Starting phenix.real_space_refine on Tue Sep 15 18:34:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmo_48396/09_2026/9mmo_48396.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmo_48396/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mmo_48396/09_2026/9mmo_48396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmo_48396/09_2026/9mmo_48396.map" model { file = "/net/cci-nas-00/data/ceres_data/9mmo_48396/09_2026/9mmo_48396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmo_48396/09_2026/9mmo_48396.cif" } 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-2.2.1-6174/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: 7.38, per 1000 atoms: 0.17 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: 3.91 Conformation dependent library (CDL) restraints added in 817.0 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: 7.35 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: 10.19 Time building geometry restraints manager: 5.47 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: 71989 1.54 - 3.08: 7310 3.08 - 4.62: 683 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: 5.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.280 Extract box with map and model: 0.890 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 44.790 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.220 ------------------------------------------------------------------------------- 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 : 1.057 7.698 36519 Z= 0.880 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 1.05700 / 0.88 (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 : 0.906 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: 0.7618 (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: 0.8626 (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: 0.8374 (m110) REVERT: P 47 VAL cc_start: 0.8762 (t) cc_final: 0.8238 (t) REVERT: P 51 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8662 (mt-10) REVERT: Q 59 LEU cc_start: 0.9100 (tp) cc_final: 0.8494 (tp) REVERT: R 91 ASP cc_start: 0.7931 (t70) cc_final: 0.7206 (t0) outliers start: 4 outliers final: 0 residues processed: 535 average time/residue: 0.4372 time to fit residues: 335.7687 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 : 0.894 ------------------------------------------------------------------------------- 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: 30.0000 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.063646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.050422 restraints weight = 381740.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.052282 restraints weight = 153556.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.053476 restraints weight = 89248.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.054185 restraints weight = 64138.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.054698 restraints weight = 53008.145| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25228 Z= 0.238 Angle : 0.771 7.030 36519 Z= 0.498 Chirality : 0.048 0.224 4149 Planarity : 0.006 0.059 2640 Dihedral : 29.527 86.233 7924 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.65 % Allowed : 13.41 % Favored : 83.94 % 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: 1.39 (0.20), residues: 1475 helix: 1.50 (0.15), residues: 1071 sheet: None (None), residues: 0 loop : -0.58 (0.26), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 80 TYR 0.026 0.002 TYR Q 89 PHE 0.020 0.002 PHE D 66 HIS 0.012 0.002 HIS O 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.24 (25228) covalent geometry : angle 0.77078 / 0.50 (36519) hydrogen bonds : bond 0.08541 / 5.61 ( 1483) hydrogen bonds : angle 4.05159 / 2.94 ( 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 348 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 315 time to evaluate : 0.915 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: A 63 ILE cc_start: 0.5655 (mm) cc_final: 0.4748 (mm) REVERT: E 94 GLN cc_start: 0.7650 (tt0) cc_final: 0.6818 (tp-100) REVERT: F 68 ARG cc_start: 0.9050 (tpt170) cc_final: 0.8408 (tpm170) REVERT: G 85 GLN cc_start: 0.7520 (tp40) cc_final: 0.6734 (tm-30) REVERT: H 96 GLN cc_start: 0.9249 (tt0) cc_final: 0.8920 (tp40) REVERT: L 98 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8211 (mt-10) REVERT: M 45 LYS cc_start: 0.9135 (tttt) cc_final: 0.8750 (ttpp) REVERT: O 94 GLU cc_start: 0.9171 (mp0) cc_final: 0.8763 (mp0) REVERT: P 82 ASP cc_start: 0.7981 (t70) cc_final: 0.7756 (t70) REVERT: P 95 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8907 (mm-30) REVERT: P 98 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7585 (mt-10) REVERT: P 111 CYS cc_start: 0.8734 (m) cc_final: 0.8530 (t) REVERT: Q 53 GLU cc_start: 0.9445 (mp0) cc_final: 0.9190 (pm20) REVERT: R 74 ASN cc_start: 0.8860 (t0) cc_final: 0.8660 (t0) REVERT: R 91 ASP cc_start: 0.7280 (t70) cc_final: 0.6669 (t0) outliers start: 33 outliers final: 27 residues processed: 332 average time/residue: 0.3670 time to fit residues: 183.0257 Evaluate side-chains 317 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 290 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP 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 D residue 55 ILE Chi-restraints excluded: chain E residue 125 ILE 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 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 N residue 77 THR 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: 6.9990 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 193 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 81 optimal weight: 30.0000 chunk 10 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.062773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.049671 restraints weight = 385439.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.051472 restraints weight = 156236.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.052651 restraints weight = 91451.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.053333 restraints weight = 66052.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.053825 restraints weight = 54948.337| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 25228 Z= 0.220 Angle : 0.691 7.253 36519 Z= 0.460 Chirality : 0.044 0.172 4149 Planarity : 0.005 0.051 2640 Dihedral : 29.793 85.353 7922 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.57 % Allowed : 15.02 % 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: 1.05 (0.20), residues: 1475 helix: 1.29 (0.15), residues: 1075 sheet: None (None), residues: 0 loop : -0.86 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 80 TYR 0.038 0.002 TYR Q 89 PHE 0.018 0.002 PHE D 66 HIS 0.005 0.001 HIS Q 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.22 (25228) covalent geometry : angle 0.69091 / 0.46 (36519) hydrogen bonds : bond 0.07895 / 5.22 ( 1483) hydrogen bonds : angle 3.89338 / 2.83 ( 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 329 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 297 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9315 (mt-10) cc_final: 0.9054 (mt-10) REVERT: A 63 ILE cc_start: 0.5713 (mm) cc_final: 0.5343 (mm) REVERT: E 94 GLN cc_start: 0.7725 (tt0) cc_final: 0.6864 (tp-100) REVERT: G 105 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7216 (mp10) REVERT: H 96 GLN cc_start: 0.9263 (tt0) cc_final: 0.9012 (tp40) REVERT: M 45 LYS cc_start: 0.9123 (tttt) cc_final: 0.8736 (ttpp) REVERT: N 65 GLU cc_start: 0.9630 (tp30) cc_final: 0.9296 (mm-30) REVERT: O 94 GLU cc_start: 0.9141 (mp0) cc_final: 0.8760 (mp0) REVERT: P 82 ASP cc_start: 0.8154 (t70) cc_final: 0.7825 (t70) REVERT: P 98 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7640 (mt-10) REVERT: Q 53 GLU cc_start: 0.9424 (mp0) cc_final: 0.9165 (pm20) REVERT: R 74 ASN cc_start: 0.8945 (OUTLIER) cc_final: 0.8706 (t0) outliers start: 32 outliers final: 23 residues processed: 315 average time/residue: 0.3788 time to fit residues: 179.8928 Evaluate side-chains 301 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 276 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 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 88 ILE Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain H residue 53 THR 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 L residue 125 ILE Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 77 THR 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 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: 8.9990 chunk 121 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 86 optimal weight: 40.0000 chunk 190 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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** R 74 ASN R 111 ASN R 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.061838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.048817 restraints weight = 391168.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.050584 restraints weight = 160286.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.051732 restraints weight = 94262.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.052405 restraints weight = 68344.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.052896 restraints weight = 56898.838| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 25228 Z= 0.242 Angle : 0.703 7.922 36519 Z= 0.458 Chirality : 0.043 0.241 4149 Planarity : 0.005 0.050 2640 Dihedral : 29.922 85.672 7922 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.37 % Allowed : 14.22 % 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: 0.67 (0.20), residues: 1475 helix: 1.09 (0.15), residues: 1071 sheet: None (None), residues: 0 loop : -1.19 (0.25), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 68 TYR 0.023 0.002 TYR F 89 PHE 0.018 0.002 PHE D 66 HIS 0.006 0.001 HIS Q 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.24 (25228) covalent geometry : angle 0.70253 / 0.46 (36519) hydrogen bonds : bond 0.08263 / 5.46 ( 1483) hydrogen bonds : angle 4.02244 / 2.92 ( 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: 42 poor density : 281 time to evaluate : 0.927 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: A 51 GLU cc_start: 0.9368 (mt-10) cc_final: 0.9103 (mt-10) REVERT: D 102 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8827 (mm) REVERT: E 91 MET cc_start: 0.7827 (mmm) cc_final: 0.7395 (mmm) REVERT: E 94 GLN cc_start: 0.7842 (tt0) cc_final: 0.7503 (tt0) REVERT: M 45 LYS cc_start: 0.9125 (tttt) cc_final: 0.8734 (ttpp) REVERT: N 65 GLU cc_start: 0.9616 (tp30) cc_final: 0.9290 (mm-30) REVERT: O 94 GLU cc_start: 0.9105 (mp0) cc_final: 0.8774 (mp0) REVERT: P 82 ASP cc_start: 0.8187 (t70) cc_final: 0.7792 (t70) REVERT: S 60 MET cc_start: 0.7358 (tpp) cc_final: 0.7153 (tpp) outliers start: 42 outliers final: 35 residues processed: 304 average time/residue: 0.3775 time to fit residues: 172.1514 Evaluate side-chains 298 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 262 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 102 LEU Chi-restraints excluded: chain E residue 51 GLU 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 69 ASP Chi-restraints excluded: chain G residue 35 LEU 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 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 N residue 77 THR Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain Q residue 31 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 74 ASN 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=3.50 ------------------------------------------------------------------------------- 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: 30.0000 chunk 104 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.063266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.049470 restraints weight = 374843.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.051315 restraints weight = 163095.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.052494 restraints weight = 99156.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.053208 restraints weight = 73159.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.053689 restraints weight = 61065.355| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4213 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= 0.181 Angle : 0.656 7.480 36519 Z= 0.435 Chirality : 0.042 0.193 4149 Planarity : 0.005 0.047 2640 Dihedral : 29.953 86.685 7922 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.57 % Allowed : 16.22 % Favored : 81.20 % 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: 1.17 (0.20), residues: 1475 helix: 1.49 (0.15), residues: 1075 sheet: None (None), residues: 0 loop : -1.18 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 93 TYR 0.017 0.002 TYR Q 89 PHE 0.019 0.002 PHE D 66 HIS 0.004 0.001 HIS M 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.18 (25228) covalent geometry : angle 0.65620 / 0.43 (36519) hydrogen bonds : bond 0.07065 / 4.68 ( 1483) hydrogen bonds : angle 3.67763 / 2.67 ( 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 315 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 283 time to evaluate : 1.193 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: A 51 GLU cc_start: 0.9314 (mt-10) cc_final: 0.9021 (mt-10) REVERT: D 102 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8872 (mm) REVERT: E 121 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6464 (tpp) REVERT: M 45 LYS cc_start: 0.9164 (tttt) cc_final: 0.8795 (ttpp) REVERT: M 85 MET cc_start: 0.9115 (mmm) cc_final: 0.8765 (mmm) REVERT: N 65 GLU cc_start: 0.9547 (tp30) cc_final: 0.9212 (mm-30) REVERT: O 100 ARG cc_start: 0.9095 (ttm110) cc_final: 0.8829 (ttm110) REVERT: P 82 ASP cc_start: 0.8187 (t70) cc_final: 0.7759 (t70) REVERT: S 72 GLU cc_start: 0.8727 (tp30) cc_final: 0.8518 (mm-30) outliers start: 32 outliers final: 26 residues processed: 301 average time/residue: 0.3861 time to fit residues: 175.6406 Evaluate side-chains 293 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 265 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 124 ASP 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 55 THR Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain G residue 35 LEU 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 75 ILE 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 N residue 56 LEU Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain P residue 81 THR 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 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: 0.1980 chunk 80 optimal weight: 30.0000 chunk 112 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 180 optimal weight: 30.0000 chunk 126 optimal weight: 0.3980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.063168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.049446 restraints weight = 378446.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.051295 restraints weight = 164719.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.052465 restraints weight = 99940.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.053174 restraints weight = 73630.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.053655 restraints weight = 61460.871| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25228 Z= 0.180 Angle : 0.656 11.371 36519 Z= 0.429 Chirality : 0.042 0.176 4149 Planarity : 0.005 0.055 2640 Dihedral : 29.969 87.836 7922 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.21 % Allowed : 16.06 % 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: 1.29 (0.21), residues: 1475 helix: 1.70 (0.15), residues: 1059 sheet: None (None), residues: 0 loop : -1.40 (0.25), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 100 TYR 0.017 0.002 TYR D 41 PHE 0.018 0.002 PHE D 66 HIS 0.006 0.001 HIS M 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.18 (25228) covalent geometry : angle 0.65605 / 0.43 (36519) hydrogen bonds : bond 0.06797 / 4.51 ( 1483) hydrogen bonds : angle 3.57577 / 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 315 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 275 time to evaluate : 0.943 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 51 GLU cc_start: 0.9338 (mt-10) cc_final: 0.9051 (mt-10) REVERT: A 94 GLN cc_start: 0.9171 (tt0) cc_final: 0.8438 (tp40) REVERT: A 124 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7351 (t70) REVERT: D 102 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8874 (mm) REVERT: E 121 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6734 (tpp) REVERT: M 45 LYS cc_start: 0.9150 (tttt) cc_final: 0.8777 (ttpp) REVERT: M 85 MET cc_start: 0.9103 (mmm) cc_final: 0.8741 (mmm) REVERT: N 65 GLU cc_start: 0.9540 (tp30) cc_final: 0.9185 (mm-30) REVERT: O 100 ARG cc_start: 0.9096 (ttm110) cc_final: 0.8846 (ttm110) REVERT: P 82 ASP cc_start: 0.8181 (t70) cc_final: 0.7705 (t70) REVERT: S 60 MET cc_start: 0.7521 (tpp) cc_final: 0.7218 (tpp) REVERT: S 72 GLU cc_start: 0.8731 (tp30) cc_final: 0.8520 (mm-30) outliers start: 40 outliers final: 31 residues processed: 299 average time/residue: 0.3942 time to fit residues: 175.5146 Evaluate side-chains 300 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 266 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 124 ASP 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 F residue 55 THR Chi-restraints excluded: chain G residue 35 LEU 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 M residue 87 VAL Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 88 VAL 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 S residue 36 GLU Chi-restraints excluded: chain S residue 117 LYS 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: 2.9990 chunk 71 optimal weight: 8.9990 chunk 198 optimal weight: 30.0000 chunk 154 optimal weight: 4.9990 chunk 192 optimal weight: 30.0000 chunk 40 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 40.0000 chunk 29 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.063168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.049463 restraints weight = 377050.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.051307 restraints weight = 163536.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.052489 restraints weight = 99139.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.053184 restraints weight = 72975.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.053681 restraints weight = 61165.919| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 25228 Z= 0.173 Angle : 0.645 8.146 36519 Z= 0.423 Chirality : 0.041 0.203 4149 Planarity : 0.005 0.051 2640 Dihedral : 29.994 89.128 7922 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.73 % Allowed : 16.55 % 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: 1.35 (0.21), residues: 1475 helix: 1.77 (0.15), residues: 1063 sheet: None (None), residues: 0 loop : -1.48 (0.25), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 100 TYR 0.017 0.002 TYR F 89 PHE 0.027 0.002 PHE P 68 HIS 0.004 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.17 (25228) covalent geometry : angle 0.64548 / 0.42 (36519) hydrogen bonds : bond 0.06389 / 4.25 ( 1483) hydrogen bonds : angle 3.51089 / 2.55 ( 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 308 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 274 time to evaluate : 0.909 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: A 51 GLU cc_start: 0.9323 (mt-10) cc_final: 0.9021 (mt-10) REVERT: A 124 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7333 (t70) REVERT: D 102 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8886 (mm) REVERT: E 121 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6771 (tpp) REVERT: F 68 ARG cc_start: 0.9029 (tpt170) cc_final: 0.8594 (tpm170) REVERT: H 97 THR cc_start: 0.9190 (m) cc_final: 0.8936 (t) REVERT: M 45 LYS cc_start: 0.9122 (tttt) cc_final: 0.8784 (ttpp) REVERT: M 75 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8949 (mm-30) REVERT: M 85 MET cc_start: 0.9097 (mmm) cc_final: 0.8689 (mmm) REVERT: N 65 GLU cc_start: 0.9511 (tp30) cc_final: 0.9108 (mm-30) REVERT: O 94 GLU cc_start: 0.9084 (mp0) cc_final: 0.8849 (mp0) REVERT: P 82 ASP cc_start: 0.8185 (t70) cc_final: 0.7702 (t70) REVERT: S 60 MET cc_start: 0.7602 (tpp) cc_final: 0.7267 (tpp) REVERT: S 72 GLU cc_start: 0.8719 (tp30) cc_final: 0.8499 (mm-30) outliers start: 34 outliers final: 25 residues processed: 294 average time/residue: 0.3845 time to fit residues: 170.2773 Evaluate side-chains 286 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 124 ASP 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 G residue 35 LEU Chi-restraints excluded: chain G residue 44 VAL 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 N residue 77 THR Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain P residue 81 THR 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 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: 0.5980 chunk 47 optimal weight: 9.9990 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: 9.9990 chunk 46 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.061873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.049180 restraints weight = 398100.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.050951 restraints weight = 165095.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.052083 restraints weight = 97327.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.052772 restraints weight = 70646.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.053249 restraints weight = 58472.609| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25228 Z= 0.185 Angle : 0.646 7.930 36519 Z= 0.422 Chirality : 0.041 0.174 4149 Planarity : 0.005 0.101 2640 Dihedral : 29.997 89.931 7922 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.81 % Allowed : 16.87 % Favored : 80.32 % 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: 1.29 (0.21), residues: 1475 helix: 1.74 (0.15), residues: 1067 sheet: None (None), residues: 0 loop : -1.60 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 100 TYR 0.024 0.002 TYR F 89 PHE 0.027 0.002 PHE E 68 HIS 0.005 0.001 HIS M 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.19 (25228) covalent geometry : angle 0.64628 / 0.42 (36519) hydrogen bonds : bond 0.06648 / 4.40 ( 1483) hydrogen bonds : angle 3.57490 / 2.60 ( 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 297 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 262 time to evaluate : 1.156 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 94 GLN cc_start: 0.9262 (tt0) cc_final: 0.8468 (tp40) REVERT: A 124 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7242 (t70) REVERT: D 102 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8848 (mm) REVERT: H 97 THR cc_start: 0.9209 (m) cc_final: 0.8987 (t) REVERT: M 45 LYS cc_start: 0.9101 (tttt) cc_final: 0.8731 (ttpp) REVERT: M 85 MET cc_start: 0.9098 (mmm) cc_final: 0.8699 (mmm) REVERT: N 65 GLU cc_start: 0.9558 (tp30) cc_final: 0.9177 (mm-30) REVERT: O 83 HIS cc_start: 0.8818 (OUTLIER) cc_final: 0.8598 (t-90) REVERT: O 94 GLU cc_start: 0.9159 (mp0) cc_final: 0.8891 (mp0) REVERT: P 82 ASP cc_start: 0.8218 (t70) cc_final: 0.7733 (t70) REVERT: S 60 MET cc_start: 0.7483 (tpp) cc_final: 0.7180 (tpp) outliers start: 35 outliers final: 29 residues processed: 281 average time/residue: 0.3814 time to fit residues: 161.8630 Evaluate side-chains 288 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 256 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 124 ASP 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 G residue 35 LEU 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 L residue 125 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 93 GLU 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 31 THR Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 19 SER 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: 4.9990 chunk 47 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 180 optimal weight: 20.0000 chunk 105 optimal weight: 0.7980 chunk 187 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 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 = 0.3924 r_free = 0.3924 target = 0.061174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.048222 restraints weight = 393625.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.049972 restraints weight = 165692.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.051087 restraints weight = 98745.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.051771 restraints weight = 72269.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.052225 restraints weight = 60126.570| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25228 Z= 0.191 Angle : 0.649 12.028 36519 Z= 0.421 Chirality : 0.041 0.179 4149 Planarity : 0.005 0.046 2640 Dihedral : 30.030 89.241 7922 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.89 % Allowed : 17.19 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.21), residues: 1475 helix: 1.69 (0.15), residues: 1067 sheet: None (None), residues: 0 loop : -1.71 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Q 93 TYR 0.052 0.002 TYR F 89 PHE 0.018 0.002 PHE P 68 HIS 0.005 0.001 HIS M 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.19 (25228) covalent geometry : angle 0.64929 / 0.42 (36519) hydrogen bonds : bond 0.06779 / 4.50 ( 1483) hydrogen bonds : angle 3.63900 / 2.64 ( 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 295 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 259 time to evaluate : 0.922 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 94 GLN cc_start: 0.9234 (tt0) cc_final: 0.8466 (tp40) REVERT: A 124 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7276 (t70) REVERT: F 54 GLU cc_start: 0.8982 (mp0) cc_final: 0.8737 (pm20) REVERT: F 68 ARG cc_start: 0.9095 (tpt170) cc_final: 0.8688 (tpm170) REVERT: H 97 THR cc_start: 0.9222 (m) cc_final: 0.9009 (t) REVERT: M 45 LYS cc_start: 0.9101 (tttt) cc_final: 0.8723 (ttpp) REVERT: M 75 GLU cc_start: 0.9400 (mm-30) cc_final: 0.9032 (mm-30) REVERT: M 85 MET cc_start: 0.9092 (mmm) cc_final: 0.8705 (mmm) REVERT: N 65 GLU cc_start: 0.9562 (tp30) cc_final: 0.9181 (mm-30) REVERT: O 83 HIS cc_start: 0.8834 (OUTLIER) cc_final: 0.8631 (t-90) REVERT: O 94 GLU cc_start: 0.9153 (mp0) cc_final: 0.8904 (mp0) REVERT: P 82 ASP cc_start: 0.8236 (t70) cc_final: 0.7761 (t70) REVERT: S 60 MET cc_start: 0.7491 (tpp) cc_final: 0.7235 (tpp) outliers start: 36 outliers final: 28 residues processed: 279 average time/residue: 0.3793 time to fit residues: 160.4143 Evaluate side-chains 281 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 251 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 124 ASP 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 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 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 N residue 77 THR 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 88 VAL Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain S residue 36 GLU 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 131 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 89 optimal weight: 30.0000 chunk 188 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 151 optimal weight: 0.8980 chunk 191 optimal weight: 20.0000 chunk 163 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.062991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.049363 restraints weight = 377679.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.051238 restraints weight = 163392.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.052437 restraints weight = 98684.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.053156 restraints weight = 72455.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.053650 restraints weight = 60459.632| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.5173 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= 0.159 Angle : 0.630 8.698 36519 Z= 0.409 Chirality : 0.040 0.247 4149 Planarity : 0.005 0.077 2640 Dihedral : 30.028 88.136 7922 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.85 % Allowed : 18.39 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.21), residues: 1475 helix: 2.04 (0.15), residues: 1067 sheet: None (None), residues: 0 loop : -1.64 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Q 93 TYR 0.024 0.002 TYR F 89 PHE 0.020 0.002 PHE E 68 HIS 0.004 0.001 HIS M 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.16 (25228) covalent geometry : angle 0.63033 / 0.41 (36519) hydrogen bonds : bond 0.05827 / 3.88 ( 1483) hydrogen bonds : angle 3.38462 / 2.46 ( 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 296 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 273 time to evaluate : 0.982 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: A 124 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7329 (t70) REVERT: D 102 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8873 (mm) REVERT: F 68 ARG cc_start: 0.9079 (tpt170) cc_final: 0.8665 (tpm170) REVERT: H 97 THR cc_start: 0.9184 (m) cc_final: 0.8955 (t) REVERT: M 75 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8970 (mm-30) REVERT: N 65 GLU cc_start: 0.9510 (tp30) cc_final: 0.9166 (mm-30) REVERT: O 94 GLU cc_start: 0.9124 (mp0) cc_final: 0.8845 (mp0) REVERT: P 82 ASP cc_start: 0.8225 (t70) cc_final: 0.7750 (t70) REVERT: S 60 MET cc_start: 0.7583 (tpp) cc_final: 0.7328 (tpp) outliers start: 23 outliers final: 19 residues processed: 288 average time/residue: 0.3912 time to fit residues: 169.2970 Evaluate side-chains 279 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 258 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 124 ASP 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 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 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 N residue 77 THR Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain R residue 19 SER 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 127 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 178 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 chunk 124 optimal weight: 0.4980 chunk 140 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 88 optimal weight: 30.0000 chunk 159 optimal weight: 0.8980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 94 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 = 0.3888 r_free = 0.3888 target = 0.062728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.048958 restraints weight = 381242.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.050815 restraints weight = 166247.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.051995 restraints weight = 101070.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.052686 restraints weight = 74635.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.053178 restraints weight = 62569.041| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25228 Z= 0.156 Angle : 0.625 10.049 36519 Z= 0.405 Chirality : 0.040 0.207 4149 Planarity : 0.004 0.060 2640 Dihedral : 29.968 88.444 7922 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.85 % Allowed : 19.12 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.21), residues: 1475 helix: 2.11 (0.16), residues: 1075 sheet: None (None), residues: 0 loop : -1.60 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 93 TYR 0.026 0.001 TYR F 89 PHE 0.019 0.001 PHE D 66 HIS 0.005 0.001 HIS M 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.16 (25228) covalent geometry : angle 0.62529 / 0.40 (36519) hydrogen bonds : bond 0.05556 / 3.69 ( 1483) hydrogen bonds : angle 3.28639 / 2.39 ( 3687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8007.55 seconds wall clock time: 137 minutes 0.21 seconds (8220.21 seconds total)