Starting phenix.real_space_refine on Fri Jun 27 08:54:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e9z_9021/06_2025/6e9z_9021.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e9z_9021/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6e9z_9021/06_2025/6e9z_9021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e9z_9021/06_2025/6e9z_9021.map" model { file = "/net/cci-nas-00/data/ceres_data/6e9z_9021/06_2025/6e9z_9021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e9z_9021/06_2025/6e9z_9021.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32652 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3628 Classifications: {'peptide': 225} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Restraints were copied for chains: C, B, E, D, G, F, I, H Time building chain proxies: 10.08, per 1000 atoms: 0.31 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: 8.60 Conformation dependent library (CDL) restraints added in 2.5 seconds 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3924 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 92.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 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: 11.76 Time building geometry restraints manager: 10.49 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' } 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.560 Extract box with map and model: 1.120 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 61.210 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.930 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.29 (0.13), residues: 2007 helix: -4.32 (0.07), residues: 1719 sheet: None (None), residues: 0 loop : -0.54 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG E 147 Details of bonding type rmsd hydrogen bonds : bond 0.27668 ( 1207) hydrogen bonds : angle 11.34365 ( 3567) covalent geometry : bond 0.01107 (15849) covalent geometry : angle 0.84728 (21222) *********************** 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 : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 1.2918 time to fit residues: 536.0240 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 : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN A 112 GLN C 112 GLN F 112 GLN D 112 GLN H 112 GLN E 112 GLN I 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.144368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122044 restraints weight = 65890.125| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.22 r_work: 0.3307 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15849 Z= 0.146 Angle : 0.606 7.540 21222 Z= 0.331 Chirality : 0.031 0.121 2583 Planarity : 0.004 0.050 2763 Dihedral : 4.940 21.539 2250 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.40 % Allowed : 1.59 % Favored : 98.01 % Rotamer: Outliers : 0.62 % Allowed : 9.44 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.16), residues: 2007 helix: -1.92 (0.10), residues: 1809 sheet: None (None), residues: 0 loop : -1.81 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 147 Details of bonding type rmsd hydrogen bonds : bond 0.04849 ( 1207) hydrogen bonds : angle 5.44925 ( 3567) covalent geometry : bond 0.00307 (15849) covalent geometry : angle 0.60555 (21222) *********************** 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 199 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 2.553 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: B 55 GLU cc_start: 0.6569 (mp0) cc_final: 0.6352 (mt-10) REVERT: A 206 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6850 (pt0) REVERT: C 33 LYS cc_start: 0.8387 (ttmm) cc_final: 0.8181 (tttp) REVERT: F 50 VAL cc_start: 0.8862 (t) cc_final: 0.8648 (m) REVERT: H 50 VAL cc_start: 0.8908 (t) cc_final: 0.8706 (m) REVERT: E 206 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7027 (pt0) outliers start: 10 outliers final: 2 residues processed: 194 average time/residue: 0.9216 time to fit residues: 241.3716 Evaluate side-chains 125 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 206 GLU 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 39 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.133796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109882 restraints weight = 68580.521| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.27 r_work: 0.3186 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15849 Z= 0.198 Angle : 0.611 8.030 21222 Z= 0.330 Chirality : 0.033 0.113 2583 Planarity : 0.005 0.057 2763 Dihedral : 4.827 21.420 2250 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.17 % Allowed : 10.31 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.18), residues: 2007 helix: -0.67 (0.11), residues: 1809 sheet: None (None), residues: 0 loop : -1.19 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 147 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 1207) hydrogen bonds : angle 4.68184 ( 3567) covalent geometry : bond 0.00470 (15849) covalent geometry : angle 0.61103 (21222) *********************** 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 172 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 2.654 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: 0.7785 (mm-40) cc_final: 0.7557 (mm110) REVERT: B 114 ASP cc_start: 0.8254 (m-30) cc_final: 0.7795 (m-30) REVERT: A 30 ASP cc_start: 0.8464 (m-30) cc_final: 0.8177 (m-30) REVERT: A 114 ASP cc_start: 0.8124 (m-30) cc_final: 0.7664 (m-30) REVERT: C 33 LYS cc_start: 0.9114 (ttmm) cc_final: 0.8863 (tttp) REVERT: C 40 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8137 (tp30) REVERT: C 114 ASP cc_start: 0.8247 (m-30) cc_final: 0.7930 (m-30) REVERT: D 40 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7971 (tt0) REVERT: H 30 ASP cc_start: 0.7775 (m-30) cc_final: 0.7527 (m-30) REVERT: G 32 GLU cc_start: 0.7900 (tp30) cc_final: 0.7673 (tp30) REVERT: G 40 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8205 (tt0) REVERT: G 114 ASP cc_start: 0.8331 (m-30) cc_final: 0.7898 (m-30) REVERT: G 206 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7011 (pt0) REVERT: E 114 ASP cc_start: 0.8266 (m-30) cc_final: 0.8062 (m-30) REVERT: E 206 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7035 (pt0) REVERT: I 114 ASP cc_start: 0.8228 (m-30) cc_final: 0.7936 (m-30) REVERT: I 206 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7220 (pt0) outliers start: 19 outliers final: 7 residues processed: 167 average time/residue: 0.8482 time to fit residues: 197.2609 Evaluate side-chains 118 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 2.852 ------------------------------------------------------------------------------- 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 F residue 76 LEU Chi-restraints excluded: chain H residue 76 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 79 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.131728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107670 restraints weight = 68837.214| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.27 r_work: 0.3165 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.6082 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= 0.179 Angle : 0.554 8.229 21222 Z= 0.299 Chirality : 0.031 0.115 2583 Planarity : 0.004 0.056 2763 Dihedral : 4.602 21.617 2250 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.17 % Allowed : 10.74 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.19), residues: 2007 helix: -0.06 (0.12), residues: 1809 sheet: None (None), residues: 0 loop : -1.07 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 150 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 1207) hydrogen bonds : angle 4.41649 ( 3567) covalent geometry : bond 0.00420 (15849) covalent geometry : angle 0.55415 (21222) *********************** 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 145 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 114 ASP cc_start: 0.8211 (m-30) cc_final: 0.7811 (m-30) REVERT: A 30 ASP cc_start: 0.8473 (m-30) cc_final: 0.8218 (m-30) REVERT: A 114 ASP cc_start: 0.8081 (m-30) cc_final: 0.7630 (m-30) REVERT: C 33 LYS cc_start: 0.9089 (ttmm) cc_final: 0.8838 (tttp) REVERT: C 40 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8103 (tp30) REVERT: C 114 ASP cc_start: 0.8240 (m-30) cc_final: 0.7867 (m-30) REVERT: F 114 ASP cc_start: 0.8260 (m-30) cc_final: 0.7979 (m-30) REVERT: D 40 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7947 (tt0) REVERT: D 177 MET cc_start: 0.8645 (mtp) cc_final: 0.8400 (mtp) REVERT: D 202 LYS cc_start: 0.7370 (mmtt) cc_final: 0.7117 (mmtt) REVERT: H 30 ASP cc_start: 0.7800 (m-30) cc_final: 0.7573 (m-30) REVERT: G 40 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8185 (tt0) REVERT: G 114 ASP cc_start: 0.8262 (m-30) cc_final: 0.7983 (m-30) REVERT: G 206 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7112 (pt0) REVERT: E 114 ASP cc_start: 0.8158 (m-30) cc_final: 0.7944 (m-30) REVERT: E 206 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7098 (pt0) REVERT: I 114 ASP cc_start: 0.8248 (m-30) cc_final: 0.7965 (m-30) REVERT: I 171 ASP cc_start: 0.8061 (t0) cc_final: 0.7808 (t70) REVERT: I 206 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7258 (pt0) REVERT: I 214 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7884 (tm-30) outliers start: 19 outliers final: 10 residues processed: 140 average time/residue: 0.8589 time to fit residues: 169.3938 Evaluate side-chains 119 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 2.699 ------------------------------------------------------------------------------- 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 74 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain E residue 14 GLU 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 192 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.129556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105568 restraints weight = 68897.938| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.25 r_work: 0.3115 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.6473 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= 0.178 Angle : 0.549 7.988 21222 Z= 0.295 Chirality : 0.031 0.114 2583 Planarity : 0.004 0.047 2763 Dihedral : 4.519 20.812 2250 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.86 % Allowed : 11.05 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.19), residues: 2007 helix: 0.37 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.89 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 150 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 1207) hydrogen bonds : angle 4.29392 ( 3567) covalent geometry : bond 0.00419 (15849) covalent geometry : angle 0.54913 (21222) *********************** 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 134 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 ASP cc_start: 0.8186 (m-30) cc_final: 0.7801 (m-30) REVERT: A 30 ASP cc_start: 0.8446 (m-30) cc_final: 0.8154 (m-30) REVERT: A 114 ASP cc_start: 0.8107 (m-30) cc_final: 0.7693 (m-30) REVERT: C 33 LYS cc_start: 0.9108 (ttmm) cc_final: 0.8873 (tttp) REVERT: C 114 ASP cc_start: 0.8257 (m-30) cc_final: 0.7920 (m-30) REVERT: D 40 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7980 (tt0) REVERT: D 177 MET cc_start: 0.8673 (mtp) cc_final: 0.8448 (mtp) REVERT: D 202 LYS cc_start: 0.7435 (mmtt) cc_final: 0.7184 (mmtt) REVERT: G 40 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8196 (tt0) REVERT: G 114 ASP cc_start: 0.8258 (m-30) cc_final: 0.7987 (m-30) REVERT: G 206 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7134 (pt0) REVERT: E 114 ASP cc_start: 0.8132 (m-30) cc_final: 0.7927 (m-30) REVERT: E 206 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7086 (pt0) REVERT: I 114 ASP cc_start: 0.8247 (m-30) cc_final: 0.7948 (m-30) REVERT: I 171 ASP cc_start: 0.8087 (t0) cc_final: 0.7846 (t0) REVERT: I 206 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7278 (pt0) REVERT: I 214 GLU cc_start: 0.8245 (tm-30) cc_final: 0.8016 (tm-30) outliers start: 14 outliers final: 12 residues processed: 132 average time/residue: 1.0184 time to fit residues: 193.6037 Evaluate side-chains 120 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 2.682 ------------------------------------------------------------------------------- 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 F residue 76 LEU Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 165 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 88 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 182 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.131421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107631 restraints weight = 68693.355| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.24 r_work: 0.3194 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.6700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15849 Z= 0.104 Angle : 0.490 8.163 21222 Z= 0.264 Chirality : 0.029 0.131 2583 Planarity : 0.003 0.030 2763 Dihedral : 4.245 19.897 2250 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.74 % Allowed : 11.05 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.19), residues: 2007 helix: 1.02 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.73 (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 hydrogen bonds : bond 0.02754 ( 1207) hydrogen bonds : angle 3.93628 ( 3567) covalent geometry : bond 0.00234 (15849) covalent geometry : angle 0.48958 (21222) *********************** 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 130 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 3 ASP cc_start: 0.7995 (m-30) cc_final: 0.7603 (t0) REVERT: B 114 ASP cc_start: 0.8215 (m-30) cc_final: 0.7939 (m-30) REVERT: A 30 ASP cc_start: 0.8466 (m-30) cc_final: 0.8244 (m-30) REVERT: A 114 ASP cc_start: 0.8089 (m-30) cc_final: 0.7817 (m-30) REVERT: C 3 ASP cc_start: 0.8184 (m-30) cc_final: 0.7846 (t0) REVERT: C 33 LYS cc_start: 0.9078 (ttmm) cc_final: 0.8869 (tttp) REVERT: C 114 ASP cc_start: 0.8237 (m-30) cc_final: 0.7930 (m-30) REVERT: F 114 ASP cc_start: 0.8237 (m-30) cc_final: 0.7987 (m-30) REVERT: D 40 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7938 (tt0) REVERT: D 177 MET cc_start: 0.8588 (mtp) cc_final: 0.8318 (mtp) REVERT: D 202 LYS cc_start: 0.7374 (mmtt) cc_final: 0.7084 (mmtt) REVERT: G 40 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8147 (tt0) REVERT: G 214 GLU cc_start: 0.8249 (tm-30) cc_final: 0.8014 (tm-30) REVERT: E 114 ASP cc_start: 0.8121 (m-30) cc_final: 0.7834 (m-30) REVERT: E 206 GLU cc_start: 0.7612 (mm-30) cc_final: 0.6397 (mt-10) REVERT: I 114 ASP cc_start: 0.8243 (m-30) cc_final: 0.8016 (m-30) REVERT: I 171 ASP cc_start: 0.8064 (t0) cc_final: 0.7818 (t0) REVERT: I 206 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7123 (pt0) outliers start: 12 outliers final: 11 residues processed: 130 average time/residue: 0.9571 time to fit residues: 173.4040 Evaluate side-chains 115 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 76 LEU Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain D 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 Chi-restraints excluded: chain I residue 176 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 195 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 150 optimal weight: 0.4980 chunk 183 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 GLN ** F 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3580 r_free = 0.3580 target = 0.126442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.102476 restraints weight = 68886.803| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.20 r_work: 0.3191 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.6844 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= 0.118 Angle : 0.496 7.382 21222 Z= 0.266 Chirality : 0.029 0.123 2583 Planarity : 0.003 0.028 2763 Dihedral : 4.167 18.353 2250 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.80 % Allowed : 11.30 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.19), residues: 2007 helix: 1.39 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.70 (0.43), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 184 Details of bonding type rmsd hydrogen bonds : bond 0.02810 ( 1207) hydrogen bonds : angle 3.90215 ( 3567) covalent geometry : bond 0.00271 (15849) covalent geometry : angle 0.49649 (21222) *********************** 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 128 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 3 ASP cc_start: 0.7989 (m-30) cc_final: 0.7629 (t0) REVERT: B 114 ASP cc_start: 0.8249 (m-30) cc_final: 0.7889 (m-30) REVERT: A 30 ASP cc_start: 0.8485 (m-30) cc_final: 0.8215 (m-30) REVERT: A 114 ASP cc_start: 0.8109 (m-30) cc_final: 0.7741 (m-30) REVERT: C 3 ASP cc_start: 0.8194 (m-30) cc_final: 0.7892 (t0) REVERT: C 33 LYS cc_start: 0.9081 (ttmm) cc_final: 0.8873 (tttp) REVERT: C 114 ASP cc_start: 0.8240 (m-30) cc_final: 0.7938 (m-30) REVERT: F 114 ASP cc_start: 0.8257 (m-30) cc_final: 0.8008 (m-30) REVERT: D 40 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7930 (tt0) REVERT: D 177 MET cc_start: 0.8618 (mtp) cc_final: 0.8390 (mtp) REVERT: D 202 LYS cc_start: 0.7410 (mmtt) cc_final: 0.7111 (mmtt) REVERT: G 40 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8229 (tt0) REVERT: G 114 ASP cc_start: 0.8082 (m-30) cc_final: 0.7817 (m-30) REVERT: G 214 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7998 (tm-30) REVERT: E 114 ASP cc_start: 0.8166 (m-30) cc_final: 0.7811 (m-30) REVERT: E 206 GLU cc_start: 0.7543 (mm-30) cc_final: 0.6360 (mt-10) REVERT: I 114 ASP cc_start: 0.8270 (m-30) cc_final: 0.7944 (m-30) REVERT: I 171 ASP cc_start: 0.8060 (t0) cc_final: 0.7842 (t0) REVERT: I 206 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7165 (pt0) outliers start: 13 outliers final: 9 residues processed: 128 average time/residue: 0.8586 time to fit residues: 151.9191 Evaluate side-chains 115 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 176 LYS Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain I residue 176 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 125 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108450 restraints weight = 69198.746| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.24 r_work: 0.3182 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.6964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15849 Z= 0.152 Angle : 0.529 8.152 21222 Z= 0.283 Chirality : 0.030 0.147 2583 Planarity : 0.003 0.058 2763 Dihedral : 4.207 19.128 2250 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.17 % Allowed : 11.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.19), residues: 2007 helix: 1.50 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.79 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 29 Details of bonding type rmsd hydrogen bonds : bond 0.03016 ( 1207) hydrogen bonds : angle 4.00421 ( 3567) covalent geometry : bond 0.00354 (15849) covalent geometry : angle 0.52945 (21222) *********************** 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 134 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 ASP cc_start: 0.8308 (m-30) cc_final: 0.7980 (m-30) REVERT: A 30 ASP cc_start: 0.8500 (m-30) cc_final: 0.8223 (m-30) REVERT: A 114 ASP cc_start: 0.8142 (m-30) cc_final: 0.7770 (m-30) REVERT: C 114 ASP cc_start: 0.8261 (m-30) cc_final: 0.7962 (m-30) REVERT: D 40 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7968 (tt0) REVERT: D 177 MET cc_start: 0.8674 (mtp) cc_final: 0.8442 (mtp) REVERT: D 202 LYS cc_start: 0.7471 (mmtt) cc_final: 0.7161 (mmtt) REVERT: G 40 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8287 (tt0) REVERT: G 214 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7948 (tm-30) REVERT: E 114 ASP cc_start: 0.8187 (m-30) cc_final: 0.7834 (m-30) REVERT: E 206 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7101 (pt0) REVERT: I 114 ASP cc_start: 0.8277 (m-30) cc_final: 0.7972 (m-30) REVERT: I 171 ASP cc_start: 0.8082 (t0) cc_final: 0.7860 (t0) REVERT: I 206 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7131 (pt0) outliers start: 19 outliers final: 12 residues processed: 133 average time/residue: 0.9053 time to fit residues: 162.9278 Evaluate side-chains 117 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL 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 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 Chi-restraints excluded: chain I residue 176 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 169 optimal weight: 4.9990 chunk 177 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 186 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 112 GLN H 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.131368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108005 restraints weight = 69112.493| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.20 r_work: 0.3164 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.7116 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= 0.156 Angle : 0.540 8.246 21222 Z= 0.287 Chirality : 0.030 0.153 2583 Planarity : 0.003 0.044 2763 Dihedral : 4.220 19.262 2250 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.86 % Allowed : 11.48 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.19), residues: 2007 helix: 1.60 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.90 (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 hydrogen bonds : bond 0.03039 ( 1207) hydrogen bonds : angle 4.02045 ( 3567) covalent geometry : bond 0.00365 (15849) covalent geometry : angle 0.53968 (21222) *********************** 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 127 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 ASP cc_start: 0.8072 (m-30) cc_final: 0.7672 (t0) REVERT: B 114 ASP cc_start: 0.8335 (m-30) cc_final: 0.7998 (m-30) REVERT: B 203 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6984 (tm-30) REVERT: A 3 ASP cc_start: 0.8148 (m-30) cc_final: 0.7754 (t0) REVERT: A 30 ASP cc_start: 0.8493 (m-30) cc_final: 0.8200 (m-30) REVERT: A 114 ASP cc_start: 0.8131 (m-30) cc_final: 0.7860 (m-30) REVERT: C 114 ASP cc_start: 0.8245 (m-30) cc_final: 0.7949 (m-30) REVERT: D 40 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7966 (tt0) REVERT: D 177 MET cc_start: 0.8699 (mtp) cc_final: 0.8472 (mtp) REVERT: D 202 LYS cc_start: 0.7483 (mmtt) cc_final: 0.7177 (mmtt) REVERT: G 40 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8283 (tt0) REVERT: G 214 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7958 (tm-30) REVERT: E 114 ASP cc_start: 0.8160 (m-30) cc_final: 0.7818 (m-30) REVERT: E 206 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7152 (pt0) REVERT: I 114 ASP cc_start: 0.8280 (m-30) cc_final: 0.7986 (m-30) REVERT: I 171 ASP cc_start: 0.8024 (t0) cc_final: 0.7795 (t0) REVERT: I 206 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7115 (pt0) outliers start: 14 outliers final: 11 residues processed: 127 average time/residue: 0.8668 time to fit residues: 152.5298 Evaluate side-chains 120 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL 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 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 G residue 176 LYS Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain I residue 176 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 148 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.130989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107734 restraints weight = 68924.636| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.19 r_work: 0.3158 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.7201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15849 Z= 0.151 Angle : 0.556 10.595 21222 Z= 0.295 Chirality : 0.030 0.167 2583 Planarity : 0.003 0.046 2763 Dihedral : 4.186 19.550 2250 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.68 % Allowed : 11.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.19), residues: 2007 helix: 1.76 (0.12), residues: 1800 sheet: None (None), residues: 0 loop : -1.30 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 29 Details of bonding type rmsd hydrogen bonds : bond 0.02995 ( 1207) hydrogen bonds : angle 3.99118 ( 3567) covalent geometry : bond 0.00351 (15849) covalent geometry : angle 0.55642 (21222) ********************** 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 125 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 ASP cc_start: 0.8032 (m-30) cc_final: 0.7664 (t0) REVERT: B 50 VAL cc_start: 0.8991 (OUTLIER) cc_final: 0.8744 (t) REVERT: B 114 ASP cc_start: 0.8318 (m-30) cc_final: 0.8052 (m-30) REVERT: B 203 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6967 (tm-30) REVERT: A 3 ASP cc_start: 0.8174 (m-30) cc_final: 0.7776 (t0) REVERT: A 29 ARG cc_start: 0.5441 (mtm180) cc_final: 0.5216 (mtp180) REVERT: A 30 ASP cc_start: 0.8465 (m-30) cc_final: 0.8183 (m-30) REVERT: A 114 ASP cc_start: 0.8130 (m-30) cc_final: 0.7858 (m-30) REVERT: C 114 ASP cc_start: 0.8235 (m-30) cc_final: 0.7943 (m-30) REVERT: D 40 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7961 (tt0) REVERT: D 177 MET cc_start: 0.8702 (mtp) cc_final: 0.8473 (mtp) REVERT: D 202 LYS cc_start: 0.7456 (mmtt) cc_final: 0.7149 (mmtt) REVERT: G 40 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8272 (tt0) REVERT: G 214 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7948 (tm-30) REVERT: E 114 ASP cc_start: 0.8160 (m-30) cc_final: 0.7808 (m-30) REVERT: E 206 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7236 (pt0) REVERT: I 114 ASP cc_start: 0.8260 (m-30) cc_final: 0.7966 (m-30) REVERT: I 171 ASP cc_start: 0.7895 (t0) cc_final: 0.7669 (t0) REVERT: I 206 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7113 (pt0) outliers start: 11 outliers final: 10 residues processed: 125 average time/residue: 0.8487 time to fit residues: 149.9335 Evaluate side-chains 119 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL 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 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 G residue 176 LYS Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain I residue 176 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 127 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 182 optimal weight: 0.0670 chunk 177 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.132853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.109778 restraints weight = 68640.908| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.18 r_work: 0.3208 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.7277 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= 0.112 Angle : 0.534 10.508 21222 Z= 0.283 Chirality : 0.030 0.170 2583 Planarity : 0.003 0.044 2763 Dihedral : 4.092 19.450 2250 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.74 % Allowed : 11.60 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.19), residues: 2007 helix: 1.95 (0.12), residues: 1800 sheet: None (None), residues: 0 loop : -1.32 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 29 Details of bonding type rmsd hydrogen bonds : bond 0.02721 ( 1207) hydrogen bonds : angle 3.84012 ( 3567) covalent geometry : bond 0.00257 (15849) covalent geometry : angle 0.53414 (21222) =============================================================================== Job complete usr+sys time: 14195.07 seconds wall clock time: 245 minutes 28.61 seconds (14728.61 seconds total)