Starting phenix.real_space_refine on Mon Sep 14 15:54:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e9z_9021/09_2026/6e9z_9021.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e9z_9021/09_2026/6e9z_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/cci-nas-00/data/ceres_data/6e9z_9021/09_2026/6e9z_9021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e9z_9021/09_2026/6e9z_9021.map" model { file = "/net/cci-nas-00/data/ceres_data/6e9z_9021/09_2026/6e9z_9021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e9z_9021/09_2026/6e9z_9021.cif" } 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 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. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32652 Number of models: 1 Model: "" Number of chains: 1 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} Restraints were copied for chains: A, C, F, D, H, G, E, I Time building chain proxies: 4.18, per 1000 atoms: 0.13 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 - 3.00 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: 2.74 Conformation dependent library (CDL) restraints added in 735.0 milliseconds 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: 0.58 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: 7.02 Time building geometry restraints manager: 3.84 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: 0.00 - 1.32: 54177 1.32 - 2.63: 4976 2.63 - 3.95: 508 3.95 - 5.26: 99 5.26 - 6.58: 18 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 - 11.81: 12728 11.81 - 23.61: 1231 23.61 - 35.42: 522 35.42 - 47.22: 87 47.22 - 59.03: 48 Dihedral angle restraints: 14616 sinusoidal: 8676 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 14613 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 2.450 nonbonded pdb=" HZ2 LYS C 100 " pdb=" O ILE F 24 " model vdw 0.653 2.450 nonbonded pdb=" HZ2 LYS B 100 " pdb=" O ILE D 24 " model vdw 0.653 2.450 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 Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'F' selection = chain 'D' selection = chain 'H' selection = chain 'G' selection = chain 'E' selection = chain 'I' } 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 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.220 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 26.250 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.680 ------------------------------------------------------------------------------- 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= 0.446 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 % Allowed : 3.89 % Favored : 96.11 % 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: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG E 147 Details of bonding type rmsd/Z covalent geometry : bond 0.01107 / 0.45 (15849) covalent geometry : angle 0.84728 / 0.44 (21222) hydrogen bonds : bond 0.27668 / 18.57 ( 1207) hydrogen bonds : angle 11.34365 / 7.81 ( 3567) *********************** 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 to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.979 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: 0.6300 time to fit residues: 264.2558 Evaluate side-chains 119 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.6766 > 50:) chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 112 GLN A 112 GLN C 112 GLN F 112 GLN D 112 GLN H 112 GLN G 112 GLN E 112 GLN I 112 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.143883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121312 restraints weight = 66629.311| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.25 r_work: 0.3348 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15849 Z= 0.149 Angle : 0.610 7.504 21222 Z= 0.332 Chirality : 0.031 0.116 2583 Planarity : 0.004 0.051 2763 Dihedral : 4.956 21.469 2250 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.35 % Allowed : 1.64 % Favored : 98.01 % Rotamer: Outliers : 0.62 % Allowed : 9.51 % Favored : 89.88 % 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: -3.19 (0.16), residues: 2007 helix: -1.88 (0.10), residues: 1809 sheet: None (None), residues: 0 loop : -1.76 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (15849) covalent geometry : angle 0.61049 / 0.33 (21222) hydrogen bonds : bond 0.04799 / 3.22 ( 1207) hydrogen bonds : angle 5.36461 / 3.74 ( 3567) *********************** 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 204 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 GLU cc_start: 0.6542 (mp0) cc_final: 0.6303 (mt-10) REVERT: A 203 GLU cc_start: 0.6717 (tm-30) cc_final: 0.6436 (tm-30) REVERT: A 206 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6845 (pt0) REVERT: F 50 VAL cc_start: 0.8875 (t) cc_final: 0.8656 (m) REVERT: H 50 VAL cc_start: 0.8917 (t) cc_final: 0.8714 (m) REVERT: E 206 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7050 (pt0) outliers start: 10 outliers final: 3 residues processed: 199 average time/residue: 0.4307 time to fit residues: 116.7821 Evaluate side-chains 116 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain E residue 14 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 180 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.134766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110930 restraints weight = 67584.937| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.26 r_work: 0.3214 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5371 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= 0.187 Angle : 0.590 8.163 21222 Z= 0.320 Chirality : 0.032 0.113 2583 Planarity : 0.005 0.050 2763 Dihedral : 4.753 21.161 2250 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.23 % Allowed : 10.19 % Favored : 88.58 % 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: -1.39 (0.18), residues: 2007 helix: -0.70 (0.11), residues: 1809 sheet: None (None), residues: 0 loop : -1.18 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (15849) covalent geometry : angle 0.59021 / 0.32 (21222) hydrogen bonds : bond 0.03970 / 2.64 ( 1207) hydrogen bonds : angle 4.68900 / 3.25 ( 3567) *********************** 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 166 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7492 (mm110) REVERT: B 114 ASP cc_start: 0.8201 (m-30) cc_final: 0.7816 (m-30) REVERT: A 30 ASP cc_start: 0.8455 (m-30) cc_final: 0.8176 (m-30) REVERT: A 114 ASP cc_start: 0.8115 (m-30) cc_final: 0.7671 (m-30) REVERT: C 40 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8076 (tp30) REVERT: C 114 ASP cc_start: 0.8244 (m-30) cc_final: 0.7922 (m-30) REVERT: F 177 MET cc_start: 0.8855 (mtp) cc_final: 0.8650 (mtp) REVERT: D 40 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7915 (tt0) REVERT: G 32 GLU cc_start: 0.7834 (tp30) cc_final: 0.7625 (tp30) REVERT: G 40 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8117 (tt0) REVERT: G 114 ASP cc_start: 0.8350 (m-30) cc_final: 0.7906 (m-30) REVERT: G 206 GLU cc_start: 0.7661 (mm-30) cc_final: 0.6948 (pt0) REVERT: E 114 ASP cc_start: 0.8229 (m-30) cc_final: 0.8024 (m-30) REVERT: E 206 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7015 (pt0) REVERT: I 40 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7996 (mt-10) REVERT: I 114 ASP cc_start: 0.8167 (m-30) cc_final: 0.7914 (m-30) REVERT: I 206 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7282 (pt0) outliers start: 20 outliers final: 9 residues processed: 162 average time/residue: 0.3588 time to fit residues: 82.8491 Evaluate side-chains 117 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain E residue 14 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 130 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108461 restraints weight = 68486.282| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.27 r_work: 0.3199 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.5943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15849 Z= 0.134 Angle : 0.517 8.314 21222 Z= 0.280 Chirality : 0.030 0.112 2583 Planarity : 0.003 0.056 2763 Dihedral : 4.468 20.627 2250 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.80 % Allowed : 11.42 % Favored : 87.78 % 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: -0.28 (0.19), residues: 2007 helix: 0.04 (0.12), residues: 1809 sheet: None (None), residues: 0 loop : -0.99 (0.49), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (15849) covalent geometry : angle 0.51707 / 0.28 (21222) hydrogen bonds : bond 0.03218 / 2.16 ( 1207) hydrogen bonds : angle 4.27211 / 2.96 ( 3567) *********************** 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 134 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 ASP cc_start: 0.8199 (m-30) cc_final: 0.7761 (m-30) REVERT: A 30 ASP cc_start: 0.8450 (m-30) cc_final: 0.8194 (m-30) REVERT: A 114 ASP cc_start: 0.8075 (m-30) cc_final: 0.7635 (m-30) REVERT: C 40 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8066 (tp30) REVERT: C 114 ASP cc_start: 0.8234 (m-30) cc_final: 0.7880 (m-30) REVERT: F 114 ASP cc_start: 0.8231 (m-30) cc_final: 0.7948 (m-30) REVERT: D 40 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7909 (tt0) REVERT: D 202 LYS cc_start: 0.7315 (mmtt) cc_final: 0.7104 (mmtt) REVERT: G 40 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8168 (tt0) REVERT: G 114 ASP cc_start: 0.8268 (m-30) cc_final: 0.7866 (m-30) REVERT: G 206 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7056 (pt0) REVERT: E 114 ASP cc_start: 0.8239 (m-30) cc_final: 0.7995 (m-30) REVERT: I 114 ASP cc_start: 0.8198 (m-30) cc_final: 0.7939 (m-30) REVERT: I 171 ASP cc_start: 0.8050 (t0) cc_final: 0.7808 (t70) outliers start: 13 outliers final: 5 residues processed: 133 average time/residue: 0.3844 time to fit residues: 71.8364 Evaluate side-chains 107 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain E residue 46 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.125802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.101692 restraints weight = 69294.628| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.21 r_work: 0.3114 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15849 Z= 0.168 Angle : 0.541 7.728 21222 Z= 0.290 Chirality : 0.030 0.113 2583 Planarity : 0.004 0.059 2763 Dihedral : 4.449 20.731 2250 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.99 % Allowed : 10.99 % Favored : 88.02 % 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: 0.35 (0.19), residues: 2007 helix: 0.47 (0.12), residues: 1809 sheet: None (None), residues: 0 loop : -0.96 (0.49), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (15849) covalent geometry : angle 0.54108 / 0.29 (21222) hydrogen bonds : bond 0.03331 / 2.24 ( 1207) hydrogen bonds : angle 4.25133 / 2.94 ( 3567) *********************** 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 130 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 ASP cc_start: 0.8191 (m-30) cc_final: 0.7755 (m-30) REVERT: A 30 ASP cc_start: 0.8468 (m-30) cc_final: 0.8169 (m-30) REVERT: A 114 ASP cc_start: 0.8067 (m-30) cc_final: 0.7608 (m-30) REVERT: C 114 ASP cc_start: 0.8220 (m-30) cc_final: 0.7858 (m-30) REVERT: D 40 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7940 (tt0) REVERT: G 40 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8135 (tt0) REVERT: G 114 ASP cc_start: 0.8205 (m-30) cc_final: 0.7782 (m-30) REVERT: G 206 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7107 (pt0) REVERT: E 114 ASP cc_start: 0.8093 (m-30) cc_final: 0.7871 (m-30) REVERT: I 114 ASP cc_start: 0.8204 (m-30) cc_final: 0.7924 (m-30) REVERT: I 171 ASP cc_start: 0.8071 (t0) cc_final: 0.7834 (t0) REVERT: I 206 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7223 (pt0) outliers start: 16 outliers final: 10 residues processed: 127 average time/residue: 0.3809 time to fit residues: 68.9196 Evaluate side-chains 112 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain E residue 46 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 12 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 182 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.132705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108902 restraints weight = 68698.183| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.23 r_work: 0.3114 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.6619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15849 Z= 0.150 Angle : 0.525 8.097 21222 Z= 0.281 Chirality : 0.030 0.123 2583 Planarity : 0.003 0.046 2763 Dihedral : 4.360 21.151 2250 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.74 % Allowed : 11.42 % Favored : 87.84 % 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: 0.80 (0.19), residues: 2007 helix: 0.84 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.76 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (15849) covalent geometry : angle 0.52464 / 0.28 (21222) hydrogen bonds : bond 0.03120 / 2.10 ( 1207) hydrogen bonds : angle 4.11243 / 2.84 ( 3567) *********************** 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 123 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 114 ASP cc_start: 0.8257 (m-30) cc_final: 0.7879 (m-30) REVERT: A 30 ASP cc_start: 0.8477 (m-30) cc_final: 0.8154 (m-30) REVERT: A 114 ASP cc_start: 0.8108 (m-30) cc_final: 0.7701 (m-30) REVERT: C 114 ASP cc_start: 0.8197 (m-30) cc_final: 0.7858 (m-30) REVERT: D 40 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7938 (tt0) REVERT: G 40 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8186 (tt0) REVERT: G 114 ASP cc_start: 0.8228 (m-30) cc_final: 0.7819 (m-30) REVERT: G 206 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7220 (pt0) REVERT: E 206 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7122 (pt0) REVERT: I 114 ASP cc_start: 0.8247 (m-30) cc_final: 0.7956 (m-30) REVERT: I 171 ASP cc_start: 0.8049 (t0) cc_final: 0.7812 (t0) REVERT: I 206 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7072 (pt0) outliers start: 12 outliers final: 12 residues processed: 122 average time/residue: 0.3723 time to fit residues: 64.9521 Evaluate side-chains 111 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 176 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 176 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 51 GLN ** H 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107714 restraints weight = 68715.851| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.14 r_work: 0.3163 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.6822 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= 0.184 Angle : 0.554 8.273 21222 Z= 0.296 Chirality : 0.031 0.129 2583 Planarity : 0.004 0.045 2763 Dihedral : 4.413 20.621 2250 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.05 % Allowed : 11.42 % Favored : 87.53 % 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: 1.07 (0.19), residues: 2007 helix: 1.03 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.86 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (15849) covalent geometry : angle 0.55442 / 0.30 (21222) hydrogen bonds : bond 0.03324 / 2.23 ( 1207) hydrogen bonds : angle 4.19109 / 2.90 ( 3567) *********************** 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 135 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 114 ASP cc_start: 0.8244 (m-30) cc_final: 0.7952 (m-30) REVERT: A 30 ASP cc_start: 0.8474 (m-30) cc_final: 0.8194 (m-30) REVERT: A 114 ASP cc_start: 0.8127 (m-30) cc_final: 0.7739 (m-30) REVERT: C 114 ASP cc_start: 0.8181 (m-30) cc_final: 0.7876 (m-30) REVERT: D 40 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8024 (tt0) REVERT: D 202 LYS cc_start: 0.7423 (mmtt) cc_final: 0.7084 (mmtt) REVERT: G 114 ASP cc_start: 0.8332 (m-30) cc_final: 0.8042 (m-30) REVERT: G 206 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7186 (pt0) REVERT: E 206 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7128 (pt0) REVERT: I 114 ASP cc_start: 0.8303 (m-30) cc_final: 0.8017 (m-30) REVERT: I 171 ASP cc_start: 0.7914 (t0) cc_final: 0.7700 (t0) REVERT: I 206 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7160 (pt0) outliers start: 17 outliers final: 14 residues processed: 135 average time/residue: 0.4079 time to fit residues: 76.7566 Evaluate side-chains 113 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 176 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 126 optimal weight: 2.9990 chunk 159 optimal weight: 0.3980 chunk 192 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.131669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108964 restraints weight = 68510.857| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.12 r_work: 0.3174 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.7062 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= 0.146 Angle : 0.528 7.387 21222 Z= 0.282 Chirality : 0.030 0.142 2583 Planarity : 0.003 0.058 2763 Dihedral : 4.305 19.724 2250 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.05 % Allowed : 11.48 % Favored : 87.47 % 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 (0.19), residues: 2007 helix: 1.33 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.86 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (15849) covalent geometry : angle 0.52835 / 0.28 (21222) hydrogen bonds : bond 0.03038 / 2.04 ( 1207) hydrogen bonds : angle 4.04326 / 2.79 ( 3567) *********************** 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 124 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 ASP cc_start: 0.8253 (m-30) cc_final: 0.7979 (m-30) REVERT: A 30 ASP cc_start: 0.8445 (m-30) cc_final: 0.8130 (m-30) REVERT: A 114 ASP cc_start: 0.8153 (m-30) cc_final: 0.7884 (m-30) REVERT: C 114 ASP cc_start: 0.8198 (m-30) cc_final: 0.7910 (m-30) REVERT: D 40 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7974 (tt0) REVERT: D 202 LYS cc_start: 0.7465 (mmtt) cc_final: 0.7151 (mmtt) REVERT: G 114 ASP cc_start: 0.8288 (m-30) cc_final: 0.8021 (m-30) REVERT: E 206 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7115 (pt0) REVERT: I 114 ASP cc_start: 0.8243 (m-30) cc_final: 0.7973 (m-30) REVERT: I 171 ASP cc_start: 0.7846 (t0) cc_final: 0.7635 (t0) REVERT: I 206 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7146 (pt0) outliers start: 17 outliers final: 13 residues processed: 124 average time/residue: 0.4216 time to fit residues: 72.3930 Evaluate side-chains 115 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain E residue 176 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 115 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 148 optimal weight: 0.1980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.133601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110994 restraints weight = 68136.320| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.11 r_work: 0.3172 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.7179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15849 Z= 0.113 Angle : 0.508 7.522 21222 Z= 0.271 Chirality : 0.030 0.150 2583 Planarity : 0.003 0.045 2763 Dihedral : 4.137 17.194 2250 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.99 % Allowed : 11.23 % Favored : 87.78 % 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: 2.04 (0.19), residues: 2007 helix: 1.69 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.80 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (15849) covalent geometry : angle 0.50769 / 0.27 (21222) hydrogen bonds : bond 0.02732 / 1.83 ( 1207) hydrogen bonds : angle 3.86018 / 2.67 ( 3567) *********************** 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 130 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 ASP cc_start: 0.8065 (m-30) cc_final: 0.7732 (t0) REVERT: B 114 ASP cc_start: 0.8211 (m-30) cc_final: 0.7929 (m-30) REVERT: A 3 ASP cc_start: 0.8082 (m-30) cc_final: 0.7716 (t0) REVERT: A 30 ASP cc_start: 0.8464 (m-30) cc_final: 0.8231 (m-30) REVERT: A 114 ASP cc_start: 0.8090 (m-30) cc_final: 0.7831 (m-30) REVERT: C 3 ASP cc_start: 0.8271 (m-30) cc_final: 0.7960 (t0) REVERT: C 114 ASP cc_start: 0.8185 (m-30) cc_final: 0.7886 (m-30) REVERT: F 114 ASP cc_start: 0.8236 (m-30) cc_final: 0.7979 (m-30) REVERT: D 40 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7885 (tt0) REVERT: D 202 LYS cc_start: 0.7442 (mmtt) cc_final: 0.7128 (mmtt) REVERT: G 114 ASP cc_start: 0.8232 (m-30) cc_final: 0.7968 (m-30) REVERT: E 206 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7189 (pt0) REVERT: I 114 ASP cc_start: 0.8234 (m-30) cc_final: 0.7954 (m-30) REVERT: I 171 ASP cc_start: 0.7870 (t0) cc_final: 0.7642 (t0) REVERT: I 206 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7163 (pt0) outliers start: 16 outliers final: 10 residues processed: 130 average time/residue: 0.4157 time to fit residues: 75.6583 Evaluate side-chains 114 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain E residue 176 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 20 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.132406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109677 restraints weight = 69021.941| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.12 r_work: 0.3199 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.7223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15849 Z= 0.141 Angle : 0.549 10.640 21222 Z= 0.291 Chirality : 0.030 0.166 2583 Planarity : 0.003 0.051 2763 Dihedral : 4.162 19.159 2250 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.62 % Allowed : 11.79 % Favored : 87.59 % 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: 2.11 (0.19), residues: 2007 helix: 1.74 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.81 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (15849) covalent geometry : angle 0.54884 / 0.29 (21222) hydrogen bonds : bond 0.02915 / 1.95 ( 1207) hydrogen bonds : angle 3.93683 / 2.72 ( 3567) ********************** 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 122 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 ASP cc_start: 0.8007 (m-30) cc_final: 0.7676 (t0) REVERT: B 114 ASP cc_start: 0.8278 (m-30) cc_final: 0.8014 (m-30) REVERT: A 3 ASP cc_start: 0.8138 (m-30) cc_final: 0.7791 (t0) REVERT: A 30 ASP cc_start: 0.8434 (m-30) cc_final: 0.8144 (m-30) REVERT: A 114 ASP cc_start: 0.8132 (m-30) cc_final: 0.7891 (m-30) REVERT: C 114 ASP cc_start: 0.8206 (m-30) cc_final: 0.7915 (m-30) REVERT: F 114 ASP cc_start: 0.8264 (m-30) cc_final: 0.8020 (m-30) REVERT: D 40 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7962 (tt0) REVERT: D 202 LYS cc_start: 0.7501 (mmtt) cc_final: 0.7188 (mmtt) REVERT: G 114 ASP cc_start: 0.8279 (m-30) cc_final: 0.7919 (m-30) REVERT: E 206 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7196 (pt0) REVERT: I 114 ASP cc_start: 0.8272 (m-30) cc_final: 0.7990 (m-30) REVERT: I 206 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7179 (pt0) outliers start: 10 outliers final: 10 residues processed: 122 average time/residue: 0.4182 time to fit residues: 71.3469 Evaluate side-chains 117 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain E residue 176 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 141 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.134033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110746 restraints weight = 68882.517| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.21 r_work: 0.3186 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.7296 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= 0.107 Angle : 0.530 10.784 21222 Z= 0.281 Chirality : 0.030 0.167 2583 Planarity : 0.003 0.075 2763 Dihedral : 4.083 19.090 2250 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.62 % Allowed : 11.91 % Favored : 87.47 % 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: 2.38 (0.19), residues: 2007 helix: 1.92 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.79 (0.43), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (15849) covalent geometry : angle 0.53006 / 0.28 (21222) hydrogen bonds : bond 0.02662 / 1.78 ( 1207) hydrogen bonds : angle 3.79157 / 2.62 ( 3567) =============================================================================== Job complete usr+sys time: 6851.21 seconds wall clock time: 116 minutes 49.14 seconds (7009.14 seconds total)