Starting phenix.real_space_refine (version: dev) on Fri Dec 16 22:13:36 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9z_9021/12_2022/6e9z_9021.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9z_9021/12_2022/6e9z_9021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9z_9021/12_2022/6e9z_9021.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9z_9021/12_2022/6e9z_9021.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9z_9021/12_2022/6e9z_9021.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9z_9021/12_2022/6e9z_9021.pdb" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 126 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 32652 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3628 Classifications: {'peptide': 225} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "A" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3628 Classifications: {'peptide': 225} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "C" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3628 Classifications: {'peptide': 225} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "F" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3628 Classifications: {'peptide': 225} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "D" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3628 Classifications: {'peptide': 225} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "H" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3628 Classifications: {'peptide': 225} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "G" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3628 Classifications: {'peptide': 225} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "E" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3628 Classifications: {'peptide': 225} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "I" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3628 Classifications: {'peptide': 225} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Time building chain proxies: 14.99, per 1000 atoms: 0.46 Number of scatterers: 32652 At special positions: 0 Unit cell: (152.25, 152.25, 75.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 O 3033 8.00 N 2925 7.00 C 9846 6.00 H 16830 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 - 3.50 Amino acid : False - 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: 30.32 Conformation dependent library (CDL) restraints added in 2.7 seconds 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3924 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 92.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'B' and resid 1 through 26 removed outlier: 3.611A pdb=" N ARG B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 8 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA B 17 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.784A pdb=" N ARG B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 41 " --> pdb=" O THR B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 55 removed outlier: 3.657A pdb=" N GLN B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 83 removed outlier: 3.811A pdb=" N ARG B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU B 67 " --> pdb=" O ARG B 63 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 81 " --> pdb=" O ARG B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 113 removed outlier: 3.502A pdb=" N LEU B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET B 104 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 108 " --> pdb=" O MET B 104 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 140 removed outlier: 3.589A pdb=" N ARG B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 170 removed outlier: 4.393A pdb=" N LEU B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 195 removed outlier: 3.907A pdb=" N ALA B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 176 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU B 181 " --> pdb=" O MET B 177 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 215 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'A' and resid 2 through 26 removed outlier: 3.611A pdb=" N ARG A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.785A pdb=" N ARG A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.656A pdb=" N GLN A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 83 removed outlier: 3.811A pdb=" N ARG A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 113 removed outlier: 3.502A pdb=" N LEU A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 108 " --> pdb=" O MET A 104 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 140 removed outlier: 3.588A pdb=" N ARG A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 170 removed outlier: 4.393A pdb=" N LEU A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 195 removed outlier: 3.908A pdb=" N ALA A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 176 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU A 181 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 188 " --> pdb=" O ARG A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 215 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'C' and resid 2 through 26 removed outlier: 3.611A pdb=" N ARG C 7 " --> pdb=" O ASP C 3 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL C 8 " --> pdb=" O GLU C 4 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA C 17 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 18 " --> pdb=" O GLU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 45 removed outlier: 3.785A pdb=" N ARG C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 55 removed outlier: 3.656A pdb=" N GLN C 51 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 83 removed outlier: 3.811A pdb=" N ARG C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU C 81 " --> pdb=" O ARG C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 113 removed outlier: 3.502A pdb=" N LEU C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET C 104 " --> pdb=" O LYS C 100 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 108 " --> pdb=" O MET C 104 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 140 removed outlier: 3.589A pdb=" N ARG C 120 " --> pdb=" O GLU C 116 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 170 removed outlier: 4.393A pdb=" N LEU C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU C 165 " --> pdb=" O ARG C 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 195 removed outlier: 3.907A pdb=" N ALA C 175 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS C 176 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 188 " --> pdb=" O ARG C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 215 Processing helix chain 'C' and resid 218 through 222 Processing helix chain 'F' and resid 2 through 26 removed outlier: 3.611A pdb=" N ARG F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL F 8 " --> pdb=" O GLU F 4 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU F 18 " --> pdb=" O GLU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 45 removed outlier: 3.785A pdb=" N ARG F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA F 41 " --> pdb=" O THR F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 55 removed outlier: 3.656A pdb=" N GLN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU F 55 " --> pdb=" O GLN F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 83 removed outlier: 3.812A pdb=" N ARG F 63 " --> pdb=" O GLU F 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU F 67 " --> pdb=" O ARG F 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG F 70 " --> pdb=" O GLU F 66 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA F 79 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU F 81 " --> pdb=" O ARG F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 113 removed outlier: 3.503A pdb=" N LEU F 92 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE F 93 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU F 108 " --> pdb=" O MET F 104 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS F 111 " --> pdb=" O GLU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 140 removed outlier: 3.590A pdb=" N ARG F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA F 121 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG F 134 " --> pdb=" O GLU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 170 removed outlier: 4.394A pdb=" N LEU F 158 " --> pdb=" O GLU F 154 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS F 160 " --> pdb=" O ALA F 156 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU F 165 " --> pdb=" O ARG F 161 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 195 removed outlier: 3.908A pdb=" N ALA F 175 " --> pdb=" O ASP F 171 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS F 176 " --> pdb=" O PRO F 172 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU F 181 " --> pdb=" O MET F 177 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS F 183 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU F 188 " --> pdb=" O ARG F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 215 Processing helix chain 'F' and resid 218 through 222 Processing helix chain 'D' and resid 2 through 26 removed outlier: 3.612A pdb=" N ARG D 7 " --> pdb=" O ASP D 3 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL D 8 " --> pdb=" O GLU D 4 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA D 17 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU D 18 " --> pdb=" O GLU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 45 removed outlier: 3.785A pdb=" N ARG D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU D 40 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 41 " --> pdb=" O THR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 55 removed outlier: 3.656A pdb=" N GLN D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 55 " --> pdb=" O GLN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 83 removed outlier: 3.811A pdb=" N ARG D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG D 70 " --> pdb=" O GLU D 66 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 113 removed outlier: 3.502A pdb=" N LEU D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET D 104 " --> pdb=" O LYS D 100 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU D 108 " --> pdb=" O MET D 104 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 140 removed outlier: 3.588A pdb=" N ARG D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 170 removed outlier: 4.393A pdb=" N LEU D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU D 165 " --> pdb=" O ARG D 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 168 " --> pdb=" O GLU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 195 removed outlier: 3.908A pdb=" N ALA D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS D 176 " --> pdb=" O PRO D 172 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU D 181 " --> pdb=" O MET D 177 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 188 " --> pdb=" O ARG D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 215 Processing helix chain 'D' and resid 218 through 222 Processing helix chain 'H' and resid 2 through 26 removed outlier: 3.611A pdb=" N ARG H 7 " --> pdb=" O ASP H 3 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL H 8 " --> pdb=" O GLU H 4 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA H 17 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 45 removed outlier: 3.785A pdb=" N ARG H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU H 40 " --> pdb=" O ARG H 36 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA H 41 " --> pdb=" O THR H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 55 removed outlier: 3.657A pdb=" N GLN H 51 " --> pdb=" O LYS H 47 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU H 54 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU H 55 " --> pdb=" O GLN H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 83 removed outlier: 3.811A pdb=" N ARG H 63 " --> pdb=" O GLU H 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU H 67 " --> pdb=" O ARG H 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU H 81 " --> pdb=" O ARG H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 113 removed outlier: 3.502A pdb=" N LEU H 92 " --> pdb=" O LEU H 88 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE H 93 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET H 104 " --> pdb=" O LYS H 100 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU H 108 " --> pdb=" O MET H 104 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 140 removed outlier: 3.589A pdb=" N ARG H 120 " --> pdb=" O GLU H 116 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL H 122 " --> pdb=" O ALA H 118 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU H 133 " --> pdb=" O ALA H 129 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 170 removed outlier: 4.393A pdb=" N LEU H 158 " --> pdb=" O GLU H 154 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS H 160 " --> pdb=" O ALA H 156 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU H 165 " --> pdb=" O ARG H 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU H 168 " --> pdb=" O GLU H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 195 removed outlier: 3.906A pdb=" N ALA H 175 " --> pdb=" O ASP H 171 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS H 176 " --> pdb=" O PRO H 172 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU H 181 " --> pdb=" O MET H 177 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS H 183 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU H 188 " --> pdb=" O ARG H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 215 Processing helix chain 'H' and resid 218 through 222 Processing helix chain 'G' and resid 2 through 26 removed outlier: 3.611A pdb=" N ARG G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL G 8 " --> pdb=" O GLU G 4 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA G 17 " --> pdb=" O LYS G 13 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU G 18 " --> pdb=" O GLU G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 45 removed outlier: 3.784A pdb=" N ARG G 36 " --> pdb=" O GLU G 32 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU G 40 " --> pdb=" O ARG G 36 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA G 41 " --> pdb=" O THR G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 55 removed outlier: 3.656A pdb=" N GLN G 51 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU G 54 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU G 55 " --> pdb=" O GLN G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 83 removed outlier: 3.810A pdb=" N ARG G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG G 70 " --> pdb=" O GLU G 66 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA G 79 " --> pdb=" O LEU G 75 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU G 81 " --> pdb=" O ARG G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 113 removed outlier: 3.502A pdb=" N LEU G 92 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE G 93 " --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET G 104 " --> pdb=" O LYS G 100 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU G 108 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 140 removed outlier: 3.589A pdb=" N ARG G 120 " --> pdb=" O GLU G 116 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA G 121 " --> pdb=" O VAL G 117 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL G 122 " --> pdb=" O ALA G 118 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU G 133 " --> pdb=" O ALA G 129 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG G 134 " --> pdb=" O GLU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 170 removed outlier: 4.394A pdb=" N LEU G 158 " --> pdb=" O GLU G 154 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS G 160 " --> pdb=" O ALA G 156 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU G 165 " --> pdb=" O ARG G 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU G 168 " --> pdb=" O GLU G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 195 removed outlier: 3.907A pdb=" N ALA G 175 " --> pdb=" O ASP G 171 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS G 176 " --> pdb=" O PRO G 172 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU G 181 " --> pdb=" O MET G 177 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS G 183 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU G 188 " --> pdb=" O ARG G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 215 Processing helix chain 'G' and resid 218 through 222 Processing helix chain 'E' and resid 2 through 26 removed outlier: 3.611A pdb=" N ARG E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA E 17 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU E 18 " --> pdb=" O GLU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 45 removed outlier: 3.785A pdb=" N ARG E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU E 40 " --> pdb=" O ARG E 36 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 41 " --> pdb=" O THR E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.656A pdb=" N GLN E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU E 55 " --> pdb=" O GLN E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 83 removed outlier: 3.811A pdb=" N ARG E 63 " --> pdb=" O GLU E 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU E 81 " --> pdb=" O ARG E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 113 removed outlier: 3.502A pdb=" N LEU E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET E 104 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU E 108 " --> pdb=" O MET E 104 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 140 removed outlier: 3.588A pdb=" N ARG E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA E 121 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 170 removed outlier: 4.393A pdb=" N LEU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS E 160 " --> pdb=" O ALA E 156 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 195 removed outlier: 3.907A pdb=" N ALA E 175 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS E 176 " --> pdb=" O PRO E 172 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU E 181 " --> pdb=" O MET E 177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS E 183 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU E 188 " --> pdb=" O ARG E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 215 Processing helix chain 'E' and resid 218 through 222 Processing helix chain 'I' and resid 2 through 26 removed outlier: 3.611A pdb=" N ARG I 7 " --> pdb=" O ASP I 3 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL I 8 " --> pdb=" O GLU I 4 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA I 17 " --> pdb=" O LYS I 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU I 18 " --> pdb=" O GLU I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 45 removed outlier: 3.785A pdb=" N ARG I 36 " --> pdb=" O GLU I 32 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU I 40 " --> pdb=" O ARG I 36 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA I 41 " --> pdb=" O THR I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 55 removed outlier: 3.657A pdb=" N GLN I 51 " --> pdb=" O LYS I 47 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU I 54 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU I 55 " --> pdb=" O GLN I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 83 removed outlier: 3.811A pdb=" N ARG I 63 " --> pdb=" O GLU I 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG I 70 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA I 79 " --> pdb=" O LEU I 75 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU I 81 " --> pdb=" O ARG I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 113 removed outlier: 3.502A pdb=" N LEU I 92 " --> pdb=" O LEU I 88 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE I 93 " --> pdb=" O LEU I 89 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET I 104 " --> pdb=" O LYS I 100 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 140 removed outlier: 3.589A pdb=" N ARG I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA I 121 " --> pdb=" O VAL I 117 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL I 122 " --> pdb=" O ALA I 118 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU I 133 " --> pdb=" O ALA I 129 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG I 134 " --> pdb=" O GLU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 170 removed outlier: 4.392A pdb=" N LEU I 158 " --> pdb=" O GLU I 154 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS I 160 " --> pdb=" O ALA I 156 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU I 165 " --> pdb=" O ARG I 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU I 168 " --> pdb=" O GLU I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 195 removed outlier: 3.906A pdb=" N ALA I 175 " --> pdb=" O ASP I 171 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS I 176 " --> pdb=" O PRO I 172 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU I 181 " --> pdb=" O MET I 177 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS I 183 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU I 188 " --> pdb=" O ARG I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 215 Processing helix chain 'I' and resid 218 through 222 1207 hydrogen bonds defined for protein. 3567 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.01 Time building geometry restraints manager: 31.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16830 1.03 - 1.23: 9 1.23 - 1.42: 5769 1.42 - 1.62: 10035 1.62 - 1.81: 36 Bond restraints: 32679 Sorted by residual: bond pdb=" CB VAL F 68 " pdb=" CG1 VAL F 68 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.70e+00 bond pdb=" CG1 ILE G 78 " pdb=" CD1 ILE G 78 " ideal model delta sigma weight residual 1.513 1.438 0.075 3.90e-02 6.57e+02 3.68e+00 bond pdb=" CB VAL B 68 " pdb=" CG1 VAL B 68 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.67e+00 bond pdb=" CG1 ILE F 78 " pdb=" CD1 ILE F 78 " ideal model delta sigma weight residual 1.513 1.438 0.075 3.90e-02 6.57e+02 3.67e+00 bond pdb=" CG1 ILE I 78 " pdb=" CD1 ILE I 78 " ideal model delta sigma weight residual 1.513 1.438 0.075 3.90e-02 6.57e+02 3.65e+00 ... (remaining 32674 not shown) Histogram of bond angle deviations from ideal: 99.42 - 105.43: 151 105.43 - 111.44: 39352 111.44 - 117.45: 7195 117.45 - 123.46: 10810 123.46 - 129.47: 2270 Bond angle restraints: 59778 Sorted by residual: angle pdb=" CA ARG E 90 " pdb=" CB ARG E 90 " pdb=" CG ARG E 90 " ideal model delta sigma weight residual 114.10 109.21 4.89 2.00e+00 2.50e-01 5.98e+00 angle pdb=" CA ARG D 90 " pdb=" CB ARG D 90 " pdb=" CG ARG D 90 " ideal model delta sigma weight residual 114.10 109.22 4.88 2.00e+00 2.50e-01 5.96e+00 angle pdb=" CA ARG A 90 " pdb=" CB ARG A 90 " pdb=" CG ARG A 90 " ideal model delta sigma weight residual 114.10 109.23 4.87 2.00e+00 2.50e-01 5.93e+00 angle pdb=" CA ARG G 90 " pdb=" CB ARG G 90 " pdb=" CG ARG G 90 " ideal model delta sigma weight residual 114.10 109.25 4.85 2.00e+00 2.50e-01 5.88e+00 angle pdb=" CA ARG H 90 " pdb=" CB ARG H 90 " pdb=" CG ARG H 90 " ideal model delta sigma weight residual 114.10 109.25 4.85 2.00e+00 2.50e-01 5.88e+00 ... (remaining 59773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.38: 10573 10.38 - 20.76: 1396 20.76 - 31.15: 541 31.15 - 41.53: 153 41.53 - 51.91: 36 Dihedral angle restraints: 12699 sinusoidal: 6759 harmonic: 5940 Sorted by residual: dihedral pdb=" CA GLU C 217 " pdb=" C GLU C 217 " pdb=" N ARG C 218 " pdb=" CA ARG C 218 " ideal model delta harmonic sigma weight residual 180.00 151.12 28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA GLU G 217 " pdb=" C GLU G 217 " pdb=" N ARG G 218 " pdb=" CA ARG G 218 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLU E 217 " pdb=" C GLU E 217 " pdb=" N ARG E 218 " pdb=" CA ARG E 218 " ideal model delta harmonic sigma weight residual 180.00 151.14 28.86 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 12696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1267 0.033 - 0.066: 974 0.066 - 0.098: 222 0.098 - 0.131: 93 0.131 - 0.164: 27 Chirality restraints: 2583 Sorted by residual: chirality pdb=" CB VAL C 174 " pdb=" CA VAL C 174 " pdb=" CG1 VAL C 174 " pdb=" CG2 VAL C 174 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CB VAL E 174 " pdb=" CA VAL E 174 " pdb=" CG1 VAL E 174 " pdb=" CG2 VAL E 174 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CB VAL A 174 " pdb=" CA VAL A 174 " pdb=" CG1 VAL A 174 " pdb=" CG2 VAL A 174 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.68e-01 ... (remaining 2580 not shown) Planarity restraints: 4743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 211 " -0.036 2.00e-02 2.50e+03 7.20e-02 5.18e+01 pdb=" C GLU F 211 " 0.125 2.00e-02 2.50e+03 pdb=" O GLU F 211 " -0.047 2.00e-02 2.50e+03 pdb=" N ALA F 212 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 211 " -0.036 2.00e-02 2.50e+03 7.18e-02 5.15e+01 pdb=" C GLU B 211 " 0.124 2.00e-02 2.50e+03 pdb=" O GLU B 211 " -0.047 2.00e-02 2.50e+03 pdb=" N ALA B 212 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 211 " 0.036 2.00e-02 2.50e+03 7.17e-02 5.14e+01 pdb=" C GLU A 211 " -0.124 2.00e-02 2.50e+03 pdb=" O GLU A 211 " 0.047 2.00e-02 2.50e+03 pdb=" N ALA A 212 " 0.041 2.00e-02 2.50e+03 ... (remaining 4740 not shown) Histogram of nonbonded interaction distances: 0.65 - 1.44: 39 1.44 - 2.23: 2820 2.23 - 3.02: 101635 3.02 - 3.81: 129088 3.81 - 4.60: 221276 Warning: very small nonbonded interaction distances. Nonbonded interactions: 454858 Sorted by model distance: nonbonded pdb=" HZ2 LYS A 100 " pdb=" O ILE H 24 " model vdw 0.652 1.850 nonbonded pdb=" HZ2 LYS C 100 " pdb=" O ILE F 24 " model vdw 0.653 1.850 nonbonded pdb=" HZ2 LYS B 100 " pdb=" O ILE D 24 " model vdw 0.653 1.850 nonbonded pdb=" HB3 LYS H 176 " pdb="HD21 LEU I 89 " model vdw 0.862 2.440 nonbonded pdb="HD21 LEU C 89 " pdb=" HB3 LYS I 176 " model vdw 0.862 2.440 ... (remaining 454853 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 18 5.16 5 C 9846 2.51 5 N 2925 2.21 5 O 3033 1.98 5 H 16830 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.510 Extract box with map and model: 6.840 Check model and map are aligned: 0.520 Convert atoms to be neutral: 0.310 Process input model: 104.010 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.011 0.075 15849 Z= 0.713 Angle : 0.847 6.581 21222 Z= 0.440 Chirality : 0.048 0.164 2583 Planarity : 0.006 0.072 2763 Dihedral : 10.267 51.911 6471 Min Nonbonded Distance : 1.132 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.48 % Favored : 95.07 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.29 (0.13), residues: 2007 helix: -4.32 (0.07), residues: 1719 sheet: None (None), residues: 0 loop : -0.54 (0.39), residues: 288 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 335 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 3.691 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 outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 1.1510 time to fit residues: 490.7592 Evaluate side-chains 119 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.755 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN A 112 GLN C 112 GLN F 112 GLN D 112 GLN H 112 GLN E 112 GLN I 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 15849 Z= 0.192 Angle : 0.598 7.467 21222 Z= 0.329 Chirality : 0.031 0.111 2583 Planarity : 0.004 0.055 2763 Dihedral : 4.916 19.211 2250 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.16), residues: 2007 helix: -1.94 (0.10), residues: 1800 sheet: None (None), residues: 0 loop : -1.39 (0.41), residues: 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 191 time to evaluate : 2.919 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 outliers start: 10 outliers final: 2 residues processed: 196 average time/residue: 0.8093 time to fit residues: 219.4345 Evaluate side-chains 113 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 2.764 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3807 time to fit residues: 4.9895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 144 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 15849 Z= 0.238 Angle : 0.557 7.301 21222 Z= 0.302 Chirality : 0.031 0.109 2583 Planarity : 0.004 0.040 2763 Dihedral : 4.646 17.106 2250 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.18), residues: 2007 helix: -0.59 (0.12), residues: 1809 sheet: None (None), residues: 0 loop : -0.92 (0.49), residues: 198 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 146 time to evaluate : 3.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 155 average time/residue: 0.7709 time to fit residues: 171.9512 Evaluate side-chains 111 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 2.926 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3527 time to fit residues: 7.0042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 15849 Z= 0.279 Angle : 0.558 7.492 21222 Z= 0.301 Chirality : 0.031 0.130 2583 Planarity : 0.004 0.066 2763 Dihedral : 4.569 18.337 2250 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.19), residues: 2007 helix: 0.06 (0.12), residues: 1809 sheet: None (None), residues: 0 loop : -0.88 (0.50), residues: 198 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 137 average time/residue: 0.7990 time to fit residues: 156.2699 Evaluate side-chains 103 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 3.063 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4966 time to fit residues: 6.9437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.6498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 15849 Z= 0.245 Angle : 0.531 7.893 21222 Z= 0.285 Chirality : 0.030 0.113 2583 Planarity : 0.004 0.042 2763 Dihedral : 4.423 17.822 2250 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 2007 helix: 0.52 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.70 (0.44), residues: 189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 117 average time/residue: 0.8134 time to fit residues: 134.8847 Evaluate side-chains 100 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 2.565 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3431 time to fit residues: 4.8167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.6740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 15849 Z= 0.270 Angle : 0.541 8.003 21222 Z= 0.290 Chirality : 0.030 0.114 2583 Planarity : 0.004 0.045 2763 Dihedral : 4.396 17.710 2250 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 2007 helix: 0.84 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.77 (0.43), residues: 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 3.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 117 average time/residue: 0.8287 time to fit residues: 134.7987 Evaluate side-chains 103 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 2.666 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.5592 time to fit residues: 8.5025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 161 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.6937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 15849 Z= 0.222 Angle : 0.519 8.441 21222 Z= 0.278 Chirality : 0.030 0.119 2583 Planarity : 0.003 0.066 2763 Dihedral : 4.296 16.809 2250 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.19), residues: 2007 helix: 1.18 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.80 (0.43), residues: 189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 108 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 111 average time/residue: 0.9240 time to fit residues: 144.0313 Evaluate side-chains 95 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 2.716 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 112 GLN H 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.7088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 15849 Z= 0.263 Angle : 0.540 8.733 21222 Z= 0.289 Chirality : 0.030 0.144 2583 Planarity : 0.004 0.071 2763 Dihedral : 4.316 17.258 2250 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.19), residues: 2007 helix: 1.32 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.87 (0.43), residues: 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 2.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 114 average time/residue: 0.8448 time to fit residues: 134.1416 Evaluate side-chains 100 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 2.817 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.4970 time to fit residues: 6.6269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 160 optimal weight: 0.6980 chunk 168 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.7245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 15849 Z= 0.140 Angle : 0.499 10.030 21222 Z= 0.266 Chirality : 0.030 0.150 2583 Planarity : 0.003 0.051 2763 Dihedral : 4.065 15.851 2250 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.19), residues: 2007 helix: 1.75 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.78 (0.45), residues: 189 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 114 average time/residue: 0.7697 time to fit residues: 124.7803 Evaluate side-chains 103 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 2.537 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.9587 time to fit residues: 4.5770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 181 optimal weight: 0.0570 chunk 157 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.7317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 15849 Z= 0.160 Angle : 0.515 10.566 21222 Z= 0.275 Chirality : 0.029 0.158 2583 Planarity : 0.003 0.055 2763 Dihedral : 4.020 16.030 2250 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.19), residues: 2007 helix: 1.90 (0.12), residues: 1827 sheet: None (None), residues: 0 loop : -1.58 (0.47), residues: 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 2.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 105 average time/residue: 0.7678 time to fit residues: 116.6011 Evaluate side-chains 102 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 3.070 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 1.0313 time to fit residues: 5.1759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.132334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.109164 restraints weight = 68417.184| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.17 r_work: 0.3144 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.7361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 15849 Z= 0.191 Angle : 0.525 10.932 21222 Z= 0.279 Chirality : 0.029 0.164 2583 Planarity : 0.004 0.073 2763 Dihedral : 4.050 16.233 2250 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.19), residues: 2007 helix: 1.96 (0.12), residues: 1827 sheet: None (None), residues: 0 loop : -1.72 (0.45), residues: 180 =============================================================================== Job complete usr+sys time: 5664.78 seconds wall clock time: 101 minutes 16.67 seconds (6076.67 seconds total)