Starting phenix.real_space_refine on Sun Feb 8 07:59:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmo_48396/02_2026/9mmo_48396.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmo_48396/02_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_48396/02_2026/9mmo_48396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmo_48396/02_2026/9mmo_48396.map" model { file = "/net/cci-nas-00/data/ceres_data/9mmo_48396/02_2026/9mmo_48396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmo_48396/02_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-2.0-5952/lib/python3.9/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: 7.36, 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: 3.57 Conformation dependent library (CDL) restraints added in 866.3 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: 7.93 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: 11.18 Time building geometry restraints manager: 5.04 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 1.525 1.561 -0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" N ARG C 12 " pdb=" CA ARG C 12 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" N SER O 33 " pdb=" CA SER O 33 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N ASP M 25 " pdb=" CA ASP M 25 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N ARG Q 24 " pdb=" CA ARG Q 24 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 ... (remaining 44191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 72324 1.54 - 3.08: 7299 3.08 - 4.62: 456 4.62 - 6.16: 32 6.16 - 7.70: 3 Bond angle restraints: 80114 Sorted by residual: angle pdb=" C2' DT X -26 " pdb=" C1' DT X -26 " pdb=" N1 DT X -26 " ideal model delta sigma weight residual 113.50 120.03 -6.53 1.50e+00 4.44e-01 1.90e+01 angle pdb=" O4' DA I -35 " pdb=" C1' DA I -35 " pdb=" N9 DA I -35 " ideal model delta sigma weight residual 108.40 102.26 6.14 1.50e+00 4.44e-01 1.67e+01 angle pdb=" O4' DG X 47 " pdb=" C1' DG X 47 " pdb=" N9 DG X 47 " ideal model delta sigma weight residual 108.40 102.81 5.59 1.50e+00 4.44e-01 1.39e+01 angle pdb=" C2' DA X 17 " pdb=" C1' DA X 17 " pdb=" N9 DA X 17 " ideal model delta sigma weight residual 113.50 118.96 -5.46 1.50e+00 4.44e-01 1.33e+01 angle pdb=" C2' DA I -69 " pdb=" C1' DA I -69 " pdb=" N9 DA I -69 " ideal model delta sigma weight residual 113.50 118.91 -5.41 1.50e+00 4.44e-01 1.30e+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 - 0.044: 2515 0.044 - 0.088: 1182 0.088 - 0.132: 380 0.132 - 0.176: 54 0.176 - 0.220: 18 Chirality restraints: 4149 Sorted by residual: 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 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C4' DC I 21 " pdb=" C5' DC I 21 " pdb=" O4' DC I 21 " pdb=" C3' DC I 21 " both_signs ideal model delta sigma weight residual False -2.53 -2.31 -0.22 2.00e-01 2.50e+01 1.19e+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 2.42 2.20 0.22 2.00e-01 2.50e+01 1.17e+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: 5.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.210 Extract box with map and model: 0.610 Check model and map are aligned: 0.130 Set scattering table: 0.130 Process input model: 45.680 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.090 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 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 : 0.006 0.081 25228 Z= 0.284 Angle : 0.962 7.698 36519 Z= 0.622 Chirality : 0.054 0.220 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 covalent geometry : bond 0.00607 (25228) covalent geometry : angle 0.96181 (36519) hydrogen bonds : bond 0.13286 ( 1483) hydrogen bonds : angle 4.20581 ( 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 : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8100 (tt0) cc_final: 0.7616 (tp40) REVERT: G 74 ASN cc_start: 0.7830 (OUTLIER) cc_final: 0.7401 (t0) REVERT: G 101 VAL cc_start: 0.8105 (t) cc_final: 0.7855 (t) REVERT: H 46 LEU cc_start: 0.8847 (tp) cc_final: 0.8624 (tp) REVERT: L 94 GLN cc_start: 0.7509 (tt0) cc_final: 0.7219 (tt0) REVERT: N 69 ASN cc_start: 0.8958 (m-40) cc_final: 0.8373 (m110) REVERT: P 47 VAL cc_start: 0.8762 (t) cc_final: 0.8557 (m) REVERT: P 51 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8685 (mt-10) REVERT: Q 59 LEU cc_start: 0.9100 (tp) cc_final: 0.8493 (tp) REVERT: R 91 ASP cc_start: 0.7931 (t70) cc_final: 0.7205 (t0) outliers start: 4 outliers final: 0 residues processed: 535 average time/residue: 0.4339 time to fit residues: 325.1332 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 : 0.825 ------------------------------------------------------------------------------- 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: 10.0000 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 HIS B 94 GLN O 110 HIS R 74 ASN R 111 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.062827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.049656 restraints weight = 385184.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.051474 restraints weight = 157906.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.052634 restraints weight = 93073.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.053327 restraints weight = 67701.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.053819 restraints weight = 56193.739| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25228 Z= 0.239 Angle : 0.711 6.318 36519 Z= 0.440 Chirality : 0.044 0.153 4149 Planarity : 0.005 0.060 2640 Dihedral : 29.499 83.916 7924 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.65 % Allowed : 12.77 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.66 (0.21), residues: 1475 helix: 1.70 (0.15), residues: 1075 sheet: None (None), residues: 0 loop : -0.48 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 53 TYR 0.014 0.002 TYR O 84 PHE 0.020 0.002 PHE D 66 HIS 0.010 0.001 HIS O 110 Details of bonding type rmsd covalent geometry : bond 0.00502 (25228) covalent geometry : angle 0.71092 (36519) hydrogen bonds : bond 0.07334 ( 1483) hydrogen bonds : angle 3.57929 ( 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 349 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 316 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.5673 (mm) cc_final: 0.4839 (mm) REVERT: A 108 THR cc_start: 0.9624 (m) cc_final: 0.9210 (m) REVERT: A 124 ASP cc_start: 0.7893 (m-30) cc_final: 0.7299 (t70) REVERT: E 94 GLN cc_start: 0.7709 (tt0) cc_final: 0.6727 (tp-100) REVERT: L 98 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8135 (mt-10) REVERT: M 80 LYS cc_start: 0.8084 (tppt) cc_final: 0.7822 (tppt) REVERT: O 94 GLU cc_start: 0.9100 (mp0) cc_final: 0.8873 (mp0) REVERT: O 100 ARG cc_start: 0.9193 (ttm170) cc_final: 0.8855 (ttm110) REVERT: O 106 GLU cc_start: 0.8798 (tp30) cc_final: 0.8361 (tp30) REVERT: O 109 LYS cc_start: 0.9550 (ttpp) cc_final: 0.9222 (ttpp) REVERT: P 82 ASP cc_start: 0.8251 (t70) cc_final: 0.8035 (t70) REVERT: P 95 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8957 (mm-30) REVERT: P 98 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7735 (mt-10) REVERT: Q 53 GLU cc_start: 0.9453 (mp0) cc_final: 0.9222 (pm20) REVERT: R 74 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8713 (t0) REVERT: S 72 GLU cc_start: 0.8750 (tp30) cc_final: 0.8544 (mm-30) REVERT: S 102 LEU cc_start: 0.6489 (mp) cc_final: 0.6285 (mp) outliers start: 33 outliers final: 23 residues processed: 336 average time/residue: 0.3858 time to fit residues: 190.7078 Evaluate side-chains 305 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 281 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 25 GLN Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 69 ASP 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 81 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 69 ASP 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 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 R residue 111 ASN Chi-restraints excluded: chain S residue 36 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 142 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 153 optimal weight: 0.0570 chunk 160 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 overall best weight: 2.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.063129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.050093 restraints weight = 383966.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.051923 restraints weight = 155388.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.053106 restraints weight = 91052.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.053816 restraints weight = 65913.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.054315 restraints weight = 54460.144| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25228 Z= 0.192 Angle : 0.652 7.312 36519 Z= 0.408 Chirality : 0.039 0.174 4149 Planarity : 0.004 0.052 2640 Dihedral : 29.303 85.974 7922 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.25 % Allowed : 13.57 % Favored : 84.18 % 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: 2.00 (0.21), residues: 1475 helix: 2.06 (0.15), residues: 1075 sheet: None (None), residues: 0 loop : -0.70 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 93 TYR 0.012 0.001 TYR B 89 PHE 0.017 0.002 PHE D 66 HIS 0.005 0.001 HIS M 76 Details of bonding type rmsd covalent geometry : bond 0.00404 (25228) covalent geometry : angle 0.65233 (36519) hydrogen bonds : bond 0.05786 ( 1483) hydrogen bonds : angle 3.26496 ( 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 328 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 300 time to evaluate : 0.823 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: A 51 GLU cc_start: 0.9716 (mt-10) cc_final: 0.9371 (mt-10) REVERT: A 63 ILE cc_start: 0.5500 (mm) cc_final: 0.4882 (mm) REVERT: A 108 THR cc_start: 0.9640 (m) cc_final: 0.9078 (m) REVERT: A 124 ASP cc_start: 0.7786 (m-30) cc_final: 0.7239 (t70) REVERT: D 121 LYS cc_start: 0.9368 (ttpp) cc_final: 0.9124 (ttpt) REVERT: L 63 ILE cc_start: 0.6323 (mm) cc_final: 0.5977 (tp) REVERT: M 75 GLU cc_start: 0.9440 (mm-30) cc_final: 0.9129 (mm-30) REVERT: O 94 GLU cc_start: 0.9216 (mp0) cc_final: 0.8852 (mp0) REVERT: O 100 ARG cc_start: 0.9200 (ttm170) cc_final: 0.8847 (ttm110) REVERT: O 106 GLU cc_start: 0.8795 (tp30) cc_final: 0.8491 (tp30) REVERT: O 109 LYS cc_start: 0.9532 (ttpp) cc_final: 0.9236 (ttpp) REVERT: P 82 ASP cc_start: 0.8349 (t70) cc_final: 0.7995 (t70) REVERT: P 95 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8997 (mm-30) REVERT: P 98 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7697 (mt-10) REVERT: P 121 MET cc_start: 0.6853 (mtm) cc_final: 0.6574 (mtt) REVERT: Q 54 GLU cc_start: 0.9190 (mp0) cc_final: 0.8962 (mp0) outliers start: 28 outliers final: 18 residues processed: 317 average time/residue: 0.3682 time to fit residues: 172.3800 Evaluate side-chains 290 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 272 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 N residue 56 LEU Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain Q residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 52 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 145 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 ASN R 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.060027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.046346 restraints weight = 385992.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.048088 restraints weight = 172734.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.049180 restraints weight = 106848.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.049837 restraints weight = 80098.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.050285 restraints weight = 67623.588| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 25228 Z= 0.298 Angle : 0.709 7.349 36519 Z= 0.440 Chirality : 0.046 0.149 4149 Planarity : 0.005 0.051 2640 Dihedral : 29.502 89.212 7922 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.29 % Allowed : 15.90 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.20), residues: 1475 helix: 1.33 (0.15), residues: 1071 sheet: None (None), residues: 0 loop : -1.32 (0.25), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 43 TYR 0.017 0.002 TYR R 58 PHE 0.025 0.003 PHE O 66 HIS 0.005 0.002 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00620 (25228) covalent geometry : angle 0.70875 (36519) hydrogen bonds : bond 0.08947 ( 1483) hydrogen bonds : angle 4.00966 ( 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 306 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 265 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9696 (mt-10) cc_final: 0.9348 (mt-10) REVERT: A 108 THR cc_start: 0.9578 (m) cc_final: 0.9105 (m) REVERT: A 124 ASP cc_start: 0.7931 (m-30) cc_final: 0.7640 (t70) REVERT: E 91 MET cc_start: 0.8308 (mmm) cc_final: 0.7978 (mmp) REVERT: F 68 ARG cc_start: 0.9009 (tpt170) cc_final: 0.8417 (tpm170) REVERT: H 97 THR cc_start: 0.9281 (m) cc_final: 0.9077 (t) REVERT: M 75 GLU cc_start: 0.9360 (mm-30) cc_final: 0.9130 (mm-30) REVERT: M 85 MET cc_start: 0.9135 (mmm) cc_final: 0.8740 (mmm) REVERT: N 93 GLU cc_start: 0.7665 (mt-10) cc_final: 0.6954 (mm-30) REVERT: O 94 GLU cc_start: 0.9085 (mp0) cc_final: 0.8810 (mp0) REVERT: P 82 ASP cc_start: 0.8304 (t70) cc_final: 0.7918 (t70) REVERT: S 60 MET cc_start: 0.7761 (tpp) cc_final: 0.7544 (tpp) outliers start: 41 outliers final: 31 residues processed: 291 average time/residue: 0.3738 time to fit residues: 160.3325 Evaluate side-chains 281 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 250 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 125 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 102 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 83 LEU Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 93 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 0 optimal weight: 20.0000 chunk 184 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 104 optimal weight: 0.4980 chunk 14 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 8 optimal weight: 0.2980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3863 r_free = 0.3863 target = 0.062049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.048562 restraints weight = 386972.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.050362 restraints weight = 171681.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.051517 restraints weight = 105002.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.052214 restraints weight = 77838.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.052698 restraints weight = 65405.366| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25228 Z= 0.194 Angle : 0.652 7.724 36519 Z= 0.405 Chirality : 0.040 0.156 4149 Planarity : 0.004 0.047 2640 Dihedral : 29.458 89.961 7922 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.89 % Allowed : 16.39 % 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: 1.51 (0.21), residues: 1475 helix: 1.84 (0.15), residues: 1075 sheet: None (None), residues: 0 loop : -1.35 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 68 TYR 0.019 0.002 TYR F 89 PHE 0.021 0.002 PHE O 66 HIS 0.005 0.001 HIS M 76 Details of bonding type rmsd covalent geometry : bond 0.00404 (25228) covalent geometry : angle 0.65241 (36519) hydrogen bonds : bond 0.05581 ( 1483) hydrogen bonds : angle 3.42834 ( 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 314 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 278 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9605 (m) cc_final: 0.9141 (m) REVERT: A 124 ASP cc_start: 0.7862 (m-30) cc_final: 0.7495 (t70) REVERT: H 97 THR cc_start: 0.9214 (m) cc_final: 0.8993 (t) REVERT: L 63 ILE cc_start: 0.6565 (mm) cc_final: 0.6215 (tp) REVERT: M 75 GLU cc_start: 0.9381 (mm-30) cc_final: 0.9132 (mm-30) REVERT: N 93 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7166 (mm-30) REVERT: O 94 GLU cc_start: 0.9117 (mp0) cc_final: 0.8886 (mp0) REVERT: P 82 ASP cc_start: 0.8380 (t70) cc_final: 0.7972 (t70) REVERT: S 60 MET cc_start: 0.7661 (tpp) cc_final: 0.7387 (tpp) REVERT: S 96 GLN cc_start: 0.9440 (tt0) cc_final: 0.8733 (tp40) outliers start: 36 outliers final: 30 residues processed: 300 average time/residue: 0.3700 time to fit residues: 164.1497 Evaluate side-chains 287 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 257 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 102 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 L residue 72 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain O residue 81 LEU 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 Q residue 93 ARG Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain S residue 74 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 33 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 180 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3826 r_free = 0.3826 target = 0.059951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.046500 restraints weight = 391757.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.048230 restraints weight = 173352.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.049338 restraints weight = 106190.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.049998 restraints weight = 78983.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.050467 restraints weight = 66376.488| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 25228 Z= 0.264 Angle : 0.674 7.433 36519 Z= 0.419 Chirality : 0.044 0.147 4149 Planarity : 0.005 0.054 2640 Dihedral : 29.499 89.333 7922 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.37 % Allowed : 16.55 % Favored : 80.08 % 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: 0.95 (0.21), residues: 1475 helix: 1.46 (0.15), residues: 1070 sheet: None (None), residues: 0 loop : -1.64 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 100 TYR 0.027 0.002 TYR C 58 PHE 0.020 0.002 PHE O 66 HIS 0.005 0.001 HIS M 76 Details of bonding type rmsd covalent geometry : bond 0.00548 (25228) covalent geometry : angle 0.67447 (36519) hydrogen bonds : bond 0.07890 ( 1483) hydrogen bonds : angle 3.82046 ( 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 285 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 243 time to evaluate : 0.995 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 108 THR cc_start: 0.9605 (m) cc_final: 0.9171 (m) REVERT: A 124 ASP cc_start: 0.7940 (m-30) cc_final: 0.7474 (t0) REVERT: B 64 GLU cc_start: 0.9354 (tp30) cc_final: 0.9138 (tp30) REVERT: B 85 MET cc_start: 0.8725 (mtm) cc_final: 0.8124 (pmm) REVERT: C 58 TYR cc_start: 0.8750 (t80) cc_final: 0.8003 (t80) REVERT: O 83 HIS cc_start: 0.8858 (OUTLIER) cc_final: 0.8612 (t-90) REVERT: P 82 ASP cc_start: 0.8334 (t70) cc_final: 0.7939 (t70) outliers start: 42 outliers final: 34 residues processed: 269 average time/residue: 0.3628 time to fit residues: 145.2282 Evaluate side-chains 271 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain C residue 60 THR 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 81 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 120 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 63 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 102 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 83 LEU Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 83 HIS Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 93 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 65 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3836 r_free = 0.3836 target = 0.060404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.046924 restraints weight = 384420.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.048685 restraints weight = 169385.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.049805 restraints weight = 103444.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.050491 restraints weight = 76698.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.050968 restraints weight = 64286.455| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25228 Z= 0.223 Angle : 0.657 8.029 36519 Z= 0.408 Chirality : 0.041 0.143 4149 Planarity : 0.005 0.048 2640 Dihedral : 29.521 89.463 7922 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.21 % Allowed : 17.43 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.21), residues: 1475 helix: 1.55 (0.15), residues: 1070 sheet: None (None), residues: 0 loop : -1.80 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 100 TYR 0.019 0.002 TYR H 41 PHE 0.021 0.002 PHE O 66 HIS 0.005 0.001 HIS M 76 Details of bonding type rmsd covalent geometry : bond 0.00462 (25228) covalent geometry : angle 0.65739 (36519) hydrogen bonds : bond 0.06335 ( 1483) hydrogen bonds : angle 3.66025 ( 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 289 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 249 time to evaluate : 0.834 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 108 THR cc_start: 0.9614 (m) cc_final: 0.9183 (m) REVERT: A 124 ASP cc_start: 0.7863 (m-30) cc_final: 0.7407 (t0) REVERT: C 58 TYR cc_start: 0.8764 (t80) cc_final: 0.8484 (t80) REVERT: L 63 ILE cc_start: 0.6792 (mm) cc_final: 0.6405 (tp) REVERT: O 83 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.8590 (t-90) REVERT: O 94 GLU cc_start: 0.9170 (mp0) cc_final: 0.8920 (mp0) REVERT: P 82 ASP cc_start: 0.8376 (t70) cc_final: 0.7977 (t70) outliers start: 40 outliers final: 34 residues processed: 275 average time/residue: 0.3555 time to fit residues: 144.7639 Evaluate side-chains 271 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 101 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 77 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 102 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 72 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 83 HIS Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 93 ARG 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: 6.9990 chunk 47 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3822 r_free = 0.3822 target = 0.059413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.045839 restraints weight = 388532.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.047573 restraints weight = 172231.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.048677 restraints weight = 105754.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.049331 restraints weight = 78736.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.049803 restraints weight = 66514.778| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.6247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 25228 Z= 0.240 Angle : 0.657 7.945 36519 Z= 0.407 Chirality : 0.042 0.141 4149 Planarity : 0.005 0.050 2640 Dihedral : 29.554 89.892 7922 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.86 % Allowed : 17.35 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.21), residues: 1475 helix: 1.46 (0.15), residues: 1070 sheet: None (None), residues: 0 loop : -1.93 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 100 TYR 0.020 0.002 TYR H 41 PHE 0.020 0.002 PHE O 66 HIS 0.008 0.001 HIS M 76 Details of bonding type rmsd covalent geometry : bond 0.00502 (25228) covalent geometry : angle 0.65696 (36519) hydrogen bonds : bond 0.07283 ( 1483) hydrogen bonds : angle 3.75215 ( 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 289 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 241 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8296 (m-10) REVERT: A 94 GLN cc_start: 0.9201 (tt0) cc_final: 0.8485 (tp40) REVERT: A 108 THR cc_start: 0.9616 (m) cc_final: 0.9138 (m) REVERT: A 124 ASP cc_start: 0.7929 (m-30) cc_final: 0.7588 (t70) REVERT: B 71 VAL cc_start: 0.9310 (t) cc_final: 0.9012 (p) REVERT: C 58 TYR cc_start: 0.8724 (t80) cc_final: 0.8480 (t80) REVERT: O 83 HIS cc_start: 0.8809 (OUTLIER) cc_final: 0.8600 (t-90) REVERT: O 94 GLU cc_start: 0.9055 (mp0) cc_final: 0.8827 (mp0) REVERT: P 82 ASP cc_start: 0.8378 (t70) cc_final: 0.7981 (t70) outliers start: 48 outliers final: 37 residues processed: 273 average time/residue: 0.3642 time to fit residues: 147.3572 Evaluate side-chains 273 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain C residue 60 THR 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 81 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 127 LEU 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 63 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 66 PHE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 83 HIS Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain Q residue 74 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 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: 6.9990 chunk 136 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 34 optimal weight: 0.0870 chunk 6 optimal weight: 6.9990 overall best weight: 4.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3830 r_free = 0.3830 target = 0.059897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.046241 restraints weight = 382098.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.047985 restraints weight = 170418.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.049101 restraints weight = 104820.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.049778 restraints weight = 77999.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.050244 restraints weight = 65536.898| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.6414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25228 Z= 0.216 Angle : 0.654 8.398 36519 Z= 0.403 Chirality : 0.041 0.140 4149 Planarity : 0.005 0.049 2640 Dihedral : 29.553 89.687 7922 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.21 % Allowed : 18.47 % Favored : 78.31 % 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: 0.97 (0.21), residues: 1475 helix: 1.58 (0.15), residues: 1068 sheet: None (None), residues: 0 loop : -1.96 (0.26), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 100 TYR 0.019 0.001 TYR H 41 PHE 0.020 0.002 PHE O 66 HIS 0.006 0.001 HIS M 76 Details of bonding type rmsd covalent geometry : bond 0.00450 (25228) covalent geometry : angle 0.65384 (36519) hydrogen bonds : bond 0.06382 ( 1483) hydrogen bonds : angle 3.63062 ( 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 281 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 241 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8446 (m-10) REVERT: A 94 GLN cc_start: 0.9179 (tt0) cc_final: 0.8419 (tp-100) REVERT: A 108 THR cc_start: 0.9617 (m) cc_final: 0.9148 (m) REVERT: A 124 ASP cc_start: 0.7920 (m-30) cc_final: 0.7537 (t70) REVERT: C 58 TYR cc_start: 0.8801 (t80) cc_final: 0.8573 (t80) REVERT: O 94 GLU cc_start: 0.9101 (mp0) cc_final: 0.8867 (mp0) REVERT: P 82 ASP cc_start: 0.8442 (t70) cc_final: 0.8045 (t70) outliers start: 40 outliers final: 34 residues processed: 268 average time/residue: 0.3543 time to fit residues: 142.3170 Evaluate side-chains 264 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 127 LEU 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 63 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 102 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 72 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 81 LEU 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 Q residue 93 ARG Chi-restraints excluded: chain R residue 19 SER 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: 9.9990 chunk 129 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.059835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.046460 restraints weight = 387949.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.048195 restraints weight = 170909.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.049309 restraints weight = 104309.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.049975 restraints weight = 77342.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.050438 restraints weight = 64926.397| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25228 Z= 0.218 Angle : 0.652 8.359 36519 Z= 0.402 Chirality : 0.041 0.140 4149 Planarity : 0.005 0.052 2640 Dihedral : 29.540 89.242 7922 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.05 % Allowed : 18.88 % Favored : 78.07 % 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: 0.93 (0.21), residues: 1475 helix: 1.57 (0.15), residues: 1058 sheet: None (None), residues: 0 loop : -1.97 (0.26), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 100 TYR 0.019 0.001 TYR H 41 PHE 0.020 0.002 PHE O 66 HIS 0.006 0.001 HIS M 76 Details of bonding type rmsd covalent geometry : bond 0.00456 (25228) covalent geometry : angle 0.65178 (36519) hydrogen bonds : bond 0.06685 ( 1483) hydrogen bonds : angle 3.65137 ( 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 275 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 0.638 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: A 68 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8205 (m-10) REVERT: A 94 GLN cc_start: 0.9174 (tt0) cc_final: 0.8421 (tp40) REVERT: A 108 THR cc_start: 0.9616 (m) cc_final: 0.9151 (m) REVERT: A 124 ASP cc_start: 0.7920 (m-30) cc_final: 0.7539 (t70) REVERT: C 58 TYR cc_start: 0.8782 (t80) cc_final: 0.8553 (t80) REVERT: G 63 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8143 (tp) REVERT: O 94 GLU cc_start: 0.9095 (mp0) cc_final: 0.8856 (mp0) REVERT: P 82 ASP cc_start: 0.8434 (t70) cc_final: 0.8040 (t70) REVERT: Q 64 GLU cc_start: 0.9501 (mt-10) cc_final: 0.9268 (mt-10) outliers start: 38 outliers final: 34 residues processed: 263 average time/residue: 0.3480 time to fit residues: 136.7051 Evaluate side-chains 267 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 102 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 72 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain Q residue 74 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 88 ILE Chi-restraints excluded: chain S residue 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 127 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 159 optimal weight: 0.0980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.062109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.048463 restraints weight = 377249.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.050327 restraints weight = 164966.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.051504 restraints weight = 100120.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.052214 restraints weight = 73643.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.052734 restraints weight = 61527.123| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.6640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25228 Z= 0.164 Angle : 0.632 8.805 36519 Z= 0.385 Chirality : 0.037 0.156 4149 Planarity : 0.004 0.058 2640 Dihedral : 29.368 89.928 7922 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.09 % Allowed : 19.92 % Favored : 77.99 % 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: 1.74 (0.22), residues: 1475 helix: 2.24 (0.16), residues: 1058 sheet: None (None), residues: 0 loop : -1.86 (0.26), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 100 TYR 0.016 0.001 TYR H 41 PHE 0.020 0.001 PHE D 66 HIS 0.006 0.001 HIS M 76 Details of bonding type rmsd covalent geometry : bond 0.00356 (25228) covalent geometry : angle 0.63188 (36519) hydrogen bonds : bond 0.04578 ( 1483) hydrogen bonds : angle 3.12848 ( 3687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7754.08 seconds wall clock time: 132 minutes 41.65 seconds (7961.65 seconds total)