Starting phenix.real_space_refine on Thu May 22 02:35:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tqz_41566/05_2025/8tqz_41566.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tqz_41566/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tqz_41566/05_2025/8tqz_41566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tqz_41566/05_2025/8tqz_41566.map" model { file = "/net/cci-nas-00/data/ceres_data/8tqz_41566/05_2025/8tqz_41566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tqz_41566/05_2025/8tqz_41566.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.68, per 1000 atoms: 0.61 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: 5.00 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 3.08 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: 7.91 Time building geometry restraints manager: 5.92 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: 3.690 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: 0.030 Extract box with map and model: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 49.980 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.750 ------------------------------------------------------------------------------- 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 : 6.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (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 TRP 0.013 0.001 TRP A 97 HIS 0.008 0.000 HIS A 352 PHE 0.039 0.001 PHE G 10 TYR 0.023 0.001 TYR F 173 ARG 0.019 0.000 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.18820 ( 885) hydrogen bonds : angle 5.70400 ( 2532) covalent geometry : bond 0.00221 (22743) covalent geometry : angle 0.50091 (30830) *********************** 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 : 2.473 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: 0.8952 time to fit residues: 378.8960 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 : 2.512 ------------------------------------------------------------------------------- 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 237 optimal weight: 0.9990 chunk 212 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** H 156 GLN A 118 ASN A 197 HIS A 248 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 F 486 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.134033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.104465 restraints weight = 33262.587| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.29 r_work: 0.3426 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 22743 Z= 0.253 Angle : 0.663 9.974 30830 Z= 0.339 Chirality : 0.050 0.248 3636 Planarity : 0.005 0.099 3926 Dihedral : 7.651 85.534 3231 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 8.44 % Allowed : 24.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.17), residues: 2803 helix: 1.36 (0.16), residues: 1095 sheet: -0.15 (0.28), residues: 406 loop : -0.46 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 97 HIS 0.010 0.001 HIS A 352 PHE 0.024 0.002 PHE B 56 TYR 0.017 0.002 TYR J 210 ARG 0.011 0.001 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.05089 ( 885) hydrogen bonds : angle 4.40613 ( 2532) covalent geometry : bond 0.00637 (22743) covalent geometry : angle 0.66268 (30830) *********************** 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 438 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 230 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6281 (mm) REVERT: A 181 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7882 (ttp) REVERT: A 324 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7054 (pp20) REVERT: D 186 LYS cc_start: 0.8012 (tmmt) cc_final: 0.7494 (tmtm) REVERT: D 203 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.6991 (tpt) REVERT: D 226 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7892 (mmt) REVERT: E 234 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7409 (pp30) REVERT: E 325 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: E 378 HIS cc_start: 0.8185 (m170) cc_final: 0.7874 (t-170) REVERT: C 217 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8531 (ptt) REVERT: F 517 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6813 (ptm160) REVERT: J 49 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7562 (mm-30) REVERT: J 57 ARG cc_start: 0.6400 (OUTLIER) cc_final: 0.5972 (tpm170) REVERT: J 227 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7066 (mt-10) outliers start: 208 outliers final: 95 residues processed: 406 average time/residue: 1.0153 time to fit residues: 486.4164 Evaluate side-chains 312 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 207 time to evaluate : 2.415 ------------------------------------------------------------------------------- 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 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 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 298 ASP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 63 VAL 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 166 LYS Chi-restraints excluded: chain H residue 176 THR 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 134 VAL Chi-restraints excluded: chain A residue 174 LEU 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 289 MET Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 140 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 226 MET Chi-restraints excluded: chain D residue 268 CYS Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain E residue 234 GLN 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 51 SER 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 138 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 301 SER 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 171 SER 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 F residue 179 LEU Chi-restraints excluded: chain F residue 198 ILE 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 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 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 57 ARG Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 315 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 260 optimal weight: 0.9990 chunk 187 optimal weight: 0.7980 chunk 272 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 262 optimal weight: 0.3980 chunk 3 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 GLN ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS A 352 HIS A 359 ASN E 406 HIS E 411 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.138098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.106935 restraints weight = 33337.409| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.44 r_work: 0.3462 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: 0.8257 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22743 Z= 0.112 Angle : 0.528 7.810 30830 Z= 0.270 Chirality : 0.044 0.224 3636 Planarity : 0.004 0.065 3926 Dihedral : 6.468 85.773 3161 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 6.04 % Allowed : 27.14 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.17), residues: 2803 helix: 1.59 (0.17), residues: 1096 sheet: 0.01 (0.28), residues: 385 loop : -0.36 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 97 HIS 0.008 0.001 HIS A 352 PHE 0.019 0.001 PHE G 75 TYR 0.016 0.001 TYR F 173 ARG 0.015 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 885) hydrogen bonds : angle 4.04474 ( 2532) covalent geometry : bond 0.00262 (22743) covalent geometry : angle 0.52817 (30830) *********************** 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 375 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 226 time to evaluate : 2.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 166 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7826 (ttmm) REVERT: A 129 ARG cc_start: 0.8123 (tpp-160) cc_final: 0.7739 (mpt180) REVERT: A 172 ARG cc_start: 0.5591 (OUTLIER) cc_final: 0.5246 (mtt180) REVERT: A 174 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6278 (mm) REVERT: D 186 LYS cc_start: 0.7922 (tmmt) cc_final: 0.7405 (tmtm) REVERT: D 230 ASN cc_start: 0.8504 (m110) cc_final: 0.8267 (m110) REVERT: D 287 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7943 (ptpt) REVERT: E 234 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7478 (pp30) REVERT: E 325 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7613 (pm20) REVERT: E 378 HIS cc_start: 0.8165 (m170) cc_final: 0.7807 (t-170) REVERT: E 456 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6716 (pt0) REVERT: B 62 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6587 (p0) REVERT: C 217 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8557 (ptt) REVERT: J 49 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7431 (mm-30) REVERT: J 227 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7153 (mt-10) outliers start: 149 outliers final: 76 residues processed: 354 average time/residue: 1.0512 time to fit residues: 436.8284 Evaluate side-chains 300 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 215 time to evaluate : 2.577 ------------------------------------------------------------------------------- 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 121 ASP 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 175 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 223 ASN 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 300 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER 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 160 ASN Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 174 LEU 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 332 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain D residue 16 GLU 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 286 HIS Chi-restraints excluded: chain D residue 287 LYS Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 325 GLN 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 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 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 76 THR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 173 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 195 PHE Chi-restraints excluded: chain F residue 392 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 164 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 219 optimal weight: 5.9990 chunk 203 optimal weight: 0.3980 chunk 169 optimal weight: 0.9980 chunk 216 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 E 406 HIS B 359 ASN B 376 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 = 0.3959 r_free = 0.3959 target = 0.138108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.106614 restraints weight = 33702.216| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.37 r_work: 0.3463 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22743 Z= 0.110 Angle : 0.516 7.835 30830 Z= 0.264 Chirality : 0.044 0.239 3636 Planarity : 0.004 0.062 3926 Dihedral : 6.045 86.148 3146 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 6.00 % Allowed : 27.46 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.17), residues: 2803 helix: 1.65 (0.17), residues: 1099 sheet: -0.08 (0.28), residues: 392 loop : -0.30 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 97 HIS 0.008 0.001 HIS A 352 PHE 0.019 0.001 PHE G 75 TYR 0.018 0.001 TYR F 173 ARG 0.013 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.03213 ( 885) hydrogen bonds : angle 3.88566 ( 2532) covalent geometry : bond 0.00262 (22743) covalent geometry : angle 0.51591 (30830) *********************** 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 374 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 226 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8146 (tpp-160) cc_final: 0.7785 (mpt180) REVERT: A 172 ARG cc_start: 0.5562 (OUTLIER) cc_final: 0.5240 (mtt180) REVERT: A 174 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6236 (mm) REVERT: D 203 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.6634 (tpt) REVERT: D 230 ASN cc_start: 0.8542 (m110) cc_final: 0.8249 (m110) REVERT: E 234 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7455 (pp30) REVERT: E 305 ASP cc_start: 0.8380 (m-30) cc_final: 0.8026 (p0) REVERT: E 325 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7621 (pm20) REVERT: E 378 HIS cc_start: 0.8161 (m170) cc_final: 0.7779 (t70) REVERT: E 456 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6752 (pt0) REVERT: I 187 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6505 (mp) REVERT: B 62 ASP cc_start: 0.6853 (OUTLIER) cc_final: 0.6600 (p0) REVERT: B 258 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7214 (mp10) REVERT: C 217 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8552 (ptt) REVERT: F 229 LEU cc_start: 0.8395 (tp) cc_final: 0.8145 (tp) REVERT: J 227 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7107 (mt-10) outliers start: 148 outliers final: 75 residues processed: 350 average time/residue: 1.0489 time to fit residues: 431.3719 Evaluate side-chains 301 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 216 time to evaluate : 2.615 ------------------------------------------------------------------------------- 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 121 ASP 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 170 HIS 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 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 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 292 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 124 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 174 LEU 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 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 140 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 226 MET Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 325 GLN 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 181 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 126 GLU Chi-restraints excluded: chain B residue 134 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 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 159 ILE 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 248 LEU 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 59 VAL Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain J residue 311 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 76 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 75 optimal weight: 0.0270 chunk 211 optimal weight: 0.7980 chunk 149 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- 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 304 HIS A 341 ASN A 352 HIS A 359 ASN E 406 HIS E 411 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.134891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.103581 restraints weight = 33857.105| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.34 r_work: 0.3418 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22743 Z= 0.175 Angle : 0.584 10.285 30830 Z= 0.297 Chirality : 0.046 0.267 3636 Planarity : 0.005 0.104 3926 Dihedral : 5.967 87.236 3133 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 7.46 % Allowed : 26.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2803 helix: 1.46 (0.16), residues: 1105 sheet: -0.27 (0.28), residues: 397 loop : -0.47 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 97 HIS 0.032 0.001 HIS G 170 PHE 0.021 0.001 PHE G 75 TYR 0.018 0.001 TYR F 173 ARG 0.014 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 885) hydrogen bonds : angle 4.01920 ( 2532) covalent geometry : bond 0.00440 (22743) covalent geometry : angle 0.58402 (30830) *********************** 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 403 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 219 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 166 LYS cc_start: 0.8193 (ttmm) cc_final: 0.7882 (ttmp) REVERT: A 129 ARG cc_start: 0.8174 (tpp-160) cc_final: 0.7839 (mpt180) REVERT: A 163 ARG cc_start: 0.7720 (ttm110) cc_final: 0.7320 (mtm-85) REVERT: A 174 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6255 (mm) REVERT: A 305 MET cc_start: 0.8033 (tpp) cc_final: 0.7682 (mmm) REVERT: A 357 GLU cc_start: 0.7825 (tt0) cc_final: 0.7295 (tt0) REVERT: D 178 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7487 (mp) REVERT: D 203 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.6635 (tpt) REVERT: D 230 ASN cc_start: 0.8556 (m110) cc_final: 0.8245 (m110) REVERT: D 287 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7997 (ptpt) REVERT: E 234 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7460 (pp30) REVERT: E 325 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7696 (pm20) REVERT: E 347 GLN cc_start: 0.7777 (tt0) cc_final: 0.7148 (tp40) REVERT: E 378 HIS cc_start: 0.8154 (m170) cc_final: 0.7816 (t-170) REVERT: E 456 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6721 (pt0) REVERT: E 464 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7438 (mm-40) REVERT: E 509 CYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6693 (t) REVERT: I 187 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6460 (mp) REVERT: B 62 ASP cc_start: 0.6884 (OUTLIER) cc_final: 0.6646 (p0) REVERT: B 104 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8374 (pt0) outliers start: 184 outliers final: 97 residues processed: 377 average time/residue: 1.0116 time to fit residues: 451.4537 Evaluate side-chains 320 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 212 time to evaluate : 2.365 ------------------------------------------------------------------------------- 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 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 152 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 175 VAL 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 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 63 VAL 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 152 VAL Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 155 SER 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 93 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 174 LEU 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 253 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain D residue 16 GLU 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 286 HIS Chi-restraints excluded: chain D residue 287 LYS 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 456 GLU Chi-restraints excluded: chain E residue 509 CYS 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 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 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 328 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 171 SER 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 179 LEU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 SER Chi-restraints excluded: chain F residue 320 SER 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 59 VAL Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain J residue 311 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 115 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 269 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 6 optimal weight: 0.0070 chunk 76 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 E 406 HIS J 236 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.138007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.107001 restraints weight = 33367.721| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.33 r_work: 0.3459 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22743 Z= 0.103 Angle : 0.531 8.706 30830 Z= 0.271 Chirality : 0.044 0.273 3636 Planarity : 0.004 0.103 3926 Dihedral : 5.422 54.246 3127 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.35 % Allowed : 28.64 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2803 helix: 1.61 (0.16), residues: 1108 sheet: -0.16 (0.28), residues: 389 loop : -0.32 (0.18), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 97 HIS 0.009 0.001 HIS A 304 PHE 0.019 0.001 PHE G 75 TYR 0.019 0.001 TYR F 173 ARG 0.014 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.03034 ( 885) hydrogen bonds : angle 3.83914 ( 2532) covalent geometry : bond 0.00236 (22743) covalent geometry : angle 0.53130 (30830) *********************** 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 363 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 231 time to evaluate : 2.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 166 LYS cc_start: 0.8153 (ttmm) cc_final: 0.7852 (ttmp) REVERT: A 129 ARG cc_start: 0.8168 (tpp-160) cc_final: 0.7824 (mpt180) REVERT: A 174 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6247 (mm) REVERT: A 305 MET cc_start: 0.7970 (tpp) cc_final: 0.7645 (mmm) REVERT: A 357 GLU cc_start: 0.7742 (tt0) cc_final: 0.7220 (tt0) REVERT: E 234 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7447 (pp30) REVERT: E 305 ASP cc_start: 0.8360 (m-30) cc_final: 0.8023 (p0) REVERT: E 347 GLN cc_start: 0.7675 (tt0) cc_final: 0.7101 (tp40) REVERT: E 378 HIS cc_start: 0.8107 (m170) cc_final: 0.7770 (t70) REVERT: E 464 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7368 (mm-40) REVERT: I 187 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6516 (mp) REVERT: B 62 ASP cc_start: 0.6897 (p0) cc_final: 0.6686 (p0) REVERT: B 258 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7205 (mp10) REVERT: C 217 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8427 (ptt) REVERT: J 49 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7231 (mm-30) REVERT: J 104 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8421 (mp) REVERT: J 173 GLU cc_start: 0.5621 (mp0) cc_final: 0.5397 (mp0) REVERT: J 227 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7074 (mt-10) REVERT: J 321 GLU cc_start: 0.8503 (tp30) cc_final: 0.8232 (tp30) outliers start: 132 outliers final: 76 residues processed: 344 average time/residue: 0.9627 time to fit residues: 392.3177 Evaluate side-chains 296 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 214 time to evaluate : 2.466 ------------------------------------------------------------------------------- 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 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 170 HIS 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 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 155 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 131 LEU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 194 THR 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 432 THR Chi-restraints excluded: chain D residue 16 GLU 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 286 HIS Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 234 GLN 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 51 SER 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 230 LEU Chi-restraints excluded: chain B residue 258 GLN 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 429 SER 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 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 198 ILE Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 SER Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 320 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 8 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 52 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 chunk 256 optimal weight: 2.9990 chunk 265 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 176 optimal weight: 0.0980 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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 E 406 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.138152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.107620 restraints weight = 33426.790| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.29 r_work: 0.3459 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22743 Z= 0.113 Angle : 0.541 8.911 30830 Z= 0.275 Chirality : 0.044 0.281 3636 Planarity : 0.004 0.107 3926 Dihedral : 5.342 55.073 3124 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.95 % Allowed : 28.76 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.17), residues: 2803 helix: 1.64 (0.16), residues: 1104 sheet: -0.17 (0.28), residues: 388 loop : -0.33 (0.18), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 97 HIS 0.009 0.001 HIS B 304 PHE 0.022 0.001 PHE G 75 TYR 0.019 0.001 TYR F 173 ARG 0.017 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.03096 ( 885) hydrogen bonds : angle 3.83492 ( 2532) covalent geometry : bond 0.00271 (22743) covalent geometry : angle 0.54050 (30830) *********************** 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 346 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 224 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 166 LYS cc_start: 0.8157 (ttmm) cc_final: 0.7851 (ttmp) REVERT: A 129 ARG cc_start: 0.8180 (tpp-160) cc_final: 0.7845 (mpt180) REVERT: A 174 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.6266 (mm) REVERT: A 305 MET cc_start: 0.7963 (tpp) cc_final: 0.7639 (mmm) REVERT: A 357 GLU cc_start: 0.7747 (tt0) cc_final: 0.7241 (tt0) REVERT: D 178 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7518 (mp) REVERT: E 234 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7477 (pp30) REVERT: E 347 GLN cc_start: 0.7648 (tt0) cc_final: 0.7045 (tp40) REVERT: E 378 HIS cc_start: 0.8098 (m170) cc_final: 0.7765 (t70) REVERT: E 464 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7370 (mm-40) REVERT: I 187 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6554 (mp) REVERT: B 62 ASP cc_start: 0.6905 (OUTLIER) cc_final: 0.6695 (p0) REVERT: B 258 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: B 274 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8069 (mtp-110) REVERT: F 283 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8167 (tp30) REVERT: J 104 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8408 (mp) REVERT: J 227 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7075 (mt-10) outliers start: 122 outliers final: 85 residues processed: 327 average time/residue: 1.0666 time to fit residues: 411.1024 Evaluate side-chains 307 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 214 time to evaluate : 2.451 ------------------------------------------------------------------------------- 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 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 170 HIS Chi-restraints excluded: chain G residue 175 VAL 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 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 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 174 LEU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 194 THR 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 D residue 16 GLU Chi-restraints excluded: chain D residue 140 LEU 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 286 HIS Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 234 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 170 MET Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 300 CYS 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 230 LEU Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 274 ARG 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 96 LEU Chi-restraints excluded: chain C residue 171 SER 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 197 SER Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 SER 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 8 MET 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 Chi-restraints excluded: chain J residue 220 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 194 optimal weight: 4.9990 chunk 274 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 252 optimal weight: 0.9980 chunk 226 optimal weight: 9.9990 chunk 71 optimal weight: 30.0000 chunk 243 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS A 352 HIS A 359 ASN E 406 HIS B 376 ASN F 486 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.136351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.109144 restraints weight = 33507.983| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.06 r_work: 0.3573 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22743 Z= 0.160 Angle : 0.580 9.423 30830 Z= 0.295 Chirality : 0.046 0.302 3636 Planarity : 0.005 0.113 3926 Dihedral : 5.493 59.407 3123 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 5.44 % Allowed : 28.40 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.17), residues: 2803 helix: 1.54 (0.16), residues: 1103 sheet: -0.28 (0.28), residues: 388 loop : -0.42 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 97 HIS 0.011 0.001 HIS G 170 PHE 0.022 0.001 PHE G 75 TYR 0.020 0.001 TYR F 173 ARG 0.013 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 885) hydrogen bonds : angle 3.92543 ( 2532) covalent geometry : bond 0.00398 (22743) covalent geometry : angle 0.57952 (30830) *********************** 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 355 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 221 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 166 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7935 (ttmp) REVERT: A 129 ARG cc_start: 0.8163 (tpp-160) cc_final: 0.7877 (mpt180) REVERT: A 163 ARG cc_start: 0.7733 (ttm110) cc_final: 0.7362 (mtm-85) REVERT: A 174 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6443 (mm) REVERT: A 305 MET cc_start: 0.8072 (tpp) cc_final: 0.7805 (mmm) REVERT: A 357 GLU cc_start: 0.7749 (tt0) cc_final: 0.7324 (tt0) REVERT: E 234 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7435 (pp30) REVERT: E 306 ARG cc_start: 0.8772 (ttp-110) cc_final: 0.8266 (mtm-85) REVERT: E 347 GLN cc_start: 0.7754 (tt0) cc_final: 0.7220 (tp40) REVERT: E 378 HIS cc_start: 0.8103 (m170) cc_final: 0.7826 (t70) REVERT: E 464 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7590 (mm-40) REVERT: I 187 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6672 (mp) REVERT: B 258 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7238 (mp10) REVERT: C 58 MET cc_start: 0.8601 (mtm) cc_final: 0.8252 (mtm) REVERT: C 217 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8307 (ptt) REVERT: F 283 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8214 (tp30) REVERT: J 104 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8453 (mp) REVERT: J 227 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7145 (mt-10) REVERT: J 324 ARG cc_start: 0.7598 (mtm-85) cc_final: 0.7386 (mtm-85) outliers start: 134 outliers final: 90 residues processed: 337 average time/residue: 1.0360 time to fit residues: 411.2815 Evaluate side-chains 310 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 214 time to evaluate : 2.298 ------------------------------------------------------------------------------- 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 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 170 HIS Chi-restraints excluded: chain G residue 175 VAL 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 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 160 SER 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 174 LEU 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 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 286 HIS Chi-restraints excluded: chain E residue 234 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 187 LEU Chi-restraints excluded: chain I residue 300 CYS 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 328 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 60 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 171 SER 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 F residue 179 LEU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 SER 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 99 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 217 GLU Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain J residue 311 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 190 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 257 optimal weight: 0.0000 chunk 144 optimal weight: 0.0370 chunk 263 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 251 optimal weight: 0.4980 chunk 211 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 overall best weight: 0.6264 ------------------------------------------------------------------------------- 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 ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS F 486 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.138043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.110794 restraints weight = 33285.329| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.16 r_work: 0.3606 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22743 Z= 0.109 Angle : 0.548 9.164 30830 Z= 0.280 Chirality : 0.044 0.302 3636 Planarity : 0.005 0.112 3926 Dihedral : 5.376 55.377 3123 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.42 % Allowed : 29.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2803 helix: 1.64 (0.17), residues: 1104 sheet: -0.24 (0.28), residues: 388 loop : -0.37 (0.18), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 97 HIS 0.010 0.001 HIS G 170 PHE 0.024 0.001 PHE G 75 TYR 0.021 0.001 TYR A 128 ARG 0.018 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.03092 ( 885) hydrogen bonds : angle 3.82457 ( 2532) covalent geometry : bond 0.00253 (22743) covalent geometry : angle 0.54779 (30830) *********************** 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 330 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 221 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 166 LYS cc_start: 0.8181 (ttmm) cc_final: 0.7902 (ttmp) REVERT: A 129 ARG cc_start: 0.8148 (tpp-160) cc_final: 0.7829 (mpt180) REVERT: A 174 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6440 (mm) REVERT: A 357 GLU cc_start: 0.7732 (tt0) cc_final: 0.7305 (tt0) REVERT: E 234 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7446 (pp30) REVERT: E 306 ARG cc_start: 0.8797 (ttp-110) cc_final: 0.8299 (mtm-85) REVERT: E 347 GLN cc_start: 0.7724 (tt0) cc_final: 0.7166 (tp40) REVERT: E 378 HIS cc_start: 0.8081 (m170) cc_final: 0.7804 (t70) REVERT: E 464 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7560 (mm-40) REVERT: I 187 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6627 (mp) REVERT: B 258 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: C 58 MET cc_start: 0.8533 (mtm) cc_final: 0.8175 (mtm) REVERT: C 217 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8470 (ptt) REVERT: F 283 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8185 (tp30) REVERT: J 49 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7204 (mm-30) REVERT: J 104 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8373 (mp) REVERT: J 227 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7166 (mt-10) outliers start: 109 outliers final: 80 residues processed: 318 average time/residue: 1.0666 time to fit residues: 398.9279 Evaluate side-chains 296 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 210 time to evaluate : 2.626 ------------------------------------------------------------------------------- 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 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 170 HIS 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 279 SER 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 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 174 LEU 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 332 THR Chi-restraints excluded: chain D residue 16 GLU 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 286 HIS Chi-restraints excluded: chain E residue 234 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 187 LEU Chi-restraints excluded: chain I residue 300 CYS 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 258 GLN 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 60 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 149 GLU 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 197 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 SER 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 99 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 220 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 23 optimal weight: 0.9980 chunk 195 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 279 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.139578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.112588 restraints weight = 33352.046| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.07 r_work: 0.3547 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22743 Z= 0.117 Angle : 0.558 9.700 30830 Z= 0.283 Chirality : 0.044 0.309 3636 Planarity : 0.005 0.117 3926 Dihedral : 5.305 55.585 3122 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.14 % Allowed : 29.94 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2803 helix: 1.66 (0.17), residues: 1097 sheet: -0.24 (0.28), residues: 388 loop : -0.37 (0.18), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 97 HIS 0.007 0.001 HIS B 304 PHE 0.021 0.001 PHE G 75 TYR 0.021 0.001 TYR A 128 ARG 0.017 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.03121 ( 885) hydrogen bonds : angle 3.81485 ( 2532) covalent geometry : bond 0.00281 (22743) covalent geometry : angle 0.55756 (30830) ********************** 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 318 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 216 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 166 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7918 (ttmp) REVERT: A 129 ARG cc_start: 0.8156 (tpp-160) cc_final: 0.7818 (mpt180) REVERT: A 131 LEU cc_start: 0.6835 (tp) cc_final: 0.6604 (tm) REVERT: A 174 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.6374 (mm) REVERT: A 305 MET cc_start: 0.7945 (tpp) cc_final: 0.7632 (mmm) REVERT: A 357 GLU cc_start: 0.7748 (tt0) cc_final: 0.7317 (tt0) REVERT: E 234 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7423 (pp30) REVERT: E 306 ARG cc_start: 0.8820 (ttp-110) cc_final: 0.8328 (mtm-85) REVERT: E 347 GLN cc_start: 0.7745 (tt0) cc_final: 0.7163 (tp40) REVERT: E 378 HIS cc_start: 0.8100 (m170) cc_final: 0.7795 (t70) REVERT: E 464 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7513 (mm-40) REVERT: I 187 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6583 (mp) REVERT: B 62 ASP cc_start: 0.6886 (OUTLIER) cc_final: 0.6631 (p0) REVERT: B 258 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7237 (mp10) REVERT: C 58 MET cc_start: 0.8535 (mtm) cc_final: 0.8168 (mtm) REVERT: C 217 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8249 (ptt) REVERT: F 229 LEU cc_start: 0.8369 (tp) cc_final: 0.8096 (tp) REVERT: F 283 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8236 (tp30) REVERT: F 517 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6798 (ptm160) REVERT: J 49 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7287 (mm-30) REVERT: J 104 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8397 (mp) REVERT: J 227 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7172 (mt-10) outliers start: 102 outliers final: 84 residues processed: 309 average time/residue: 1.0656 time to fit residues: 390.8929 Evaluate side-chains 303 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 211 time to evaluate : 2.333 ------------------------------------------------------------------------------- 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 121 ASP Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 175 VAL 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 279 SER 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 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 174 LEU 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 332 THR Chi-restraints excluded: chain D residue 16 GLU 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 286 HIS Chi-restraints excluded: chain E residue 234 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 187 LEU Chi-restraints excluded: chain I residue 300 CYS 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 221 LEU Chi-restraints excluded: chain B residue 258 GLN 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 60 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 149 GLU 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 197 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 SER 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 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 99 THR Chi-restraints excluded: chain J residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 192 optimal weight: 4.9990 chunk 51 optimal weight: 0.0370 chunk 122 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 241 optimal weight: 0.9980 chunk 279 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- 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 A 376 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS F 371 HIS F 486 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.137733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.107748 restraints weight = 34005.057| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.42 r_work: 0.3553 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22743 Z= 0.166 Angle : 0.596 9.433 30830 Z= 0.304 Chirality : 0.046 0.324 3636 Planarity : 0.005 0.122 3926 Dihedral : 5.411 54.922 3121 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.46 % Allowed : 29.82 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2803 helix: 1.54 (0.16), residues: 1102 sheet: -0.34 (0.28), residues: 388 loop : -0.48 (0.18), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 97 HIS 0.012 0.001 HIS G 170 PHE 0.021 0.001 PHE G 75 TYR 0.021 0.001 TYR A 128 ARG 0.016 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 885) hydrogen bonds : angle 3.92938 ( 2532) covalent geometry : bond 0.00413 (22743) covalent geometry : angle 0.59608 (30830) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14777.67 seconds wall clock time: 255 minutes 37.68 seconds (15337.68 seconds total)