc_final: 0.5963 (m-30) REVERT: J 435 GLU cc_start: 0.6166 (tp30) cc_final: 0.5929 (tp30) REVERT: K 800 SER cc_start: 0.8301 (m) cc_final: 0.7762 (m) REVERT: K 818 ARG cc_start: 0.7114 (ttm170) cc_final: 0.6854 (ttp-170) REVERT: L 793 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7642 (tt) REVERT: L 807 MET cc_start: 0.7932 (pmm) cc_final: 0.7572 (pmm) REVERT: L 861 GLU cc_start: 0.6202 (pp20) cc_final: 0.5887 (pp20) REVERT: L 866 TYR cc_start: 0.7734 (m-10) cc_final: 0.7253 (m-10) REVERT: L 876 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7104 (mm-30) REVERT: M 42 TYR cc_start: 0.5813 (m-10) cc_final: 0.5112 (m-10) REVERT: M 46 HIS cc_start: 0.7077 (m90) cc_final: 0.6824 (m170) REVERT: M 52 ILE cc_start: 0.7969 (mm) cc_final: 0.7450 (mm) REVERT: M 63 GLU cc_start: 0.6408 (tm-30) cc_final: 0.5938 (tm-30) REVERT: M 151 LEU cc_start: 0.7007 (mt) cc_final: 0.6414 (mt) REVERT: M 152 GLN cc_start: 0.6895 (pp30) cc_final: 0.6574 (pp30) REVERT: M 177 ASP cc_start: 0.5890 (t70) cc_final: 0.5629 (t0) REVERT: M 264 ARG cc_start: 0.6667 (ttp-170) cc_final: 0.6448 (ttp-110) REVERT: N 62 ILE cc_start: 0.7647 (mp) cc_final: 0.7288 (mm) REVERT: N 73 VAL cc_start: 0.7112 (t) cc_final: 0.6558 (t) REVERT: N 80 ARG cc_start: 0.5372 (mtm-85) cc_final: 0.4817 (mtm-85) REVERT: N 126 ASP cc_start: 0.6292 (t70) cc_final: 0.6035 (t0) REVERT: N 130 GLN cc_start: 0.8049 (mt0) cc_final: 0.7817 (mt0) REVERT: N 145 ARG cc_start: 0.6131 (ttp80) cc_final: 0.5923 (tmm-80) REVERT: O 392 LEU cc_start: 0.6129 (mm) cc_final: 0.5897 (tp) REVERT: P 378 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.5932 (tp) REVERT: P 413 ILE cc_start: 0.7970 (mm) cc_final: 0.7646 (mm) REVERT: P 421 GLU cc_start: 0.6699 (tp30) cc_final: 0.6215 (tp30) REVERT: P 445 GLN cc_start: 0.6914 (tm-30) cc_final: 0.6630 (tm-30) REVERT: Q 792 ARG cc_start: 0.7159 (ttm-80) cc_final: 0.6309 (ttm-80) REVERT: Q 825 THR cc_start: 0.8099 (p) cc_final: 0.7806 (p) REVERT: Q 835 SER cc_start: 0.7652 (p) cc_final: 0.7237 (t) REVERT: Q 845 ASP cc_start: 0.7202 (t70) cc_final: 0.6852 (t70) REVERT: Q 850 THR cc_start: 0.8004 (p) cc_final: 0.7585 (p) REVERT: R 794 SER cc_start: 0.5169 (m) cc_final: 0.4933 (t) REVERT: R 834 ASP cc_start: 0.6748 (m-30) cc_final: 0.5993 (m-30) REVERT: R 852 TYR cc_start: 0.6381 (m-80) cc_final: 0.5963 (m-80) REVERT: R 867 SER cc_start: 0.7692 (t) cc_final: 0.7342 (p) REVERT: T 84 HIS cc_start: 0.5739 (t-90) cc_final: 0.5249 (t-90) REVERT: T 87 LEU cc_start: 0.7431 (mm) cc_final: 0.6921 (tp) REVERT: T 115 LEU cc_start: 0.6715 (tp) cc_final: 0.6117 (tp) REVERT: U 412 LYS cc_start: 0.7662 (tppt) cc_final: 0.7166 (tptp) REVERT: U 426 GLU cc_start: 0.6427 (mt-10) cc_final: 0.6224 (mt-10) REVERT: U 438 ARG cc_start: 0.6980 (mmt90) cc_final: 0.6585 (mtt90) REVERT: V 376 LYS cc_start: 0.8461 (mtmm) cc_final: 0.5650 (mtmm) REVERT: V 383 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.5810 (pm20) REVERT: V 386 GLN cc_start: 0.6951 (pp30) cc_final: 0.6717 (pp30) REVERT: W 804 ILE cc_start: 0.7653 (tp) cc_final: 0.7429 (mm) REVERT: W 811 ARG cc_start: 0.6390 (ttm170) cc_final: 0.5991 (ttm170) REVERT: W 820 MET cc_start: 0.6904 (tmm) cc_final: 0.6189 (ttp) REVERT: X 866 TYR cc_start: 0.8491 (m-80) cc_final: 0.8100 (m-80) outliers start: 32 outliers final: 11 residues processed: 1035 average time/residue: 0.2389 time to fit residues: 362.9538 Evaluate side-chains 899 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 883 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 314 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 175 optimal weight: 0.1980 chunk 137 optimal weight: 0.9990 chunk 364 optimal weight: 0.2980 chunk 202 optimal weight: 0.1980 chunk 269 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 241 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS B 100 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 812 GLN K 817 GLN L 856 ASN M 36 GLN ** M 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 ASN O 240 GLN ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 409 HIS ** R 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 100 GLN ** S 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 GLN U 374 GLN V 374 GLN W 817 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.187424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.176211 restraints weight = 52913.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.176096 restraints weight = 61871.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.175514 restraints weight = 51176.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.175197 restraints weight = 46968.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.175497 restraints weight = 42387.087| |-----------------------------------------------------------------------------| r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5690 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30280 Z= 0.227 Angle : 0.784 14.518 40742 Z= 0.419 Chirality : 0.046 0.311 4646 Planarity : 0.005 0.081 5518 Dihedral : 4.944 31.713 4368 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.33 % Allowed : 6.46 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 1.99 (0.13), residues: 3834 helix: 2.30 (0.09), residues: 2908 sheet: -2.39 (0.24), residues: 368 loop : -1.35 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 873 TYR 0.029 0.003 TYR W 810 PHE 0.036 0.005 PHE B 77 TRP 0.044 0.004 TRP F 809 HIS 0.015 0.001 HIS N 58 Details of bonding type rmsd covalent geometry : bond 0.00468 (30270) covalent geometry : angle 0.78191 (40726) SS BOND : bond 0.01288 ( 8) SS BOND : angle 2.93217 ( 16) hydrogen bonds : bond 0.05726 ( 3024) hydrogen bonds : angle 4.59151 ( 9000) Misc. bond : bond 0.00279 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1026 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.6483 (m-10) cc_final: 0.5988 (m-10) REVERT: A 63 GLU cc_start: 0.6982 (tm-30) cc_final: 0.6572 (tm-30) REVERT: A 151 LEU cc_start: 0.6743 (mt) cc_final: 0.6306 (mt) REVERT: A 152 GLN cc_start: 0.6474 (pp30) cc_final: 0.6187 (pp30) REVERT: A 168 THR cc_start: 0.7441 (t) cc_final: 0.7172 (t) REVERT: A 171 ILE cc_start: 0.8060 (mm) cc_final: 0.7751 (mm) REVERT: B 56 MET cc_start: 0.4801 (mpp) cc_final: 0.4546 (mpp) REVERT: B 76 GLU cc_start: 0.5642 (mt-10) cc_final: 0.5222 (mt-10) REVERT: B 80 ARG cc_start: 0.4757 (mtm-85) cc_final: 0.4011 (mtm-85) REVERT: B 91 ARG cc_start: 0.5572 (mtt90) cc_final: 0.4746 (tpp-160) REVERT: B 119 GLU cc_start: 0.6158 (pp20) cc_final: 0.5866 (tm-30) REVERT: B 126 ASP cc_start: 0.6192 (t70) cc_final: 0.5754 (t0) REVERT: B 128 ARG cc_start: 0.6730 (mtp-110) cc_final: 0.6488 (mtm110) REVERT: B 138 ASP cc_start: 0.6043 (m-30) cc_final: 0.4862 (m-30) REVERT: B 170 ARG cc_start: 0.6601 (ttm-80) cc_final: 0.6373 (ttt180) REVERT: B 172 GLU cc_start: 0.5731 (tp30) cc_final: 0.5499 (tp30) REVERT: C 325 LEU cc_start: 0.7538 (mt) cc_final: 0.6780 (mm) REVERT: C 375 GLU cc_start: 0.5317 (pp20) cc_final: 0.4995 (tm-30) REVERT: C 404 ARG cc_start: 0.6816 (ptt90) cc_final: 0.6536 (mtm-85) REVERT: C 426 GLU cc_start: 0.6806 (pp20) cc_final: 0.6475 (tm-30) REVERT: C 431 GLU cc_start: 0.6684 (pp20) cc_final: 0.6296 (tm-30) REVERT: D 286 ARG cc_start: 0.6343 (ptp-170) cc_final: 0.6095 (ptp90) REVERT: D 372 VAL cc_start: 0.7456 (t) cc_final: 0.6845 (p) REVERT: D 380 ARG cc_start: 0.6901 (mtp180) cc_final: 0.6399 (ttm110) REVERT: D 426 GLU cc_start: 0.7103 (tt0) cc_final: 0.6777 (tt0) REVERT: D 440 ASP cc_start: 0.5449 (t0) cc_final: 0.5179 (t0) REVERT: E 876 GLU cc_start: 0.7075 (tp30) cc_final: 0.6524 (tp30) REVERT: F 841 ILE cc_start: 0.6443 (tp) cc_final: 0.6010 (mm) REVERT: F 867 SER cc_start: 0.7862 (t) cc_final: 0.7486 (p) REVERT: F 873 ARG cc_start: 0.6909 (mpt-90) cc_final: 0.6479 (mmt90) REVERT: G 101 ILE cc_start: 0.6347 (tp) cc_final: 0.6025 (tp) REVERT: G 103 LEU cc_start: 0.7905 (tp) cc_final: 0.7700 (tp) REVERT: G 157 VAL cc_start: 0.6771 (t) cc_final: 0.6428 (t) REVERT: H 41 ARG cc_start: 0.6597 (tpp-160) cc_final: 0.6056 (ptt180) REVERT: H 94 LEU cc_start: 0.7579 (tp) cc_final: 0.6767 (tt) REVERT: I 395 MET cc_start: 0.6090 (ttp) cc_final: 0.5603 (ttt) REVERT: I 416 LEU cc_start: 0.7683 (tt) cc_final: 0.7309 (tp) REVERT: I 421 GLU cc_start: 0.6020 (mm-30) cc_final: 0.5761 (mm-30) REVERT: I 426 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6638 (mt-10) REVERT: J 367 LEU cc_start: 0.7990 (mt) cc_final: 0.6957 (mt) REVERT: J 387 GLN cc_start: 0.6331 (pp30) cc_final: 0.6005 (pp30) REVERT: J 404 ARG cc_start: 0.7535 (ptt-90) cc_final: 0.7291 (ptt90) REVERT: K 800 SER cc_start: 0.8167 (m) cc_final: 0.7125 (p) REVERT: K 811 ARG cc_start: 0.6784 (ttm170) cc_final: 0.6204 (ttm170) REVERT: K 825 THR cc_start: 0.8378 (t) cc_final: 0.7430 (t) REVERT: K 865 VAL cc_start: 0.8021 (t) cc_final: 0.7758 (p) REVERT: L 807 MET cc_start: 0.7963 (pmm) cc_final: 0.7727 (ptp) REVERT: L 856 ASN cc_start: 0.6495 (m110) cc_final: 0.6261 (m-40) REVERT: L 861 GLU cc_start: 0.6341 (pp20) cc_final: 0.5959 (pp20) REVERT: L 876 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7086 (mm-30) REVERT: M 42 TYR cc_start: 0.6148 (m-10) cc_final: 0.5782 (m-10) REVERT: M 63 GLU cc_start: 0.6188 (tm-30) cc_final: 0.5975 (tm-30) REVERT: M 151 LEU cc_start: 0.7149 (mt) cc_final: 0.6548 (mt) REVERT: M 152 GLN cc_start: 0.7031 (pp30) cc_final: 0.6728 (pp30) REVERT: M 177 ASP cc_start: 0.6034 (t70) cc_final: 0.5706 (t0) REVERT: M 264 ARG cc_start: 0.6851 (ttp-170) cc_final: 0.6559 (ttp-110) REVERT: N 62 ILE cc_start: 0.7390 (mp) cc_final: 0.7179 (mm) REVERT: N 77 PHE cc_start: 0.6552 (m-80) cc_final: 0.5891 (m-80) REVERT: N 80 ARG cc_start: 0.5390 (mtm-85) cc_final: 0.4004 (mtm-85) REVERT: N 124 GLU cc_start: 0.6739 (pp20) cc_final: 0.6153 (pp20) REVERT: N 126 ASP cc_start: 0.6270 (t70) cc_final: 0.5987 (t0) REVERT: N 130 GLN cc_start: 0.7915 (mt0) cc_final: 0.7681 (mt0) REVERT: O 329 LEU cc_start: 0.7052 (tp) cc_final: 0.6687 (tp) REVERT: O 392 LEU cc_start: 0.5909 (mm) cc_final: 0.5671 (tp) REVERT: O 409 HIS cc_start: 0.5725 (m90) cc_final: 0.5182 (m-70) REVERT: O 434 LEU cc_start: 0.5014 (tp) cc_final: 0.4714 (tt) REVERT: O 446 MET cc_start: 0.4685 (mmt) cc_final: 0.4202 (mmt) REVERT: P 321 ARG cc_start: 0.6667 (tmt-80) cc_final: 0.5376 (tpt90) REVERT: P 325 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.7029 (mp) REVERT: P 331 ARG cc_start: 0.7264 (ttm-80) cc_final: 0.6956 (ttm-80) REVERT: P 340 GLU cc_start: 0.7283 (pp20) cc_final: 0.6914 (pp20) REVERT: P 438 ARG cc_start: 0.6297 (tmm160) cc_final: 0.5384 (tmm160) REVERT: P 445 GLN cc_start: 0.6802 (tm-30) cc_final: 0.6394 (tm-30) REVERT: Q 825 THR cc_start: 0.8345 (p) cc_final: 0.7381 (p) REVERT: Q 835 SER cc_start: 0.7623 (p) cc_final: 0.7188 (t) REVERT: Q 843 SER cc_start: 0.8255 (t) cc_final: 0.7979 (p) REVERT: Q 845 ASP cc_start: 0.7273 (t70) cc_final: 0.6986 (t70) REVERT: Q 850 THR cc_start: 0.8108 (p) cc_final: 0.7806 (p) REVERT: Q 875 SER cc_start: 0.7597 (t) cc_final: 0.7307 (t) REVERT: R 805 ASN cc_start: 0.5132 (m-40) cc_final: 0.4385 (t0) REVERT: R 867 SER cc_start: 0.7834 (t) cc_final: 0.7504 (p) REVERT: R 873 ARG cc_start: 0.7245 (mmt90) cc_final: 0.7006 (mtt-85) REVERT: S 153 SER cc_start: 0.6250 (p) cc_final: 0.5909 (m) REVERT: T 84 HIS cc_start: 0.5018 (t-90) cc_final: 0.4407 (t-90) REVERT: T 104 ILE cc_start: 0.7467 (tt) cc_final: 0.6860 (tt) REVERT: T 115 LEU cc_start: 0.6436 (tp) cc_final: 0.6211 (tt) REVERT: U 391 ARG cc_start: 0.7848 (ttp80) cc_final: 0.6009 (ttp80) REVERT: U 403 ARG cc_start: 0.7191 (mtt180) cc_final: 0.6477 (mtt180) REVERT: U 412 LYS cc_start: 0.7519 (tppt) cc_final: 0.7203 (tptm) REVERT: U 426 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6722 (mt-10) REVERT: U 438 ARG cc_start: 0.6963 (mmt90) cc_final: 0.6107 (mmt-90) REVERT: V 359 THR cc_start: 0.7641 (t) cc_final: 0.7165 (t) REVERT: V 384 ARG cc_start: 0.7030 (ptp-170) cc_final: 0.6754 (ptt180) REVERT: V 412 LYS cc_start: 0.7094 (mtpp) cc_final: 0.6734 (mtpp) REVERT: V 434 LEU cc_start: 0.6945 (mm) cc_final: 0.6258 (mm) REVERT: W 855 MET cc_start: 0.7149 (mmm) cc_final: 0.6733 (mmt) REVERT: X 810 TYR cc_start: 0.6275 (m-80) cc_final: 0.5598 (m-80) REVERT: X 854 GLN cc_start: 0.7159 (tp40) cc_final: 0.6849 (tp-100) outliers start: 10 outliers final: 4 residues processed: 1031 average time/residue: 0.2409 time to fit residues: 366.3807 Evaluate side-chains 928 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 923 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 148 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 298 optimal weight: 0.0970 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 chunk 358 optimal weight: 0.0870 chunk 254 optimal weight: 0.9980 chunk 278 optimal weight: 0.0970 chunk 119 optimal weight: 0.8980 overall best weight: 0.1954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS B 93 ASN B 100 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN D 303 GLN ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 GLN I 366 GLN ** I 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 401 GLN K 3 GLN K 817 GLN K 831 ASN M 176 GLN M 272 GLN ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 ASN ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 401 GLN Q 817 GLN ** R 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 100 GLN S 139 ASN T 93 ASN T 96 GLN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 817 GLN X 812 GLN X 817 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.190115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.178948 restraints weight = 52642.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.178935 restraints weight = 60162.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.179107 restraints weight = 44672.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.178409 restraints weight = 42494.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.178699 restraints weight = 42196.442| |-----------------------------------------------------------------------------| r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5612 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30280 Z= 0.179 Angle : 0.725 14.375 40742 Z= 0.384 Chirality : 0.043 0.247 4646 Planarity : 0.005 0.073 5518 Dihedral : 4.699 32.586 4368 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.40 % Allowed : 4.68 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 2.59 (0.13), residues: 3834 helix: 2.75 (0.09), residues: 2884 sheet: -2.02 (0.25), residues: 388 loop : -1.16 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 384 TYR 0.030 0.002 TYR E 810 PHE 0.044 0.005 PHE N 77 TRP 0.043 0.003 TRP F 809 HIS 0.011 0.001 HIS P 409 Details of bonding type rmsd covalent geometry : bond 0.00358 (30270) covalent geometry : angle 0.72345 (40726) SS BOND : bond 0.00604 ( 8) SS BOND : angle 2.39022 ( 16) hydrogen bonds : bond 0.05497 ( 3024) hydrogen bonds : angle 4.33312 ( 9000) Misc. bond : bond 0.00189 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1022 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.6425 (m-10) cc_final: 0.5894 (m-10) REVERT: A 57 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6638 (mt-10) REVERT: A 63 GLU cc_start: 0.6610 (tm-30) cc_final: 0.6353 (tm-30) REVERT: A 152 GLN cc_start: 0.6479 (pp30) cc_final: 0.6237 (pp30) REVERT: A 176 GLN cc_start: 0.6094 (mp10) cc_final: 0.5537 (mp10) REVERT: A 231 SER cc_start: 0.3592 (t) cc_final: 0.3337 (t) REVERT: B 80 ARG cc_start: 0.4793 (mtm-85) cc_final: 0.4110 (mtm-85) REVERT: B 91 ARG cc_start: 0.5466 (mtt90) cc_final: 0.4951 (tpp-160) REVERT: B 119 GLU cc_start: 0.6222 (pp20) cc_final: 0.5794 (tm-30) REVERT: B 126 ASP cc_start: 0.6244 (t70) cc_final: 0.5990 (t0) REVERT: B 138 ASP cc_start: 0.5897 (m-30) cc_final: 0.5666 (m-30) REVERT: B 170 ARG cc_start: 0.6587 (ttm-80) cc_final: 0.6175 (ttt-90) REVERT: C 259 GLN cc_start: 0.6166 (mp10) cc_final: 0.5706 (mp10) REVERT: C 404 ARG cc_start: 0.6868 (ptt90) cc_final: 0.6589 (mtm-85) REVERT: C 416 LEU cc_start: 0.7506 (mt) cc_final: 0.7209 (mm) REVERT: C 426 GLU cc_start: 0.7003 (pp20) cc_final: 0.6665 (tm-30) REVERT: C 431 GLU cc_start: 0.6378 (pp20) cc_final: 0.5881 (tm-30) REVERT: C 434 LEU cc_start: 0.5870 (tp) cc_final: 0.5511 (tp) REVERT: D 286 ARG cc_start: 0.6313 (ptp-170) cc_final: 0.6004 (ptp90) REVERT: D 372 VAL cc_start: 0.7436 (t) cc_final: 0.6677 (p) REVERT: D 380 ARG cc_start: 0.7162 (mtp180) cc_final: 0.6331 (mtp180) REVERT: D 415 GLU cc_start: 0.5537 (tp30) cc_final: 0.5267 (tp30) REVERT: E 820 MET cc_start: 0.7106 (ptt) cc_final: 0.6863 (ptt) REVERT: E 825 THR cc_start: 0.7753 (p) cc_final: 0.7505 (p) REVERT: F 795 CYS cc_start: 0.4695 (p) cc_final: 0.3254 (p) REVERT: F 837 LYS cc_start: 0.8033 (mmpt) cc_final: 0.7744 (mmmm) REVERT: F 841 ILE cc_start: 0.6370 (tp) cc_final: 0.6128 (mm) REVERT: F 853 LEU cc_start: 0.4549 (tt) cc_final: 0.4344 (tp) REVERT: F 867 SER cc_start: 0.7857 (t) cc_final: 0.7380 (p) REVERT: G 115 LEU cc_start: 0.7909 (tp) cc_final: 0.7365 (tp) REVERT: G 156 LYS cc_start: 0.4616 (tmtt) cc_final: 0.4379 (tttt) REVERT: G 157 VAL cc_start: 0.6824 (t) cc_final: 0.6527 (t) REVERT: H 41 ARG cc_start: 0.6428 (tpp-160) cc_final: 0.5826 (ptt180) REVERT: H 75 GLN cc_start: 0.7333 (mp10) cc_final: 0.6409 (mp10) REVERT: I 416 LEU cc_start: 0.7480 (tt) cc_final: 0.7220 (tp) REVERT: I 421 GLU cc_start: 0.6263 (mm-30) cc_final: 0.5086 (mm-30) REVERT: I 426 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6639 (mt-10) REVERT: J 367 LEU cc_start: 0.7933 (mt) cc_final: 0.7007 (tp) REVERT: J 404 ARG cc_start: 0.7408 (ptt-90) cc_final: 0.7024 (ptt90) REVERT: K 800 SER cc_start: 0.8042 (m) cc_final: 0.6990 (p) REVERT: K 825 THR cc_start: 0.8337 (t) cc_final: 0.7537 (t) REVERT: K 865 VAL cc_start: 0.8180 (t) cc_final: 0.7847 (p) REVERT: K 866 TYR cc_start: 0.8319 (m-10) cc_final: 0.8001 (m-10) REVERT: L 823 VAL cc_start: 0.8430 (t) cc_final: 0.8178 (t) REVERT: L 861 GLU cc_start: 0.6314 (pp20) cc_final: 0.5922 (pp20) REVERT: L 865 VAL cc_start: 0.7531 (p) cc_final: 0.7018 (m) REVERT: L 876 GLU cc_start: 0.7507 (mm-30) cc_final: 0.6980 (mm-30) REVERT: M 94 LEU cc_start: 0.7406 (mm) cc_final: 0.6894 (tp) REVERT: M 151 LEU cc_start: 0.7286 (mt) cc_final: 0.6668 (mt) REVERT: M 177 ASP cc_start: 0.5936 (t70) cc_final: 0.5571 (t0) REVERT: M 264 ARG cc_start: 0.6888 (ttp-170) cc_final: 0.6501 (ttp-110) REVERT: M 272 GLN cc_start: -0.1366 (OUTLIER) cc_final: -0.2062 (tm-30) REVERT: N 62 ILE cc_start: 0.7317 (mp) cc_final: 0.6714 (tp) REVERT: N 66 ILE cc_start: 0.6607 (tt) cc_final: 0.6373 (tt) REVERT: N 77 PHE cc_start: 0.6113 (m-80) cc_final: 0.5807 (m-80) REVERT: N 80 ARG cc_start: 0.5006 (mtm-85) cc_final: 0.3326 (mtm-85) REVERT: N 124 GLU cc_start: 0.6385 (pp20) cc_final: 0.5965 (pp20) REVERT: O 392 LEU cc_start: 0.5383 (mm) cc_final: 0.4946 (tp) REVERT: O 396 GLN cc_start: 0.6017 (tp40) cc_final: 0.5408 (tm-30) REVERT: O 446 MET cc_start: 0.4714 (mmt) cc_final: 0.4093 (mmt) REVERT: P 340 GLU cc_start: 0.7062 (pp20) cc_final: 0.6317 (tm-30) REVERT: P 395 MET cc_start: 0.7357 (ppp) cc_final: 0.7055 (ppp) REVERT: P 421 GLU cc_start: 0.6697 (tp30) cc_final: 0.6270 (tp30) REVERT: P 445 GLN cc_start: 0.6904 (tm-30) cc_final: 0.6564 (tm-30) REVERT: Q 820 MET cc_start: 0.6273 (tmm) cc_final: 0.5459 (ttp) REVERT: Q 850 THR cc_start: 0.8074 (p) cc_final: 0.7866 (p) REVERT: Q 880 GLN cc_start: 0.6583 (mm110) cc_final: 0.6088 (mm110) REVERT: R 805 ASN cc_start: 0.5200 (m-40) cc_final: 0.4875 (t0) REVERT: R 845 ASP cc_start: 0.5386 (t0) cc_final: 0.4877 (t0) REVERT: R 867 SER cc_start: 0.7655 (t) cc_final: 0.6562 (p) REVERT: S 91 ARG cc_start: 0.7279 (ptp-170) cc_final: 0.6961 (ptp-170) REVERT: S 153 SER cc_start: 0.6446 (p) cc_final: 0.5968 (m) REVERT: T 84 HIS cc_start: 0.4275 (t-90) cc_final: 0.3976 (t-90) REVERT: T 96 GLN cc_start: 0.6437 (tp40) cc_final: 0.6096 (tp40) REVERT: T 104 ILE cc_start: 0.7488 (tt) cc_final: 0.6861 (tt) REVERT: T 115 LEU cc_start: 0.6689 (tp) cc_final: 0.6407 (tp) REVERT: U 403 ARG cc_start: 0.7216 (mtt180) cc_final: 0.6434 (mtt180) REVERT: U 412 LYS cc_start: 0.7650 (tppt) cc_final: 0.7312 (tptt) REVERT: U 426 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6746 (mt-10) REVERT: U 438 ARG cc_start: 0.6457 (mmt90) cc_final: 0.6100 (mtt90) REVERT: V 376 LYS cc_start: 0.7984 (mtmm) cc_final: 0.7560 (mtmm) REVERT: V 384 ARG cc_start: 0.7088 (ptp-170) cc_final: 0.6545 (ptm160) REVERT: V 386 GLN cc_start: 0.7020 (pp30) cc_final: 0.6787 (pp30) REVERT: V 412 LYS cc_start: 0.7004 (mtpp) cc_final: 0.6660 (mtpp) REVERT: V 426 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7131 (mt-10) REVERT: V 434 LEU cc_start: 0.6870 (mm) cc_final: 0.6504 (mm) REVERT: W 804 ILE cc_start: 0.7967 (tp) cc_final: 0.7718 (mm) REVERT: X 810 TYR cc_start: 0.6127 (m-80) cc_final: 0.5471 (m-80) outliers start: 12 outliers final: 4 residues processed: 1029 average time/residue: 0.2370 time to fit residues: 360.9988 Evaluate side-chains 931 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 926 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 82 optimal weight: 0.9980 chunk 298 optimal weight: 0.0870 chunk 315 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 291 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 205 optimal weight: 0.8980 chunk 321 optimal weight: 0.1980 chunk 193 optimal weight: 0.5980 chunk 115 optimal weight: 0.4980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN B 276 ASN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN D 303 GLN ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 GLN H 139 ASN ** I 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 396 GLN ** J 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 817 GLN K 831 ASN L 856 ASN M 46 HIS M 148 ASN ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 249 GLN ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 399 GLN ** P 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 805 ASN ** R 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 100 GLN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 831 ASN X 812 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.187607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.176411 restraints weight = 52996.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.176414 restraints weight = 55173.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.176371 restraints weight = 44723.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.175852 restraints weight = 39223.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.176105 restraints weight = 39590.219| |-----------------------------------------------------------------------------| r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5680 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30280 Z= 0.203 Angle : 0.748 14.600 40742 Z= 0.399 Chirality : 0.044 0.252 4646 Planarity : 0.005 0.065 5518 Dihedral : 4.705 34.614 4368 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.26 % Allowed : 3.99 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 2.51 (0.13), residues: 3834 helix: 2.71 (0.09), residues: 2878 sheet: -1.93 (0.25), residues: 390 loop : -1.33 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 349 TYR 0.023 0.002 TYR G 42 PHE 0.036 0.005 PHE B 77 TRP 0.038 0.003 TRP F 809 HIS 0.008 0.001 HIS P 409 Details of bonding type rmsd covalent geometry : bond 0.00418 (30270) covalent geometry : angle 0.74672 (40726) SS BOND : bond 0.01094 ( 8) SS BOND : angle 2.17186 ( 16) hydrogen bonds : bond 0.05525 ( 3024) hydrogen bonds : angle 4.40325 ( 9000) Misc. bond : bond 0.00141 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1010 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.6517 (m-10) cc_final: 0.6014 (m-10) REVERT: A 51 SER cc_start: 0.7647 (p) cc_final: 0.6953 (p) REVERT: A 57 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6760 (mt-10) REVERT: A 63 GLU cc_start: 0.6892 (tm-30) cc_final: 0.6463 (tm-30) REVERT: A 151 LEU cc_start: 0.6739 (mt) cc_final: 0.6337 (mt) REVERT: A 152 GLN cc_start: 0.6532 (pp30) cc_final: 0.6119 (pp30) REVERT: A 172 GLU cc_start: 0.5632 (pp20) cc_final: 0.5253 (pp20) REVERT: A 220 VAL cc_start: 0.7087 (t) cc_final: 0.6698 (p) REVERT: B 76 GLU cc_start: 0.5713 (mt-10) cc_final: 0.4913 (mt-10) REVERT: B 80 ARG cc_start: 0.4927 (mtm-85) cc_final: 0.3369 (mtp180) REVERT: B 105 GLN cc_start: 0.7327 (tp-100) cc_final: 0.7055 (tp-100) REVERT: B 119 GLU cc_start: 0.6214 (pp20) cc_final: 0.5937 (tm-30) REVERT: B 126 ASP cc_start: 0.6416 (t70) cc_final: 0.6063 (t0) REVERT: B 138 ASP cc_start: 0.6284 (m-30) cc_final: 0.5635 (m-30) REVERT: B 170 ARG cc_start: 0.6657 (ttm-80) cc_final: 0.6335 (ttt-90) REVERT: C 259 GLN cc_start: 0.6435 (mp10) cc_final: 0.6097 (mp10) REVERT: C 404 ARG cc_start: 0.6782 (ptt90) cc_final: 0.6452 (mtm-85) REVERT: C 426 GLU cc_start: 0.6929 (pp20) cc_final: 0.6564 (tm-30) REVERT: C 431 GLU cc_start: 0.6788 (pp20) cc_final: 0.6315 (tm-30) REVERT: C 434 LEU cc_start: 0.6091 (tp) cc_final: 0.5722 (tp) REVERT: C 438 ARG cc_start: 0.6956 (ptt90) cc_final: 0.6098 (ptt-90) REVERT: D 372 VAL cc_start: 0.7919 (t) cc_final: 0.7563 (p) REVERT: D 380 ARG cc_start: 0.7248 (mtp180) cc_final: 0.6397 (ttm110) REVERT: D 409 HIS cc_start: 0.6818 (m-70) cc_final: 0.6618 (m-70) REVERT: D 421 GLU cc_start: 0.7150 (tp30) cc_final: 0.6899 (tp30) REVERT: D 422 ARG cc_start: 0.7798 (tpp-160) cc_final: 0.7577 (tpp-160) REVERT: E 862 ASP cc_start: 0.6736 (m-30) cc_final: 0.6453 (m-30) REVERT: F 795 CYS cc_start: 0.4476 (p) cc_final: 0.3181 (p) REVERT: F 809 TRP cc_start: 0.7823 (m100) cc_final: 0.7557 (m100) REVERT: F 837 LYS cc_start: 0.8033 (mmpt) cc_final: 0.7655 (mmmm) REVERT: F 841 ILE cc_start: 0.6255 (tp) cc_final: 0.5808 (mm) REVERT: F 867 SER cc_start: 0.7860 (t) cc_final: 0.7406 (p) REVERT: G 83 GLU cc_start: 0.6343 (mt-10) cc_final: 0.5197 (mt-10) REVERT: G 160 LEU cc_start: 0.7151 (mm) cc_final: 0.6853 (mm) REVERT: H 41 ARG cc_start: 0.6573 (tpp-160) cc_final: 0.6255 (ptt180) REVERT: H 75 GLN cc_start: 0.7346 (mp10) cc_final: 0.6667 (mp10) REVERT: H 101 ILE cc_start: 0.8119 (mt) cc_final: 0.7864 (mt) REVERT: I 396 GLN cc_start: 0.6099 (OUTLIER) cc_final: 0.5848 (tm-30) REVERT: I 426 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6663 (mt-10) REVERT: J 367 LEU cc_start: 0.8025 (mt) cc_final: 0.7303 (mt) REVERT: J 422 ARG cc_start: 0.7911 (tpp-160) cc_final: 0.7688 (tpp-160) REVERT: J 426 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6667 (mt-10) REVERT: K 818 ARG cc_start: 0.7566 (ttm170) cc_final: 0.7226 (ptm160) REVERT: K 865 VAL cc_start: 0.8206 (t) cc_final: 0.7989 (p) REVERT: L 861 GLU cc_start: 0.6387 (pp20) cc_final: 0.6005 (pp20) REVERT: L 876 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7220 (mm-30) REVERT: M 94 LEU cc_start: 0.7358 (mm) cc_final: 0.6930 (tp) REVERT: M 151 LEU cc_start: 0.7107 (mt) cc_final: 0.6564 (mt) REVERT: M 152 GLN cc_start: 0.7097 (pp30) cc_final: 0.6749 (pp30) REVERT: M 177 ASP cc_start: 0.5929 (t70) cc_final: 0.5603 (t0) REVERT: M 264 ARG cc_start: 0.6950 (ttp-170) cc_final: 0.6645 (ttp-110) REVERT: N 66 ILE cc_start: 0.6443 (tt) cc_final: 0.6204 (tt) REVERT: N 80 ARG cc_start: 0.5205 (mtm-85) cc_final: 0.3950 (mtm-85) REVERT: N 124 GLU cc_start: 0.6245 (pp20) cc_final: 0.6021 (pp20) REVERT: N 126 ASP cc_start: 0.6575 (t0) cc_final: 0.6209 (t0) REVERT: N 130 GLN cc_start: 0.8193 (mt0) cc_final: 0.7813 (mt0) REVERT: O 320 ARG cc_start: 0.6832 (tpp80) cc_final: 0.6630 (tpp80) REVERT: O 389 ARG cc_start: 0.6491 (mtm110) cc_final: 0.6271 (mtm-85) REVERT: O 392 LEU cc_start: 0.5714 (mm) cc_final: 0.5459 (tp) REVERT: O 397 GLU cc_start: 0.5878 (mm-30) cc_final: 0.5642 (tp30) REVERT: O 412 LYS cc_start: 0.7211 (pttp) cc_final: 0.6770 (ttpp) REVERT: P 421 GLU cc_start: 0.6715 (tp30) cc_final: 0.6338 (tp30) REVERT: P 438 ARG cc_start: 0.6513 (tmm160) cc_final: 0.5896 (ttp80) REVERT: P 445 GLN cc_start: 0.6890 (tm-30) cc_final: 0.6445 (tm-30) REVERT: Q 797 SER cc_start: 0.8046 (t) cc_final: 0.7453 (p) REVERT: Q 850 THR cc_start: 0.7875 (p) cc_final: 0.7551 (p) REVERT: Q 880 GLN cc_start: 0.6570 (mm110) cc_final: 0.6084 (mm110) REVERT: R 806 ILE cc_start: 0.7200 (mt) cc_final: 0.6998 (mt) REVERT: R 867 SER cc_start: 0.7451 (t) cc_final: 0.7251 (p) REVERT: R 872 TYR cc_start: 0.7339 (t80) cc_final: 0.6625 (t80) REVERT: S 91 ARG cc_start: 0.7328 (ptp-170) cc_final: 0.6809 (ptp-170) REVERT: S 153 SER cc_start: 0.6456 (p) cc_final: 0.5904 (m) REVERT: S 186 GLN cc_start: 0.5906 (OUTLIER) cc_final: 0.5533 (pm20) REVERT: T 56 MET cc_start: 0.5962 (ppp) cc_final: 0.5760 (ppp) REVERT: T 80 ARG cc_start: 0.7230 (ttm-80) cc_final: 0.6965 (ttm-80) REVERT: T 101 ILE cc_start: 0.7006 (mt) cc_final: 0.6537 (mt) REVERT: T 104 ILE cc_start: 0.7481 (tt) cc_final: 0.6346 (tt) REVERT: U 382 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7243 (mm-30) REVERT: U 410 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7108 (mm-30) REVERT: U 412 LYS cc_start: 0.7515 (tppt) cc_final: 0.7175 (tptt) REVERT: U 415 GLU cc_start: 0.6819 (tm-30) cc_final: 0.6579 (tm-30) REVERT: U 426 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6889 (mt-10) REVERT: V 376 LYS cc_start: 0.8027 (mtmm) cc_final: 0.7576 (mtmm) REVERT: V 383 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.6101 (pm20) REVERT: V 384 ARG cc_start: 0.7061 (ptp-170) cc_final: 0.6427 (ptm160) REVERT: V 386 GLN cc_start: 0.7030 (pp30) cc_final: 0.6761 (pp30) REVERT: V 404 ARG cc_start: 0.7319 (ptp-110) cc_final: 0.6887 (ttp-110) REVERT: V 405 ASP cc_start: 0.5481 (m-30) cc_final: 0.5029 (m-30) REVERT: V 431 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7577 (tm-30) REVERT: V 434 LEU cc_start: 0.6907 (mm) cc_final: 0.6179 (mm) REVERT: W 852 TYR cc_start: 0.6544 (m-80) cc_final: 0.6217 (m-80) REVERT: X 810 TYR cc_start: 0.6319 (m-80) cc_final: 0.5647 (m-80) outliers start: 8 outliers final: 1 residues processed: 1016 average time/residue: 0.2335 time to fit residues: 348.9794 Evaluate side-chains 943 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 939 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 345 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 226 optimal weight: 0.7980 chunk 262 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 181 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 113 optimal weight: 0.5980 chunk 303 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 96 GLN ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 GLN D 303 GLN ** F 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 HIS G 100 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 GLN H 139 ASN ** I 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 817 GLN K 831 ASN M 98 GLN M 176 GLN M 272 GLN ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 GLN N 84 HIS ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 366 GLN R 831 ASN T 93 ASN T 96 GLN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 132 GLN U 386 GLN X 812 GLN X 854 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.185032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.173093 restraints weight = 52283.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.172667 restraints weight = 61733.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.172832 restraints weight = 47796.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.172545 restraints weight = 37078.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.172526 restraints weight = 37382.422| |-----------------------------------------------------------------------------| r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 moved from start: 0.6410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30280 Z= 0.247 Angle : 0.802 15.208 40742 Z= 0.428 Chirality : 0.046 0.261 4646 Planarity : 0.005 0.064 5518 Dihedral : 4.905 31.330 4368 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.36 % Allowed : 3.46 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 2.13 (0.13), residues: 3834 helix: 2.40 (0.09), residues: 2908 sheet: -1.97 (0.26), residues: 352 loop : -1.59 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 129 TYR 0.037 0.003 TYR R 810 PHE 0.032 0.005 PHE B 77 TRP 0.032 0.004 TRP F 809 HIS 0.006 0.001 HIS V 409 Details of bonding type rmsd covalent geometry : bond 0.00518 (30270) covalent geometry : angle 0.80071 (40726) SS BOND : bond 0.00769 ( 8) SS BOND : angle 2.71785 ( 16) hydrogen bonds : bond 0.05693 ( 3024) hydrogen bonds : angle 4.60715 ( 9000) Misc. bond : bond 0.00182 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 1029 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.5952 (mmp) cc_final: 0.5343 (mmt) REVERT: A 63 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6672 (tm-30) REVERT: A 124 GLU cc_start: 0.7877 (pp20) cc_final: 0.7554 (pp20) REVERT: A 133 ASP cc_start: 0.6927 (t70) cc_final: 0.6695 (t70) REVERT: A 151 LEU cc_start: 0.6511 (mt) cc_final: 0.6169 (mt) REVERT: B 80 ARG cc_start: 0.4901 (mtm-85) cc_final: 0.4388 (mtm-85) REVERT: B 105 GLN cc_start: 0.7490 (tp-100) cc_final: 0.7051 (tp-100) REVERT: B 126 ASP cc_start: 0.6116 (t70) cc_final: 0.5736 (t0) REVERT: B 170 ARG cc_start: 0.6762 (ttm-80) cc_final: 0.6462 (ttt-90) REVERT: C 259 GLN cc_start: 0.6277 (mp10) cc_final: 0.6041 (mp10) REVERT: C 389 ARG cc_start: 0.6639 (ptt-90) cc_final: 0.5988 (ptt-90) REVERT: C 404 ARG cc_start: 0.6837 (ptt90) cc_final: 0.6398 (mtm-85) REVERT: C 426 GLU cc_start: 0.6915 (pp20) cc_final: 0.6485 (tm-30) REVERT: C 431 GLU cc_start: 0.6644 (pp20) cc_final: 0.6259 (tm-30) REVERT: C 434 LEU cc_start: 0.6083 (tp) cc_final: 0.5875 (tp) REVERT: C 438 ARG cc_start: 0.6917 (ptt90) cc_final: 0.5930 (ptt-90) REVERT: D 341 GLU cc_start: 0.7527 (tp30) cc_final: 0.6739 (tp30) REVERT: D 354 ASP cc_start: 0.6163 (t0) cc_final: 0.5917 (t0) REVERT: D 375 GLU cc_start: 0.5627 (pp20) cc_final: 0.5144 (pp20) REVERT: D 380 ARG cc_start: 0.7447 (mtp180) cc_final: 0.6960 (ttm170) REVERT: D 409 HIS cc_start: 0.6951 (m-70) cc_final: 0.6684 (m-70) REVERT: E 855 MET cc_start: 0.6715 (mmt) cc_final: 0.6096 (mmt) REVERT: E 862 ASP cc_start: 0.6918 (m-30) cc_final: 0.6534 (m-30) REVERT: E 866 TYR cc_start: 0.7888 (m-10) cc_final: 0.7543 (m-10) REVERT: F 795 CYS cc_start: 0.4868 (p) cc_final: 0.4650 (p) REVERT: F 837 LYS cc_start: 0.8137 (mmpt) cc_final: 0.7728 (mmmm) REVERT: F 841 ILE cc_start: 0.6342 (tp) cc_final: 0.6023 (mm) REVERT: F 867 SER cc_start: 0.7735 (t) cc_final: 0.7194 (p) REVERT: G 83 GLU cc_start: 0.5921 (mt-10) cc_final: 0.4901 (mt-10) REVERT: G 91 ARG cc_start: 0.6727 (ptp-170) cc_final: 0.6354 (ptp-170) REVERT: G 160 LEU cc_start: 0.7105 (mm) cc_final: 0.6858 (mm) REVERT: H 41 ARG cc_start: 0.6776 (tpp-160) cc_final: 0.6391 (ptt-90) REVERT: H 75 GLN cc_start: 0.7503 (mp10) cc_final: 0.6778 (mp10) REVERT: H 94 LEU cc_start: 0.7691 (tp) cc_final: 0.7096 (tt) REVERT: H 101 ILE cc_start: 0.8219 (mt) cc_final: 0.7733 (mt) REVERT: I 393 ASP cc_start: 0.6356 (m-30) cc_final: 0.6146 (m-30) REVERT: I 416 LEU cc_start: 0.7512 (tt) cc_final: 0.7295 (tp) REVERT: I 426 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6552 (mt-10) REVERT: I 429 LEU cc_start: 0.8125 (tt) cc_final: 0.7892 (mt) REVERT: I 434 LEU cc_start: 0.6400 (mt) cc_final: 0.6100 (mt) REVERT: I 438 ARG cc_start: 0.6352 (mpt180) cc_final: 0.5636 (mpt180) REVERT: I 446 MET cc_start: 0.6452 (tmm) cc_final: 0.6053 (tmm) REVERT: J 367 LEU cc_start: 0.8230 (mt) cc_final: 0.7307 (mt) REVERT: J 388 LEU cc_start: 0.8195 (tt) cc_final: 0.7634 (tp) REVERT: J 404 ARG cc_start: 0.7536 (ptt-90) cc_final: 0.7166 (ptt90) REVERT: J 426 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6783 (mt-10) REVERT: K 862 ASP cc_start: 0.7328 (t70) cc_final: 0.7083 (t0) REVERT: K 865 VAL cc_start: 0.8349 (t) cc_final: 0.8097 (p) REVERT: L 807 MET cc_start: 0.7887 (pmm) cc_final: 0.7551 (pmm) REVERT: L 818 ARG cc_start: 0.6398 (tpp-160) cc_final: 0.5513 (mmm-85) REVERT: L 861 GLU cc_start: 0.6808 (pp20) cc_final: 0.6444 (pp20) REVERT: L 865 VAL cc_start: 0.7646 (p) cc_final: 0.7191 (m) REVERT: L 876 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6458 (mm-30) REVERT: M 166 ASP cc_start: 0.7049 (t70) cc_final: 0.6843 (t70) REVERT: M 177 ASP cc_start: 0.6003 (t70) cc_final: 0.5672 (t0) REVERT: M 264 ARG cc_start: 0.6870 (ttp-170) cc_final: 0.6556 (ttp-110) REVERT: N 68 GLU cc_start: 0.6948 (mp0) cc_final: 0.6699 (pm20) REVERT: N 77 PHE cc_start: 0.5501 (m-10) cc_final: 0.5055 (m-10) REVERT: N 80 ARG cc_start: 0.5250 (mtm-85) cc_final: 0.3764 (mtm-85) REVERT: N 109 ARG cc_start: 0.7423 (mmm-85) cc_final: 0.6879 (mmm-85) REVERT: N 126 ASP cc_start: 0.6821 (t0) cc_final: 0.6311 (t0) REVERT: N 130 GLN cc_start: 0.8383 (mt0) cc_final: 0.8027 (mt0) REVERT: N 133 ASP cc_start: 0.5519 (t0) cc_final: 0.5253 (t70) REVERT: N 157 VAL cc_start: 0.6284 (t) cc_final: 0.6007 (p) REVERT: N 262 SER cc_start: 0.6015 (p) cc_final: 0.5788 (p) REVERT: O 392 LEU cc_start: 0.6602 (mm) cc_final: 0.6268 (tp) REVERT: P 326 ASN cc_start: 0.7277 (t0) cc_final: 0.6549 (t0) REVERT: P 340 GLU cc_start: 0.7188 (pp20) cc_final: 0.6890 (tm-30) REVERT: P 413 ILE cc_start: 0.8244 (mm) cc_final: 0.7886 (mm) REVERT: P 421 GLU cc_start: 0.6705 (tp30) cc_final: 0.6450 (tp30) REVERT: P 426 GLU cc_start: 0.7187 (pp20) cc_final: 0.6928 (pp20) REVERT: P 438 ARG cc_start: 0.6585 (tmm160) cc_final: 0.6109 (ttp80) REVERT: P 445 GLN cc_start: 0.6834 (tm-30) cc_final: 0.6145 (tm-30) REVERT: Q 850 THR cc_start: 0.7955 (p) cc_final: 0.7746 (p) REVERT: Q 861 GLU cc_start: 0.7306 (pm20) cc_final: 0.6121 (tp30) REVERT: Q 880 GLN cc_start: 0.6586 (mm110) cc_final: 0.6042 (mm110) REVERT: R 867 SER cc_start: 0.7480 (t) cc_final: 0.7226 (p) REVERT: R 872 TYR cc_start: 0.7511 (t80) cc_final: 0.7000 (t80) REVERT: R 873 ARG cc_start: 0.7449 (mtt-85) cc_final: 0.6981 (ttm110) REVERT: S 91 ARG cc_start: 0.7327 (ptp-170) cc_final: 0.7009 (ptp-170) REVERT: S 99 ARG cc_start: 0.6230 (mtm-85) cc_final: 0.5940 (ptp90) REVERT: S 146 LEU cc_start: 0.6416 (mm) cc_final: 0.6197 (mt) REVERT: S 147 ARG cc_start: 0.6251 (mmt-90) cc_final: 0.5861 (mmt-90) REVERT: S 153 SER cc_start: 0.6566 (p) cc_final: 0.5857 (m) REVERT: T 96 GLN cc_start: 0.6634 (tp40) cc_final: 0.6406 (tp40) REVERT: T 101 ILE cc_start: 0.7316 (mt) cc_final: 0.6429 (mt) REVERT: T 104 ILE cc_start: 0.7574 (tt) cc_final: 0.6649 (tt) REVERT: U 382 GLU cc_start: 0.7713 (mm-30) cc_final: 0.6829 (mm-30) REVERT: U 412 LYS cc_start: 0.7592 (tppt) cc_final: 0.7236 (tptm) REVERT: U 426 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6797 (mt-10) REVERT: U 438 ARG cc_start: 0.7226 (mmt90) cc_final: 0.6528 (mtt90) REVERT: V 357 ARG cc_start: 0.7205 (tpt90) cc_final: 0.6926 (tpt90) REVERT: V 431 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7274 (tm-30) REVERT: V 434 LEU cc_start: 0.6725 (mm) cc_final: 0.6182 (mm) REVERT: W 840 PHE cc_start: 0.6836 (m-80) cc_final: 0.6538 (m-10) REVERT: W 852 TYR cc_start: 0.6751 (m-80) cc_final: 0.6489 (m-80) REVERT: W 875 SER cc_start: 0.7747 (t) cc_final: 0.7487 (t) REVERT: X 4 LEU cc_start: 0.8209 (mt) cc_final: 0.7734 (mt) REVERT: X 810 TYR cc_start: 0.6697 (m-80) cc_final: 0.5770 (m-80) REVERT: X 859 LYS cc_start: 0.7341 (mmpt) cc_final: 0.6981 (mmpt) REVERT: X 866 TYR cc_start: 0.8121 (m-10) cc_final: 0.7779 (m-10) outliers start: 11 outliers final: 5 residues processed: 1033 average time/residue: 0.2398 time to fit residues: 362.9564 Evaluate side-chains 935 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 930 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 292 optimal weight: 0.5980 chunk 343 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 282 optimal weight: 0.5980 chunk 111 optimal weight: 0.2980 chunk 106 optimal weight: 0.0970 chunk 68 optimal weight: 0.2980 chunk 279 optimal weight: 0.0570 chunk 380 optimal weight: 0.9990 chunk 313 optimal weight: 0.8980 chunk 145 optimal weight: 0.3980 overall best weight: 0.2296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN B 100 GLN B 139 ASN C 303 GLN ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 366 GLN ** I 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 817 GLN K 831 ASN M 276 ASN ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 HIS O 259 GLN ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 350 HIS ** R 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 40 GLN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 831 ASN X 5 GLN X 812 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.184555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.172398 restraints weight = 54695.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.170715 restraints weight = 69939.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.170157 restraints weight = 56580.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.170110 restraints weight = 50840.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.170104 restraints weight = 44593.218| |-----------------------------------------------------------------------------| r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5780 moved from start: 0.6649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30280 Z= 0.186 Angle : 0.764 16.744 40742 Z= 0.406 Chirality : 0.044 0.264 4646 Planarity : 0.005 0.065 5518 Dihedral : 4.688 31.035 4368 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.03 % Allowed : 2.08 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 2.40 (0.13), residues: 3834 helix: 2.61 (0.09), residues: 2910 sheet: -2.00 (0.26), residues: 352 loop : -1.54 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 129 TYR 0.031 0.002 TYR R 810 PHE 0.027 0.005 PHE B 77 TRP 0.023 0.003 TRP L 827 HIS 0.005 0.001 HIS V 409 Details of bonding type rmsd covalent geometry : bond 0.00383 (30270) covalent geometry : angle 0.76353 (40726) SS BOND : bond 0.00474 ( 8) SS BOND : angle 1.96679 ( 16) hydrogen bonds : bond 0.05486 ( 3024) hydrogen bonds : angle 4.41550 ( 9000) Misc. bond : bond 0.00100 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1029 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 51 SER cc_start: 0.7749 (p) cc_final: 0.6954 (p) REVERT: A 56 MET cc_start: 0.6135 (mmp) cc_final: 0.5820 (mmp) REVERT: A 63 GLU cc_start: 0.6757 (tm-30) cc_final: 0.6415 (tm-30) REVERT: A 151 LEU cc_start: 0.6617 (mt) cc_final: 0.6230 (mt) REVERT: A 152 GLN cc_start: 0.6615 (pp30) cc_final: 0.6282 (pp30) REVERT: B 80 ARG cc_start: 0.4459 (mtm-85) cc_final: 0.3903 (mtm-85) REVERT: B 107 GLU cc_start: 0.6275 (tt0) cc_final: 0.5558 (tt0) REVERT: B 126 ASP cc_start: 0.6179 (t70) cc_final: 0.5734 (t0) REVERT: B 144 ASP cc_start: 0.6586 (t0) cc_final: 0.6042 (t0) REVERT: B 157 VAL cc_start: 0.7385 (t) cc_final: 0.7145 (p) REVERT: B 170 ARG cc_start: 0.6713 (ttm-80) cc_final: 0.6470 (ttt-90) REVERT: C 375 GLU cc_start: 0.5411 (pp20) cc_final: 0.5095 (pp20) REVERT: C 389 ARG cc_start: 0.6579 (ptt-90) cc_final: 0.5962 (ptt-90) REVERT: C 404 ARG cc_start: 0.6798 (ptt90) cc_final: 0.6410 (mtm-85) REVERT: C 415 GLU cc_start: 0.6150 (tp30) cc_final: 0.5509 (tp30) REVERT: C 426 GLU cc_start: 0.6989 (pp20) cc_final: 0.6471 (tm-30) REVERT: C 431 GLU cc_start: 0.6638 (pp20) cc_final: 0.6308 (tm-30) REVERT: D 286 ARG cc_start: 0.6217 (mtm110) cc_final: 0.5981 (ptp-110) REVERT: D 341 GLU cc_start: 0.7438 (tp30) cc_final: 0.6679 (tp30) REVERT: D 375 GLU cc_start: 0.5387 (pp20) cc_final: 0.5015 (pp20) REVERT: D 404 ARG cc_start: 0.6108 (mtm-85) cc_final: 0.5735 (mtm-85) REVERT: D 440 ASP cc_start: 0.6377 (t0) cc_final: 0.6119 (t0) REVERT: E 855 MET cc_start: 0.6605 (mmt) cc_final: 0.5731 (mmt) REVERT: E 878 TRP cc_start: 0.8289 (m100) cc_final: 0.7453 (m-90) REVERT: F 810 TYR cc_start: 0.7681 (m-80) cc_final: 0.7428 (m-80) REVERT: F 837 LYS cc_start: 0.8046 (mmpt) cc_final: 0.7631 (mmmm) REVERT: F 841 ILE cc_start: 0.6390 (tp) cc_final: 0.5999 (mm) REVERT: F 849 ASP cc_start: 0.5173 (t0) cc_final: 0.4934 (t0) REVERT: F 867 SER cc_start: 0.7897 (t) cc_final: 0.7436 (p) REVERT: G 76 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7312 (mt-10) REVERT: G 83 GLU cc_start: 0.6341 (mt-10) cc_final: 0.4844 (mt-10) REVERT: G 91 ARG cc_start: 0.6861 (ptp-170) cc_final: 0.6277 (ttp80) REVERT: H 41 ARG cc_start: 0.6690 (tpp-160) cc_final: 0.6196 (ptt180) REVERT: H 90 VAL cc_start: 0.7643 (t) cc_final: 0.7266 (m) REVERT: I 416 LEU cc_start: 0.7514 (tt) cc_final: 0.7222 (tp) REVERT: I 421 GLU cc_start: 0.6936 (tp30) cc_final: 0.6706 (tp30) REVERT: J 357 ARG cc_start: 0.5038 (ttm-80) cc_final: 0.4771 (tpp-160) REVERT: J 367 LEU cc_start: 0.8319 (mt) cc_final: 0.7174 (mt) REVERT: J 396 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7519 (tm-30) REVERT: K 865 VAL cc_start: 0.8376 (t) cc_final: 0.8139 (p) REVERT: L 861 GLU cc_start: 0.6924 (pp20) cc_final: 0.6567 (pp20) REVERT: L 865 VAL cc_start: 0.7506 (p) cc_final: 0.7145 (m) REVERT: L 876 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7439 (mm-30) REVERT: M 42 TYR cc_start: 0.6006 (m-10) cc_final: 0.5745 (m-10) REVERT: M 59 LEU cc_start: 0.7537 (tt) cc_final: 0.7155 (pp) REVERT: M 94 LEU cc_start: 0.7338 (mm) cc_final: 0.7008 (tp) REVERT: M 107 GLU cc_start: 0.6066 (mm-30) cc_final: 0.5848 (tp30) REVERT: M 147 ARG cc_start: 0.6678 (mtm110) cc_final: 0.6475 (ttm110) REVERT: M 151 LEU cc_start: 0.7273 (mt) cc_final: 0.6684 (mt) REVERT: M 152 GLN cc_start: 0.7135 (pp30) cc_final: 0.6853 (pp30) REVERT: M 170 ARG cc_start: 0.6710 (tmm-80) cc_final: 0.6214 (tmm-80) REVERT: M 177 ASP cc_start: 0.6001 (t70) cc_final: 0.5726 (t0) REVERT: N 80 ARG cc_start: 0.4921 (mtm-85) cc_final: 0.3725 (mtm-85) REVERT: N 86 GLU cc_start: 0.6206 (tm-30) cc_final: 0.5968 (tm-30) REVERT: N 124 GLU cc_start: 0.6621 (pp20) cc_final: 0.6387 (pp20) REVERT: N 126 ASP cc_start: 0.6864 (t0) cc_final: 0.6178 (t0) REVERT: N 128 ARG cc_start: 0.6364 (ttt90) cc_final: 0.6135 (ttt90) REVERT: N 130 GLN cc_start: 0.8157 (mt0) cc_final: 0.7721 (mt0) REVERT: N 133 ASP cc_start: 0.5547 (t0) cc_final: 0.5205 (t70) REVERT: N 216 LEU cc_start: 0.5559 (mt) cc_final: 0.5356 (mt) REVERT: P 375 GLU cc_start: 0.5669 (pp20) cc_final: 0.5457 (pp20) REVERT: P 389 ARG cc_start: 0.6309 (tmm-80) cc_final: 0.6085 (ttp-170) REVERT: P 438 ARG cc_start: 0.6716 (tmm160) cc_final: 0.5806 (ttp80) REVERT: P 445 GLN cc_start: 0.6885 (tm-30) cc_final: 0.5917 (tm-30) REVERT: Q 790 SER cc_start: 0.5961 (t) cc_final: 0.5631 (p) REVERT: Q 880 GLN cc_start: 0.6555 (mm110) cc_final: 0.5908 (mm110) REVERT: R 2 VAL cc_start: 0.7564 (m) cc_final: 0.7303 (t) REVERT: S 91 ARG cc_start: 0.7303 (ptp-170) cc_final: 0.6854 (ptp-170) REVERT: S 146 LEU cc_start: 0.6661 (mm) cc_final: 0.6444 (mt) REVERT: S 147 ARG cc_start: 0.6493 (mmt-90) cc_final: 0.6024 (mmt-90) REVERT: S 153 SER cc_start: 0.6581 (p) cc_final: 0.5843 (m) REVERT: T 40 GLN cc_start: 0.6616 (tp40) cc_final: 0.6369 (tp40) REVERT: T 43 GLU cc_start: 0.5858 (mp0) cc_final: 0.5570 (mp0) REVERT: T 80 ARG cc_start: 0.7138 (ttm-80) cc_final: 0.6676 (ttm170) REVERT: T 114 ARG cc_start: 0.7523 (mtp85) cc_final: 0.7117 (mtp85) REVERT: U 375 GLU cc_start: 0.6299 (tm-30) cc_final: 0.5746 (tm-30) REVERT: U 380 ARG cc_start: 0.7469 (ttp80) cc_final: 0.7135 (tpt90) REVERT: U 395 MET cc_start: 0.7704 (tmm) cc_final: 0.7128 (ppp) REVERT: U 412 LYS cc_start: 0.7711 (tppt) cc_final: 0.7334 (tptt) REVERT: U 438 ARG cc_start: 0.7360 (mmt90) cc_final: 0.6923 (ttm170) REVERT: V 357 ARG cc_start: 0.7415 (tpt90) cc_final: 0.7141 (tpt90) REVERT: V 376 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7815 (mtmm) REVERT: V 404 ARG cc_start: 0.7177 (ptp-110) cc_final: 0.6908 (mtp-110) REVERT: V 412 LYS cc_start: 0.7242 (mtpp) cc_final: 0.6813 (mtpp) REVERT: V 434 LEU cc_start: 0.7148 (mm) cc_final: 0.6601 (mm) REVERT: W 840 PHE cc_start: 0.6862 (m-80) cc_final: 0.6514 (m-10) REVERT: W 855 MET cc_start: 0.7935 (mmm) cc_final: 0.7461 (mmm) REVERT: X 810 TYR cc_start: 0.6433 (m-80) cc_final: 0.5601 (m-80) outliers start: 1 outliers final: 0 residues processed: 1030 average time/residue: 0.2295 time to fit residues: 349.6068 Evaluate side-chains 937 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 937 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 137 optimal weight: 0.6980 chunk 380 optimal weight: 0.9990 chunk 260 optimal weight: 0.7980 chunk 334 optimal weight: 0.6980 chunk 305 optimal weight: 0.8980 chunk 117 optimal weight: 0.4980 chunk 161 optimal weight: 0.9990 chunk 344 optimal weight: 0.2980 chunk 343 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 317 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN G 173 HIS ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 366 GLN I 374 GLN I 396 GLN ** J 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 374 GLN K 817 GLN K 831 ASN M 98 GLN M 176 GLN ** M 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 276 ASN ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 366 GLN P 401 GLN R 817 GLN ** R 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 854 GLN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 445 GLN V 445 GLN W 812 GLN X 812 GLN X 854 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.180312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.168048 restraints weight = 55469.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.166802 restraints weight = 70236.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.165190 restraints weight = 54319.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.165010 restraints weight = 55803.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.165427 restraints weight = 48008.588| |-----------------------------------------------------------------------------| r_work (final): 0.4342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 0.7084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30280 Z= 0.254 Angle : 0.845 17.673 40742 Z= 0.451 Chirality : 0.048 0.317 4646 Planarity : 0.006 0.118 5518 Dihedral : 4.981 32.076 4368 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.13 % Allowed : 1.95 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 1.92 (0.13), residues: 3834 helix: 2.23 (0.09), residues: 2906 sheet: -1.99 (0.25), residues: 354 loop : -1.59 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG O 293 TYR 0.037 0.003 TYR W 872 PHE 0.042 0.006 PHE B 77 TRP 0.058 0.005 TRP F 809 HIS 0.007 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00538 (30270) covalent geometry : angle 0.84330 (40726) SS BOND : bond 0.00797 ( 8) SS BOND : angle 2.71503 ( 16) hydrogen bonds : bond 0.05768 ( 3024) hydrogen bonds : angle 4.68168 ( 9000) Misc. bond : bond 0.00113 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1023 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1019 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 42 TYR cc_start: 0.6513 (m-10) cc_final: 0.6138 (m-10) REVERT: A 59 LEU cc_start: 0.7179 (mt) cc_final: 0.6913 (mt) REVERT: A 63 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6458 (tm-30) REVERT: A 151 LEU cc_start: 0.6819 (mt) cc_final: 0.6365 (mt) REVERT: A 152 GLN cc_start: 0.6661 (pp30) cc_final: 0.6233 (pp30) REVERT: A 161 ASP cc_start: 0.6921 (t0) cc_final: 0.6666 (t0) REVERT: B 91 ARG cc_start: 0.6789 (mtt180) cc_final: 0.6402 (ptp90) REVERT: B 126 ASP cc_start: 0.6062 (t70) cc_final: 0.5692 (t0) REVERT: B 170 ARG cc_start: 0.6805 (ttm-80) cc_final: 0.6533 (ttt-90) REVERT: B 172 GLU cc_start: 0.5664 (tp30) cc_final: 0.5435 (tp30) REVERT: C 389 ARG cc_start: 0.6665 (ptt-90) cc_final: 0.6275 (ptt-90) REVERT: C 392 LEU cc_start: 0.6800 (mm) cc_final: 0.6471 (mt) REVERT: C 410 GLU cc_start: 0.6180 (mm-30) cc_final: 0.5400 (mm-30) REVERT: C 426 GLU cc_start: 0.6986 (pp20) cc_final: 0.6580 (tm-30) REVERT: C 431 GLU cc_start: 0.6790 (pp20) cc_final: 0.6224 (tm-30) REVERT: D 286 ARG cc_start: 0.6475 (mtm110) cc_final: 0.6096 (ptp-110) REVERT: D 315 GLN cc_start: 0.7203 (tm-30) cc_final: 0.6965 (tm-30) REVERT: D 341 GLU cc_start: 0.7522 (tp30) cc_final: 0.6767 (tp30) REVERT: D 369 LYS cc_start: 0.8144 (mmpt) cc_final: 0.7864 (mmtm) REVERT: D 375 GLU cc_start: 0.5685 (pp20) cc_final: 0.4307 (pp20) REVERT: D 440 ASP cc_start: 0.6809 (t0) cc_final: 0.6055 (t0) REVERT: D 442 SER cc_start: 0.8091 (t) cc_final: 0.7615 (p) REVERT: E 809 TRP cc_start: 0.8166 (m100) cc_final: 0.6771 (m100) REVERT: E 855 MET cc_start: 0.6894 (mmt) cc_final: 0.5962 (mmt) REVERT: E 866 TYR cc_start: 0.7485 (m-10) cc_final: 0.7002 (m-10) REVERT: E 878 TRP cc_start: 0.8343 (m100) cc_final: 0.7670 (m-90) REVERT: E 883 GLN cc_start: 0.7600 (tp40) cc_final: 0.7165 (tp40) REVERT: F 810 TYR cc_start: 0.8179 (m-80) cc_final: 0.7774 (m-80) REVERT: F 816 LYS cc_start: 0.7612 (mttm) cc_final: 0.7373 (mtmm) REVERT: F 837 LYS cc_start: 0.8130 (mmpt) cc_final: 0.7756 (mmmm) REVERT: F 841 ILE cc_start: 0.6357 (tp) cc_final: 0.6070 (mm) REVERT: F 849 ASP cc_start: 0.5494 (t0) cc_final: 0.5277 (t70) REVERT: F 867 SER cc_start: 0.8089 (t) cc_final: 0.7585 (p) REVERT: G 56 MET cc_start: 0.5910 (ttm) cc_final: 0.5088 (mtm) REVERT: G 76 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7055 (mt-10) REVERT: G 91 ARG cc_start: 0.6885 (ptp-170) cc_final: 0.6456 (ptp-170) REVERT: G 160 LEU cc_start: 0.7199 (mm) cc_final: 0.6991 (mm) REVERT: H 41 ARG cc_start: 0.6815 (tpp-160) cc_final: 0.6171 (ptp90) REVERT: H 70 ARG cc_start: 0.6021 (ttp80) cc_final: 0.5048 (ttp80) REVERT: H 75 GLN cc_start: 0.7439 (mp10) cc_final: 0.6781 (mp10) REVERT: H 98 GLN cc_start: 0.7331 (mp-120) cc_final: 0.6623 (mp-120) REVERT: I 421 GLU cc_start: 0.6979 (tp30) cc_final: 0.6660 (mm-30) REVERT: I 438 ARG cc_start: 0.6379 (mpt180) cc_final: 0.6073 (mpt180) REVERT: J 396 GLN cc_start: 0.7857 (tm-30) cc_final: 0.7533 (tm-30) REVERT: J 422 ARG cc_start: 0.8065 (tpp-160) cc_final: 0.7146 (tpt90) REVERT: K 837 LYS cc_start: 0.8348 (mtmm) cc_final: 0.8125 (mtmm) REVERT: K 861 GLU cc_start: 0.7923 (pp20) cc_final: 0.7531 (pp20) REVERT: K 865 VAL cc_start: 0.8572 (t) cc_final: 0.8291 (p) REVERT: L 2 VAL cc_start: 0.7646 (t) cc_final: 0.7439 (t) REVERT: L 5 GLN cc_start: 0.6964 (pm20) cc_final: 0.6494 (pm20) REVERT: L 807 MET cc_start: 0.7901 (pmm) cc_final: 0.7462 (pmm) REVERT: L 861 GLU cc_start: 0.6949 (pp20) cc_final: 0.6613 (pp20) REVERT: L 862 ASP cc_start: 0.7812 (p0) cc_final: 0.7543 (p0) REVERT: L 865 VAL cc_start: 0.7831 (p) cc_final: 0.7457 (m) REVERT: L 872 TYR cc_start: 0.7678 (t80) cc_final: 0.7389 (t80) REVERT: M 42 TYR cc_start: 0.6156 (m-10) cc_final: 0.5954 (m-10) REVERT: M 124 GLU cc_start: 0.7366 (pp20) cc_final: 0.7137 (pp20) REVERT: M 148 ASN cc_start: 0.8197 (m110) cc_final: 0.7848 (m110) REVERT: M 151 LEU cc_start: 0.7503 (mt) cc_final: 0.6759 (mt) REVERT: M 152 GLN cc_start: 0.7210 (pp30) cc_final: 0.6920 (pp30) REVERT: M 170 ARG cc_start: 0.6723 (tmm-80) cc_final: 0.6485 (tmm-80) REVERT: M 177 ASP cc_start: 0.6161 (t70) cc_final: 0.5819 (t0) REVERT: M 264 ARG cc_start: 0.7212 (ttp-110) cc_final: 0.6922 (ttp-110) REVERT: N 126 ASP cc_start: 0.6870 (t0) cc_final: 0.6493 (t0) REVERT: N 128 ARG cc_start: 0.6347 (ttt90) cc_final: 0.6043 (ttt90) REVERT: N 130 GLN cc_start: 0.8307 (mt0) cc_final: 0.7982 (mt0) REVERT: N 133 ASP cc_start: 0.5695 (t0) cc_final: 0.5354 (t70) REVERT: N 154 ASP cc_start: 0.5507 (t70) cc_final: 0.5245 (t0) REVERT: N 201 ARG cc_start: 0.5471 (ptt-90) cc_final: 0.5178 (ptt-90) REVERT: N 262 SER cc_start: 0.6135 (p) cc_final: 0.5929 (p) REVERT: O 403 ARG cc_start: 0.7626 (mmp80) cc_final: 0.7248 (mmp80) REVERT: P 331 ARG cc_start: 0.7688 (tpp-160) cc_final: 0.7351 (tpp-160) REVERT: P 340 GLU cc_start: 0.7162 (pp20) cc_final: 0.6870 (pp20) REVERT: P 399 GLN cc_start: 0.7248 (tp40) cc_final: 0.7001 (tp40) REVERT: P 438 ARG cc_start: 0.7073 (tmm160) cc_final: 0.5917 (ttp80) REVERT: P 445 GLN cc_start: 0.6863 (tm-30) cc_final: 0.6143 (tm-30) REVERT: Q 790 SER cc_start: 0.6274 (t) cc_final: 0.5964 (p) REVERT: Q 880 GLN cc_start: 0.6483 (mm110) cc_final: 0.6022 (mm110) REVERT: R 806 ILE cc_start: 0.7282 (mt) cc_final: 0.7063 (mt) REVERT: R 865 VAL cc_start: 0.7512 (p) cc_final: 0.7243 (m) REVERT: R 872 TYR cc_start: 0.7546 (t80) cc_final: 0.7115 (t80) REVERT: S 91 ARG cc_start: 0.7294 (ptp-170) cc_final: 0.6803 (ptp-170) REVERT: S 146 LEU cc_start: 0.6693 (mm) cc_final: 0.6334 (mt) REVERT: S 147 ARG cc_start: 0.6623 (mmt-90) cc_final: 0.6094 (mmt-90) REVERT: S 153 SER cc_start: 0.6721 (p) cc_final: 0.6133 (m) REVERT: T 43 GLU cc_start: 0.5613 (mp0) cc_final: 0.5379 (mp0) REVERT: T 56 MET cc_start: 0.5038 (ppp) cc_final: 0.4326 (ppp) REVERT: T 104 ILE cc_start: 0.7520 (tt) cc_final: 0.6928 (tt) REVERT: T 114 ARG cc_start: 0.7575 (mtp85) cc_final: 0.7287 (mtp85) REVERT: T 191 ARG cc_start: 0.5516 (mmp80) cc_final: 0.5182 (mmp80) REVERT: U 375 GLU cc_start: 0.6379 (tm-30) cc_final: 0.6001 (tm-30) REVERT: U 395 MET cc_start: 0.7810 (tmm) cc_final: 0.6529 (ppp) REVERT: U 412 LYS cc_start: 0.7841 (tppt) cc_final: 0.7474 (tptt) REVERT: U 438 ARG cc_start: 0.7353 (mmt90) cc_final: 0.6958 (ttm170) REVERT: V 357 ARG cc_start: 0.7546 (tpt90) cc_final: 0.7255 (tpt90) REVERT: V 376 LYS cc_start: 0.8279 (mtmm) cc_final: 0.7821 (mtmm) REVERT: V 384 ARG cc_start: 0.7335 (ptp-170) cc_final: 0.6661 (ptm160) REVERT: V 412 LYS cc_start: 0.7204 (mtpp) cc_final: 0.6791 (mtpp) REVERT: V 429 LEU cc_start: 0.8183 (tt) cc_final: 0.7875 (tt) REVERT: V 431 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7238 (tm-30) REVERT: V 434 LEU cc_start: 0.7047 (mm) cc_final: 0.6143 (mm) REVERT: W 797 SER cc_start: 0.7658 (t) cc_final: 0.7452 (p) REVERT: W 840 PHE cc_start: 0.7017 (m-80) cc_final: 0.6604 (m-10) REVERT: W 855 MET cc_start: 0.8023 (mmm) cc_final: 0.7484 (mmm) REVERT: W 885 THR cc_start: 0.7194 (m) cc_final: 0.6880 (p) REVERT: X 810 TYR cc_start: 0.6737 (m-80) cc_final: 0.5892 (m-80) REVERT: X 861 GLU cc_start: 0.7817 (pp20) cc_final: 0.7218 (pp20) outliers start: 4 outliers final: 1 residues processed: 1021 average time/residue: 0.2381 time to fit residues: 358.2797 Evaluate side-chains 937 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 936 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 164 optimal weight: 0.5980 chunk 155 optimal weight: 0.0870 chunk 180 optimal weight: 0.9990 chunk 377 optimal weight: 0.0030 chunk 216 optimal weight: 0.8980 chunk 166 optimal weight: 0.2980 chunk 121 optimal weight: 0.1980 chunk 63 optimal weight: 0.1980 chunk 261 optimal weight: 0.3980 chunk 363 optimal weight: 0.0980 chunk 223 optimal weight: 0.2980 overall best weight: 0.1168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN A 276 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN C 303 GLN ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 366 GLN ** I 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 374 GLN K 817 GLN K 831 ASN M 98 GLN ** N 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 276 ASN ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 817 GLN ** R 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 40 GLN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 399 GLN W 831 ASN ** X 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 812 GLN X 854 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.186116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.174210 restraints weight = 55183.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.173654 restraints weight = 62509.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.171843 restraints weight = 53548.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.171461 restraints weight = 52183.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.171743 restraints weight = 43415.809| |-----------------------------------------------------------------------------| r_work (final): 0.4414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5742 moved from start: 0.7236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30280 Z= 0.178 Angle : 0.785 14.322 40742 Z= 0.419 Chirality : 0.044 0.268 4646 Planarity : 0.005 0.066 5518 Dihedral : 4.676 32.581 4368 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.03 % Allowed : 1.12 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 are not related in a simple way. whole: 2.47 (0.13), residues: 3834 helix: 2.67 (0.09), residues: 2900 sheet: -1.98 (0.26), residues: 354 loop : -1.46 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 443 TYR 0.039 0.002 TYR G 42 PHE 0.085 0.006 PHE A 77 TRP 0.042 0.003 TRP Q 827 HIS 0.013 0.001 HIS G 173 Details of bonding type rmsd covalent geometry : bond 0.00358 (30270) covalent geometry : angle 0.78491 (40726) SS BOND : bond 0.00380 ( 8) SS BOND : angle 1.53909 ( 16) hydrogen bonds : bond 0.05457 ( 3024) hydrogen bonds : angle 4.39666 ( 9000) Misc. bond : bond 0.00084 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1010 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.6320 (m-10) cc_final: 0.6098 (m-10) REVERT: A 51 SER cc_start: 0.7869 (p) cc_final: 0.7638 (p) REVERT: A 56 MET cc_start: 0.6237 (mmp) cc_final: 0.5863 (mmt) REVERT: A 57 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7089 (mm-30) REVERT: A 144 ASP cc_start: 0.6082 (m-30) cc_final: 0.5845 (m-30) REVERT: A 151 LEU cc_start: 0.6603 (mt) cc_final: 0.6230 (mt) REVERT: A 152 GLN cc_start: 0.6495 (pp30) cc_final: 0.6236 (pp30) REVERT: A 154 ASP cc_start: 0.7082 (t0) cc_final: 0.6750 (t0) REVERT: B 80 ARG cc_start: 0.4006 (mtm-85) cc_final: 0.3664 (mtm-85) REVERT: B 157 VAL cc_start: 0.7250 (t) cc_final: 0.7038 (p) REVERT: B 170 ARG cc_start: 0.6720 (ttm-80) cc_final: 0.6482 (ttt-90) REVERT: C 325 LEU cc_start: 0.7192 (mp) cc_final: 0.6964 (mt) REVERT: C 375 GLU cc_start: 0.5357 (pp20) cc_final: 0.4965 (pp20) REVERT: C 410 GLU cc_start: 0.6178 (mm-30) cc_final: 0.5703 (mm-30) REVERT: C 415 GLU cc_start: 0.6139 (tp30) cc_final: 0.5529 (tp30) REVERT: C 426 GLU cc_start: 0.6983 (pp20) cc_final: 0.6443 (tm-30) REVERT: C 431 GLU cc_start: 0.6609 (pp20) cc_final: 0.6019 (tm-30) REVERT: D 286 ARG cc_start: 0.6335 (mtm110) cc_final: 0.5873 (ptp-110) REVERT: D 341 GLU cc_start: 0.7301 (tp30) cc_final: 0.6656 (tp30) REVERT: D 375 GLU cc_start: 0.5676 (pp20) cc_final: 0.4992 (pp20) REVERT: D 412 LYS cc_start: 0.7367 (ttmm) cc_final: 0.7074 (ttmm) REVERT: D 439 ARG cc_start: 0.6508 (ttp80) cc_final: 0.6194 (tmm160) REVERT: D 440 ASP cc_start: 0.5884 (t0) cc_final: 0.5421 (t0) REVERT: E 825 THR cc_start: 0.7943 (p) cc_final: 0.7602 (p) REVERT: E 866 TYR cc_start: 0.7819 (m-10) cc_final: 0.7519 (m-10) REVERT: E 883 GLN cc_start: 0.7423 (tp40) cc_final: 0.7019 (tp40) REVERT: F 810 TYR cc_start: 0.7569 (m-80) cc_final: 0.7361 (m-80) REVERT: F 837 LYS cc_start: 0.7898 (mmpt) cc_final: 0.7562 (mmmm) REVERT: F 841 ILE cc_start: 0.6547 (tp) cc_final: 0.6320 (mm) REVERT: F 849 ASP cc_start: 0.4991 (t0) cc_final: 0.4782 (t70) REVERT: F 867 SER cc_start: 0.7866 (t) cc_final: 0.7515 (p) REVERT: G 56 MET cc_start: 0.5369 (ttm) cc_final: 0.4503 (mtm) REVERT: G 76 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6859 (mt-10) REVERT: G 91 ARG cc_start: 0.6660 (ptp-170) cc_final: 0.6094 (ttp80) REVERT: G 160 LEU cc_start: 0.7051 (mm) cc_final: 0.6758 (mm) REVERT: H 41 ARG cc_start: 0.6783 (tpp-160) cc_final: 0.6076 (ttp-170) REVERT: H 94 LEU cc_start: 0.7527 (tp) cc_final: 0.7214 (tt) REVERT: I 354 ASP cc_start: 0.3572 (t0) cc_final: 0.3289 (m-30) REVERT: I 421 GLU cc_start: 0.6930 (tp30) cc_final: 0.6657 (tp30) REVERT: I 431 GLU cc_start: 0.6244 (tm-30) cc_final: 0.5943 (tm-30) REVERT: I 438 ARG cc_start: 0.5820 (mpt180) cc_final: 0.5509 (mpt180) REVERT: K 861 GLU cc_start: 0.7733 (pp20) cc_final: 0.7437 (pp20) REVERT: K 865 VAL cc_start: 0.8471 (t) cc_final: 0.8248 (p) REVERT: L 861 GLU cc_start: 0.6849 (pp20) cc_final: 0.6568 (pp20) REVERT: L 865 VAL cc_start: 0.7837 (p) cc_final: 0.7427 (m) REVERT: M 94 LEU cc_start: 0.7200 (mm) cc_final: 0.6965 (mt) REVERT: M 151 LEU cc_start: 0.7495 (mt) cc_final: 0.6801 (mt) REVERT: M 177 ASP cc_start: 0.6249 (t70) cc_final: 0.5878 (t0) REVERT: N 126 ASP cc_start: 0.6639 (t0) cc_final: 0.6259 (t0) REVERT: N 130 GLN cc_start: 0.8155 (mt0) cc_final: 0.7858 (mt0) REVERT: O 267 ARG cc_start: 0.6600 (mtt180) cc_final: 0.6299 (mtt90) REVERT: O 272 GLN cc_start: 0.6194 (pt0) cc_final: 0.5914 (pp30) REVERT: O 308 LEU cc_start: 0.6270 (mm) cc_final: 0.5956 (mt) REVERT: P 330 GLU cc_start: 0.6316 (mp0) cc_final: 0.5915 (mp0) REVERT: P 331 ARG cc_start: 0.7806 (tpp-160) cc_final: 0.7502 (tpp-160) REVERT: P 334 ASP cc_start: 0.5941 (m-30) cc_final: 0.5132 (m-30) REVERT: P 340 GLU cc_start: 0.7240 (pp20) cc_final: 0.6913 (pp20) REVERT: P 438 ARG cc_start: 0.7079 (tmm160) cc_final: 0.5761 (tmm160) REVERT: P 446 MET cc_start: 0.7165 (mpp) cc_final: 0.6659 (mpp) REVERT: Q 880 GLN cc_start: 0.6490 (mm110) cc_final: 0.5913 (mm110) REVERT: R 806 ILE cc_start: 0.6967 (mt) cc_final: 0.6765 (mt) REVERT: S 91 ARG cc_start: 0.7253 (ptp-170) cc_final: 0.6797 (ptp-170) REVERT: S 99 ARG cc_start: 0.6167 (mtm-85) cc_final: 0.5957 (ptp90) REVERT: S 146 LEU cc_start: 0.6643 (mm) cc_final: 0.6361 (mt) REVERT: S 147 ARG cc_start: 0.6531 (mmt-90) cc_final: 0.6003 (mmt-90) REVERT: S 153 SER cc_start: 0.6647 (p) cc_final: 0.5936 (m) REVERT: T 56 MET cc_start: 0.4629 (ppp) cc_final: 0.3920 (ppp) REVERT: T 70 ARG cc_start: 0.6835 (ptt-90) cc_final: 0.6597 (mmm-85) REVERT: T 104 ILE cc_start: 0.7510 (tt) cc_final: 0.6907 (tt) REVERT: T 110 GLU cc_start: 0.6798 (tm-30) cc_final: 0.6077 (tm-30) REVERT: T 191 ARG cc_start: 0.5582 (mmp80) cc_final: 0.5329 (mmp80) REVERT: U 375 GLU cc_start: 0.6607 (tm-30) cc_final: 0.6207 (tm-30) REVERT: U 395 MET cc_start: 0.7561 (tmm) cc_final: 0.6752 (ppp) REVERT: U 403 ARG cc_start: 0.7315 (mtt180) cc_final: 0.6456 (ptp-170) REVERT: U 438 ARG cc_start: 0.6904 (mmt90) cc_final: 0.6485 (ttm170) REVERT: V 335 ARG cc_start: 0.6459 (tmm-80) cc_final: 0.5543 (ptm-80) REVERT: V 357 ARG cc_start: 0.7420 (tpt90) cc_final: 0.7133 (tpt90) REVERT: V 376 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7805 (mtmm) REVERT: V 384 ARG cc_start: 0.7623 (ptp-170) cc_final: 0.7087 (ptt-90) REVERT: V 399 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7055 (tp40) REVERT: V 412 LYS cc_start: 0.6854 (mtpp) cc_final: 0.6626 (mtpp) REVERT: V 426 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7404 (mt-10) REVERT: V 429 LEU cc_start: 0.8247 (tt) cc_final: 0.7792 (tt) REVERT: V 431 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7222 (tm-30) REVERT: V 434 LEU cc_start: 0.7037 (mm) cc_final: 0.6638 (mm) REVERT: W 812 GLN cc_start: 0.6388 (tp-100) cc_final: 0.6160 (tp-100) REVERT: W 837 LYS cc_start: 0.8130 (mttt) cc_final: 0.7901 (mtmt) REVERT: W 840 PHE cc_start: 0.6975 (m-80) cc_final: 0.6585 (m-10) REVERT: W 854 GLN cc_start: 0.7454 (tp40) cc_final: 0.7197 (mm-40) REVERT: W 855 MET cc_start: 0.7981 (mmm) cc_final: 0.7647 (mmm) REVERT: X 4 LEU cc_start: 0.8204 (mt) cc_final: 0.7990 (mt) REVERT: X 810 TYR cc_start: 0.6698 (m-80) cc_final: 0.5559 (m-80) REVERT: X 833 VAL cc_start: 0.8165 (p) cc_final: 0.7956 (m) REVERT: X 855 MET cc_start: 0.5389 (mmt) cc_final: 0.5061 (mmt) outliers start: 1 outliers final: 0 residues processed: 1010 average time/residue: 0.2257 time to fit residues: 335.2114 Evaluate side-chains 927 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 926 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 143 optimal weight: 0.5980 chunk 20 optimal weight: 0.0470 chunk 41 optimal weight: 0.9980 chunk 167 optimal weight: 0.0980 chunk 363 optimal weight: 0.8980 chunk 300 optimal weight: 0.5980 chunk 134 optimal weight: 0.0970 chunk 130 optimal weight: 0.2980 chunk 259 optimal weight: 0.2980 chunk 118 optimal weight: 0.5980 chunk 172 optimal weight: 0.5980 overall best weight: 0.1676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN C 303 GLN ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** I 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 817 GLN K 831 ASN M 98 GLN M 176 GLN ** M 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 401 GLN R 817 GLN ** R 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 40 GLN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 399 GLN V 399 GLN ** W 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 812 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.190518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.179060 restraints weight = 51734.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.178807 restraints weight = 56181.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.178156 restraints weight = 44371.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.177853 restraints weight = 42128.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.178423 restraints weight = 36301.900| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5681 moved from start: 0.7459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30280 Z= 0.182 Angle : 0.804 14.576 40742 Z= 0.428 Chirality : 0.046 0.499 4646 Planarity : 0.006 0.295 5518 Dihedral : 4.686 42.416 4368 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.03 % Allowed : 0.56 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 2.48 (0.13), residues: 3834 helix: 2.68 (0.09), residues: 2888 sheet: -1.96 (0.26), residues: 354 loop : -1.42 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG P 286 TYR 0.049 0.003 TYR H 42 PHE 0.054 0.005 PHE A 77 TRP 0.059 0.003 TRP F 809 HIS 0.011 0.001 HIS G 173 Details of bonding type rmsd covalent geometry : bond 0.00374 (30270) covalent geometry : angle 0.80387 (40726) SS BOND : bond 0.00507 ( 8) SS BOND : angle 1.41151 ( 16) hydrogen bonds : bond 0.05502 ( 3024) hydrogen bonds : angle 4.39138 ( 9000) Misc. bond : bond 0.00074 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 995 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 994 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7215 (mm-30) REVERT: A 151 LEU cc_start: 0.6513 (mt) cc_final: 0.5954 (mt) REVERT: A 152 GLN cc_start: 0.6534 (pp30) cc_final: 0.6214 (pp30) REVERT: A 154 ASP cc_start: 0.6988 (t0) cc_final: 0.6695 (t0) REVERT: B 56 MET cc_start: 0.4568 (mpp) cc_final: 0.4326 (mpp) REVERT: B 80 ARG cc_start: 0.4063 (mtm-85) cc_final: 0.3828 (mtm-85) REVERT: B 156 LYS cc_start: 0.7005 (tptm) cc_final: 0.6570 (tptm) REVERT: B 157 VAL cc_start: 0.7213 (t) cc_final: 0.6964 (p) REVERT: B 170 ARG cc_start: 0.6792 (ttm-80) cc_final: 0.6550 (ttt-90) REVERT: C 375 GLU cc_start: 0.5388 (pp20) cc_final: 0.4934 (pp20) REVERT: C 410 GLU cc_start: 0.5949 (mm-30) cc_final: 0.5570 (mm-30) REVERT: C 426 GLU cc_start: 0.7175 (pp20) cc_final: 0.6682 (tm-30) REVERT: C 431 GLU cc_start: 0.6776 (pp20) cc_final: 0.6223 (tm-30) REVERT: D 341 GLU cc_start: 0.7111 (tp30) cc_final: 0.6498 (tp30) REVERT: D 404 ARG cc_start: 0.7061 (mtm180) cc_final: 0.6516 (mtm-85) REVERT: D 439 ARG cc_start: 0.6503 (ttp80) cc_final: 0.6243 (ttp80) REVERT: D 440 ASP cc_start: 0.7023 (t0) cc_final: 0.6231 (t0) REVERT: D 442 SER cc_start: 0.8043 (t) cc_final: 0.7419 (p) REVERT: E 824 VAL cc_start: 0.8194 (t) cc_final: 0.7622 (t) REVERT: E 825 THR cc_start: 0.8083 (p) cc_final: 0.7335 (p) REVERT: E 855 MET cc_start: 0.6978 (mmt) cc_final: 0.5933 (mmt) REVERT: E 878 TRP cc_start: 0.8444 (m100) cc_final: 0.7612 (m-90) REVERT: E 883 GLN cc_start: 0.6859 (tp40) cc_final: 0.6640 (tp40) REVERT: F 809 TRP cc_start: 0.7585 (m100) cc_final: 0.7200 (m100) REVERT: F 837 LYS cc_start: 0.7927 (mmpt) cc_final: 0.7645 (mmmm) REVERT: F 841 ILE cc_start: 0.6298 (tp) cc_final: 0.6048 (mm) REVERT: F 867 SER cc_start: 0.8087 (t) cc_final: 0.7788 (p) REVERT: F 885 THR cc_start: 0.1764 (p) cc_final: 0.1422 (p) REVERT: G 56 MET cc_start: 0.5296 (ttm) cc_final: 0.4781 (ttp) REVERT: G 73 VAL cc_start: 0.6678 (p) cc_final: 0.6105 (m) REVERT: G 76 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6830 (mt-10) REVERT: G 83 GLU cc_start: 0.6235 (pt0) cc_final: 0.5887 (pt0) REVERT: G 91 ARG cc_start: 0.6762 (ptp-170) cc_final: 0.6294 (ttp80) REVERT: G 160 LEU cc_start: 0.6826 (mm) cc_final: 0.6615 (mm) REVERT: H 41 ARG cc_start: 0.6769 (tpp-160) cc_final: 0.6424 (ptm160) REVERT: H 45 ILE cc_start: 0.6584 (mt) cc_final: 0.6384 (mt) REVERT: I 354 ASP cc_start: 0.3266 (t0) cc_final: 0.2986 (m-30) REVERT: I 400 ASP cc_start: 0.7258 (m-30) cc_final: 0.7018 (m-30) REVERT: I 431 GLU cc_start: 0.6231 (tm-30) cc_final: 0.5954 (tm-30) REVERT: I 438 ARG cc_start: 0.5800 (mpt180) cc_final: 0.5490 (mpt180) REVERT: J 389 ARG cc_start: 0.6786 (mtm-85) cc_final: 0.6215 (mtm-85) REVERT: J 404 ARG cc_start: 0.7510 (ptt90) cc_final: 0.7205 (ptt90) REVERT: K 841 ILE cc_start: 0.5253 (mp) cc_final: 0.4938 (mp) REVERT: K 855 MET cc_start: 0.7317 (mpp) cc_final: 0.6573 (mtp) REVERT: K 859 LYS cc_start: 0.7736 (ptpp) cc_final: 0.7451 (ptpp) REVERT: K 861 GLU cc_start: 0.7960 (pp20) cc_final: 0.7674 (pp20) REVERT: K 865 VAL cc_start: 0.8485 (t) cc_final: 0.8241 (p) REVERT: L 820 MET cc_start: 0.5482 (ttp) cc_final: 0.5164 (ttm) REVERT: L 865 VAL cc_start: 0.7795 (p) cc_final: 0.7394 (m) REVERT: M 94 LEU cc_start: 0.7383 (mm) cc_final: 0.7047 (mt) REVERT: M 124 GLU cc_start: 0.7139 (pp20) cc_final: 0.6754 (pp20) REVERT: M 151 LEU cc_start: 0.7286 (mt) cc_final: 0.6693 (mt) REVERT: M 152 GLN cc_start: 0.7237 (pp30) cc_final: 0.7022 (pp30) REVERT: M 170 ARG cc_start: 0.7006 (ttp80) cc_final: 0.6657 (ttp80) REVERT: M 177 ASP cc_start: 0.6367 (t70) cc_final: 0.6066 (t0) REVERT: N 62 ILE cc_start: 0.6759 (mm) cc_final: 0.6506 (mm) REVERT: N 115 LEU cc_start: 0.7152 (tp) cc_final: 0.6798 (tp) REVERT: N 126 ASP cc_start: 0.6632 (t0) cc_final: 0.6201 (t0) REVERT: N 128 ARG cc_start: 0.6201 (ttt90) cc_final: 0.5856 (ttt90) REVERT: N 130 GLN cc_start: 0.8158 (mt0) cc_final: 0.7800 (mt0) REVERT: N 133 ASP cc_start: 0.5278 (t0) cc_final: 0.4889 (t70) REVERT: N 191 ARG cc_start: 0.6407 (ttp-110) cc_final: 0.6193 (ttp-110) REVERT: O 272 GLN cc_start: 0.6065 (pt0) cc_final: 0.5851 (pp30) REVERT: O 389 ARG cc_start: 0.6635 (mtm-85) cc_final: 0.6434 (mtm-85) REVERT: P 331 ARG cc_start: 0.7666 (tpp-160) cc_final: 0.7431 (tpp-160) REVERT: P 438 ARG cc_start: 0.7130 (tmm160) cc_final: 0.5789 (tmm160) REVERT: P 445 GLN cc_start: 0.6804 (tm-30) cc_final: 0.5677 (tm-30) REVERT: Q 880 GLN cc_start: 0.6546 (mm110) cc_final: 0.5984 (mm110) REVERT: R 872 TYR cc_start: 0.7454 (t80) cc_final: 0.7146 (t80) REVERT: S 91 ARG cc_start: 0.7252 (ptp-170) cc_final: 0.6826 (ptp-170) REVERT: S 146 LEU cc_start: 0.6524 (mm) cc_final: 0.6282 (mt) REVERT: S 147 ARG cc_start: 0.6304 (mmt-90) cc_final: 0.5857 (mmt-90) REVERT: S 156 LYS cc_start: 0.5279 (pttt) cc_final: 0.5044 (pttm) REVERT: T 56 MET cc_start: 0.4580 (ppp) cc_final: 0.3830 (ppp) REVERT: T 80 ARG cc_start: 0.6963 (ttm-80) cc_final: 0.6699 (ttm170) REVERT: T 104 ILE cc_start: 0.7500 (tt) cc_final: 0.6797 (tt) REVERT: U 375 GLU cc_start: 0.6414 (tm-30) cc_final: 0.6119 (tm-30) REVERT: U 395 MET cc_start: 0.7273 (tmm) cc_final: 0.6943 (ppp) REVERT: U 412 LYS cc_start: 0.7320 (tptt) cc_final: 0.7065 (ttmm) REVERT: U 438 ARG cc_start: 0.6920 (mmt90) cc_final: 0.6471 (ttm170) REVERT: V 357 ARG cc_start: 0.7149 (tpt90) cc_final: 0.6941 (tpt90) REVERT: V 376 LYS cc_start: 0.8149 (mtmm) cc_final: 0.7758 (mtmm) REVERT: V 384 ARG cc_start: 0.7437 (ptp-170) cc_final: 0.6937 (ptt-90) REVERT: V 412 LYS cc_start: 0.6967 (mtpp) cc_final: 0.6608 (mtpp) REVERT: V 415 GLU cc_start: 0.5928 (tp30) cc_final: 0.5639 (tp30) REVERT: V 426 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7364 (mt-10) REVERT: V 429 LEU cc_start: 0.8249 (tt) cc_final: 0.7871 (tt) REVERT: V 431 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7565 (tm-30) REVERT: V 434 LEU cc_start: 0.7060 (mm) cc_final: 0.6698 (mm) REVERT: W 804 ILE cc_start: 0.7965 (mm) cc_final: 0.7730 (mm) REVERT: W 805 ASN cc_start: 0.8066 (m-40) cc_final: 0.7754 (m-40) REVERT: W 837 LYS cc_start: 0.8139 (mttt) cc_final: 0.7931 (mtmt) REVERT: W 840 PHE cc_start: 0.7052 (m-80) cc_final: 0.6731 (m-10) REVERT: W 854 GLN cc_start: 0.7460 (tp40) cc_final: 0.7199 (mm-40) REVERT: W 855 MET cc_start: 0.7979 (mmm) cc_final: 0.7574 (mmm) REVERT: X 810 TYR cc_start: 0.6568 (m-80) cc_final: 0.5494 (m-80) REVERT: X 855 MET cc_start: 0.5012 (mmt) cc_final: 0.4723 (mmt) REVERT: X 857 ASN cc_start: 0.8250 (p0) cc_final: 0.8025 (p0) outliers start: 1 outliers final: 1 residues processed: 994 average time/residue: 0.2381 time to fit residues: 348.0152 Evaluate side-chains 907 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 906 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 121 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 100 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 255 optimal weight: 0.0980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 817 GLN K 831 ASN L 856 ASN M 98 GLN M 105 GLN ** M 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 272 GLN ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 366 GLN Q 831 ASN R 817 GLN ** R 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 399 GLN ** W 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 812 GLN X 854 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.185355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.173634 restraints weight = 52380.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.173070 restraints weight = 62855.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.173296 restraints weight = 54373.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.173121 restraints weight = 50475.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.173121 restraints weight = 40406.694| |-----------------------------------------------------------------------------| r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 moved from start: 0.7710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 30280 Z= 0.249 Angle : 0.882 14.723 40742 Z= 0.471 Chirality : 0.049 0.289 4646 Planarity : 0.006 0.089 5518 Dihedral : 4.956 29.312 4368 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.07 % Allowed : 0.89 % Favored : 99.04 % 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 are not related in a simple way. whole: 1.95 (0.13), residues: 3834 helix: 2.30 (0.09), residues: 2898 sheet: -2.24 (0.24), residues: 366 loop : -1.60 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG I 404 TYR 0.055 0.003 TYR G 42 PHE 0.076 0.007 PHE A 77 TRP 0.051 0.004 TRP E 827 HIS 0.009 0.001 HIS G 173 Details of bonding type rmsd covalent geometry : bond 0.00527 (30270) covalent geometry : angle 0.88146 (40726) SS BOND : bond 0.00683 ( 8) SS BOND : angle 2.03383 ( 16) hydrogen bonds : bond 0.05739 ( 3024) hydrogen bonds : angle 4.66313 ( 9000) Misc. bond : bond 0.00107 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7475.11 seconds wall clock time: 128 minutes 56.49 seconds (7736.49 seconds total)