Starting phenix.real_space_refine on Sun Aug 24 19:07:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tqz_41566/08_2025/8tqz_41566.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tqz_41566/08_2025/8tqz_41566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tqz_41566/08_2025/8tqz_41566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tqz_41566/08_2025/8tqz_41566.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tqz_41566/08_2025/8tqz_41566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tqz_41566/08_2025/8tqz_41566.map" } resolution = 2.9 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= 0.043 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 121 5.16 5 C 14206 2.51 5 N 3912 2.21 5 O 4095 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22334 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2039 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 256} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2002 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3244 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 395} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2483 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1983 Classifications: {'peptide': 256} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 245} Chain breaks: 2 Chain: "I" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 380 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain breaks: 3 Chain: "B" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3239 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 394} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2486 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 1 Chain: "F" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2690 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 328} Chain: "J" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1788 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 5.30, per 1000 atoms: 0.24 Number of scatterers: 22334 At special positions: 0 Unit cell: (133.6, 177.02, 122.745, 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 121 16.00 O 4095 8.00 N 3912 7.00 C 14206 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: 1.93 Conformation dependent library (CDL) restraints added in 875.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5430 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 29 sheets defined 45.5% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'G' and resid 10 through 15 Processing helix chain 'G' and resid 21 through 35 removed outlier: 4.101A pdb=" N LYS G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 60 removed outlier: 3.553A pdb=" N ASN G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 74 Processing helix chain 'G' and resid 75 through 77 No H-bonds generated for 'chain 'G' and resid 75 through 77' Processing helix chain 'G' and resid 90 through 116 removed outlier: 3.913A pdb=" N GLU G 95 " --> pdb=" O LYS G 91 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG G 96 " --> pdb=" O ILE G 92 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY G 97 " --> pdb=" O MET G 93 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU G 98 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG G 108 " --> pdb=" O ILE G 104 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 119 No H-bonds generated for 'chain 'G' and resid 117 through 119' Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 160 through 170 removed outlier: 4.096A pdb=" N HIS G 170 " --> pdb=" O LYS G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 211 No H-bonds generated for 'chain 'G' and resid 209 through 211' Processing helix chain 'G' and resid 212 through 222 Processing helix chain 'G' and resid 231 through 235 removed outlier: 3.863A pdb=" N LYS G 234 " --> pdb=" O GLU G 231 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE G 235 " --> pdb=" O SER G 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 231 through 235' Processing helix chain 'G' and resid 247 through 252 removed outlier: 3.626A pdb=" N LYS G 251 " --> pdb=" O PRO G 247 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR G 252 " --> pdb=" O ASP G 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 247 through 252' Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 295 through 303 removed outlier: 3.703A pdb=" N GLU G 299 " --> pdb=" O ALA G 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 17 removed outlier: 3.692A pdb=" N ASP H 17 " --> pdb=" O GLN H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 35 removed outlier: 4.235A pdb=" N LYS H 35 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 60 Processing helix chain 'H' and resid 62 through 76 removed outlier: 3.684A pdb=" N SER H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 116 removed outlier: 4.489A pdb=" N PHE H 100 " --> pdb=" O ARG H 96 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU H 101 " --> pdb=" O GLY H 97 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU H 106 " --> pdb=" O ARG H 102 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG H 108 " --> pdb=" O ILE H 104 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 119 No H-bonds generated for 'chain 'H' and resid 117 through 119' Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 160 through 170 removed outlier: 4.268A pdb=" N HIS H 170 " --> pdb=" O LYS H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 183 removed outlier: 3.876A pdb=" N VAL H 183 " --> pdb=" O ASP H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 190 Processing helix chain 'H' and resid 211 through 222 removed outlier: 3.841A pdb=" N MET H 215 " --> pdb=" O GLY H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 246 removed outlier: 3.763A pdb=" N VAL H 246 " --> pdb=" O GLN H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 Processing helix chain 'H' and resid 277 through 281 Processing helix chain 'H' and resid 292 through 294 No H-bonds generated for 'chain 'H' and resid 292 through 294' Processing helix chain 'H' and resid 295 through 304 removed outlier: 3.534A pdb=" N GLU H 299 " --> pdb=" O ALA H 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.526A pdb=" N TYR A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.653A pdb=" N LYS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 130 through 142 removed outlier: 3.608A pdb=" N VAL A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 removed outlier: 3.652A pdb=" N GLU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.545A pdb=" N ALA A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'D' and resid 9 through 25 removed outlier: 3.694A pdb=" N GLY D 25 " --> pdb=" O THR D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 48 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.687A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 98 Processing helix chain 'D' and resid 128 through 145 removed outlier: 3.869A pdb=" N ASN D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 153 removed outlier: 3.741A pdb=" N ASN D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 159 removed outlier: 3.932A pdb=" N HIS D 158 " --> pdb=" O GLN D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 181 removed outlier: 3.952A pdb=" N ALA D 181 " --> pdb=" O PHE D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.730A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 222 removed outlier: 3.838A pdb=" N ALA D 221 " --> pdb=" O THR D 218 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE D 222 " --> pdb=" O ASP D 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 218 through 222' Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.652A pdb=" N LYS D 273 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU D 274 " --> pdb=" O MET D 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 270 through 274' Processing helix chain 'D' and resid 296 through 305 removed outlier: 4.394A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU D 304 " --> pdb=" O ASP D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 344 removed outlier: 3.591A pdb=" N LEU D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.588A pdb=" N HIS D 349 " --> pdb=" O PRO D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 238 removed outlier: 3.549A pdb=" N VAL E 236 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE E 237 " --> pdb=" O LEU E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 283 Processing helix chain 'E' and resid 294 through 312 Processing helix chain 'E' and resid 312 through 325 removed outlier: 4.354A pdb=" N GLN E 325 " --> pdb=" O ARG E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 353 removed outlier: 3.507A pdb=" N GLY E 353 " --> pdb=" O ALA E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 380 removed outlier: 4.069A pdb=" N THR E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 379 " --> pdb=" O SER E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 396 through 398 No H-bonds generated for 'chain 'E' and resid 396 through 398' Processing helix chain 'E' and resid 418 through 430 removed outlier: 4.360A pdb=" N GLN E 422 " --> pdb=" O VAL E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 463 removed outlier: 3.852A pdb=" N ASP E 462 " --> pdb=" O ASP E 459 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU E 463 " --> pdb=" O PRO E 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 459 through 463' Processing helix chain 'E' and resid 493 through 497 Processing helix chain 'E' and resid 508 through 510 No H-bonds generated for 'chain 'E' and resid 508 through 510' Processing helix chain 'E' and resid 511 through 516 Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 230 through 235 Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.633A pdb=" N ILE B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.555A pdb=" N GLU B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 253 through 263 removed outlier: 4.111A pdb=" N ALA B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 277 removed outlier: 3.804A pdb=" N LEU B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.849A pdb=" N SER B 334 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 30 through 48 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.702A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 98 Processing helix chain 'C' and resid 128 through 153 removed outlier: 4.422A pdb=" N MET C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 199 through 209 removed outlier: 3.579A pdb=" N MET C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 223 removed outlier: 3.592A pdb=" N ILE C 222 " --> pdb=" O ASP C 219 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N PHE C 223 " --> pdb=" O ALA C 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 219 through 223' Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.635A pdb=" N LYS C 273 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 274 " --> pdb=" O MET C 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 270 through 274' Processing helix chain 'C' and resid 296 through 304 removed outlier: 4.438A pdb=" N GLY C 300 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU C 304 " --> pdb=" O ASP C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.784A pdb=" N GLU C 342 " --> pdb=" O ARG C 338 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 Processing helix chain 'F' and resid 191 through 196 removed outlier: 4.144A pdb=" N GLN F 194 " --> pdb=" O SER F 191 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE F 195 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 217 Processing helix chain 'F' and resid 221 through 239 removed outlier: 3.649A pdb=" N CYS F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 267 removed outlier: 4.785A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASN F 254 " --> pdb=" O ARG F 250 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 270 through 286 Processing helix chain 'F' and resid 292 through 312 Processing helix chain 'F' and resid 312 through 325 removed outlier: 3.889A pdb=" N GLN F 317 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN F 325 " --> pdb=" O ARG F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 353 Processing helix chain 'F' and resid 368 through 379 removed outlier: 4.133A pdb=" N THR F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 removed outlier: 3.599A pdb=" N VAL F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 398 No H-bonds generated for 'chain 'F' and resid 396 through 398' Processing helix chain 'F' and resid 420 through 430 Processing helix chain 'F' and resid 439 through 443 removed outlier: 3.510A pdb=" N LYS F 442 " --> pdb=" O GLU F 439 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE F 443 " --> pdb=" O THR F 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 439 through 443' Processing helix chain 'F' and resid 459 through 464 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 493 through 497 Processing helix chain 'F' and resid 511 through 517 removed outlier: 3.806A pdb=" N VAL F 515 " --> pdb=" O SER F 511 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 33 removed outlier: 4.030A pdb=" N ASN J 32 " --> pdb=" O PRO J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 35 No H-bonds generated for 'chain 'J' and resid 34 through 35' Processing helix chain 'J' and resid 36 through 44 Processing helix chain 'J' and resid 86 through 93 Processing helix chain 'J' and resid 114 through 124 removed outlier: 4.243A pdb=" N LEU J 120 " --> pdb=" O GLU J 116 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE J 121 " --> pdb=" O VAL J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'J' and resid 208 through 218 removed outlier: 3.727A pdb=" N VAL J 212 " --> pdb=" O LYS J 208 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU J 217 " --> pdb=" O ASP J 213 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN J 218 " --> pdb=" O PHE J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 236 removed outlier: 4.984A pdb=" N ILE J 229 " --> pdb=" O ARG J 225 " (cutoff:3.500A) Proline residue: J 230 - end of helix Processing helix chain 'J' and resid 315 through 334 Proline residue: J 327 - end of helix removed outlier: 3.865A pdb=" N ALA J 332 " --> pdb=" O LYS J 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 175 through 178 removed outlier: 8.795A pdb=" N THR G 176 " --> pdb=" O PHE G 148 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL G 150 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL G 178 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL G 152 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE G 194 " --> pdb=" O LEU G 126 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL G 193 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL G 229 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL G 195 " --> pdb=" O VAL G 229 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE G 226 " --> pdb=" O LEU G 283 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N PHE G 285 " --> pdb=" O PHE G 226 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL G 228 " --> pdb=" O PHE G 285 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR G 286 " --> pdb=" O GLY G 289 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 199 through 200 Processing sheet with id=AA3, first strand: chain 'H' and resid 175 through 178 removed outlier: 6.509A pdb=" N VAL H 150 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL H 178 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL H 152 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N THR H 124 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE H 194 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU H 126 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N GLY H 196 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL H 193 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL H 229 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL H 195 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE H 226 " --> pdb=" O LEU H 283 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N PHE H 285 " --> pdb=" O PHE H 226 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL H 228 " --> pdb=" O PHE H 285 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR H 286 " --> pdb=" O GLY H 289 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 124 removed outlier: 6.779A pdb=" N THR A 91 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 48 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 250 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR A 152 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N HIS A 248 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N CYS A 247 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N LYS A 186 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE A 249 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN A 286 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET A 181 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE A 287 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG A 211 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 206 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 202 " --> pdb=" O GLN A 216 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 216 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 119 through 124 removed outlier: 6.779A pdb=" N THR A 91 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 48 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 250 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR A 152 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N HIS A 248 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N CYS A 247 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N LYS A 186 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE A 249 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN A 286 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET A 181 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE A 287 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG A 211 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 206 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL A 238 " --> pdb=" O PHE I 195 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE I 195 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL I 160 " --> pdb=" O ARG I 194 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS I 196 " --> pdb=" O ILE I 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AA7, first strand: chain 'A' and resid 223 through 226 removed outlier: 3.814A pdb=" N PHE A 224 " --> pdb=" O ILE I 182 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU I 180 " --> pdb=" O PHE A 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 336 through 338 removed outlier: 3.616A pdb=" N ILE A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU A 361 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TYR A 395 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 430 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.228A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE A 373 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLN A 407 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR A 424 " --> pdb=" O LEU A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 384 through 385 removed outlier: 6.376A pdb=" N HIS A 384 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG A 401 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N GLU A 418 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 323 through 325 removed outlier: 3.829A pdb=" N LEU D 323 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE D 168 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 238 through 239 removed outlier: 3.822A pdb=" N THR D 238 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D 247 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 307 through 308 removed outlier: 6.042A pdb=" N SER D 307 " --> pdb=" O TYR E 385 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N LEU E 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL E 332 " --> pdb=" O LYS E 400 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU E 402 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU E 334 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'B' and resid 119 through 124 removed outlier: 3.556A pdb=" N PHE B 148 " --> pdb=" O CYS B 252 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 250 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR B 152 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N HIS B 248 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS B 247 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE B 184 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE B 249 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N THR B 182 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE B 251 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 180 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLN B 286 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET B 181 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AB8, first strand: chain 'B' and resid 212 through 217 removed outlier: 6.554A pdb=" N ALA B 204 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE B 215 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL B 202 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 223 through 226 Processing sheet with id=AC1, first strand: chain 'B' and resid 336 through 337 removed outlier: 6.040A pdb=" N LEU B 361 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL B 378 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR B 395 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 412 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 430 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 355 through 356 removed outlier: 6.279A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE B 373 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL B 390 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLN B 407 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR B 424 " --> pdb=" O LEU B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 401 through 402 removed outlier: 6.776A pdb=" N ARG B 401 " --> pdb=" O VAL B 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 323 through 325 removed outlier: 6.737A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL C 164 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE C 233 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET C 217 " --> pdb=" O VAL C 191 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 238 through 239 removed outlier: 3.898A pdb=" N LEU C 245 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 316 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA C 247 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.300A pdb=" N SER C 307 " --> pdb=" O TYR F 385 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N LEU F 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL F 332 " --> pdb=" O LYS F 400 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU F 402 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU F 334 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLY F 404 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N TYR F 336 " --> pdb=" O GLY F 404 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL F 401 " --> pdb=" O LEU F 435 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N CYS F 437 " --> pdb=" O VAL F 401 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU F 403 " --> pdb=" O CYS F 437 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL F 434 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE F 501 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL F 436 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 407 through 408 Processing sheet with id=AC8, first strand: chain 'J' and resid 52 through 55 removed outlier: 3.945A pdb=" N THR J 55 " --> pdb=" O ILE J 78 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 101 through 103 removed outlier: 3.540A pdb=" N VAL J 101 " --> pdb=" O LEU J 207 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 199 through 201 Processing sheet with id=AD2, first strand: chain 'J' and resid 167 through 170 removed outlier: 3.516A pdb=" N PHE J 169 " --> pdb=" O GLY J 159 " (cutoff:3.500A) 905 hydrogen bonds defined for protein. 2532 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: 4.72 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7385 1.34 - 1.46: 4221 1.46 - 1.58: 10955 1.58 - 1.70: 1 1.70 - 1.82: 181 Bond restraints: 22743 Sorted by residual: bond pdb=" CB PRO J 79 " pdb=" CG PRO J 79 " ideal model delta sigma weight residual 1.492 1.626 -0.134 5.00e-02 4.00e+02 7.18e+00 bond pdb=" CB ASN F 190 " pdb=" CG ASN F 190 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 1.99e+00 bond pdb=" CB GLU J 178 " pdb=" CG GLU J 178 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" CG ARG A 163 " pdb=" CD ARG A 163 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.51e+00 bond pdb=" C PHE A 57 " pdb=" N PRO A 58 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.20e-02 6.94e+03 1.47e+00 ... (remaining 22738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 30517 2.19 - 4.38: 256 4.38 - 6.56: 41 6.56 - 8.75: 14 8.75 - 10.94: 2 Bond angle restraints: 30830 Sorted by residual: angle pdb=" CA PRO J 79 " pdb=" N PRO J 79 " pdb=" CD PRO J 79 " ideal model delta sigma weight residual 112.00 103.74 8.26 1.40e+00 5.10e-01 3.48e+01 angle pdb=" CA GLU C 75 " pdb=" CB GLU C 75 " pdb=" CG GLU C 75 " ideal model delta sigma weight residual 114.10 120.78 -6.68 2.00e+00 2.50e-01 1.12e+01 angle pdb=" CA GLN E 309 " pdb=" CB GLN E 309 " pdb=" CG GLN E 309 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CA GLU J 178 " pdb=" CB GLU J 178 " pdb=" CG GLU J 178 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 angle pdb=" N PRO J 79 " pdb=" CD PRO J 79 " pdb=" CG PRO J 79 " ideal model delta sigma weight residual 103.20 98.34 4.86 1.50e+00 4.44e-01 1.05e+01 ... (remaining 30825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 11830 17.84 - 35.67: 1370 35.67 - 53.51: 482 53.51 - 71.34: 84 71.34 - 89.18: 34 Dihedral angle restraints: 13800 sinusoidal: 5459 harmonic: 8341 Sorted by residual: dihedral pdb=" CA PHE B 57 " pdb=" C PHE B 57 " pdb=" N PRO B 58 " pdb=" CA PRO B 58 " ideal model delta harmonic sigma weight residual 180.00 148.31 31.69 0 5.00e+00 4.00e-02 4.02e+01 dihedral pdb=" CA PRO A 453 " pdb=" C PRO A 453 " pdb=" N PRO A 454 " pdb=" CA PRO A 454 " ideal model delta harmonic sigma weight residual -180.00 -158.69 -21.31 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA PRO B 58 " pdb=" C PRO B 58 " pdb=" N ILE B 59 " pdb=" CA ILE B 59 " ideal model delta harmonic sigma weight residual -180.00 -161.55 -18.45 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 13797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3059 0.055 - 0.111: 512 0.111 - 0.166: 61 0.166 - 0.222: 3 0.222 - 0.277: 1 Chirality restraints: 3636 Sorted by residual: chirality pdb=" CB VAL B 238 " pdb=" CA VAL B 238 " pdb=" CG1 VAL B 238 " pdb=" CG2 VAL B 238 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CG LEU A 174 " pdb=" CB LEU A 174 " pdb=" CD1 LEU A 174 " pdb=" CD2 LEU A 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PHE A 57 " pdb=" N PHE A 57 " pdb=" C PHE A 57 " pdb=" CB PHE A 57 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.59e-01 ... (remaining 3633 not shown) Planarity restraints: 3926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 57 " -0.084 5.00e-02 4.00e+02 1.30e-01 2.70e+01 pdb=" N PRO B 58 " 0.225 5.00e-02 4.00e+02 pdb=" CA PRO B 58 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 58 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE J 78 " 0.087 5.00e-02 4.00e+02 1.26e-01 2.53e+01 pdb=" N PRO J 79 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO J 79 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO J 79 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 190 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.58e+00 pdb=" C ASN F 190 " 0.041 2.00e-02 2.50e+03 pdb=" O ASN F 190 " -0.016 2.00e-02 2.50e+03 pdb=" N SER F 191 " -0.013 2.00e-02 2.50e+03 ... (remaining 3923 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 220 2.62 - 3.19: 18479 3.19 - 3.76: 33897 3.76 - 4.33: 45134 4.33 - 4.90: 78110 Nonbonded interactions: 175840 Sorted by model distance: nonbonded pdb=" N GLY I 159 " pdb=" O PHE I 169 " model vdw 2.049 3.120 nonbonded pdb=" O PHE B 56 " pdb=" OG SER B 60 " model vdw 2.136 3.040 nonbonded pdb=" OH TYR F 240 " pdb=" OD1 ASP F 251 " model vdw 2.175 3.040 nonbonded pdb=" OG1 THR A 268 " pdb=" OD2 ASP A 271 " model vdw 2.226 3.040 nonbonded pdb=" N GLN D 128 " pdb=" OE1 GLN D 128 " model vdw 2.236 3.120 ... (remaining 175835 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 41 through 175 or (resid 176 and (name N or name CA or nam \ e C or name O or name CB )) or resid 177 through 233 or (resid 234 and (name N o \ r name CA or name C or name O or name CB )) or resid 235 through 346 or (resid 3 \ 47 and (name N or name CA or name C or name O or name CB )) or resid 348 through \ 458)) selection = (chain 'B' and (resid 41 through 218 or (resid 219 and (name N or name CA or nam \ e C or name O or name CB )) or resid 220 through 293 or (resid 294 and (name N o \ r name CA or name C or name O or name CB )) or resid 295 through 420 or (resid 4 \ 21 and (name N or name CA or name C or name O or name CB )) or resid 422 through \ 458)) } ncs_group { reference = (chain 'C' and (resid 8 through 279 or (resid 280 and (name N or name CA or name \ C or name O or name CB )) or resid 281 through 351)) selection = chain 'D' } ncs_group { reference = (chain 'G' and (resid 9 through 14 or (resid 15 through 16 and (name N or name C \ A or name C or name O or name CB )) or resid 17 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 36 or resid \ 45 through 76 or resid 94 through 305)) selection = (chain 'H' and (resid 9 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 58 or (resid 59 through 60 and (nam \ e N or name CA or name C or name O or name CB )) or resid 61 through 72 or (resi \ d 73 and (name N or name CA or name C or name O or name CB )) or resid 74 throug \ h 144 or (resid 145 and (name N or name CA or name C or name O or name CB )) or \ resid 146 through 305)) } 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: 5.170 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.620 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:7.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 0.134 22743 Z= 0.095 Angle : 0.501 10.939 30830 Z= 0.254 Chirality : 0.042 0.277 3636 Planarity : 0.005 0.130 3926 Dihedral : 17.764 89.181 8370 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.50 % Allowed : 29.61 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.17), residues: 2803 helix: 1.83 (0.17), residues: 1076 sheet: 0.35 (0.29), residues: 405 loop : -0.02 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A 163 TYR 0.023 0.001 TYR F 173 PHE 0.039 0.001 PHE G 10 TRP 0.013 0.001 TRP A 97 HIS 0.008 0.000 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00221 (22743) covalent geometry : angle 0.50091 (30830) hydrogen bonds : bond 0.18820 ( 885) hydrogen bonds : angle 5.70400 ( 2532) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 247 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 305 ASP cc_start: 0.8209 (m-30) cc_final: 0.8005 (p0) REVERT: C 338 ARG cc_start: 0.7744 (mmm160) cc_final: 0.7016 (tpm-80) REVERT: F 299 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: J 132 MET cc_start: 0.7871 (mtp) cc_final: 0.7343 (mmt) REVERT: J 227 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6657 (mt-10) outliers start: 111 outliers final: 97 residues processed: 352 average time/residue: 0.4635 time to fit residues: 195.3233 Evaluate side-chains 330 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 232 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 297 SER Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 268 CYS Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain J residue 315 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.0270 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 overall best weight: 0.9044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN A 197 HIS A 258 GLN A 263 ASN A 352 HIS A 359 ASN E 406 HIS I 190 HIS B 409 HIS B 416 ASN C 230 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.141667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.112910 restraints weight = 32904.746| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.20 r_work: 0.3549 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22743 Z= 0.123 Angle : 0.525 8.673 30830 Z= 0.269 Chirality : 0.044 0.242 3636 Planarity : 0.004 0.095 3926 Dihedral : 7.006 83.738 3231 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 6.98 % Allowed : 25.72 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.17), residues: 2803 helix: 1.77 (0.17), residues: 1103 sheet: 0.44 (0.29), residues: 386 loop : -0.19 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 163 TYR 0.010 0.001 TYR J 210 PHE 0.020 0.001 PHE G 75 TRP 0.013 0.001 TRP B 97 HIS 0.008 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00291 (22743) covalent geometry : angle 0.52527 (30830) hydrogen bonds : bond 0.03696 ( 885) hydrogen bonds : angle 4.20043 ( 2532) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 245 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 163 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7986 (ptmm) REVERT: H 31 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7310 (pp) REVERT: H 164 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7402 (tpt) REVERT: A 287 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7527 (mm) REVERT: D 145 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7981 (pm20) REVERT: D 203 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7095 (tpt) REVERT: E 234 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7418 (pp30) REVERT: E 325 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7539 (pm20) REVERT: E 378 HIS cc_start: 0.8196 (m170) cc_final: 0.7881 (t-170) REVERT: C 217 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8497 (ptt) REVERT: J 49 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7556 (mm-30) REVERT: J 57 ARG cc_start: 0.6135 (OUTLIER) cc_final: 0.5794 (tpm170) REVERT: J 173 GLU cc_start: 0.5317 (mp0) cc_final: 0.5022 (mp0) REVERT: J 227 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7011 (mt-10) outliers start: 172 outliers final: 82 residues processed: 386 average time/residue: 0.5162 time to fit residues: 235.2497 Evaluate side-chains 312 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 220 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 437 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 243 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 232 optimal weight: 1.9990 chunk 140 optimal weight: 0.1980 chunk 277 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 170 HIS ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS A 352 HIS A 359 ASN D 230 ASN E 406 HIS E 411 ASN F 486 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.139438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.109039 restraints weight = 33690.986| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.27 r_work: 0.3525 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22743 Z= 0.133 Angle : 0.539 8.643 30830 Z= 0.275 Chirality : 0.045 0.265 3636 Planarity : 0.004 0.092 3926 Dihedral : 6.408 84.906 3160 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 6.94 % Allowed : 26.09 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.17), residues: 2803 helix: 1.74 (0.17), residues: 1093 sheet: 0.18 (0.29), residues: 388 loop : -0.22 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 223 TYR 0.016 0.001 TYR F 173 PHE 0.018 0.001 PHE G 75 TRP 0.014 0.001 TRP B 97 HIS 0.009 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00324 (22743) covalent geometry : angle 0.53931 (30830) hydrogen bonds : bond 0.03680 ( 885) hydrogen bonds : angle 3.94991 ( 2532) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 231 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7543 (pt) REVERT: H 164 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7480 (tpt) REVERT: H 166 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7823 (ttmm) REVERT: A 129 ARG cc_start: 0.8102 (tpp-160) cc_final: 0.7761 (mpt180) REVERT: A 259 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.6135 (tt) REVERT: A 287 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7440 (mm) REVERT: D 178 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7481 (mp) REVERT: D 203 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.6809 (tpt) REVERT: E 234 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7443 (pp30) REVERT: E 325 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: E 378 HIS cc_start: 0.8123 (m170) cc_final: 0.7813 (t-170) REVERT: E 456 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6456 (pt0) REVERT: I 187 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6504 (mp) REVERT: B 61 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7689 (mtmm) REVERT: C 217 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8578 (ptt) REVERT: F 517 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6070 (ptm160) REVERT: J 107 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7403 (p0) REVERT: J 227 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7054 (mt-10) REVERT: J 316 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7898 (tm) outliers start: 171 outliers final: 97 residues processed: 372 average time/residue: 0.5048 time to fit residues: 222.0989 Evaluate side-chains 328 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 215 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 456 GLU Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 437 CYS Chi-restraints excluded: chain F residue 458 ASP Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 517 ARG Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain J residue 315 THR Chi-restraints excluded: chain J residue 316 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 112 optimal weight: 0.3980 chunk 177 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 233 optimal weight: 0.6980 chunk 144 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 272 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 170 HIS H 13 GLN H 48 ASN A 197 HIS A 352 HIS A 359 ASN D 230 ASN E 406 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.139083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.107657 restraints weight = 33715.457| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.38 r_work: 0.3462 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22743 Z= 0.117 Angle : 0.524 8.275 30830 Z= 0.266 Chirality : 0.044 0.311 3636 Planarity : 0.004 0.096 3926 Dihedral : 6.001 85.985 3151 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 6.25 % Allowed : 27.10 % Favored : 66.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.17), residues: 2803 helix: 1.72 (0.17), residues: 1103 sheet: 0.07 (0.28), residues: 390 loop : -0.23 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 145 TYR 0.018 0.001 TYR F 173 PHE 0.035 0.001 PHE A 57 TRP 0.014 0.001 TRP B 97 HIS 0.009 0.001 HIS G 170 Details of bonding type rmsd covalent geometry : bond 0.00280 (22743) covalent geometry : angle 0.52427 (30830) hydrogen bonds : bond 0.03252 ( 885) hydrogen bonds : angle 3.86829 ( 2532) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 224 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 163 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8147 (ptmm) REVERT: H 164 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7409 (tpt) REVERT: H 166 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7842 (ttmm) REVERT: A 129 ARG cc_start: 0.8122 (tpp-160) cc_final: 0.7712 (mpt180) REVERT: A 287 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7397 (mm) REVERT: E 234 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7450 (pp30) REVERT: E 325 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: E 362 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8155 (t0) REVERT: E 378 HIS cc_start: 0.8182 (m170) cc_final: 0.7770 (t70) REVERT: E 456 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6637 (pt0) REVERT: E 464 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7356 (mm-40) REVERT: I 187 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6526 (mp) REVERT: C 217 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8561 (ptt) REVERT: F 283 GLU cc_start: 0.8379 (tp30) cc_final: 0.8158 (tp30) REVERT: J 107 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7500 (p0) REVERT: J 227 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7108 (mt-10) outliers start: 154 outliers final: 88 residues processed: 350 average time/residue: 0.5086 time to fit residues: 210.7022 Evaluate side-chains 310 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 211 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 362 ASP Chi-restraints excluded: chain E residue 456 GLU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 437 CYS Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 220 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 134 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 258 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 255 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 250 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 170 HIS H 13 GLN A 197 HIS A 352 HIS A 359 ASN D 230 ASN E 406 HIS F 486 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.138282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.106958 restraints weight = 33439.092| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.36 r_work: 0.3469 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22743 Z= 0.120 Angle : 0.530 9.205 30830 Z= 0.268 Chirality : 0.044 0.318 3636 Planarity : 0.004 0.096 3926 Dihedral : 5.728 86.415 3142 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 6.53 % Allowed : 27.14 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.17), residues: 2803 helix: 1.69 (0.17), residues: 1103 sheet: -0.04 (0.28), residues: 391 loop : -0.24 (0.18), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 163 TYR 0.019 0.001 TYR F 173 PHE 0.036 0.001 PHE A 57 TRP 0.014 0.001 TRP B 97 HIS 0.014 0.001 HIS G 170 Details of bonding type rmsd covalent geometry : bond 0.00289 (22743) covalent geometry : angle 0.52996 (30830) hydrogen bonds : bond 0.03229 ( 885) hydrogen bonds : angle 3.82476 ( 2532) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 218 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: G 163 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8091 (ptmm) REVERT: H 166 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7925 (ttmm) REVERT: A 129 ARG cc_start: 0.8151 (tpp-160) cc_final: 0.7759 (mpt180) REVERT: A 163 ARG cc_start: 0.7731 (ttm110) cc_final: 0.6999 (mtm110) REVERT: A 287 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7364 (mm) REVERT: E 234 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7451 (pp30) REVERT: E 305 ASP cc_start: 0.8473 (m-30) cc_final: 0.8047 (p0) REVERT: E 325 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: E 362 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8155 (t0) REVERT: E 378 HIS cc_start: 0.8150 (m170) cc_final: 0.7763 (t70) REVERT: E 456 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6693 (pt0) REVERT: E 464 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7411 (mm-40) REVERT: I 187 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6523 (mp) REVERT: B 104 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8379 (pt0) REVERT: B 274 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8068 (mtp-110) REVERT: C 217 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8513 (ptt) REVERT: J 104 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8427 (mp) REVERT: J 107 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7576 (p0) outliers start: 161 outliers final: 95 residues processed: 352 average time/residue: 0.5097 time to fit residues: 212.3295 Evaluate side-chains 323 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 215 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 362 ASP Chi-restraints excluded: chain E residue 456 GLU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 437 CYS Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 458 ASP Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain J residue 315 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 270 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 208 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 255 optimal weight: 0.0770 chunk 262 optimal weight: 0.3980 chunk 136 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS A 352 HIS A 359 ASN D 230 ASN E 406 HIS B 359 ASN B 376 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.138453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.107875 restraints weight = 33634.357| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.41 r_work: 0.3469 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22743 Z= 0.111 Angle : 0.519 7.997 30830 Z= 0.265 Chirality : 0.044 0.277 3636 Planarity : 0.004 0.101 3926 Dihedral : 5.355 58.139 3134 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 6.37 % Allowed : 27.55 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.17), residues: 2803 helix: 1.73 (0.17), residues: 1103 sheet: 0.00 (0.29), residues: 383 loop : -0.23 (0.18), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 223 TYR 0.019 0.001 TYR F 173 PHE 0.039 0.001 PHE A 57 TRP 0.014 0.001 TRP B 97 HIS 0.008 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00263 (22743) covalent geometry : angle 0.51938 (30830) hydrogen bonds : bond 0.03064 ( 885) hydrogen bonds : angle 3.78035 ( 2532) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 224 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 163 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8111 (ptmm) REVERT: H 166 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7882 (ttmm) REVERT: A 129 ARG cc_start: 0.8172 (tpp-160) cc_final: 0.7777 (mpt180) REVERT: A 163 ARG cc_start: 0.7663 (ttm110) cc_final: 0.6998 (mtm-85) REVERT: A 176 LYS cc_start: 0.8106 (mmpt) cc_final: 0.7887 (mmpt) REVERT: A 287 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7330 (mm) REVERT: E 234 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7484 (pp30) REVERT: E 325 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7593 (pm20) REVERT: E 347 GLN cc_start: 0.7682 (tt0) cc_final: 0.7082 (tp40) REVERT: E 362 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8119 (t0) REVERT: E 378 HIS cc_start: 0.8139 (m170) cc_final: 0.7753 (t70) REVERT: E 464 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7400 (mm-40) REVERT: I 187 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6575 (mp) REVERT: B 258 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: C 186 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7427 (tptp) REVERT: C 217 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8647 (ptt) REVERT: F 229 LEU cc_start: 0.8382 (tp) cc_final: 0.8138 (tp) REVERT: F 283 GLU cc_start: 0.8394 (tp30) cc_final: 0.8174 (tp30) REVERT: F 517 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.5979 (ptm160) REVERT: J 49 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7204 (mm-30) REVERT: J 104 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8465 (mp) REVERT: J 107 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7575 (p0) REVERT: J 227 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7082 (mt-10) outliers start: 157 outliers final: 90 residues processed: 354 average time/residue: 0.5247 time to fit residues: 218.5453 Evaluate side-chains 314 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 211 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 228 ARG Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 362 ASP Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 437 CYS Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain F residue 517 ARG Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 110 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 97 optimal weight: 9.9990 chunk 246 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 189 optimal weight: 0.7980 chunk 152 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 204 optimal weight: 0.9980 chunk 251 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 170 HIS H 13 GLN A 197 HIS A 341 ASN A 352 HIS A 359 ASN D 230 ASN E 406 HIS E 411 ASN F 486 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.136922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.105819 restraints weight = 33470.219| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.32 r_work: 0.3445 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22743 Z= 0.140 Angle : 0.557 9.804 30830 Z= 0.282 Chirality : 0.045 0.299 3636 Planarity : 0.004 0.105 3926 Dihedral : 5.425 59.492 3131 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 6.25 % Allowed : 27.55 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.17), residues: 2803 helix: 1.66 (0.17), residues: 1103 sheet: -0.11 (0.28), residues: 388 loop : -0.33 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 338 TYR 0.018 0.001 TYR F 173 PHE 0.040 0.001 PHE A 57 TRP 0.014 0.001 TRP B 97 HIS 0.008 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00343 (22743) covalent geometry : angle 0.55671 (30830) hydrogen bonds : bond 0.03435 ( 885) hydrogen bonds : angle 3.85209 ( 2532) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 227 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: H 166 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.8006 (ttmm) REVERT: A 57 PHE cc_start: 0.7270 (p90) cc_final: 0.7048 (p90) REVERT: A 129 ARG cc_start: 0.8175 (tpp-160) cc_final: 0.7778 (mpt180) REVERT: A 163 ARG cc_start: 0.7699 (ttm110) cc_final: 0.7014 (mtm-85) REVERT: A 357 GLU cc_start: 0.7740 (tt0) cc_final: 0.7223 (tt0) REVERT: A 450 SER cc_start: 0.7557 (m) cc_final: 0.7217 (p) REVERT: E 234 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7444 (pp30) REVERT: E 305 ASP cc_start: 0.8431 (m-30) cc_final: 0.8018 (p0) REVERT: E 325 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: E 347 GLN cc_start: 0.7709 (tt0) cc_final: 0.7117 (tp40) REVERT: E 378 HIS cc_start: 0.8151 (m170) cc_final: 0.7773 (t70) REVERT: E 464 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7540 (mm-40) REVERT: I 187 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6619 (mp) REVERT: B 62 ASP cc_start: 0.6909 (OUTLIER) cc_final: 0.6607 (p0) REVERT: B 258 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7192 (mp10) REVERT: C 96 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8219 (tp) REVERT: C 186 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7436 (tptp) REVERT: F 283 GLU cc_start: 0.8499 (tp30) cc_final: 0.8233 (tp30) REVERT: F 517 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.5993 (ptm160) REVERT: J 104 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8440 (mp) REVERT: J 107 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7675 (p0) outliers start: 154 outliers final: 98 residues processed: 361 average time/residue: 0.5290 time to fit residues: 224.7976 Evaluate side-chains 325 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 216 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 228 ARG Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 437 CYS Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain F residue 517 ARG Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 315 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 20 optimal weight: 1.9990 chunk 238 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 104 optimal weight: 0.2980 chunk 97 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 203 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 170 HIS H 13 GLN A 197 HIS A 352 HIS A 359 ASN D 230 ASN E 406 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.137947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.106584 restraints weight = 33426.420| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.36 r_work: 0.3461 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22743 Z= 0.108 Angle : 0.539 8.834 30830 Z= 0.274 Chirality : 0.044 0.292 3636 Planarity : 0.004 0.106 3926 Dihedral : 5.298 57.483 3130 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.99 % Allowed : 29.25 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.17), residues: 2803 helix: 1.69 (0.17), residues: 1104 sheet: -0.10 (0.28), residues: 383 loop : -0.30 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 223 TYR 0.020 0.001 TYR F 173 PHE 0.040 0.001 PHE A 57 TRP 0.013 0.001 TRP B 97 HIS 0.009 0.001 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00253 (22743) covalent geometry : angle 0.53871 (30830) hydrogen bonds : bond 0.03015 ( 885) hydrogen bonds : angle 3.77724 ( 2532) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 221 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 166 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7927 (ttmm) REVERT: H 180 ASP cc_start: 0.8412 (m-30) cc_final: 0.8124 (m-30) REVERT: A 57 PHE cc_start: 0.7230 (p90) cc_final: 0.7026 (p90) REVERT: A 129 ARG cc_start: 0.8164 (tpp-160) cc_final: 0.7768 (mpt180) REVERT: A 357 GLU cc_start: 0.7710 (tt0) cc_final: 0.7188 (tt0) REVERT: D 178 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7564 (mp) REVERT: E 234 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7431 (pp30) REVERT: E 305 ASP cc_start: 0.8429 (m-30) cc_final: 0.7997 (p0) REVERT: E 325 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7645 (pm20) REVERT: E 347 GLN cc_start: 0.7651 (tt0) cc_final: 0.7205 (tp40) REVERT: E 378 HIS cc_start: 0.8119 (m170) cc_final: 0.7744 (t70) REVERT: E 464 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7543 (mm-40) REVERT: I 187 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6678 (mp) REVERT: B 62 ASP cc_start: 0.6789 (p0) cc_final: 0.6568 (p0) REVERT: B 258 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7199 (mp10) REVERT: C 58 MET cc_start: 0.8559 (mtm) cc_final: 0.8212 (mtm) REVERT: C 186 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7400 (tptp) REVERT: C 217 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8610 (ptt) REVERT: F 283 GLU cc_start: 0.8503 (tp30) cc_final: 0.8225 (tp30) REVERT: J 49 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7177 (mm-30) REVERT: J 104 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8432 (mp) REVERT: J 107 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7613 (p0) REVERT: J 227 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7088 (mt-10) outliers start: 123 outliers final: 88 residues processed: 328 average time/residue: 0.5301 time to fit residues: 204.9872 Evaluate side-chains 305 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 207 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 228 ARG Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 437 CYS Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 107 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 198 optimal weight: 0.6980 chunk 236 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 255 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 170 HIS H 13 GLN A 197 HIS A 352 HIS A 359 ASN D 230 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS E 411 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.136116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.104775 restraints weight = 33807.042| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.36 r_work: 0.3437 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22743 Z= 0.145 Angle : 0.575 9.170 30830 Z= 0.291 Chirality : 0.046 0.308 3636 Planarity : 0.005 0.112 3926 Dihedral : 5.374 55.116 3129 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 5.31 % Allowed : 29.01 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.17), residues: 2803 helix: 1.63 (0.16), residues: 1104 sheet: -0.16 (0.28), residues: 386 loop : -0.39 (0.18), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 338 TYR 0.020 0.001 TYR F 173 PHE 0.038 0.001 PHE A 57 TRP 0.013 0.001 TRP B 97 HIS 0.008 0.001 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00359 (22743) covalent geometry : angle 0.57480 (30830) hydrogen bonds : bond 0.03417 ( 885) hydrogen bonds : angle 3.84951 ( 2532) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 223 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 166 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7879 (ttmp) REVERT: H 180 ASP cc_start: 0.8408 (m-30) cc_final: 0.8151 (m-30) REVERT: A 57 PHE cc_start: 0.7167 (p90) cc_final: 0.6854 (p90) REVERT: A 129 ARG cc_start: 0.8160 (tpp-160) cc_final: 0.7771 (mpt180) REVERT: A 163 ARG cc_start: 0.7675 (ttm110) cc_final: 0.7061 (mtm-85) REVERT: A 172 ARG cc_start: 0.5639 (OUTLIER) cc_final: 0.5182 (mmm160) REVERT: A 357 GLU cc_start: 0.7812 (tt0) cc_final: 0.7281 (tt0) REVERT: A 450 SER cc_start: 0.7583 (m) cc_final: 0.7192 (p) REVERT: E 234 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7426 (pp30) REVERT: E 325 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: E 347 GLN cc_start: 0.7825 (tt0) cc_final: 0.7238 (tp40) REVERT: E 378 HIS cc_start: 0.8122 (m170) cc_final: 0.7775 (t70) REVERT: E 464 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7644 (mm-40) REVERT: I 187 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6634 (mp) REVERT: B 62 ASP cc_start: 0.6786 (p0) cc_final: 0.6577 (p0) REVERT: B 258 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7205 (mp10) REVERT: C 58 MET cc_start: 0.8594 (mtm) cc_final: 0.8234 (mtm) REVERT: C 186 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7416 (tptp) REVERT: F 283 GLU cc_start: 0.8547 (tp30) cc_final: 0.8317 (tp30) REVERT: J 49 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7244 (mm-30) REVERT: J 104 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8427 (mp) outliers start: 131 outliers final: 94 residues processed: 338 average time/residue: 0.5215 time to fit residues: 207.8166 Evaluate side-chains 321 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 219 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 228 ARG Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 437 CYS Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 217 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 29 optimal weight: 8.9990 chunk 243 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 222 optimal weight: 0.4980 chunk 174 optimal weight: 4.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS A 352 HIS A 359 ASN D 230 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS F 486 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.135704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.104711 restraints weight = 33641.332| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.33 r_work: 0.3473 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.234 22743 Z= 0.249 Angle : 0.834 59.200 30830 Z= 0.443 Chirality : 0.048 0.374 3636 Planarity : 0.005 0.114 3926 Dihedral : 5.358 55.142 3127 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.54 % Allowed : 29.66 % Favored : 65.80 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.17), residues: 2803 helix: 1.59 (0.16), residues: 1104 sheet: -0.23 (0.28), residues: 396 loop : -0.40 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 223 TYR 0.019 0.002 TYR F 173 PHE 0.055 0.002 PHE A 57 TRP 0.014 0.001 TRP B 97 HIS 0.008 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00559 (22743) covalent geometry : angle 0.83399 (30830) hydrogen bonds : bond 0.03567 ( 885) hydrogen bonds : angle 3.85558 ( 2532) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 220 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 MET cc_start: 0.6863 (mmm) cc_final: 0.6639 (mmp) REVERT: H 13 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7777 (tp40) REVERT: H 166 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7876 (ttmp) REVERT: H 180 ASP cc_start: 0.8416 (m-30) cc_final: 0.8155 (m-30) REVERT: A 129 ARG cc_start: 0.8164 (tpp-160) cc_final: 0.7768 (mpt180) REVERT: A 163 ARG cc_start: 0.7672 (ttm110) cc_final: 0.7057 (mtm-85) REVERT: A 172 ARG cc_start: 0.5668 (OUTLIER) cc_final: 0.5208 (mmm160) REVERT: A 357 GLU cc_start: 0.7806 (tt0) cc_final: 0.7245 (tt0) REVERT: A 450 SER cc_start: 0.7596 (m) cc_final: 0.7204 (p) REVERT: E 234 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7397 (pp30) REVERT: E 305 ASP cc_start: 0.8437 (m-30) cc_final: 0.7953 (p0) REVERT: E 325 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7653 (pm20) REVERT: E 347 GLN cc_start: 0.7820 (tt0) cc_final: 0.7233 (tp40) REVERT: E 362 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8095 (t0) REVERT: E 378 HIS cc_start: 0.8107 (m170) cc_final: 0.7765 (t70) REVERT: E 464 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7603 (mm-40) REVERT: I 187 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6613 (mp) REVERT: B 62 ASP cc_start: 0.6806 (p0) cc_final: 0.6595 (p0) REVERT: B 258 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7197 (mp10) REVERT: C 58 MET cc_start: 0.8600 (mtm) cc_final: 0.8238 (mtm) REVERT: C 186 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7419 (tptp) REVERT: F 283 GLU cc_start: 0.8545 (tp30) cc_final: 0.8311 (tp30) REVERT: F 347 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.6381 (mp10) REVERT: J 49 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7241 (mm-30) REVERT: J 104 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8425 (mp) REVERT: J 227 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7139 (mt-10) outliers start: 112 outliers final: 96 residues processed: 319 average time/residue: 0.5373 time to fit residues: 201.7501 Evaluate side-chains 324 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 218 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 228 ARG Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 362 ASP Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 347 GLN Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 437 CYS Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 217 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 239 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 253 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 220 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 271 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS A 352 HIS A 359 ASN D 230 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS F 486 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.135701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.104734 restraints weight = 33690.750| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.32 r_work: 0.3474 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.234 22743 Z= 0.249 Angle : 0.834 59.200 30830 Z= 0.443 Chirality : 0.048 0.374 3636 Planarity : 0.005 0.117 3926 Dihedral : 5.358 55.142 3127 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.46 % Allowed : 29.74 % Favored : 65.80 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.17), residues: 2803 helix: 1.59 (0.16), residues: 1104 sheet: -0.23 (0.28), residues: 396 loop : -0.40 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 223 TYR 0.019 0.002 TYR F 173 PHE 0.055 0.002 PHE A 57 TRP 0.014 0.001 TRP B 97 HIS 0.008 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00559 (22743) covalent geometry : angle 0.83407 (30830) hydrogen bonds : bond 0.03567 ( 885) hydrogen bonds : angle 3.85558 ( 2532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8061.56 seconds wall clock time: 138 minutes 23.21 seconds (8303.21 seconds total)