Starting phenix.real_space_refine on Thu Mar 5 05:13:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dk1_27480/03_2026/8dk1_27480.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dk1_27480/03_2026/8dk1_27480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dk1_27480/03_2026/8dk1_27480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dk1_27480/03_2026/8dk1_27480.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dk1_27480/03_2026/8dk1_27480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dk1_27480/03_2026/8dk1_27480.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 12210 2.51 5 N 3622 2.21 5 O 3624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19500 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2796 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 336} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2796 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 336} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 4035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4035 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 14, 'TRANS': 494} Chain breaks: 5 Chain: "D" Number of atoms: 4035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4035 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 14, 'TRANS': 494} Chain breaks: 5 Chain: "E" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1413 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain breaks: 2 Chain: "F" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1506 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "G" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1413 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain breaks: 2 Chain: "H" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1506 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Time building chain proxies: 3.84, per 1000 atoms: 0.20 Number of scatterers: 19500 At special positions: 0 Unit cell: (183.96, 101.64, 138.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 3624 8.00 N 3622 7.00 C 12210 6.00 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: 1.66 Conformation dependent library (CDL) restraints added in 889.3 milliseconds 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 16 sheets defined 65.2% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 removed outlier: 3.852A pdb=" N SER A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 10 " --> pdb=" O GLN A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 26 Processing helix chain 'A' and resid 29 through 41 Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.847A pdb=" N ALA A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.718A pdb=" N GLU A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 143 Processing helix chain 'A' and resid 148 through 170 removed outlier: 3.555A pdb=" N ALA A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 Processing helix chain 'A' and resid 194 through 197 removed outlier: 3.533A pdb=" N ALA A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 198 through 220 removed outlier: 3.665A pdb=" N VAL A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 234 removed outlier: 3.793A pdb=" N VAL A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.501A pdb=" N VAL A 246 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 255 " --> pdb=" O GLN A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 272 removed outlier: 3.508A pdb=" N LEU A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 290 through 320 removed outlier: 3.908A pdb=" N VAL A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN A 304 " --> pdb=" O GLN A 300 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 339 Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'B' and resid 6 through 19 removed outlier: 3.509A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 26 Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 52 through 63 removed outlier: 3.973A pdb=" N ALA B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 91 Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.680A pdb=" N GLU B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 143 Processing helix chain 'B' and resid 146 through 170 removed outlier: 3.559A pdb=" N ARG B 150 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 193 Processing helix chain 'B' and resid 194 through 197 removed outlier: 3.531A pdb=" N ALA B 197 " --> pdb=" O SER B 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 194 through 197' Processing helix chain 'B' and resid 198 through 220 removed outlier: 3.678A pdb=" N VAL B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 234 removed outlier: 3.789A pdb=" N VAL B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.501A pdb=" N VAL B 246 " --> pdb=" O PRO B 242 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 255 " --> pdb=" O GLN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 272 removed outlier: 3.507A pdb=" N LEU B 260 " --> pdb=" O GLN B 256 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 272 " --> pdb=" O ARG B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 281 through 290 Processing helix chain 'B' and resid 290 through 320 removed outlier: 3.908A pdb=" N VAL B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN B 304 " --> pdb=" O GLN B 300 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 339 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'C' and resid 48 through 59 removed outlier: 3.759A pdb=" N VAL C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 86 Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 152 through 164 Processing helix chain 'C' and resid 165 through 171 removed outlier: 3.798A pdb=" N MET C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 195 Processing helix chain 'C' and resid 200 through 208 Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 231 through 274 removed outlier: 3.581A pdb=" N ALA C 235 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA C 236 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP C 247 " --> pdb=" O ASP C 243 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) Proline residue: C 264 - end of helix Processing helix chain 'C' and resid 793 through 808 removed outlier: 3.510A pdb=" N ALA C 807 " --> pdb=" O ASP C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 835 Processing helix chain 'C' and resid 835 through 855 removed outlier: 3.589A pdb=" N GLU C 839 " --> pdb=" O GLU C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 882 removed outlier: 3.662A pdb=" N LEU C 859 " --> pdb=" O GLY C 855 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C 860 " --> pdb=" O VAL C 856 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER C 861 " --> pdb=" O THR C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 917 Processing helix chain 'C' and resid 918 through 920 No H-bonds generated for 'chain 'C' and resid 918 through 920' Processing helix chain 'C' and resid 924 through 944 removed outlier: 3.685A pdb=" N ALA C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS C 944 " --> pdb=" O ASP C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 955 removed outlier: 3.638A pdb=" N LEU C 953 " --> pdb=" O GLY C 949 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 954 " --> pdb=" O ALA C 950 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 958 No H-bonds generated for 'chain 'C' and resid 956 through 958' Processing helix chain 'C' and resid 989 through 1005 Processing helix chain 'C' and resid 1028 through 1043 removed outlier: 3.914A pdb=" N ARG C1034 " --> pdb=" O ALA C1030 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE C1035 " --> pdb=" O VAL C1031 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA C1037 " --> pdb=" O GLY C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1057 through 1062 Processing helix chain 'D' and resid 48 through 59 removed outlier: 3.759A pdb=" N VAL D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 86 removed outlier: 3.520A pdb=" N TYR D 83 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 137 No H-bonds generated for 'chain 'D' and resid 135 through 137' Processing helix chain 'D' and resid 152 through 164 Processing helix chain 'D' and resid 165 through 170 Processing helix chain 'D' and resid 171 through 174 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 200 through 208 Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 231 through 274 removed outlier: 3.599A pdb=" N ALA D 235 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA D 236 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP D 247 " --> pdb=" O ASP D 243 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) Proline residue: D 264 - end of helix Processing helix chain 'D' and resid 793 through 808 Processing helix chain 'D' and resid 818 through 820 No H-bonds generated for 'chain 'D' and resid 818 through 820' Processing helix chain 'D' and resid 821 through 835 Processing helix chain 'D' and resid 835 through 855 removed outlier: 3.611A pdb=" N GLU D 839 " --> pdb=" O GLU D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 855 through 881 removed outlier: 3.652A pdb=" N LEU D 859 " --> pdb=" O GLY D 855 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU D 860 " --> pdb=" O VAL D 856 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER D 861 " --> pdb=" O THR D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 901 through 917 Processing helix chain 'D' and resid 918 through 920 No H-bonds generated for 'chain 'D' and resid 918 through 920' Processing helix chain 'D' and resid 924 through 944 removed outlier: 3.682A pdb=" N ALA D 933 " --> pdb=" O LYS D 929 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS D 944 " --> pdb=" O ASP D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 947 through 955 removed outlier: 3.637A pdb=" N LEU D 953 " --> pdb=" O GLY D 949 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 954 " --> pdb=" O ALA D 950 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 958 No H-bonds generated for 'chain 'D' and resid 956 through 958' Processing helix chain 'D' and resid 989 through 1005 Processing helix chain 'D' and resid 1028 through 1043 removed outlier: 3.902A pdb=" N ARG D1034 " --> pdb=" O ALA D1030 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE D1035 " --> pdb=" O VAL D1031 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE D1036 " --> pdb=" O ALA D1032 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D1037 " --> pdb=" O GLY D1033 " (cutoff:3.500A) Processing helix chain 'D' and resid 1057 through 1062 Processing helix chain 'E' and resid 49 through 63 Processing helix chain 'E' and resid 70 through 79 Processing helix chain 'E' and resid 80 through 89 Processing helix chain 'E' and resid 130 through 150 removed outlier: 4.075A pdb=" N LEU E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 174 removed outlier: 3.791A pdb=" N ILE E 166 " --> pdb=" O VAL E 162 " (cutoff:3.500A) Proline residue: E 167 - end of helix removed outlier: 4.119A pdb=" N TYR E 172 " --> pdb=" O GLN E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 196 removed outlier: 3.571A pdb=" N HIS E 196 " --> pdb=" O GLN E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 217 Processing helix chain 'E' and resid 219 through 236 Processing helix chain 'F' and resid 49 through 63 Processing helix chain 'F' and resid 70 through 79 Processing helix chain 'F' and resid 80 through 89 Processing helix chain 'F' and resid 130 through 150 removed outlier: 3.689A pdb=" N GLU F 150 " --> pdb=" O ALA F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 174 Proline residue: F 167 - end of helix removed outlier: 4.001A pdb=" N TYR F 172 " --> pdb=" O GLN F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 195 removed outlier: 3.899A pdb=" N GLU F 182 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 217 Processing helix chain 'F' and resid 219 through 235 Processing helix chain 'G' and resid 49 through 63 Processing helix chain 'G' and resid 70 through 79 Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 130 through 150 removed outlier: 4.119A pdb=" N LEU G 136 " --> pdb=" O GLU G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 174 removed outlier: 3.769A pdb=" N ILE G 166 " --> pdb=" O VAL G 162 " (cutoff:3.500A) Proline residue: G 167 - end of helix removed outlier: 4.019A pdb=" N TYR G 172 " --> pdb=" O GLN G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 196 removed outlier: 3.528A pdb=" N HIS G 196 " --> pdb=" O GLN G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 217 Processing helix chain 'G' and resid 219 through 236 Processing helix chain 'H' and resid 49 through 63 Processing helix chain 'H' and resid 70 through 79 Processing helix chain 'H' and resid 80 through 89 Processing helix chain 'H' and resid 130 through 150 removed outlier: 3.689A pdb=" N GLU H 150 " --> pdb=" O ALA H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 174 Proline residue: H 167 - end of helix removed outlier: 4.000A pdb=" N TYR H 172 " --> pdb=" O GLN H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 195 removed outlier: 3.983A pdb=" N GLU H 182 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 217 Processing helix chain 'H' and resid 219 through 235 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 96 Processing sheet with id=AA2, first strand: chain 'B' and resid 94 through 96 Processing sheet with id=AA3, first strand: chain 'C' and resid 29 through 33 removed outlier: 6.934A pdb=" N THR C 113 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ILE C 18 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA C 111 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LEU C 20 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA C 109 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 119 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 1017 through 1021 removed outlier: 3.980A pdb=" N THR C 39 " --> pdb=" O ALA C1046 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR C1050 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL C1066 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA C 40 " --> pdb=" O VAL C1066 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL C1068 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE C 42 " --> pdb=" O VAL C1068 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N ARG C1070 " --> pdb=" O ILE C 42 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 893 through 898 Processing sheet with id=AA6, first strand: chain 'D' and resid 29 through 33 removed outlier: 6.925A pdb=" N THR D 113 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ILE D 18 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA D 111 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU D 20 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA D 109 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA D 119 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 1017 through 1021 removed outlier: 3.977A pdb=" N THR D 39 " --> pdb=" O ALA D1046 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR D1050 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL D1066 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA D 40 " --> pdb=" O VAL D1066 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL D1068 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE D 42 " --> pdb=" O VAL D1068 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N ARG D1070 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU D1074 " --> pdb=" O ARG D1071 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 893 through 898 Processing sheet with id=AA9, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AB1, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.291A pdb=" N ALA E 158 " --> pdb=" O ILE E 210 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AB3, first strand: chain 'F' and resid 158 through 161 removed outlier: 4.733A pdb=" N ALA F 158 " --> pdb=" O ILE F 210 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 64 through 66 Processing sheet with id=AB5, first strand: chain 'G' and resid 158 through 161 removed outlier: 4.290A pdb=" N ALA G 158 " --> pdb=" O ILE G 210 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 64 through 66 Processing sheet with id=AB7, first strand: chain 'H' and resid 158 through 161 removed outlier: 4.730A pdb=" N ALA H 158 " --> pdb=" O ILE H 210 " (cutoff:3.500A) 1176 hydrogen bonds defined for protein. 3435 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: 3.20 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6808 1.34 - 1.46: 2728 1.46 - 1.57: 10178 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 19792 Sorted by residual: bond pdb=" CA ILE H 166 " pdb=" CB ILE H 166 " ideal model delta sigma weight residual 1.539 1.532 0.007 5.40e-03 3.43e+04 1.63e+00 bond pdb=" CA ILE F 166 " pdb=" CB ILE F 166 " ideal model delta sigma weight residual 1.539 1.533 0.006 5.40e-03 3.43e+04 1.17e+00 bond pdb=" CA VAL D 822 " pdb=" CB VAL D 822 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 9.74e-01 bond pdb=" CA VAL C 822 " pdb=" CB VAL C 822 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.46e-01 bond pdb=" CA GLN D 263 " pdb=" C GLN D 263 " ideal model delta sigma weight residual 1.522 1.532 -0.011 1.26e-02 6.30e+03 7.18e-01 ... (remaining 19787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 26217 1.16 - 2.33: 415 2.33 - 3.49: 76 3.49 - 4.66: 20 4.66 - 5.82: 12 Bond angle restraints: 26740 Sorted by residual: angle pdb=" C GLN F 116 " pdb=" N ASP F 117 " pdb=" CA ASP F 117 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 7.99e+00 angle pdb=" N VAL C 225 " pdb=" CA VAL C 225 " pdb=" C VAL C 225 " ideal model delta sigma weight residual 111.62 109.47 2.15 7.90e-01 1.60e+00 7.42e+00 angle pdb=" C GLN H 116 " pdb=" N ASP H 117 " pdb=" CA ASP H 117 " ideal model delta sigma weight residual 121.54 126.11 -4.57 1.91e+00 2.74e-01 5.71e+00 angle pdb=" C VAL A 114 " pdb=" N ASP A 115 " pdb=" CA ASP A 115 " ideal model delta sigma weight residual 122.38 118.39 3.99 1.81e+00 3.05e-01 4.86e+00 angle pdb=" C LEU C 224 " pdb=" N VAL C 225 " pdb=" CA VAL C 225 " ideal model delta sigma weight residual 123.16 120.87 2.29 1.06e+00 8.90e-01 4.66e+00 ... (remaining 26735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 11516 16.31 - 32.61: 501 32.61 - 48.92: 112 48.92 - 65.22: 15 65.22 - 81.53: 6 Dihedral angle restraints: 12150 sinusoidal: 5048 harmonic: 7102 Sorted by residual: dihedral pdb=" N LEU B 54 " pdb=" CA LEU B 54 " pdb=" CB LEU B 54 " pdb=" CG LEU B 54 " ideal model delta sinusoidal sigma weight residual -60.00 -118.75 58.75 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU A 85 " pdb=" CA LEU A 85 " pdb=" CB LEU A 85 " pdb=" CG LEU A 85 " ideal model delta sinusoidal sigma weight residual -60.00 -118.28 58.28 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N ARG F 183 " pdb=" CA ARG F 183 " pdb=" CB ARG F 183 " pdb=" CG ARG F 183 " ideal model delta sinusoidal sigma weight residual -60.00 -117.68 57.68 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 12147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1864 0.026 - 0.051: 696 0.051 - 0.077: 312 0.077 - 0.103: 116 0.103 - 0.129: 68 Chirality restraints: 3056 Sorted by residual: chirality pdb=" CA PRO H 220 " pdb=" N PRO H 220 " pdb=" C PRO H 220 " pdb=" CB PRO H 220 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA PRO F 220 " pdb=" N PRO F 220 " pdb=" C PRO F 220 " pdb=" CB PRO F 220 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA VAL B 94 " pdb=" N VAL B 94 " pdb=" C VAL B 94 " pdb=" CB VAL B 94 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 3053 not shown) Planarity restraints: 3488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 366 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO A 367 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 367 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 367 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 357 " 0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO B 358 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 358 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 358 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 179 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO C 180 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 180 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 180 " -0.018 5.00e-02 4.00e+02 ... (remaining 3485 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 4963 2.82 - 3.34: 17809 3.34 - 3.86: 29525 3.86 - 4.38: 32661 4.38 - 4.90: 59821 Nonbonded interactions: 144779 Sorted by model distance: nonbonded pdb=" O LEU B 93 " pdb=" OG1 THR B 104 " model vdw 2.294 3.040 nonbonded pdb=" O LEU A 93 " pdb=" OG1 THR A 104 " model vdw 2.296 3.040 nonbonded pdb=" OE2 GLU D 147 " pdb=" OH TYR D 194 " model vdw 2.298 3.040 nonbonded pdb=" OE2 GLU C 147 " pdb=" OH TYR C 194 " model vdw 2.304 3.040 nonbonded pdb=" OG SER C 133 " pdb=" OD2 ASP C 138 " model vdw 2.309 3.040 ... (remaining 144774 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 48 through 110 or resid 120 through 151 or resid 156 throu \ gh 236)) selection = chain 'G' selection = (chain 'H' and (resid 48 through 110 or resid 120 through 151 or resid 156 throu \ gh 236)) } 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: 4.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.010 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 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 : 0.002 0.036 19792 Z= 0.110 Angle : 0.421 5.822 26740 Z= 0.227 Chirality : 0.038 0.129 3056 Planarity : 0.004 0.042 3488 Dihedral : 9.972 81.528 7518 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.44 % Allowed : 3.55 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.18), residues: 2390 helix: 2.68 (0.14), residues: 1428 sheet: 0.30 (0.34), residues: 250 loop : -0.93 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 286 TYR 0.010 0.001 TYR C 825 PHE 0.010 0.001 PHE A 250 TRP 0.008 0.001 TRP D 128 HIS 0.002 0.001 HIS B 19 Details of bonding type rmsd covalent geometry : bond 0.00238 (19792) covalent geometry : angle 0.42079 (26740) hydrogen bonds : bond 0.13017 ( 1176) hydrogen bonds : angle 4.81129 ( 3435) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.840 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: C 869 MET cc_start: 0.9033 (mmm) cc_final: 0.8819 (mmp) REVERT: D 171 MET cc_start: 0.9049 (mtm) cc_final: 0.8843 (mtp) REVERT: D 869 MET cc_start: 0.9021 (mmm) cc_final: 0.8804 (mmp) REVERT: E 147 TYR cc_start: 0.7115 (t80) cc_final: 0.6881 (t80) REVERT: F 92 ASP cc_start: 0.9118 (m-30) cc_final: 0.8805 (m-30) REVERT: F 178 SER cc_start: 0.8509 (t) cc_final: 0.8291 (p) REVERT: F 206 ASP cc_start: 0.8796 (t0) cc_final: 0.8556 (t0) REVERT: G 147 TYR cc_start: 0.7230 (t80) cc_final: 0.6972 (t80) REVERT: H 92 ASP cc_start: 0.9097 (m-30) cc_final: 0.8776 (m-30) REVERT: H 178 SER cc_start: 0.8560 (t) cc_final: 0.8357 (p) REVERT: H 206 ASP cc_start: 0.8791 (t0) cc_final: 0.8552 (t0) outliers start: 30 outliers final: 7 residues processed: 225 average time/residue: 0.8067 time to fit residues: 197.9505 Evaluate side-chains 105 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 916 SER Chi-restraints excluded: chain D residue 916 SER Chi-restraints excluded: chain E residue 168 GLN Chi-restraints excluded: chain F residue 117 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 19 HIS A 80 GLN B 6 GLN B 19 HIS B 80 GLN C 858 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 858 GLN D 887 GLN E 57 GLN E 110 GLN E 127 GLN E 130 ASN F 57 GLN F 80 ASN F 110 GLN F 116 GLN F 127 GLN F 142 GLN F 149 GLN F 157 GLN F 168 GLN F 205 HIS G 57 GLN G 110 GLN G 127 GLN G 130 ASN H 57 GLN H 110 GLN H 116 GLN H 127 GLN H 142 GLN H 149 GLN H 157 GLN H 168 GLN H 205 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.089695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.060033 restraints weight = 52136.119| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.34 r_work: 0.2877 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19792 Z= 0.116 Angle : 0.488 8.473 26740 Z= 0.250 Chirality : 0.038 0.153 3056 Planarity : 0.004 0.068 3488 Dihedral : 3.825 72.632 2731 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.30 % Allowed : 9.03 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.18), residues: 2390 helix: 2.84 (0.14), residues: 1442 sheet: 0.30 (0.34), residues: 250 loop : -1.02 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 75 TYR 0.018 0.001 TYR G 74 PHE 0.007 0.001 PHE A 247 TRP 0.009 0.001 TRP D 128 HIS 0.003 0.001 HIS C1061 Details of bonding type rmsd covalent geometry : bond 0.00263 (19792) covalent geometry : angle 0.48756 (26740) hydrogen bonds : bond 0.04230 ( 1176) hydrogen bonds : angle 3.92608 ( 3435) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6947 (ttt) REVERT: B 101 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7284 (pp) REVERT: C 801 MET cc_start: 0.8332 (mtp) cc_final: 0.8044 (mtm) REVERT: C 869 MET cc_start: 0.9081 (mmm) cc_final: 0.8853 (mmp) REVERT: D 869 MET cc_start: 0.9050 (mmm) cc_final: 0.8819 (mmp) REVERT: E 74 TYR cc_start: 0.9204 (t80) cc_final: 0.8965 (t80) REVERT: F 178 SER cc_start: 0.8511 (t) cc_final: 0.8309 (p) REVERT: F 206 ASP cc_start: 0.8662 (t0) cc_final: 0.8299 (t0) REVERT: H 206 ASP cc_start: 0.8669 (t0) cc_final: 0.8326 (t0) outliers start: 27 outliers final: 7 residues processed: 123 average time/residue: 0.5825 time to fit residues: 81.1499 Evaluate side-chains 97 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 202 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 179 optimal weight: 2.9990 chunk 232 optimal weight: 0.0870 chunk 154 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 214 optimal weight: 9.9990 chunk 156 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 228 optimal weight: 0.7980 chunk 142 optimal weight: 0.2980 chunk 46 optimal weight: 4.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.092389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062594 restraints weight = 52847.086| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.38 r_work: 0.2951 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19792 Z= 0.089 Angle : 0.437 7.945 26740 Z= 0.221 Chirality : 0.037 0.146 3056 Planarity : 0.004 0.047 3488 Dihedral : 3.297 39.214 2720 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.30 % Allowed : 8.93 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.18), residues: 2390 helix: 2.99 (0.14), residues: 1446 sheet: 0.23 (0.34), residues: 254 loop : -1.08 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 51 TYR 0.010 0.001 TYR E 74 PHE 0.005 0.001 PHE C 187 TRP 0.010 0.001 TRP D 128 HIS 0.002 0.000 HIS C1060 Details of bonding type rmsd covalent geometry : bond 0.00190 (19792) covalent geometry : angle 0.43682 (26740) hydrogen bonds : bond 0.03452 ( 1176) hydrogen bonds : angle 3.66443 ( 3435) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6888 (ttt) REVERT: B 101 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7351 (pp) REVERT: C 801 MET cc_start: 0.8280 (mtp) cc_final: 0.8054 (ttm) REVERT: D 869 MET cc_start: 0.9041 (mmm) cc_final: 0.8787 (mmp) REVERT: D 1080 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8883 (mm) REVERT: F 206 ASP cc_start: 0.8628 (t0) cc_final: 0.8242 (t0) REVERT: H 206 ASP cc_start: 0.8655 (t0) cc_final: 0.8292 (t0) outliers start: 27 outliers final: 7 residues processed: 121 average time/residue: 0.6263 time to fit residues: 85.6550 Evaluate side-chains 97 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain E residue 162 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 159 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 203 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 101 optimal weight: 0.0370 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** 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 = 0.3651 r_free = 0.3651 target = 0.089945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.059787 restraints weight = 53028.184| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.48 r_work: 0.2848 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19792 Z= 0.130 Angle : 0.470 9.546 26740 Z= 0.237 Chirality : 0.038 0.145 3056 Planarity : 0.004 0.039 3488 Dihedral : 3.218 15.159 2718 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.49 % Allowed : 9.27 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.18), residues: 2390 helix: 3.02 (0.14), residues: 1450 sheet: 0.49 (0.36), residues: 230 loop : -1.07 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 125 TYR 0.022 0.001 TYR E 74 PHE 0.023 0.001 PHE D 886 TRP 0.008 0.001 TRP D 128 HIS 0.002 0.000 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00310 (19792) covalent geometry : angle 0.46962 (26740) hydrogen bonds : bond 0.04069 ( 1176) hydrogen bonds : angle 3.67628 ( 3435) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7328 (pp) REVERT: C 801 MET cc_start: 0.8225 (mtp) cc_final: 0.7981 (ttm) REVERT: C 1080 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8882 (mm) REVERT: D 869 MET cc_start: 0.8999 (mmm) cc_final: 0.8741 (mmp) REVERT: F 206 ASP cc_start: 0.8748 (t0) cc_final: 0.8258 (t0) REVERT: H 206 ASP cc_start: 0.8741 (t0) cc_final: 0.8239 (t0) outliers start: 31 outliers final: 12 residues processed: 112 average time/residue: 0.5783 time to fit residues: 73.9178 Evaluate side-chains 99 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 1080 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 162 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 156 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 204 optimal weight: 0.9980 chunk 230 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 GLN D 213 GLN G 196 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.090819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.061319 restraints weight = 52747.820| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.35 r_work: 0.2932 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19792 Z= 0.095 Angle : 0.444 8.626 26740 Z= 0.222 Chirality : 0.037 0.147 3056 Planarity : 0.003 0.039 3488 Dihedral : 3.165 15.292 2718 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.97 % Favored : 96.99 % Rotamer: Outliers : 1.59 % Allowed : 9.75 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.18), residues: 2390 helix: 3.07 (0.14), residues: 1450 sheet: 0.43 (0.35), residues: 234 loop : -1.07 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 125 TYR 0.018 0.001 TYR G 147 PHE 0.019 0.001 PHE D 886 TRP 0.009 0.001 TRP D 128 HIS 0.002 0.000 HIS C1061 Details of bonding type rmsd covalent geometry : bond 0.00214 (19792) covalent geometry : angle 0.44424 (26740) hydrogen bonds : bond 0.03363 ( 1176) hydrogen bonds : angle 3.54167 ( 3435) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7555 (pp) REVERT: B 159 GLN cc_start: 0.9371 (tt0) cc_final: 0.8840 (tm-30) REVERT: C 801 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.8026 (ttm) REVERT: F 59 MET cc_start: 0.9370 (ttp) cc_final: 0.9156 (ttp) REVERT: F 206 ASP cc_start: 0.8703 (t0) cc_final: 0.8279 (t0) REVERT: G 74 TYR cc_start: 0.9147 (t80) cc_final: 0.8920 (t80) REVERT: H 206 ASP cc_start: 0.8654 (t0) cc_final: 0.8221 (t0) outliers start: 33 outliers final: 15 residues processed: 118 average time/residue: 0.6151 time to fit residues: 82.0066 Evaluate side-chains 102 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 162 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 43 optimal weight: 0.8980 chunk 191 optimal weight: 8.9990 chunk 192 optimal weight: 5.9990 chunk 198 optimal weight: 0.3980 chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 49 optimal weight: 0.0050 chunk 15 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.092801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.062026 restraints weight = 52408.176| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.52 r_work: 0.2949 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19792 Z= 0.087 Angle : 0.448 9.034 26740 Z= 0.222 Chirality : 0.037 0.145 3056 Planarity : 0.003 0.036 3488 Dihedral : 3.107 15.021 2718 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.69 % Rotamer: Outliers : 1.25 % Allowed : 9.99 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.18), residues: 2390 helix: 3.11 (0.14), residues: 1450 sheet: 0.51 (0.36), residues: 234 loop : -1.05 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 51 TYR 0.013 0.001 TYR G 147 PHE 0.019 0.001 PHE D 886 TRP 0.010 0.001 TRP D 128 HIS 0.003 0.000 HIS G 69 Details of bonding type rmsd covalent geometry : bond 0.00191 (19792) covalent geometry : angle 0.44787 (26740) hydrogen bonds : bond 0.03085 ( 1176) hydrogen bonds : angle 3.45676 ( 3435) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7691 (pp) REVERT: B 159 GLN cc_start: 0.9369 (tt0) cc_final: 0.8836 (tm-30) REVERT: C 801 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7989 (ttm) REVERT: H 206 ASP cc_start: 0.8707 (t0) cc_final: 0.8260 (t0) outliers start: 26 outliers final: 14 residues processed: 115 average time/residue: 0.5957 time to fit residues: 77.6355 Evaluate side-chains 97 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 1080 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 162 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 104 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 196 optimal weight: 0.9980 chunk 113 optimal weight: 0.3980 chunk 72 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 216 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.091423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.061857 restraints weight = 52658.631| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.40 r_work: 0.2945 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19792 Z= 0.093 Angle : 0.461 9.240 26740 Z= 0.227 Chirality : 0.037 0.178 3056 Planarity : 0.003 0.034 3488 Dihedral : 3.067 14.793 2718 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.31 % Favored : 96.65 % Rotamer: Outliers : 1.30 % Allowed : 10.66 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.18), residues: 2390 helix: 3.13 (0.14), residues: 1450 sheet: 0.53 (0.36), residues: 234 loop : -1.03 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 51 TYR 0.035 0.001 TYR G 74 PHE 0.017 0.001 PHE D 886 TRP 0.009 0.001 TRP D 128 HIS 0.002 0.000 HIS C1061 Details of bonding type rmsd covalent geometry : bond 0.00211 (19792) covalent geometry : angle 0.46079 (26740) hydrogen bonds : bond 0.03155 ( 1176) hydrogen bonds : angle 3.43171 ( 3435) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7700 (pp) REVERT: B 159 GLN cc_start: 0.9373 (tt0) cc_final: 0.8841 (tm-30) REVERT: C 801 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.8036 (ttm) outliers start: 27 outliers final: 13 residues processed: 106 average time/residue: 0.5962 time to fit residues: 71.7114 Evaluate side-chains 93 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 162 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 197 optimal weight: 0.0670 chunk 29 optimal weight: 0.8980 chunk 204 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 181 optimal weight: 0.0970 chunk 217 optimal weight: 0.0270 chunk 103 optimal weight: 0.9980 chunk 151 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.4174 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.092861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.062042 restraints weight = 52584.597| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.57 r_work: 0.2970 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19792 Z= 0.084 Angle : 0.459 9.461 26740 Z= 0.224 Chirality : 0.037 0.212 3056 Planarity : 0.003 0.045 3488 Dihedral : 3.028 14.772 2718 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.18 % Favored : 96.78 % Rotamer: Outliers : 1.15 % Allowed : 10.57 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.18), residues: 2390 helix: 3.12 (0.14), residues: 1454 sheet: 0.57 (0.36), residues: 234 loop : -1.00 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 51 TYR 0.032 0.001 TYR G 74 PHE 0.017 0.001 PHE D 886 TRP 0.010 0.000 TRP D 128 HIS 0.001 0.000 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00184 (19792) covalent geometry : angle 0.45935 (26740) hydrogen bonds : bond 0.02791 ( 1176) hydrogen bonds : angle 3.37361 ( 3435) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7656 (pp) REVERT: B 159 GLN cc_start: 0.9365 (tt0) cc_final: 0.8827 (tm-30) REVERT: C 801 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.8009 (ttm) REVERT: D 801 MET cc_start: 0.7871 (mpp) cc_final: 0.7621 (mpp) outliers start: 24 outliers final: 12 residues processed: 99 average time/residue: 0.6070 time to fit residues: 68.6586 Evaluate side-chains 91 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 162 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 209 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 196 optimal weight: 0.0000 chunk 206 optimal weight: 0.3980 chunk 139 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 210 optimal weight: 0.0060 overall best weight: 0.4800 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.092969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.062165 restraints weight = 52497.262| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.54 r_work: 0.2962 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19792 Z= 0.087 Angle : 0.467 10.322 26740 Z= 0.227 Chirality : 0.037 0.219 3056 Planarity : 0.003 0.043 3488 Dihedral : 2.987 14.573 2718 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.05 % Favored : 96.90 % Rotamer: Outliers : 0.82 % Allowed : 10.81 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.18), residues: 2390 helix: 3.15 (0.14), residues: 1454 sheet: 0.63 (0.36), residues: 234 loop : -0.97 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 51 TYR 0.031 0.001 TYR G 74 PHE 0.017 0.001 PHE D 886 TRP 0.010 0.001 TRP D 128 HIS 0.002 0.000 HIS G 196 Details of bonding type rmsd covalent geometry : bond 0.00192 (19792) covalent geometry : angle 0.46686 (26740) hydrogen bonds : bond 0.02752 ( 1176) hydrogen bonds : angle 3.34608 ( 3435) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7647 (pp) REVERT: B 159 GLN cc_start: 0.9367 (tt0) cc_final: 0.8819 (tm-30) REVERT: C 801 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7999 (ttm) REVERT: D 801 MET cc_start: 0.7795 (mpp) cc_final: 0.7578 (mpp) outliers start: 17 outliers final: 11 residues processed: 97 average time/residue: 0.6610 time to fit residues: 72.0972 Evaluate side-chains 90 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 220 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 177 optimal weight: 9.9990 chunk 25 optimal weight: 0.3980 chunk 198 optimal weight: 0.2980 chunk 144 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.090496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.060525 restraints weight = 52634.037| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.45 r_work: 0.2890 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19792 Z= 0.097 Angle : 0.483 12.289 26740 Z= 0.234 Chirality : 0.037 0.204 3056 Planarity : 0.003 0.043 3488 Dihedral : 3.002 14.290 2718 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.74 % Rotamer: Outliers : 0.67 % Allowed : 11.05 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.18), residues: 2390 helix: 3.17 (0.14), residues: 1454 sheet: 0.64 (0.36), residues: 234 loop : -0.97 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 51 TYR 0.029 0.001 TYR G 74 PHE 0.016 0.001 PHE D 886 TRP 0.008 0.001 TRP D 128 HIS 0.002 0.000 HIS C1061 Details of bonding type rmsd covalent geometry : bond 0.00229 (19792) covalent geometry : angle 0.48325 (26740) hydrogen bonds : bond 0.03053 ( 1176) hydrogen bonds : angle 3.38768 ( 3435) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 GLN cc_start: 0.9351 (tt0) cc_final: 0.8810 (tm-30) REVERT: C 801 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7950 (ttm) REVERT: D 801 MET cc_start: 0.7783 (mpp) cc_final: 0.7531 (mpp) outliers start: 14 outliers final: 9 residues processed: 93 average time/residue: 0.6547 time to fit residues: 68.3325 Evaluate side-chains 87 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 151 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 180 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 199 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.090514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.060565 restraints weight = 52431.668| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.47 r_work: 0.2888 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19792 Z= 0.097 Angle : 0.488 12.851 26740 Z= 0.237 Chirality : 0.038 0.236 3056 Planarity : 0.003 0.043 3488 Dihedral : 3.019 14.388 2718 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.01 % Favored : 96.95 % Rotamer: Outliers : 0.62 % Allowed : 11.19 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.18), residues: 2390 helix: 3.17 (0.14), residues: 1454 sheet: 0.64 (0.36), residues: 234 loop : -0.98 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 51 TYR 0.028 0.001 TYR G 74 PHE 0.016 0.001 PHE D 886 TRP 0.009 0.001 TRP D 128 HIS 0.001 0.000 HIS C1061 Details of bonding type rmsd covalent geometry : bond 0.00228 (19792) covalent geometry : angle 0.48837 (26740) hydrogen bonds : bond 0.03062 ( 1176) hydrogen bonds : angle 3.40323 ( 3435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5662.89 seconds wall clock time: 97 minutes 43.88 seconds (5863.88 seconds total)