Starting phenix.real_space_refine on Mon Aug 25 23:32:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e9z_9021/08_2025/6e9z_9021.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e9z_9021/08_2025/6e9z_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 { model { file = "/net/cci-nas-00/data/ceres_data/6e9z_9021/08_2025/6e9z_9021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e9z_9021/08_2025/6e9z_9021.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6e9z_9021/08_2025/6e9z_9021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e9z_9021/08_2025/6e9z_9021.map" } 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-2.0-5787/lib/python3.9/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: 3.29, per 1000 atoms: 0.10 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: 2.27 Conformation dependent library (CDL) restraints added in 658.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.42 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: 6.23 Time building geometry restraints manager: 3.05 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: 0.07 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.130 Extract box with map and model: 0.310 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.440 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 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 aren 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 covalent geometry : bond 0.01107 (15849) covalent geometry : angle 0.84728 (21222) hydrogen bonds : bond 0.27668 ( 1207) hydrogen bonds : angle 11.34365 ( 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 : 0.861 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: 0.5615 time to fit residues: 231.6781 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 : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.6766 > 50: distance: 113 - 145: 3.250 distance: 116 - 155: 25.563 distance: 125 - 177: 30.710 distance: 139 - 196: 29.734 distance: 147 - 155: 23.556 distance: 148 - 206: 33.280 distance: 155 - 156: 32.010 distance: 155 - 164: 41.247 distance: 156 - 157: 45.352 distance: 156 - 159: 24.209 distance: 156 - 165: 24.149 distance: 157 - 158: 8.105 distance: 157 - 177: 4.174 distance: 159 - 160: 16.292 distance: 159 - 166: 43.323 distance: 159 - 167: 42.710 distance: 160 - 161: 30.427 distance: 160 - 168: 27.141 distance: 160 - 169: 27.141 distance: 161 - 162: 26.097 distance: 161 - 170: 3.945 distance: 161 - 171: 44.375 distance: 162 - 163: 37.882 distance: 163 - 174: 27.817 distance: 163 - 175: 27.610 distance: 163 - 176: 22.220 distance: 177 - 178: 20.950 distance: 177 - 185: 62.745 distance: 178 - 179: 42.569 distance: 178 - 181: 23.375 distance: 178 - 186: 21.861 distance: 179 - 180: 4.807 distance: 179 - 196: 25.500 distance: 180 - 245: 45.548 distance: 181 - 182: 47.680 distance: 181 - 187: 56.614 distance: 181 - 188: 13.590 distance: 182 - 183: 28.820 distance: 182 - 184: 39.859 distance: 182 - 189: 37.541 distance: 183 - 190: 23.458 distance: 184 - 193: 40.398 distance: 184 - 194: 41.017 distance: 196 - 197: 23.759 distance: 196 - 201: 47.695 distance: 197 - 198: 26.633 distance: 197 - 200: 18.230 distance: 198 - 199: 21.535 distance: 198 - 206: 48.700 distance: 199 - 261: 26.556 distance: 200 - 203: 25.592 distance: 200 - 204: 27.787 distance: 200 - 205: 30.666 distance: 206 - 207: 17.216 distance: 206 - 215: 11.462 distance: 207 - 208: 28.854 distance: 207 - 210: 18.985 distance: 207 - 216: 19.440 distance: 208 - 209: 33.038 distance: 208 - 228: 19.541 distance: 209 - 280: 33.000 distance: 210 - 211: 14.979 distance: 210 - 217: 42.412 distance: 210 - 218: 20.486 distance: 211 - 212: 39.250 distance: 211 - 219: 7.972 distance: 211 - 220: 10.550 distance: 212 - 213: 4.756 distance: 212 - 221: 20.514 distance: 212 - 222: 8.673 distance: 213 - 214: 16.597 distance: 213 - 223: 25.388 distance: 213 - 224: 9.966 distance: 214 - 225: 23.678 distance: 214 - 226: 7.147 distance: 214 - 227: 7.025 distance: 228 - 229: 40.587 distance: 228 - 236: 21.375 distance: 229 - 230: 7.123 distance: 229 - 232: 33.143 distance: 229 - 237: 4.659 distance: 230 - 245: 21.518 distance: 232 - 233: 23.522 distance: 232 - 238: 32.002 distance: 232 - 239: 51.881 distance: 233 - 234: 33.694 distance: 233 - 240: 15.322 distance: 233 - 241: 40.282 distance: 234 - 235: 31.240 distance: 235 - 243: 8.295 distance: 235 - 244: 10.889 distance: 245 - 246: 27.609 distance: 245 - 252: 14.133 distance: 246 - 247: 19.111 distance: 246 - 249: 9.930 distance: 246 - 253: 27.328 distance: 247 - 248: 33.760 distance: 247 - 261: 19.444 distance: 248 - 314: 44.155 distance: 249 - 250: 24.420 distance: 249 - 251: 21.218 distance: 249 - 254: 27.251 distance: 250 - 255: 14.774 distance: 250 - 256: 24.307 distance: 250 - 257: 27.963 distance: 251 - 258: 23.806 distance: 251 - 259: 14.795 distance: 251 - 260: 16.699 distance: 261 - 262: 4.317 distance: 261 - 269: 26.867 distance: 262 - 263: 24.917 distance: 262 - 265: 30.474 distance: 262 - 270: 17.505 distance: 263 - 264: 27.666 distance: 263 - 280: 11.560 distance: 264 - 324: 24.206 distance: 265 - 266: 14.798 distance: 265 - 271: 39.500 distance: 265 - 272: 18.530 distance: 266 - 267: 15.602 distance: 266 - 268: 24.724 distance: 266 - 273: 4.502 distance: 267 - 275: 21.796 distance: 267 - 276: 4.444 distance: 268 - 277: 13.268 distance: 268 - 278: 26.427 distance: 268 - 279: 20.019 distance: 280 - 281: 42.967 distance: 280 - 289: 16.896 distance: 281 - 282: 33.383 distance: 281 - 284: 38.362 distance: 281 - 290: 7.352 distance: 282 - 283: 4.948 distance: 282 - 295: 11.722 distance: 284 - 285: 8.403 distance: 284 - 291: 32.306 distance: 284 - 292: 27.628 distance: 285 - 286: 12.627 distance: 285 - 293: 13.648 distance: 286 - 287: 14.985 distance: 286 - 288: 25.565 distance: 295 - 296: 15.818 distance: 295 - 303: 12.342 distance: 296 - 297: 6.866 distance: 296 - 299: 15.143 distance: 296 - 304: 34.396 distance: 297 - 298: 5.461 distance: 297 - 314: 20.834 distance: 298 - 357: 33.232 distance: 299 - 300: 47.743 distance: 299 - 305: 14.815 distance: 299 - 306: 13.675 distance: 300 - 302: 6.727 distance: 300 - 307: 10.162 distance: 301 - 309: 18.126 distance: 301 - 310: 19.853 distance: 302 - 311: 23.173 distance: 302 - 312: 26.450 distance: 302 - 313: 8.048 distance: 314 - 315: 43.634 distance: 314 - 319: 31.554 distance: 315 - 316: 16.769 distance: 315 - 318: 23.855 distance: 315 - 320: 24.957 distance: 316 - 317: 9.477 distance: 316 - 324: 28.938 distance: 317 - 374: 26.363 distance: 318 - 321: 54.081 distance: 318 - 322: 7.840 distance: 318 - 323: 46.839 distance: 418 - 441: 3.109