Starting phenix.real_space_refine on Tue Jul 7 03:44:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmo_48396/07_2026/9mmo_48396.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmo_48396/07_2026/9mmo_48396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mmo_48396/07_2026/9mmo_48396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmo_48396/07_2026/9mmo_48396.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mmo_48396/07_2026/9mmo_48396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmo_48396/07_2026/9mmo_48396.map" } resolution = 3.9 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= 0.010 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: 6 Type Number sf(0) Gaussians P 570 5.49 5 S 28 5.16 5 C 13077 2.51 5 N 4434 2.21 5 O 5529 1.98 5 H 18968 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42606 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1342 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1472 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1315 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4519 Classifications: {'DNA': 143} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 142} Chain: "J" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4552 Classifications: {'DNA': 143} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 142} Chain: "L" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "M" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1283 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "N" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "O" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "P" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "Q" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1315 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "R" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "S" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "X" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4519 Classifications: {'DNA': 143} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 142} Chain: "Y" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4552 Classifications: {'DNA': 143} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 142} Time building chain proxies: 6.07, per 1000 atoms: 0.14 Number of scatterers: 42606 At special positions: 0 Unit cell: (121.66, 125.51, 174.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 570 15.00 O 5529 8.00 N 4434 7.00 C 13077 6.00 H 18968 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 781.9 milliseconds 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2802 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 19 sheets defined 72.5% alpha, 2.8% beta 282 base pairs and 481 stacking pairs defined. Time for finding SS restraints: 7.23 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.723A pdb=" N GLN A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.860A pdb=" N VAL A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.750A pdb=" N ILE A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.822A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 66 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.521A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.540A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 93 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 removed outlier: 3.923A pdb=" N ASN D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 125 removed outlier: 3.743A pdb=" N SER D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.572A pdb=" N GLN E 77 " --> pdb=" O ARG E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 removed outlier: 3.704A pdb=" N VAL E 90 " --> pdb=" O GLN E 86 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA E 115 " --> pdb=" O CYS E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 133 Processing helix chain 'F' and resid 24 through 30 removed outlier: 3.899A pdb=" N ILE F 27 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 removed outlier: 3.504A pdb=" N ILE F 35 " --> pdb=" O THR F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.866A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP F 69 " --> pdb=" O ASN F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 95 removed outlier: 3.643A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 46 through 73 removed outlier: 4.406A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'G' and resid 93 through 98 Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 removed outlier: 3.523A pdb=" N ILE H 62 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL H 67 " --> pdb=" O MET H 63 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 removed outlier: 3.596A pdb=" N HIS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 56 Processing helix chain 'L' and resid 64 through 77 removed outlier: 3.568A pdb=" N GLN L 77 " --> pdb=" O ARG L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 114 removed outlier: 3.786A pdb=" N VAL L 90 " --> pdb=" O GLN L 86 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET L 91 " --> pdb=" O SER L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 133 removed outlier: 3.539A pdb=" N ILE L 125 " --> pdb=" O MET L 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 30 Processing helix chain 'M' and resid 31 through 42 Processing helix chain 'M' and resid 50 through 77 removed outlier: 3.909A pdb=" N GLU M 54 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN M 65 " --> pdb=" O VAL M 61 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL M 66 " --> pdb=" O PHE M 62 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP M 69 " --> pdb=" O ASN M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 94 removed outlier: 3.544A pdb=" N VAL M 87 " --> pdb=" O THR M 83 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN M 94 " --> pdb=" O ALA M 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 23 Processing helix chain 'N' and resid 27 through 38 Processing helix chain 'N' and resid 46 through 74 removed outlier: 4.597A pdb=" N VAL N 50 " --> pdb=" O ALA N 46 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU N 66 " --> pdb=" O GLU N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 90 Processing helix chain 'N' and resid 93 through 98 Processing helix chain 'N' and resid 113 through 117 Processing helix chain 'O' and resid 38 through 50 Processing helix chain 'O' and resid 56 through 85 removed outlier: 4.023A pdb=" N ASN O 68 " --> pdb=" O ASN O 64 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN O 85 " --> pdb=" O LEU O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 103 Processing helix chain 'O' and resid 104 through 125 removed outlier: 3.657A pdb=" N SER O 113 " --> pdb=" O LYS O 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 58 Processing helix chain 'P' and resid 64 through 77 removed outlier: 3.536A pdb=" N PHE P 68 " --> pdb=" O ARG P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 115 removed outlier: 3.704A pdb=" N VAL P 90 " --> pdb=" O GLN P 86 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET P 91 " --> pdb=" O SER P 87 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU P 110 " --> pdb=" O GLU P 106 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA P 115 " --> pdb=" O CYS P 111 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 133 Processing helix chain 'Q' and resid 24 through 30 removed outlier: 3.946A pdb=" N ILE Q 27 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE Q 30 " --> pdb=" O ILE Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 42 Processing helix chain 'Q' and resid 50 through 77 removed outlier: 4.105A pdb=" N GLU Q 54 " --> pdb=" O LEU Q 50 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL Q 61 " --> pdb=" O GLY Q 57 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE Q 62 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP Q 69 " --> pdb=" O ASN Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 95 removed outlier: 3.723A pdb=" N VAL Q 87 " --> pdb=" O THR Q 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 23 Processing helix chain 'R' and resid 27 through 38 Processing helix chain 'R' and resid 46 through 73 removed outlier: 4.518A pdb=" N VAL R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP R 73 " --> pdb=" O ASN R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 90 removed outlier: 3.546A pdb=" N LEU R 84 " --> pdb=" O ILE R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 98 Processing helix chain 'S' and resid 38 through 50 Processing helix chain 'S' and resid 56 through 85 removed outlier: 3.593A pdb=" N ILE S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL S 67 " --> pdb=" O MET S 63 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN S 68 " --> pdb=" O ASN S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 103 Processing helix chain 'S' and resid 104 through 125 removed outlier: 3.643A pdb=" N LYS S 109 " --> pdb=" O GLY S 105 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS S 110 " --> pdb=" O GLU S 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.740A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 removed outlier: 3.542A pdb=" N ILE A 120 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.079A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.856A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 removed outlier: 3.582A pdb=" N ILE E 120 " --> pdb=" O ARG F 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.336A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB2, first strand: chain 'L' and resid 84 through 85 removed outlier: 6.842A pdb=" N ARG L 84 " --> pdb=" O VAL M 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'L' and resid 119 through 120 removed outlier: 3.587A pdb=" N ILE L 120 " --> pdb=" O ARG M 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'M' and resid 98 through 99 Processing sheet with id=AB5, first strand: chain 'N' and resid 43 through 44 removed outlier: 7.105A pdb=" N ARG N 43 " --> pdb=" O ILE O 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'N' and resid 78 through 79 Processing sheet with id=AB7, first strand: chain 'N' and resid 101 through 103 Processing sheet with id=AB8, first strand: chain 'P' and resid 84 through 85 removed outlier: 6.632A pdb=" N ARG P 84 " --> pdb=" O VAL Q 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'R' and resid 43 through 44 removed outlier: 7.467A pdb=" N ARG R 43 " --> pdb=" O ILE S 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'R' and resid 78 through 79 760 hydrogen bonds defined for protein. 2241 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 723 hydrogen bonds 1446 hydrogen bond angles 0 basepair planarities 282 basepair parallelities 481 stacking parallelities Total time for adding SS restraints: 9.07 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 18960 1.03 - 1.22: 176 1.22 - 1.42: 10757 1.42 - 1.61: 14252 1.61 - 1.81: 51 Bond restraints: 44196 Sorted by residual: bond pdb=" C3' DT Y 15 " pdb=" C2' DT Y 15 " ideal model delta sigma weight residual 1.516 1.561 -0.045 8.00e-03 1.56e+04 3.12e+01 bond pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 1.516 1.557 -0.041 8.00e-03 1.56e+04 2.58e+01 bond pdb=" C3' DC I 69 " pdb=" C2' DC I 69 " ideal model delta sigma weight residual 1.516 1.555 -0.039 8.00e-03 1.56e+04 2.40e+01 bond pdb=" C3' DC J 24 " pdb=" C2' DC J 24 " ideal model delta sigma weight residual 1.516 1.554 -0.038 8.00e-03 1.56e+04 2.21e+01 bond pdb=" C3' DG J 2 " pdb=" C2' DG J 2 " ideal model delta sigma weight residual 1.516 1.553 -0.037 8.00e-03 1.56e+04 2.12e+01 ... (remaining 44191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 72112 1.54 - 3.08: 7211 3.08 - 4.62: 659 4.62 - 6.16: 126 6.16 - 7.70: 6 Bond angle restraints: 80114 Sorted by residual: angle pdb=" O4' DG Y 27 " pdb=" C1' DG Y 27 " pdb=" N9 DG Y 27 " ideal model delta sigma weight residual 108.00 113.77 -5.77 7.00e-01 2.04e+00 6.79e+01 angle pdb=" O4' DA I -35 " pdb=" C1' DA I -35 " pdb=" N9 DA I -35 " ideal model delta sigma weight residual 108.00 102.26 5.74 7.00e-01 2.04e+00 6.71e+01 angle pdb=" O4' DG J 27 " pdb=" C1' DG J 27 " pdb=" N9 DG J 27 " ideal model delta sigma weight residual 108.00 113.44 -5.44 7.00e-01 2.04e+00 6.04e+01 angle pdb=" O4' DG X 47 " pdb=" C1' DG X 47 " pdb=" N9 DG X 47 " ideal model delta sigma weight residual 108.00 102.81 5.19 7.00e-01 2.04e+00 5.50e+01 angle pdb=" O5' DA I -69 " pdb=" C5' DA I -69 " pdb=" C4' DA I -69 " ideal model delta sigma weight residual 109.40 114.67 -5.27 8.00e-01 1.56e+00 4.35e+01 ... (remaining 80109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 12920 17.91 - 35.82: 2545 35.82 - 53.73: 1929 53.73 - 71.64: 916 71.64 - 89.55: 44 Dihedral angle restraints: 18354 sinusoidal: 13472 harmonic: 4882 Sorted by residual: dihedral pdb=" CG ARG R 36 " pdb=" CD ARG R 36 " pdb=" NE ARG R 36 " pdb=" CZ ARG R 36 " ideal model delta sinusoidal sigma weight residual 180.00 -135.43 -44.57 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG Q 56 " pdb=" CD ARG Q 56 " pdb=" NE ARG Q 56 " pdb=" CZ ARG Q 56 " ideal model delta sinusoidal sigma weight residual 180.00 135.66 44.34 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG G 36 " pdb=" CD ARG G 36 " pdb=" NE ARG G 36 " pdb=" CZ ARG G 36 " ideal model delta sinusoidal sigma weight residual -180.00 -135.96 -44.04 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 18351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2443 0.048 - 0.097: 1063 0.097 - 0.145: 422 0.145 - 0.194: 202 0.194 - 0.242: 19 Chirality restraints: 4149 Sorted by residual: chirality pdb=" C3' DA I -54 " pdb=" C4' DA I -54 " pdb=" O3' DA I -54 " pdb=" C2' DA I -54 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" C1' DA Y 16 " pdb=" O4' DA Y 16 " pdb=" C2' DA Y 16 " pdb=" N9 DA Y 16 " both_signs ideal model delta sigma weight residual False 2.43 2.20 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C4' DA J -62 " pdb=" C5' DA J -62 " pdb=" O4' DA J -62 " pdb=" C3' DA J -62 " both_signs ideal model delta sigma weight residual False -2.53 -2.31 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 4146 not shown) Planarity restraints: 4533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 24 " 0.033 2.00e-02 2.50e+03 3.49e-02 3.96e+01 pdb=" N9 DA I 24 " -0.102 2.00e-02 2.50e+03 pdb=" C8 DA I 24 " 0.065 2.00e-02 2.50e+03 pdb=" N7 DA I 24 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 24 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 24 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA I 24 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DA I 24 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 24 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 24 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 24 " -0.003 2.00e-02 2.50e+03 pdb=" H8 DA I 24 " -0.004 2.00e-02 2.50e+03 pdb=" H2 DA I 24 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 30 " -0.042 2.00e-02 2.50e+03 3.21e-02 3.10e+01 pdb=" N1 DT I 30 " 0.093 2.00e-02 2.50e+03 pdb=" C2 DT I 30 " -0.042 2.00e-02 2.50e+03 pdb=" O2 DT I 30 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DT I 30 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT I 30 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT I 30 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DT I 30 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 30 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT I 30 " -0.001 2.00e-02 2.50e+03 pdb=" H3 DT I 30 " 0.004 2.00e-02 2.50e+03 pdb=" H6 DT I 30 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 73 " 0.050 9.50e-02 1.11e+02 4.01e-02 3.02e+01 pdb=" NE ARG A 73 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 73 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG A 73 " -0.062 2.00e-02 2.50e+03 pdb=" NH2 ARG A 73 " 0.038 2.00e-02 2.50e+03 pdb="HH11 ARG A 73 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 73 " 0.066 2.00e-02 2.50e+03 pdb="HH21 ARG A 73 " 0.003 2.00e-02 2.50e+03 pdb="HH22 ARG A 73 " -0.039 2.00e-02 2.50e+03 ... (remaining 4530 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.16: 1303 2.16 - 2.77: 68304 2.77 - 3.38: 104740 3.38 - 3.99: 142362 3.99 - 4.60: 220718 Nonbonded interactions: 537427 Sorted by model distance: nonbonded pdb=" OE1 GLU P 74 " pdb="HD21 ASN Q 26 " model vdw 1.555 2.450 nonbonded pdb=" H VAL E 118 " pdb=" OP1 DA J -3 " model vdw 1.576 2.450 nonbonded pdb=" H THR H 91 " pdb=" OE1 GLU H 94 " model vdw 1.576 2.450 nonbonded pdb=" O ARG P 130 " pdb="HH11 ARG P 130 " model vdw 1.578 2.450 nonbonded pdb=" HE ARG P 129 " pdb=" OE1 GLU P 134 " model vdw 1.604 2.450 ... (remaining 537422 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'L' selection = chain 'P' } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = (chain 'F' and resid 25 through 102) selection = chain 'M' selection = (chain 'Q' and resid 25 through 102) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'N' selection = chain 'R' } ncs_group { reference = (chain 'D' and (resid 33 through 82 or (resid 83 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resi \ d 84 through 125)) selection = (chain 'H' and (resid 33 through 82 or (resid 83 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resi \ d 84 through 125)) selection = (chain 'O' and (resid 33 through 82 or (resid 83 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resi \ d 84 through 125)) selection = (chain 'S' and (resid 33 through 82 or (resid 83 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resi \ d 84 through 125)) } ncs_group { reference = chain 'I' selection = chain 'X' } ncs_group { reference = chain 'J' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.870 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: 0.250 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 38.740 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 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 0.081 25228 Z= 0.659 Angle : 1.047 7.698 36519 Z= 0.870 Chirality : 0.068 0.242 4149 Planarity : 0.013 0.119 2640 Dihedral : 26.346 89.552 10881 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.32 % Allowed : 2.33 % Favored : 97.35 % 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: 0.60 (0.19), residues: 1475 helix: 0.73 (0.14), residues: 1051 sheet: None (None), residues: 0 loop : -0.18 (0.25), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.003 ARG L 84 TYR 0.032 0.005 TYR B 89 PHE 0.030 0.004 PHE H 66 HIS 0.008 0.002 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.66 (25228) covalent geometry : angle 1.04691 / 0.87 (36519) hydrogen bonds : bond 0.13286 / 8.77 ( 1483) hydrogen bonds : angle 4.20581 / 3.05 ( 3687) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 532 time to evaluate : 0.790 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: symmetry clash REVERT: A 94 GLN cc_start: 0.8100 (tt0) cc_final: 0.7616 (tp40) REVERT: G 74 ASN cc_start: 0.7830 (OUTLIER) cc_final: 0.7401 (t0) REVERT: G 101 VAL cc_start: 0.8105 (t) cc_final: 0.7855 (t) REVERT: H 46 LEU cc_start: 0.8847 (tp) cc_final: 0.8624 (tp) REVERT: L 94 GLN cc_start: 0.7509 (tt0) cc_final: 0.7219 (tt0) REVERT: N 69 ASN cc_start: 0.8958 (m-40) cc_final: 0.8373 (m110) REVERT: P 47 VAL cc_start: 0.8762 (t) cc_final: 0.8557 (m) REVERT: P 51 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8685 (mt-10) REVERT: Q 59 LEU cc_start: 0.9100 (tp) cc_final: 0.8493 (tp) REVERT: R 91 ASP cc_start: 0.7931 (t70) cc_final: 0.7205 (t0) outliers start: 4 outliers final: 0 residues processed: 535 average time/residue: 0.3777 time to fit residues: 289.2221 Evaluate side-chains 297 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 296 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 74 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 HIS B 94 GLN O 110 HIS ** R 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.064432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.051311 restraints weight = 377063.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.053170 restraints weight = 152216.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.054363 restraints weight = 88678.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.055096 restraints weight = 63785.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.055598 restraints weight = 52364.893| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25228 Z= 0.205 Angle : 0.746 6.998 36519 Z= 0.484 Chirality : 0.047 0.213 4149 Planarity : 0.006 0.057 2640 Dihedral : 29.515 86.523 7924 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.49 % Allowed : 13.41 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.65 (0.21), residues: 1475 helix: 1.71 (0.15), residues: 1071 sheet: None (None), residues: 0 loop : -0.51 (0.26), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 80 TYR 0.024 0.002 TYR Q 89 PHE 0.019 0.002 PHE D 66 HIS 0.013 0.002 HIS O 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.21 (25228) covalent geometry : angle 0.74597 / 0.48 (36519) hydrogen bonds : bond 0.07809 / 5.12 ( 1483) hydrogen bonds : angle 3.78316 / 2.75 ( 3687) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 326 time to evaluate : 0.822 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: A 63 ILE cc_start: 0.5654 (mm) cc_final: 0.4882 (mm) REVERT: A 124 ASP cc_start: 0.7871 (m-30) cc_final: 0.6997 (t0) REVERT: E 94 GLN cc_start: 0.7581 (tt0) cc_final: 0.6815 (tp-100) REVERT: F 68 ARG cc_start: 0.9048 (tpt170) cc_final: 0.8657 (tpm170) REVERT: G 85 GLN cc_start: 0.7513 (tp40) cc_final: 0.6730 (tm-30) REVERT: H 96 GLN cc_start: 0.9230 (tt0) cc_final: 0.8895 (tp40) REVERT: L 98 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8189 (mt-10) REVERT: M 45 LYS cc_start: 0.9150 (tttt) cc_final: 0.8774 (ttpp) REVERT: M 80 LYS cc_start: 0.8000 (tppt) cc_final: 0.7694 (tppt) REVERT: M 85 MET cc_start: 0.9048 (mmm) cc_final: 0.8739 (mmm) REVERT: N 93 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7419 (mm-30) REVERT: O 94 GLU cc_start: 0.9156 (mp0) cc_final: 0.8759 (mp0) REVERT: P 82 ASP cc_start: 0.7979 (t70) cc_final: 0.7745 (t70) REVERT: P 98 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7565 (mt-10) REVERT: P 111 CYS cc_start: 0.8686 (m) cc_final: 0.8466 (t) REVERT: Q 53 GLU cc_start: 0.9430 (mp0) cc_final: 0.9191 (pm20) REVERT: R 74 ASN cc_start: 0.8848 (t0) cc_final: 0.8638 (t0) outliers start: 31 outliers final: 25 residues processed: 342 average time/residue: 0.3451 time to fit residues: 176.1464 Evaluate side-chains 325 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 300 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 111 CYS Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 74 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 142 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 193 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 81 optimal weight: 30.0000 chunk 10 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.061681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.048534 restraints weight = 388046.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.050300 restraints weight = 160503.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.051438 restraints weight = 95155.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.052113 restraints weight = 69355.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.052595 restraints weight = 57607.533| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 25228 Z= 0.262 Angle : 0.723 7.554 36519 Z= 0.476 Chirality : 0.044 0.184 4149 Planarity : 0.006 0.052 2640 Dihedral : 29.803 85.655 7922 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.05 % Allowed : 14.86 % Favored : 82.09 % 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: 0.76 (0.20), residues: 1475 helix: 1.07 (0.15), residues: 1075 sheet: None (None), residues: 0 loop : -0.92 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 80 TYR 0.041 0.002 TYR F 89 PHE 0.018 0.002 PHE O 66 HIS 0.008 0.002 HIS Q 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.26 (25228) covalent geometry : angle 0.72305 / 0.48 (36519) hydrogen bonds : bond 0.09109 / 6.02 ( 1483) hydrogen bonds : angle 4.08536 / 2.97 ( 3687) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 288 time to evaluate : 0.891 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 63 ILE cc_start: 0.5798 (mm) cc_final: 0.5401 (mm) REVERT: A 124 ASP cc_start: 0.7950 (m-30) cc_final: 0.7257 (t70) REVERT: E 94 GLN cc_start: 0.7794 (tt0) cc_final: 0.6858 (tp-100) REVERT: M 45 LYS cc_start: 0.9144 (tttt) cc_final: 0.8747 (ttpp) REVERT: N 65 GLU cc_start: 0.9627 (tp30) cc_final: 0.9356 (mm-30) REVERT: O 94 GLU cc_start: 0.9147 (mp0) cc_final: 0.8799 (mp0) REVERT: P 82 ASP cc_start: 0.8147 (t70) cc_final: 0.7819 (t70) REVERT: Q 53 GLU cc_start: 0.9420 (mp0) cc_final: 0.9217 (pm20) REVERT: R 74 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8725 (t0) outliers start: 38 outliers final: 28 residues processed: 308 average time/residue: 0.3499 time to fit residues: 161.0823 Evaluate side-chains 294 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 66 PHE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 74 ASN Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 74 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 52 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 86 optimal weight: 40.0000 chunk 190 optimal weight: 30.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 74 ASN R 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.062319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.048971 restraints weight = 380692.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.050776 restraints weight = 156910.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.051937 restraints weight = 93030.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.052628 restraints weight = 67885.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.053111 restraints weight = 56472.025| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 25228 Z= 0.184 Angle : 0.660 7.996 36519 Z= 0.438 Chirality : 0.042 0.187 4149 Planarity : 0.005 0.047 2640 Dihedral : 29.921 85.763 7922 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.49 % Allowed : 15.10 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.19 (0.20), residues: 1475 helix: 1.47 (0.15), residues: 1075 sheet: None (None), residues: 0 loop : -1.05 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 68 TYR 0.035 0.002 TYR H 84 PHE 0.019 0.002 PHE D 66 HIS 0.003 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.18 (25228) covalent geometry : angle 0.66028 / 0.44 (36519) hydrogen bonds : bond 0.07105 / 4.70 ( 1483) hydrogen bonds : angle 3.68871 / 2.68 ( 3687) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 292 time to evaluate : 0.844 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 108 THR cc_start: 0.9600 (m) cc_final: 0.9135 (m) REVERT: A 124 ASP cc_start: 0.7854 (m-30) cc_final: 0.7245 (t70) REVERT: B 80 LYS cc_start: 0.8649 (tppt) cc_final: 0.8264 (tppt) REVERT: E 65 LYS cc_start: 0.8114 (mtmm) cc_final: 0.7638 (mmmm) REVERT: G 105 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7082 (mp10) REVERT: H 96 GLN cc_start: 0.9241 (tt0) cc_final: 0.8961 (tp40) REVERT: H 106 GLU cc_start: 0.9165 (mp0) cc_final: 0.8918 (mp0) REVERT: M 45 LYS cc_start: 0.9128 (tttt) cc_final: 0.8753 (ttpp) REVERT: M 85 MET cc_start: 0.9074 (mmm) cc_final: 0.8738 (mmm) REVERT: N 65 GLU cc_start: 0.9632 (tp30) cc_final: 0.9363 (mm-30) REVERT: O 94 GLU cc_start: 0.9076 (mp0) cc_final: 0.8851 (mp0) REVERT: P 82 ASP cc_start: 0.8189 (t70) cc_final: 0.7789 (t70) REVERT: Q 53 GLU cc_start: 0.9417 (mp0) cc_final: 0.9208 (pm20) REVERT: S 72 GLU cc_start: 0.8735 (tp30) cc_final: 0.8533 (mm-30) outliers start: 31 outliers final: 25 residues processed: 309 average time/residue: 0.3316 time to fit residues: 153.5827 Evaluate side-chains 299 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 273 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 74 ASN Chi-restraints excluded: chain R residue 93 GLU Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 74 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 0 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 chunk 172 optimal weight: 30.0000 chunk 84 optimal weight: 40.0000 chunk 104 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN D 48 GLN ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.062444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.048740 restraints weight = 379291.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.050537 restraints weight = 166948.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.051692 restraints weight = 101905.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.052402 restraints weight = 75318.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.052869 restraints weight = 62846.182| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 25228 Z= 0.225 Angle : 0.676 7.671 36519 Z= 0.444 Chirality : 0.042 0.218 4149 Planarity : 0.005 0.057 2640 Dihedral : 29.965 86.768 7922 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.81 % Allowed : 15.42 % Favored : 81.77 % 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: 0.84 (0.20), residues: 1475 helix: 1.26 (0.15), residues: 1071 sheet: None (None), residues: 0 loop : -1.32 (0.25), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 100 TYR 0.027 0.002 TYR Q 89 PHE 0.017 0.002 PHE O 66 HIS 0.008 0.001 HIS M 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.23 (25228) covalent geometry : angle 0.67582 / 0.44 (36519) hydrogen bonds : bond 0.07901 / 5.23 ( 1483) hydrogen bonds : angle 3.84709 / 2.80 ( 3687) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 0.679 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: A 51 GLU cc_start: 0.9707 (mt-10) cc_final: 0.9399 (mt-10) REVERT: A 108 THR cc_start: 0.9568 (m) cc_final: 0.9122 (m) REVERT: A 124 ASP cc_start: 0.7973 (m-30) cc_final: 0.7581 (t70) REVERT: B 80 LYS cc_start: 0.8834 (tppt) cc_final: 0.8529 (tppt) REVERT: E 65 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7900 (mmmm) REVERT: E 91 MET cc_start: 0.7852 (mmm) cc_final: 0.7362 (mmm) REVERT: E 98 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7434 (mt-10) REVERT: E 121 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6460 (tpp) REVERT: H 106 GLU cc_start: 0.9149 (mp0) cc_final: 0.8859 (mp0) REVERT: M 45 LYS cc_start: 0.9170 (tttt) cc_final: 0.8795 (ttpp) REVERT: N 65 GLU cc_start: 0.9562 (tp30) cc_final: 0.9337 (mm-30) REVERT: O 94 GLU cc_start: 0.9169 (mp0) cc_final: 0.8878 (mp0) REVERT: P 82 ASP cc_start: 0.8166 (t70) cc_final: 0.7734 (t70) REVERT: Q 53 GLU cc_start: 0.9329 (mp0) cc_final: 0.9101 (pm20) outliers start: 35 outliers final: 29 residues processed: 295 average time/residue: 0.3286 time to fit residues: 145.5812 Evaluate side-chains 291 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 261 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 66 PHE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 74 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 33 optimal weight: 6.9990 chunk 80 optimal weight: 30.0000 chunk 112 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 180 optimal weight: 30.0000 chunk 126 optimal weight: 4.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.062995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.049233 restraints weight = 378186.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.051054 restraints weight = 165502.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.052230 restraints weight = 100833.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.052931 restraints weight = 74455.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.053426 restraints weight = 62355.163| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25228 Z= 0.177 Angle : 0.643 7.239 36519 Z= 0.425 Chirality : 0.042 0.271 4149 Planarity : 0.005 0.051 2640 Dihedral : 30.023 88.069 7922 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.81 % Allowed : 16.47 % Favored : 80.72 % 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: 1.23 (0.20), residues: 1475 helix: 1.67 (0.15), residues: 1059 sheet: None (None), residues: 0 loop : -1.46 (0.25), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 68 TYR 0.038 0.002 TYR S 84 PHE 0.019 0.002 PHE D 66 HIS 0.005 0.001 HIS M 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.18 (25228) covalent geometry : angle 0.64275 / 0.42 (36519) hydrogen bonds : bond 0.06717 / 4.47 ( 1483) hydrogen bonds : angle 3.57912 / 2.60 ( 3687) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 278 time to evaluate : 0.850 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: A 108 THR cc_start: 0.9586 (m) cc_final: 0.9037 (m) REVERT: A 124 ASP cc_start: 0.7912 (m-30) cc_final: 0.7458 (t70) REVERT: B 80 LYS cc_start: 0.8824 (tppt) cc_final: 0.8534 (tppt) REVERT: C 58 TYR cc_start: 0.8822 (t80) cc_final: 0.7967 (t80) REVERT: D 114 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8740 (mm-30) REVERT: E 121 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6771 (tpp) REVERT: F 68 ARG cc_start: 0.9048 (tpt170) cc_final: 0.8414 (tpm170) REVERT: G 105 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7150 (mp10) REVERT: H 97 THR cc_start: 0.9214 (m) cc_final: 0.8978 (t) REVERT: H 106 GLU cc_start: 0.9196 (mp0) cc_final: 0.8981 (mp0) REVERT: M 45 LYS cc_start: 0.9142 (tttt) cc_final: 0.8777 (ttpp) REVERT: M 85 MET cc_start: 0.9107 (mmm) cc_final: 0.8754 (mmm) REVERT: N 65 GLU cc_start: 0.9559 (tp30) cc_final: 0.9320 (mm-30) REVERT: N 105 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7887 (tm-30) REVERT: O 94 GLU cc_start: 0.9157 (mp0) cc_final: 0.8859 (mp0) REVERT: O 100 ARG cc_start: 0.9101 (ttm110) cc_final: 0.8836 (ttm110) REVERT: P 82 ASP cc_start: 0.8186 (t70) cc_final: 0.7710 (t70) REVERT: Q 53 GLU cc_start: 0.9365 (mp0) cc_final: 0.9165 (pm20) REVERT: Q 54 GLU cc_start: 0.9123 (mp0) cc_final: 0.8922 (mp0) REVERT: R 93 GLU cc_start: 0.8873 (tt0) cc_final: 0.8022 (tm-30) REVERT: S 72 GLU cc_start: 0.8725 (tp30) cc_final: 0.8523 (mm-30) REVERT: S 106 GLU cc_start: 0.8788 (tp30) cc_final: 0.8492 (tp30) outliers start: 35 outliers final: 29 residues processed: 300 average time/residue: 0.3377 time to fit residues: 150.6895 Evaluate side-chains 296 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 265 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 74 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 65 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 198 optimal weight: 30.0000 chunk 154 optimal weight: 6.9990 chunk 192 optimal weight: 30.0000 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 40.0000 chunk 29 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.065698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.052928 restraints weight = 436003.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.054614 restraints weight = 190544.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.055693 restraints weight = 117098.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.056360 restraints weight = 87757.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.056718 restraints weight = 74184.177| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25228 Z= 0.200 Angle : 0.653 8.885 36519 Z= 0.429 Chirality : 0.041 0.184 4149 Planarity : 0.005 0.049 2640 Dihedral : 30.030 88.841 7922 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.21 % Allowed : 16.63 % Favored : 80.16 % 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: 1.10 (0.20), residues: 1475 helix: 1.60 (0.15), residues: 1059 sheet: None (None), residues: 0 loop : -1.59 (0.25), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 100 TYR 0.016 0.002 TYR Q 89 PHE 0.017 0.002 PHE D 66 HIS 0.006 0.001 HIS M 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.20 (25228) covalent geometry : angle 0.65334 / 0.43 (36519) hydrogen bonds : bond 0.07086 / 4.71 ( 1483) hydrogen bonds : angle 3.65495 / 2.66 ( 3687) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 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: A 51 GLU cc_start: 0.9721 (mt-10) cc_final: 0.9412 (mt-10) REVERT: A 108 THR cc_start: 0.9573 (m) cc_final: 0.9039 (m) REVERT: A 124 ASP cc_start: 0.7883 (m-30) cc_final: 0.7495 (t70) REVERT: B 80 LYS cc_start: 0.8884 (tppt) cc_final: 0.8607 (tppt) REVERT: C 58 TYR cc_start: 0.8448 (t80) cc_final: 0.8073 (t80) REVERT: D 114 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8762 (mm-30) REVERT: E 121 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6761 (tpp) REVERT: G 93 GLU cc_start: 0.8708 (mp0) cc_final: 0.7884 (pt0) REVERT: H 97 THR cc_start: 0.9214 (m) cc_final: 0.8979 (t) REVERT: M 45 LYS cc_start: 0.9133 (tttt) cc_final: 0.8785 (ttpp) REVERT: N 65 GLU cc_start: 0.9542 (tp30) cc_final: 0.9324 (mm-30) REVERT: N 105 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7667 (tm-30) REVERT: O 94 GLU cc_start: 0.9130 (mp0) cc_final: 0.8859 (mp0) REVERT: O 100 ARG cc_start: 0.9088 (ttm110) cc_final: 0.8818 (ttm110) REVERT: P 82 ASP cc_start: 0.8187 (t70) cc_final: 0.7705 (t70) REVERT: Q 53 GLU cc_start: 0.9363 (mp0) cc_final: 0.9149 (pm20) outliers start: 40 outliers final: 37 residues processed: 287 average time/residue: 0.3381 time to fit residues: 145.7596 Evaluate side-chains 296 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 258 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain Q residue 85 MET Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 74 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 34 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 86 optimal weight: 40.0000 chunk 177 optimal weight: 30.0000 chunk 176 optimal weight: 20.0000 chunk 148 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 73 optimal weight: 30.0000 chunk 63 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.065012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.052242 restraints weight = 440040.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.053923 restraints weight = 193802.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.054980 restraints weight = 119295.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.055589 restraints weight = 89823.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.056013 restraints weight = 76663.318| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25228 Z= 0.199 Angle : 0.655 11.128 36519 Z= 0.427 Chirality : 0.041 0.178 4149 Planarity : 0.005 0.049 2640 Dihedral : 30.120 89.536 7922 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.37 % Allowed : 17.11 % Favored : 79.52 % 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: 0.84 (0.20), residues: 1475 helix: 1.44 (0.15), residues: 1059 sheet: None (None), residues: 0 loop : -1.79 (0.25), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 100 TYR 0.020 0.002 TYR S 84 PHE 0.032 0.002 PHE P 68 HIS 0.006 0.001 HIS M 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.20 (25228) covalent geometry : angle 0.65511 / 0.43 (36519) hydrogen bonds : bond 0.07153 / 4.75 ( 1483) hydrogen bonds : angle 3.69849 / 2.68 ( 3687) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 257 time to evaluate : 0.880 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: A 51 GLU cc_start: 0.9721 (mt-10) cc_final: 0.9425 (mt-10) REVERT: A 108 THR cc_start: 0.9584 (m) cc_final: 0.9065 (m) REVERT: A 124 ASP cc_start: 0.7854 (m-30) cc_final: 0.7503 (t70) REVERT: C 58 TYR cc_start: 0.8477 (t80) cc_final: 0.8112 (t80) REVERT: D 114 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8825 (mm-30) REVERT: F 68 ARG cc_start: 0.9055 (tpt170) cc_final: 0.8417 (tpm170) REVERT: H 97 THR cc_start: 0.9235 (m) cc_final: 0.9012 (t) REVERT: M 45 LYS cc_start: 0.9127 (tttt) cc_final: 0.8778 (ttpp) REVERT: M 75 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8996 (mm-30) REVERT: N 65 GLU cc_start: 0.9512 (tp30) cc_final: 0.9260 (mm-30) REVERT: O 83 HIS cc_start: 0.8805 (OUTLIER) cc_final: 0.8532 (t-90) REVERT: O 94 GLU cc_start: 0.9096 (mp0) cc_final: 0.8841 (mp0) REVERT: P 82 ASP cc_start: 0.8145 (t70) cc_final: 0.7679 (t70) REVERT: Q 53 GLU cc_start: 0.9369 (mp0) cc_final: 0.9164 (pm20) outliers start: 42 outliers final: 33 residues processed: 280 average time/residue: 0.3485 time to fit residues: 146.5565 Evaluate side-chains 285 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 251 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 66 PHE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 83 HIS Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain Q residue 85 MET Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 74 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 119 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 180 optimal weight: 30.0000 chunk 105 optimal weight: 0.9980 chunk 187 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.062493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.048563 restraints weight = 371603.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.050406 restraints weight = 163498.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.051581 restraints weight = 99874.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.052262 restraints weight = 74081.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.052743 restraints weight = 62610.299| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 25228 Z= 0.155 Angle : 0.623 9.109 36519 Z= 0.408 Chirality : 0.040 0.145 4149 Planarity : 0.005 0.059 2640 Dihedral : 30.098 88.160 7922 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.09 % Allowed : 18.55 % Favored : 79.36 % 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: 1.62 (0.21), residues: 1475 helix: 2.05 (0.15), residues: 1067 sheet: None (None), residues: 0 loop : -1.66 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 100 TYR 0.013 0.001 TYR S 41 PHE 0.020 0.002 PHE D 66 HIS 0.004 0.001 HIS M 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.15 (25228) covalent geometry : angle 0.62334 / 0.41 (36519) hydrogen bonds : bond 0.05871 / 3.92 ( 1483) hydrogen bonds : angle 3.27970 / 2.39 ( 3687) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 276 time to evaluate : 0.888 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: A 51 GLU cc_start: 0.9696 (mt-10) cc_final: 0.9397 (mt-10) REVERT: A 108 THR cc_start: 0.9608 (m) cc_final: 0.9132 (m) REVERT: A 124 ASP cc_start: 0.7826 (m-30) cc_final: 0.7485 (t70) REVERT: C 58 TYR cc_start: 0.8364 (t80) cc_final: 0.8088 (t80) REVERT: F 68 ARG cc_start: 0.9038 (tpt170) cc_final: 0.8384 (tpm170) REVERT: G 93 GLU cc_start: 0.8646 (mp0) cc_final: 0.7791 (mt-10) REVERT: H 97 THR cc_start: 0.9190 (m) cc_final: 0.8956 (t) REVERT: M 45 LYS cc_start: 0.9129 (tttt) cc_final: 0.8767 (ttpp) REVERT: O 83 HIS cc_start: 0.8711 (OUTLIER) cc_final: 0.8457 (t-90) REVERT: O 94 GLU cc_start: 0.9102 (mp0) cc_final: 0.8821 (mp0) REVERT: O 100 ARG cc_start: 0.9061 (ttm110) cc_final: 0.8844 (ptp-110) REVERT: P 82 ASP cc_start: 0.8186 (t70) cc_final: 0.7721 (t70) REVERT: Q 54 GLU cc_start: 0.9131 (mp0) cc_final: 0.8905 (mp0) REVERT: S 47 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8268 (tppt) outliers start: 26 outliers final: 21 residues processed: 292 average time/residue: 0.3450 time to fit residues: 150.6196 Evaluate side-chains 282 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 260 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 83 HIS Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain Q residue 85 MET Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain S residue 36 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 131 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 89 optimal weight: 30.0000 chunk 188 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 20.0000 chunk 151 optimal weight: 0.6980 chunk 191 optimal weight: 20.0000 chunk 163 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.062809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.048983 restraints weight = 376526.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.050846 restraints weight = 166148.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.052008 restraints weight = 101502.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.052706 restraints weight = 75244.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.053202 restraints weight = 63093.722| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25228 Z= 0.154 Angle : 0.625 12.792 36519 Z= 0.406 Chirality : 0.040 0.192 4149 Planarity : 0.005 0.055 2640 Dihedral : 30.038 87.629 7922 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.85 % Allowed : 19.36 % Favored : 78.80 % 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: 1.85 (0.21), residues: 1475 helix: 2.19 (0.15), residues: 1075 sheet: None (None), residues: 0 loop : -1.56 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 100 TYR 0.030 0.001 TYR H 41 PHE 0.020 0.001 PHE D 66 HIS 0.005 0.001 HIS M 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.15 (25228) covalent geometry : angle 0.62535 / 0.41 (36519) hydrogen bonds : bond 0.05469 / 3.65 ( 1483) hydrogen bonds : angle 3.17283 / 2.31 ( 3687) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 269 time to evaluate : 0.924 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: A 51 GLU cc_start: 0.9707 (mt-10) cc_final: 0.9418 (mt-10) REVERT: F 53 GLU cc_start: 0.9149 (mp0) cc_final: 0.8909 (pm20) REVERT: F 68 ARG cc_start: 0.9064 (tpt170) cc_final: 0.8396 (tpm170) REVERT: G 93 GLU cc_start: 0.8676 (mp0) cc_final: 0.7833 (pt0) REVERT: G 105 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7206 (mp10) REVERT: H 97 THR cc_start: 0.9159 (m) cc_final: 0.8918 (t) REVERT: M 93 ARG cc_start: 0.8586 (ttp80) cc_final: 0.8338 (ttp80) REVERT: O 83 HIS cc_start: 0.8702 (OUTLIER) cc_final: 0.8466 (t-90) REVERT: O 94 GLU cc_start: 0.9114 (mp0) cc_final: 0.8832 (mp0) REVERT: O 100 ARG cc_start: 0.9094 (ttm110) cc_final: 0.8868 (ptp-110) REVERT: P 82 ASP cc_start: 0.8261 (t70) cc_final: 0.7792 (t70) outliers start: 23 outliers final: 17 residues processed: 284 average time/residue: 0.3450 time to fit residues: 145.8227 Evaluate side-chains 278 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 259 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain O residue 83 HIS Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain Q residue 85 MET Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain S residue 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 127 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 178 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 88 optimal weight: 30.0000 chunk 159 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 94 GLN F 65 ASN ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.063312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.049691 restraints weight = 381852.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.051582 restraints weight = 164855.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.052768 restraints weight = 99202.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.053461 restraints weight = 72722.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.053983 restraints weight = 60825.605| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25228 Z= 0.152 Angle : 0.615 12.514 36519 Z= 0.401 Chirality : 0.040 0.167 4149 Planarity : 0.004 0.055 2640 Dihedral : 30.008 88.120 7922 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.45 % Allowed : 20.16 % Favored : 78.39 % 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: 1.91 (0.21), residues: 1475 helix: 2.24 (0.15), residues: 1075 sheet: None (None), residues: 0 loop : -1.55 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 100 TYR 0.019 0.001 TYR H 41 PHE 0.019 0.001 PHE O 66 HIS 0.005 0.001 HIS M 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.15 (25228) covalent geometry : angle 0.61535 / 0.40 (36519) hydrogen bonds : bond 0.05403 / 3.60 ( 1483) hydrogen bonds : angle 3.15173 / 2.30 ( 3687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7255.04 seconds wall clock time: 124 minutes 3.58 seconds (7443.58 seconds total)