Starting phenix.real_space_refine on Thu Mar 5 11:05:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q5b_13831/03_2026/7q5b_13831.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q5b_13831/03_2026/7q5b_13831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7q5b_13831/03_2026/7q5b_13831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q5b_13831/03_2026/7q5b_13831.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q5b_13831/03_2026/7q5b_13831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q5b_13831/03_2026/7q5b_13831.map" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 264 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 166 5.49 5 S 75 5.16 5 C 13330 2.51 5 N 3864 2.21 5 O 4311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21746 Number of models: 1 Model: "" Number of chains: 12 Chain: "R" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1140 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "S" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "r" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 705 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "s" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3438 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 397} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3936 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 457} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3912 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 22, 'TRANS': 459} Chain breaks: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2681 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 16, 'TRANS': 317} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "X" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 591 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 4, 'TRANS': 65} Chain: "Y" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} Chain: "Z" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2328 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 1 Chain: "t" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 390 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Restraints were copied for chains: u Time building chain proxies: 5.46, per 1000 atoms: 0.25 Number of scatterers: 21746 At special positions: 0 Unit cell: (151.58, 166.42, 151.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 P 166 15.00 O 4311 8.00 N 3864 7.00 C 13330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 134 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 998.0 milliseconds 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4368 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 13 sheets defined 43.1% alpha, 7.5% beta 75 base pairs and 127 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'A' and resid 29 through 38 removed outlier: 3.881A pdb=" N LEU A 35 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N THR A 36 " --> pdb=" O MET A 32 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 60 removed outlier: 3.637A pdb=" N TYR A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 84 through 92 Processing helix chain 'A' and resid 103 through 112 Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 232 through 243 removed outlier: 3.614A pdb=" N LEU A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 removed outlier: 4.057A pdb=" N THR A 256 " --> pdb=" O HIS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 275 Processing helix chain 'A' and resid 281 through 296 removed outlier: 4.350A pdb=" N TYR A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 334 through 362 removed outlier: 3.753A pdb=" N HIS A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'B' and resid 29 through 38 removed outlier: 3.771A pdb=" N LEU B 35 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR B 36 " --> pdb=" O MET B 32 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 60 removed outlier: 4.026A pdb=" N TYR B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 84 through 94 Processing helix chain 'B' and resid 95 through 98 removed outlier: 3.739A pdb=" N PHE B 98 " --> pdb=" O HIS B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 95 through 98' Processing helix chain 'B' and resid 103 through 112 Processing helix chain 'B' and resid 119 through 131 Processing helix chain 'B' and resid 133 through 138 removed outlier: 3.757A pdb=" N LYS B 138 " --> pdb=" O CYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.578A pdb=" N LEU B 144 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 253 through 256 removed outlier: 3.545A pdb=" N THR B 256 " --> pdb=" O HIS B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 253 through 256' Processing helix chain 'B' and resid 257 through 275 removed outlier: 3.732A pdb=" N ARG B 269 " --> pdb=" O GLN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 296 removed outlier: 3.800A pdb=" N GLN B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 311 removed outlier: 3.912A pdb=" N ASP B 309 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.539A pdb=" N ARG B 328 " --> pdb=" O VAL B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 362 removed outlier: 4.042A pdb=" N HIS B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN B 361 " --> pdb=" O MET B 357 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 454 removed outlier: 3.819A pdb=" N LYS B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 449 through 454' Processing helix chain 'B' and resid 487 through 491 Processing helix chain 'B' and resid 499 through 504 removed outlier: 3.840A pdb=" N LEU B 503 " --> pdb=" O ARG B 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 34 Processing helix chain 'C' and resid 47 through 60 removed outlier: 3.510A pdb=" N TYR C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN C 52 " --> pdb=" O PHE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 103 through 112 removed outlier: 3.673A pdb=" N SER C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 132 Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 258 through 275 removed outlier: 3.806A pdb=" N ARG C 269 " --> pdb=" O GLN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 296 Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.825A pdb=" N ASP C 309 " --> pdb=" O PRO C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 340 Processing helix chain 'C' and resid 341 through 352 removed outlier: 3.770A pdb=" N GLN C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 447 through 454 removed outlier: 3.686A pdb=" N LYS C 453 " --> pdb=" O THR C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 511 Processing helix chain 'D' and resid 28 through 34 removed outlier: 4.173A pdb=" N MET D 32 " --> pdb=" O VAL D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 60 removed outlier: 3.557A pdb=" N TYR D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 94 Processing helix chain 'D' and resid 95 through 98 removed outlier: 3.809A pdb=" N PHE D 98 " --> pdb=" O HIS D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 103 through 112 Processing helix chain 'D' and resid 119 through 131 Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 258 through 275 removed outlier: 4.090A pdb=" N LEU D 267 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN D 268 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG D 269 " --> pdb=" O GLN D 265 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 295 Processing helix chain 'D' and resid 304 through 310 removed outlier: 3.846A pdb=" N ASP D 309 " --> pdb=" O PRO D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 363 removed outlier: 3.577A pdb=" N HIS D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) Processing helix chain 'X' and resid 422 through 435 Processing helix chain 'X' and resid 438 through 446 Processing helix chain 'X' and resid 450 through 465 removed outlier: 3.856A pdb=" N LYS X 463 " --> pdb=" O VAL X 459 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS X 464 " --> pdb=" O ASN X 460 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG X 465 " --> pdb=" O GLU X 461 " (cutoff:3.500A) Processing helix chain 'X' and resid 465 through 476 removed outlier: 3.600A pdb=" N GLU X 470 " --> pdb=" O PRO X 466 " (cutoff:3.500A) Processing helix chain 'X' and resid 481 through 489 removed outlier: 4.158A pdb=" N GLU X 487 " --> pdb=" O GLU X 483 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE X 488 " --> pdb=" O TYR X 484 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS X 489 " --> pdb=" O CYS X 485 " (cutoff:3.500A) Processing helix chain 'Y' and resid 82 through 88 Processing helix chain 'Y' and resid 128 through 147 removed outlier: 3.862A pdb=" N GLY Y 147 " --> pdb=" O ILE Y 143 " (cutoff:3.500A) Processing helix chain 'Y' and resid 172 through 179 Processing helix chain 'Y' and resid 220 through 237 Proline residue: Y 232 - end of helix Processing helix chain 'Z' and resid 72 through 95 removed outlier: 3.916A pdb=" N ARG Z 76 " --> pdb=" O ALA Z 72 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU Z 77 " --> pdb=" O LEU Z 73 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA Z 78 " --> pdb=" O GLU Z 74 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR Z 79 " --> pdb=" O SER Z 75 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA Z 93 " --> pdb=" O ALA Z 89 " (cutoff:3.500A) Processing helix chain 'Z' and resid 97 through 114 Processing helix chain 'Z' and resid 121 through 137 removed outlier: 3.714A pdb=" N VAL Z 125 " --> pdb=" O ARG Z 121 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU Z 137 " --> pdb=" O ALA Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 142 through 147 Processing helix chain 'Z' and resid 153 through 169 removed outlier: 3.738A pdb=" N ILE Z 157 " --> pdb=" O SER Z 153 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS Z 166 " --> pdb=" O LEU Z 162 " (cutoff:3.500A) Processing helix chain 'Z' and resid 178 through 186 removed outlier: 3.547A pdb=" N ILE Z 182 " --> pdb=" O PRO Z 178 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN Z 183 " --> pdb=" O SER Z 179 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS Z 184 " --> pdb=" O LEU Z 180 " (cutoff:3.500A) Processing helix chain 'Z' and resid 196 through 211 removed outlier: 3.508A pdb=" N LYS Z 200 " --> pdb=" O ILE Z 196 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG Z 208 " --> pdb=" O LYS Z 204 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS Z 211 " --> pdb=" O GLN Z 207 " (cutoff:3.500A) Processing helix chain 'Z' and resid 219 through 235 Processing helix chain 'Z' and resid 241 through 247 removed outlier: 3.852A pdb=" N ILE Z 244 " --> pdb=" O HIS Z 241 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL Z 245 " --> pdb=" O THR Z 242 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA Z 246 " --> pdb=" O GLU Z 243 " (cutoff:3.500A) Processing helix chain 'Z' and resid 251 through 266 Processing helix chain 'Z' and resid 287 through 294 Processing helix chain 'Z' and resid 448 through 455 removed outlier: 4.043A pdb=" N VAL Z 455 " --> pdb=" O TYR Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 476 through 478 No H-bonds generated for 'chain 'Z' and resid 476 through 478' Processing helix chain 'Z' and resid 479 through 491 removed outlier: 3.854A pdb=" N ILE Z 486 " --> pdb=" O LEU Z 482 " (cutoff:3.500A) Processing helix chain 'Z' and resid 492 through 497 removed outlier: 4.062A pdb=" N LEU Z 496 " --> pdb=" O ALA Z 492 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU Z 497 " --> pdb=" O ASP Z 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 492 through 497' Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 195 removed outlier: 4.169A pdb=" N ASP A 164 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 183 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A 161 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 407 removed outlier: 6.365A pdb=" N LYS A 405 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU A 412 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 407 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 425 " --> pdb=" O TYR A 411 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA5, first strand: chain 'B' and resid 162 through 165 removed outlier: 3.534A pdb=" N SER B 162 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP B 164 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 181 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 180 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 424 through 426 removed outlier: 3.578A pdb=" N TYR B 411 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA B 410 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS B 405 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU B 412 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 458 through 464 removed outlier: 6.595A pdb=" N HIS B 474 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU B 461 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU B 472 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 192 through 193 Processing sheet with id=AA9, first strand: chain 'C' and resid 424 through 425 removed outlier: 3.629A pdb=" N ILE C 425 " --> pdb=" O TYR C 411 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA C 410 " --> pdb=" O ILE C 406 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 404 " --> pdb=" O GLU C 412 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 377 " --> pdb=" O LYS C 431 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 458 through 464 removed outlier: 6.920A pdb=" N LEU C 472 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 66 through 68 removed outlier: 3.706A pdb=" N TYR D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU D 68 " --> pdb=" O MET D 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 190 through 195 removed outlier: 4.096A pdb=" N VAL D 181 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP D 164 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE D 161 " --> pdb=" O THR D 221 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Y' and resid 92 through 93 removed outlier: 3.727A pdb=" N GLY Y 125 " --> pdb=" O ILE Y 70 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE Y 70 " --> pdb=" O GLY Y 125 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU Y 67 " --> pdb=" O SER Y 163 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER Y 163 " --> pdb=" O LEU Y 67 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR Y 73 " --> pdb=" O ILE Y 157 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ILE Y 157 " --> pdb=" O THR Y 73 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY Y 162 " --> pdb=" O LEU Y 214 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR Y 215 " --> pdb=" O VAL Y 203 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLU Y 186 " --> pdb=" O PHE Y 190 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLY Y 192 " --> pdb=" O SER Y 184 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N SER Y 184 " --> pdb=" O GLY Y 192 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 176 hydrogen bonds 352 hydrogen bond angles 0 basepair planarities 75 basepair parallelities 127 stacking parallelities Total time for adding SS restraints: 4.37 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5073 1.33 - 1.45: 5262 1.45 - 1.57: 11760 1.57 - 1.69: 330 1.69 - 1.81: 126 Bond restraints: 22551 Sorted by residual: bond pdb=" N GLN C 75 " pdb=" CA GLN C 75 " ideal model delta sigma weight residual 1.457 1.519 -0.062 1.29e-02 6.01e+03 2.30e+01 bond pdb=" N TYR C 74 " pdb=" CA TYR C 74 " ideal model delta sigma weight residual 1.457 1.515 -0.058 1.29e-02 6.01e+03 2.01e+01 bond pdb=" C GLN C 75 " pdb=" O GLN C 75 " ideal model delta sigma weight residual 1.235 1.291 -0.056 1.26e-02 6.30e+03 1.95e+01 bond pdb=" CA TYR C 74 " pdb=" C TYR C 74 " ideal model delta sigma weight residual 1.523 1.557 -0.034 1.34e-02 5.57e+03 6.32e+00 bond pdb=" C GLN C 75 " pdb=" N ASP C 76 " ideal model delta sigma weight residual 1.333 1.369 -0.036 1.56e-02 4.11e+03 5.42e+00 ... (remaining 22546 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 30902 3.76 - 7.52: 285 7.52 - 11.28: 27 11.28 - 15.03: 0 15.03 - 18.79: 2 Bond angle restraints: 31216 Sorted by residual: angle pdb=" C GLN C 75 " pdb=" N ASP C 76 " pdb=" CA ASP C 76 " ideal model delta sigma weight residual 122.79 104.00 18.79 1.63e+00 3.76e-01 1.33e+02 angle pdb=" C TYR C 74 " pdb=" N GLN C 75 " pdb=" CA GLN C 75 " ideal model delta sigma weight residual 121.54 137.82 -16.28 1.91e+00 2.74e-01 7.26e+01 angle pdb=" N PRO D 150 " pdb=" CA PRO D 150 " pdb=" CB PRO D 150 " ideal model delta sigma weight residual 103.25 111.59 -8.34 1.05e+00 9.07e-01 6.31e+01 angle pdb=" N PRO D 254 " pdb=" CA PRO D 254 " pdb=" CB PRO D 254 " ideal model delta sigma weight residual 103.25 111.15 -7.90 1.05e+00 9.07e-01 5.66e+01 angle pdb=" N PRO D 152 " pdb=" CA PRO D 152 " pdb=" CB PRO D 152 " ideal model delta sigma weight residual 103.25 111.07 -7.82 1.05e+00 9.07e-01 5.55e+01 ... (remaining 31211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 12459 35.90 - 71.79: 812 71.79 - 107.69: 23 107.69 - 143.59: 9 143.59 - 179.48: 11 Dihedral angle restraints: 13314 sinusoidal: 6606 harmonic: 6708 Sorted by residual: dihedral pdb=" CA THR A 231 " pdb=" C THR A 231 " pdb=" N ALA A 232 " pdb=" CA ALA A 232 " ideal model delta harmonic sigma weight residual 180.00 141.22 38.78 0 5.00e+00 4.00e-02 6.02e+01 dihedral pdb=" CA LYS B 421 " pdb=" C LYS B 421 " pdb=" N HIS B 422 " pdb=" CA HIS B 422 " ideal model delta harmonic sigma weight residual 180.00 145.85 34.15 0 5.00e+00 4.00e-02 4.67e+01 dihedral pdb=" CA VAL D 292 " pdb=" C VAL D 292 " pdb=" N TYR D 293 " pdb=" CA TYR D 293 " ideal model delta harmonic sigma weight residual 180.00 148.33 31.67 0 5.00e+00 4.00e-02 4.01e+01 ... (remaining 13311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3223 0.091 - 0.182: 265 0.182 - 0.272: 24 0.272 - 0.363: 2 0.363 - 0.454: 2 Chirality restraints: 3516 Sorted by residual: chirality pdb=" CB ILE A 395 " pdb=" CA ILE A 395 " pdb=" CG1 ILE A 395 " pdb=" CG2 ILE A 395 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CB ILE B 153 " pdb=" CA ILE B 153 " pdb=" CG1 ILE B 153 " pdb=" CG2 ILE B 153 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CB THR D 41 " pdb=" CA THR D 41 " pdb=" OG1 THR D 41 " pdb=" CG2 THR D 41 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 3513 not shown) Planarity restraints: 3379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 75 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C GLN C 75 " -0.060 2.00e-02 2.50e+03 pdb=" O GLN C 75 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP C 76 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 494 " 0.050 5.00e-02 4.00e+02 7.65e-02 9.35e+00 pdb=" N PRO C 495 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 495 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 495 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 366 " 0.046 5.00e-02 4.00e+02 7.00e-02 7.84e+00 pdb=" N PRO C 367 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 367 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 367 " 0.039 5.00e-02 4.00e+02 ... (remaining 3376 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3419 2.76 - 3.30: 20381 3.30 - 3.83: 38624 3.83 - 4.37: 43357 4.37 - 4.90: 68937 Nonbonded interactions: 174718 Sorted by model distance: nonbonded pdb=" O CYS Z 134 " pdb=" OG1 THR Z 139 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR B 202 " pdb=" O ARG B 229 " model vdw 2.234 3.040 nonbonded pdb=" O ILE B 222 " pdb=" OG1 THR B 247 " model vdw 2.238 3.040 nonbonded pdb=" O LEU A 342 " pdb=" OG1 THR A 346 " model vdw 2.266 3.040 nonbonded pdb=" NH1 ARG B 185 " pdb=" OP1 DT u 5 " model vdw 2.274 3.120 ... (remaining 174713 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 18 through 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 142 or (resid 143 and (name N or name CA or na \ me C or name O or name CB )) or resid 154 through 353 or (resid 356 through 361 \ and (name N or name CA or name C or name O or name CB )) or resid 362 through 38 \ 4 or (resid 389 and (name N or name CA or name C or name O or name CB )) or resi \ d 390 through 395 or (resid 396 and (name N or name CA or name C or name O or na \ me CB )) or resid 397 through 437)) selection = (chain 'B' and ((resid 18 through 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 142 or (resid 143 and (name N or name CA or na \ me C or name O or name CB )) or resid 154 through 197 or resid 201 through 353 o \ r (resid 356 through 361 and (name N or name CA or name C or name O or name CB ) \ ) or resid 362 through 395 or (resid 396 and (name N or name CA or name C or nam \ e O or name CB )) or resid 397 through 437)) selection = (chain 'C' and (resid 18 through 197 or resid 201 through 384 or (resid 389 and \ (name N or name CA or name C or name O or name CB )) or resid 390 through 436 or \ (resid 437 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = chain 't' selection = chain 'u' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.140 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 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 : 0.004 0.077 22552 Z= 0.214 Angle : 0.908 18.793 31218 Z= 0.509 Chirality : 0.053 0.454 3516 Planarity : 0.006 0.076 3379 Dihedral : 21.260 179.482 8943 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.23 % Favored : 86.55 % Rotamer: Outliers : 0.10 % Allowed : 0.60 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.17), residues: 2223 helix: -0.76 (0.16), residues: 837 sheet: -1.64 (0.48), residues: 100 loop : -2.84 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 269 TYR 0.024 0.002 TYR Z 155 PHE 0.045 0.002 PHE C 306 TRP 0.037 0.002 TRP B 117 HIS 0.014 0.001 HIS Z 473 Details of bonding type rmsd covalent geometry : bond 0.00434 (22551) covalent geometry : angle 0.90820 (31216) SS BOND : bond 0.00232 ( 1) SS BOND : angle 0.57827 ( 2) hydrogen bonds : bond 0.16869 ( 816) hydrogen bonds : angle 6.68761 ( 2197) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 379 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 HIS cc_start: 0.5508 (m90) cc_final: 0.5225 (m170) REVERT: A 73 TYR cc_start: 0.5813 (p90) cc_final: 0.5299 (p90) REVERT: B 89 MET cc_start: 0.7192 (ptp) cc_final: 0.6333 (ptp) REVERT: B 283 HIS cc_start: 0.6532 (p-80) cc_final: 0.6265 (p-80) REVERT: B 330 PHE cc_start: 0.5167 (p90) cc_final: 0.4581 (p90) REVERT: C 90 ARG cc_start: 0.6239 (tpt-90) cc_final: 0.5976 (tpp-160) REVERT: C 115 TYR cc_start: 0.6461 (m-10) cc_final: 0.6232 (m-10) REVERT: C 272 ARG cc_start: 0.6262 (ttt180) cc_final: 0.5908 (tpp80) REVERT: D 137 ILE cc_start: 0.7105 (mt) cc_final: 0.6890 (mt) REVERT: D 291 PHE cc_start: 0.7435 (t80) cc_final: 0.7183 (t80) REVERT: Y 97 LYS cc_start: 0.5565 (mttt) cc_final: 0.4885 (pttm) REVERT: Y 114 LEU cc_start: 0.7739 (tp) cc_final: 0.7293 (tp) REVERT: Y 131 ASP cc_start: 0.8210 (m-30) cc_final: 0.7925 (m-30) REVERT: Y 206 ILE cc_start: 0.7042 (mm) cc_final: 0.6780 (mm) REVERT: Y 233 VAL cc_start: 0.7899 (t) cc_final: 0.7542 (t) REVERT: Y 240 MET cc_start: 0.4399 (mtm) cc_final: 0.3320 (tpp) REVERT: Z 130 LEU cc_start: 0.7387 (mt) cc_final: 0.7024 (mt) REVERT: Z 460 ASP cc_start: 0.5980 (m-30) cc_final: 0.5571 (t0) REVERT: Z 494 PHE cc_start: 0.4215 (t80) cc_final: 0.2629 (m-80) outliers start: 2 outliers final: 1 residues processed: 380 average time/residue: 0.1680 time to fit residues: 96.3793 Evaluate side-chains 210 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.0970 chunk 227 optimal weight: 0.0670 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 278 ASN B 84 GLN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN C 416 ASN ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 114 ASN Z 141 HIS Z 207 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.116585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.097890 restraints weight = 86376.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.098674 restraints weight = 54797.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.099335 restraints weight = 39278.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.099563 restraints weight = 32278.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.099620 restraints weight = 31674.681| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22552 Z= 0.171 Angle : 0.721 11.867 31218 Z= 0.389 Chirality : 0.044 0.190 3516 Planarity : 0.006 0.069 3379 Dihedral : 23.988 179.961 4372 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.27 % Favored : 86.64 % Rotamer: Outliers : 1.29 % Allowed : 10.20 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.17), residues: 2223 helix: -0.16 (0.17), residues: 847 sheet: -1.62 (0.45), residues: 107 loop : -2.80 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 62 TYR 0.023 0.002 TYR C 389 PHE 0.027 0.002 PHE A 213 TRP 0.028 0.002 TRP Z 213 HIS 0.009 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00376 (22551) covalent geometry : angle 0.72124 (31216) SS BOND : bond 0.00093 ( 1) SS BOND : angle 1.09221 ( 2) hydrogen bonds : bond 0.04984 ( 816) hydrogen bonds : angle 5.30927 ( 2197) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 MET cc_start: 0.6697 (mpp) cc_final: 0.6475 (ptp) REVERT: B 283 HIS cc_start: 0.6784 (p-80) cc_final: 0.6317 (p-80) REVERT: B 310 LEU cc_start: 0.8287 (mp) cc_final: 0.7887 (mp) REVERT: B 330 PHE cc_start: 0.5200 (p90) cc_final: 0.4505 (p90) REVERT: C 90 ARG cc_start: 0.6335 (tpt-90) cc_final: 0.6004 (tpp-160) REVERT: C 129 ARG cc_start: 0.5435 (ttt180) cc_final: 0.5184 (ttp-170) REVERT: C 272 ARG cc_start: 0.6948 (ttt180) cc_final: 0.6538 (tpp80) REVERT: C 274 TYR cc_start: 0.5551 (t80) cc_final: 0.4971 (t80) REVERT: D 128 ILE cc_start: 0.7254 (mm) cc_final: 0.6937 (pt) REVERT: D 215 TYR cc_start: 0.6298 (m-10) cc_final: 0.5500 (m-10) REVERT: D 235 TYR cc_start: 0.6184 (t80) cc_final: 0.5824 (t80) REVERT: Y 97 LYS cc_start: 0.5553 (mttt) cc_final: 0.4865 (pttm) REVERT: Y 131 ASP cc_start: 0.8320 (m-30) cc_final: 0.8034 (m-30) REVERT: Y 240 MET cc_start: 0.5176 (mtm) cc_final: 0.3474 (tpp) REVERT: Z 460 ASP cc_start: 0.6059 (m-30) cc_final: 0.5646 (t0) REVERT: Z 494 PHE cc_start: 0.4445 (t80) cc_final: 0.2826 (m-80) outliers start: 26 outliers final: 16 residues processed: 240 average time/residue: 0.1635 time to fit residues: 60.5153 Evaluate side-chains 215 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 349 GLN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain X residue 442 ILE Chi-restraints excluded: chain Y residue 188 GLU Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 154 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 10 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 229 optimal weight: 0.0870 chunk 125 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 ASN A 177 ASN ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN C 349 GLN ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS Z 114 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.113131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.092606 restraints weight = 86371.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.092557 restraints weight = 63585.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.093160 restraints weight = 45736.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.093601 restraints weight = 39501.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.093609 restraints weight = 34845.299| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22552 Z= 0.227 Angle : 0.785 11.078 31218 Z= 0.421 Chirality : 0.047 0.205 3516 Planarity : 0.006 0.067 3379 Dihedral : 24.239 179.236 4372 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.30 % Favored : 85.61 % Rotamer: Outliers : 2.49 % Allowed : 15.77 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.17), residues: 2223 helix: -0.26 (0.17), residues: 853 sheet: -1.87 (0.44), residues: 114 loop : -2.92 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 401 TYR 0.027 0.002 TYR B 435 PHE 0.033 0.003 PHE C 306 TRP 0.052 0.004 TRP Z 213 HIS 0.013 0.002 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00505 (22551) covalent geometry : angle 0.78516 (31216) SS BOND : bond 0.00157 ( 1) SS BOND : angle 1.24753 ( 2) hydrogen bonds : bond 0.05360 ( 816) hydrogen bonds : angle 5.28729 ( 2197) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ILE cc_start: 0.7338 (mm) cc_final: 0.6969 (mm) REVERT: A 33 LYS cc_start: 0.7145 (ptpt) cc_final: 0.6923 (ptpt) REVERT: A 74 TYR cc_start: 0.6003 (t80) cc_final: 0.5660 (t80) REVERT: B 89 MET cc_start: 0.7151 (ptp) cc_final: 0.6317 (ptp) REVERT: B 310 LEU cc_start: 0.8466 (mp) cc_final: 0.8234 (mp) REVERT: B 328 ARG cc_start: 0.6216 (tpt-90) cc_final: 0.4992 (tpt90) REVERT: B 390 MET cc_start: 0.6165 (ptt) cc_final: 0.5657 (mtt) REVERT: C 73 TYR cc_start: 0.4754 (OUTLIER) cc_final: 0.4528 (m-80) REVERT: C 90 ARG cc_start: 0.6287 (tpt-90) cc_final: 0.5777 (tpt170) REVERT: C 272 ARG cc_start: 0.7168 (ttt180) cc_final: 0.6835 (tpp80) REVERT: D 31 HIS cc_start: 0.5925 (OUTLIER) cc_final: 0.5047 (t-90) REVERT: D 128 ILE cc_start: 0.7242 (mm) cc_final: 0.6963 (pt) REVERT: Y 131 ASP cc_start: 0.8346 (m-30) cc_final: 0.7997 (m-30) REVERT: Y 240 MET cc_start: 0.5618 (mtm) cc_final: 0.3516 (tpt) REVERT: Z 208 ARG cc_start: 0.5964 (tpt90) cc_final: 0.5693 (ptt180) REVERT: Z 213 TRP cc_start: 0.2684 (m-10) cc_final: 0.2228 (m-10) REVERT: Z 460 ASP cc_start: 0.6155 (m-30) cc_final: 0.5796 (t0) REVERT: Z 494 PHE cc_start: 0.4661 (t80) cc_final: 0.3452 (m-80) outliers start: 50 outliers final: 32 residues processed: 243 average time/residue: 0.1684 time to fit residues: 62.5379 Evaluate side-chains 216 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 31 HIS Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain X residue 442 ILE Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 103 ILE Chi-restraints excluded: chain Y residue 188 GLU Chi-restraints excluded: chain Y residue 189 LEU Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 154 VAL Chi-restraints excluded: chain Z residue 199 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 205 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN C 315 ASN ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Z 114 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.114563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.094729 restraints weight = 85296.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.095670 restraints weight = 54132.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.096213 restraints weight = 39148.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.096468 restraints weight = 32447.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.096527 restraints weight = 32894.020| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22552 Z= 0.151 Angle : 0.688 10.589 31218 Z= 0.370 Chirality : 0.043 0.191 3516 Planarity : 0.005 0.078 3379 Dihedral : 24.169 179.934 4372 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.36 % Favored : 86.55 % Rotamer: Outliers : 2.64 % Allowed : 17.96 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.17), residues: 2223 helix: -0.01 (0.18), residues: 847 sheet: -2.03 (0.44), residues: 117 loop : -2.87 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 269 TYR 0.023 0.002 TYR B 435 PHE 0.024 0.002 PHE D 209 TRP 0.018 0.002 TRP Z 213 HIS 0.010 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00331 (22551) covalent geometry : angle 0.68847 (31216) SS BOND : bond 0.00049 ( 1) SS BOND : angle 1.02594 ( 2) hydrogen bonds : bond 0.04383 ( 816) hydrogen bonds : angle 4.99084 ( 2197) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 210 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ILE cc_start: 0.7363 (mm) cc_final: 0.6905 (mm) REVERT: A 33 LYS cc_start: 0.7215 (ptpt) cc_final: 0.6978 (ptpt) REVERT: A 74 TYR cc_start: 0.5779 (t80) cc_final: 0.5492 (t80) REVERT: A 163 MET cc_start: 0.6674 (mmm) cc_final: 0.6336 (mtp) REVERT: B 390 MET cc_start: 0.6172 (ptt) cc_final: 0.5648 (mtt) REVERT: C 71 MET cc_start: 0.4136 (mmm) cc_final: 0.3778 (mmt) REVERT: C 90 ARG cc_start: 0.6211 (tpt-90) cc_final: 0.5913 (tpp-160) REVERT: C 272 ARG cc_start: 0.7152 (ttt180) cc_final: 0.6864 (tpp80) REVERT: D 128 ILE cc_start: 0.7213 (mm) cc_final: 0.6988 (pt) REVERT: Y 121 MET cc_start: 0.5392 (tpt) cc_final: 0.5084 (tpp) REVERT: Y 131 ASP cc_start: 0.8317 (m-30) cc_final: 0.7964 (m-30) REVERT: Y 186 GLU cc_start: 0.6453 (mm-30) cc_final: 0.6177 (mm-30) REVERT: Y 240 MET cc_start: 0.5246 (mtm) cc_final: 0.3544 (tpp) REVERT: Z 213 TRP cc_start: 0.2642 (m-10) cc_final: 0.2073 (m-10) REVERT: Z 460 ASP cc_start: 0.6046 (m-30) cc_final: 0.5649 (t0) REVERT: Z 494 PHE cc_start: 0.4693 (t80) cc_final: 0.3586 (m-80) outliers start: 53 outliers final: 24 residues processed: 246 average time/residue: 0.1447 time to fit residues: 55.8414 Evaluate side-chains 211 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain Y residue 189 LEU Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 154 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 169 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 178 optimal weight: 8.9990 chunk 201 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 185 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.114588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.095201 restraints weight = 85848.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.096038 restraints weight = 56309.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.096633 restraints weight = 38978.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.097054 restraints weight = 32651.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.097089 restraints weight = 32388.627| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22552 Z= 0.156 Angle : 0.685 9.645 31218 Z= 0.368 Chirality : 0.043 0.189 3516 Planarity : 0.005 0.082 3379 Dihedral : 24.145 179.506 4372 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.45 % Favored : 86.46 % Rotamer: Outliers : 3.13 % Allowed : 18.96 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.17), residues: 2223 helix: 0.02 (0.18), residues: 848 sheet: -2.05 (0.46), residues: 99 loop : -2.82 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Z 208 TYR 0.029 0.002 TYR B 435 PHE 0.020 0.002 PHE A 213 TRP 0.014 0.002 TRP C 117 HIS 0.008 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00346 (22551) covalent geometry : angle 0.68501 (31216) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.93750 ( 2) hydrogen bonds : bond 0.04344 ( 816) hydrogen bonds : angle 4.88955 ( 2197) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 202 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.5795 (t80) cc_final: 0.5500 (t80) REVERT: A 163 MET cc_start: 0.6570 (mmm) cc_final: 0.6341 (mtp) REVERT: B 98 PHE cc_start: 0.6455 (m-80) cc_final: 0.5979 (m-80) REVERT: B 161 ILE cc_start: 0.5093 (OUTLIER) cc_final: 0.4783 (tt) REVERT: B 310 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7998 (mp) REVERT: B 390 MET cc_start: 0.6155 (ptt) cc_final: 0.5726 (mtt) REVERT: C 71 MET cc_start: 0.3738 (mmm) cc_final: 0.3361 (mmt) REVERT: C 90 ARG cc_start: 0.6190 (tpt-90) cc_final: 0.5930 (tpp-160) REVERT: C 272 ARG cc_start: 0.7261 (ttt180) cc_final: 0.6998 (tpp80) REVERT: C 425 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7475 (tp) REVERT: C 434 VAL cc_start: 0.4133 (OUTLIER) cc_final: 0.3830 (p) REVERT: D 31 HIS cc_start: 0.5367 (OUTLIER) cc_final: 0.5026 (t-90) REVERT: D 128 ILE cc_start: 0.7153 (mm) cc_final: 0.6565 (tp) REVERT: D 169 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7523 (mt) REVERT: Y 121 MET cc_start: 0.5595 (tpt) cc_final: 0.5311 (tpp) REVERT: Y 131 ASP cc_start: 0.8114 (m-30) cc_final: 0.7809 (m-30) REVERT: Y 240 MET cc_start: 0.5182 (mtm) cc_final: 0.3487 (tpp) REVERT: Z 112 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7142 (mt) REVERT: Z 116 PHE cc_start: 0.6214 (OUTLIER) cc_final: 0.5660 (t80) REVERT: Z 123 GLN cc_start: 0.7184 (pm20) cc_final: 0.6903 (pm20) REVERT: Z 213 TRP cc_start: 0.2631 (m-10) cc_final: 0.2205 (m-10) REVERT: Z 460 ASP cc_start: 0.5986 (m-30) cc_final: 0.5572 (t0) REVERT: Z 494 PHE cc_start: 0.4530 (t80) cc_final: 0.3527 (m-80) outliers start: 63 outliers final: 37 residues processed: 249 average time/residue: 0.1359 time to fit residues: 53.8397 Evaluate side-chains 225 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 31 HIS Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain X residue 442 ILE Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 189 LEU Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 116 PHE Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 154 VAL Chi-restraints excluded: chain Z residue 157 ILE Chi-restraints excluded: chain Z residue 199 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 191 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 229 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 214 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 119 optimal weight: 0.0370 chunk 182 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 GLN ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.113250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.093156 restraints weight = 85557.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.092943 restraints weight = 58864.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.093509 restraints weight = 46871.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.093747 restraints weight = 39323.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.093900 restraints weight = 34241.968| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22552 Z= 0.184 Angle : 0.716 15.240 31218 Z= 0.382 Chirality : 0.044 0.224 3516 Planarity : 0.005 0.072 3379 Dihedral : 24.185 179.557 4370 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.26 % Favored : 85.65 % Rotamer: Outliers : 3.63 % Allowed : 19.25 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.17), residues: 2223 helix: -0.03 (0.18), residues: 853 sheet: -2.22 (0.45), residues: 108 loop : -2.84 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 105 TYR 0.050 0.002 TYR C 274 PHE 0.028 0.002 PHE C 506 TRP 0.019 0.002 TRP C 117 HIS 0.007 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00411 (22551) covalent geometry : angle 0.71560 (31216) SS BOND : bond 0.00081 ( 1) SS BOND : angle 1.03811 ( 2) hydrogen bonds : bond 0.04581 ( 816) hydrogen bonds : angle 4.96834 ( 2197) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 193 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ILE cc_start: 0.7249 (mm) cc_final: 0.7005 (mm) REVERT: A 74 TYR cc_start: 0.6001 (t80) cc_final: 0.5687 (t80) REVERT: A 163 MET cc_start: 0.6633 (mmm) cc_final: 0.6386 (mtp) REVERT: B 89 MET cc_start: 0.7148 (ptp) cc_final: 0.6266 (ptp) REVERT: B 161 ILE cc_start: 0.5107 (OUTLIER) cc_final: 0.4753 (tt) REVERT: B 235 TYR cc_start: 0.7706 (t80) cc_final: 0.7434 (t80) REVERT: B 310 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8068 (mp) REVERT: B 352 HIS cc_start: 0.7373 (m90) cc_final: 0.7041 (m90) REVERT: B 390 MET cc_start: 0.6231 (ptt) cc_final: 0.5837 (mtt) REVERT: C 34 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7105 (tm-30) REVERT: C 71 MET cc_start: 0.3492 (mmm) cc_final: 0.3132 (mmt) REVERT: C 90 ARG cc_start: 0.6021 (tpt-90) cc_final: 0.5760 (tpp-160) REVERT: C 272 ARG cc_start: 0.7259 (ttt180) cc_final: 0.7019 (tpp80) REVERT: C 425 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7435 (tp) REVERT: C 434 VAL cc_start: 0.4462 (OUTLIER) cc_final: 0.4174 (p) REVERT: D 31 HIS cc_start: 0.5308 (OUTLIER) cc_final: 0.4682 (t-90) REVERT: D 117 TRP cc_start: 0.7096 (OUTLIER) cc_final: 0.6216 (t60) REVERT: D 127 TYR cc_start: 0.7141 (t80) cc_final: 0.6806 (t80) REVERT: D 128 ILE cc_start: 0.7277 (mm) cc_final: 0.6881 (tp) REVERT: D 169 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7707 (mt) REVERT: Y 105 ARG cc_start: 0.5113 (tpm170) cc_final: 0.4784 (tpm170) REVERT: Y 121 MET cc_start: 0.5574 (tpt) cc_final: 0.5313 (tpp) REVERT: Y 131 ASP cc_start: 0.8224 (m-30) cc_final: 0.7910 (m-30) REVERT: Y 240 MET cc_start: 0.5428 (mtm) cc_final: 0.3640 (tpp) REVERT: Z 112 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7184 (mt) REVERT: Z 116 PHE cc_start: 0.6220 (OUTLIER) cc_final: 0.5754 (t80) REVERT: Z 213 TRP cc_start: 0.2838 (m-10) cc_final: 0.2223 (m-10) REVERT: Z 460 ASP cc_start: 0.6217 (m-30) cc_final: 0.5886 (t0) REVERT: Z 494 PHE cc_start: 0.4952 (t80) cc_final: 0.3705 (m-80) outliers start: 73 outliers final: 52 residues processed: 251 average time/residue: 0.1372 time to fit residues: 56.2819 Evaluate side-chains 243 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 182 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 31 HIS Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 114 LEU Chi-restraints excluded: chain Y residue 189 LEU Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 116 PHE Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 154 VAL Chi-restraints excluded: chain Z residue 157 ILE Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain Z residue 199 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 62 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 114 optimal weight: 0.0870 chunk 215 optimal weight: 1.9990 chunk 229 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 HIS ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.114527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.094662 restraints weight = 84933.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.095471 restraints weight = 57682.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.096147 restraints weight = 38573.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.096641 restraints weight = 31527.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.096778 restraints weight = 29988.851| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22552 Z= 0.144 Angle : 0.680 13.939 31218 Z= 0.362 Chirality : 0.042 0.206 3516 Planarity : 0.005 0.064 3379 Dihedral : 24.112 179.088 4370 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.72 % Favored : 86.19 % Rotamer: Outliers : 3.63 % Allowed : 20.15 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.17), residues: 2223 helix: 0.00 (0.18), residues: 861 sheet: -2.27 (0.46), residues: 107 loop : -2.77 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 77 TYR 0.023 0.002 TYR B 435 PHE 0.023 0.001 PHE B 209 TRP 0.012 0.002 TRP C 282 HIS 0.009 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00318 (22551) covalent geometry : angle 0.68018 (31216) SS BOND : bond 0.00035 ( 1) SS BOND : angle 0.91516 ( 2) hydrogen bonds : bond 0.04173 ( 816) hydrogen bonds : angle 4.81598 ( 2197) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 200 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ILE cc_start: 0.7118 (mm) cc_final: 0.6809 (mm) REVERT: A 74 TYR cc_start: 0.5767 (t80) cc_final: 0.5463 (t80) REVERT: A 163 MET cc_start: 0.6478 (mmm) cc_final: 0.6270 (mtp) REVERT: B 98 PHE cc_start: 0.6413 (m-80) cc_final: 0.6072 (m-80) REVERT: B 161 ILE cc_start: 0.5117 (OUTLIER) cc_final: 0.4797 (tt) REVERT: B 235 TYR cc_start: 0.7644 (t80) cc_final: 0.7324 (t80) REVERT: B 310 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7999 (mp) REVERT: B 390 MET cc_start: 0.6074 (ptt) cc_final: 0.5730 (mtt) REVERT: C 34 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7009 (tm-30) REVERT: C 259 GLN cc_start: 0.4509 (pm20) cc_final: 0.4277 (pt0) REVERT: C 425 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7293 (tp) REVERT: C 434 VAL cc_start: 0.4263 (OUTLIER) cc_final: 0.4032 (p) REVERT: D 31 HIS cc_start: 0.5343 (OUTLIER) cc_final: 0.4769 (t-90) REVERT: D 117 TRP cc_start: 0.6945 (OUTLIER) cc_final: 0.6306 (t60) REVERT: D 127 TYR cc_start: 0.7096 (t80) cc_final: 0.6777 (t80) REVERT: D 128 ILE cc_start: 0.7135 (mm) cc_final: 0.6776 (tp) REVERT: Y 105 ARG cc_start: 0.4861 (tpm170) cc_final: 0.4577 (tpm170) REVERT: Y 121 MET cc_start: 0.5547 (tpt) cc_final: 0.5297 (tpp) REVERT: Y 131 ASP cc_start: 0.8173 (m-30) cc_final: 0.7853 (m-30) REVERT: Y 240 MET cc_start: 0.5216 (mtm) cc_final: 0.3564 (tpp) REVERT: Z 112 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7097 (mt) REVERT: Z 116 PHE cc_start: 0.6234 (OUTLIER) cc_final: 0.5705 (t80) REVERT: Z 185 PHE cc_start: 0.4597 (OUTLIER) cc_final: 0.3619 (m-80) REVERT: Z 213 TRP cc_start: 0.3049 (m-10) cc_final: 0.2628 (m-10) REVERT: Z 460 ASP cc_start: 0.6040 (m-30) cc_final: 0.5615 (t0) REVERT: Z 494 PHE cc_start: 0.4710 (t80) cc_final: 0.3381 (m-80) outliers start: 73 outliers final: 40 residues processed: 259 average time/residue: 0.1498 time to fit residues: 62.1747 Evaluate side-chains 233 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 31 HIS Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain Y residue 211 LYS Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 116 PHE Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 157 ILE Chi-restraints excluded: chain Z residue 185 PHE Chi-restraints excluded: chain Z residue 198 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 178 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 78 optimal weight: 0.0970 chunk 151 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 223 optimal weight: 0.0770 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 HIS ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 352 HIS ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.114442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.094355 restraints weight = 85466.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.095165 restraints weight = 55884.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.095784 restraints weight = 38843.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.095955 restraints weight = 32722.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.096127 restraints weight = 31575.456| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22552 Z= 0.152 Angle : 0.690 14.458 31218 Z= 0.367 Chirality : 0.043 0.203 3516 Planarity : 0.005 0.062 3379 Dihedral : 24.110 178.644 4370 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 14.13 % Favored : 85.83 % Rotamer: Outliers : 3.13 % Allowed : 20.60 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.18), residues: 2223 helix: 0.06 (0.18), residues: 852 sheet: -2.32 (0.45), residues: 107 loop : -2.74 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 269 TYR 0.023 0.002 TYR B 435 PHE 0.022 0.002 PHE B 209 TRP 0.012 0.002 TRP C 117 HIS 0.011 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00337 (22551) covalent geometry : angle 0.69046 (31216) SS BOND : bond 0.00085 ( 1) SS BOND : angle 1.14522 ( 2) hydrogen bonds : bond 0.04212 ( 816) hydrogen bonds : angle 4.81437 ( 2197) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 185 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.5808 (t80) cc_final: 0.5485 (t80) REVERT: B 98 PHE cc_start: 0.6397 (m-80) cc_final: 0.6119 (m-80) REVERT: B 161 ILE cc_start: 0.5136 (OUTLIER) cc_final: 0.4790 (tt) REVERT: B 235 TYR cc_start: 0.7706 (t80) cc_final: 0.7376 (t80) REVERT: B 259 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6489 (tm-30) REVERT: B 310 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8058 (mp) REVERT: B 390 MET cc_start: 0.6022 (ptt) cc_final: 0.5660 (mtt) REVERT: C 71 MET cc_start: 0.3895 (tpp) cc_final: 0.3671 (tpt) REVERT: C 425 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7188 (tp) REVERT: C 475 MET cc_start: 0.6510 (mmm) cc_final: 0.6094 (mmm) REVERT: D 31 HIS cc_start: 0.5205 (OUTLIER) cc_final: 0.4637 (t-90) REVERT: D 117 TRP cc_start: 0.7034 (OUTLIER) cc_final: 0.6365 (t60) REVERT: D 127 TYR cc_start: 0.7111 (t80) cc_final: 0.6793 (t80) REVERT: D 128 ILE cc_start: 0.7168 (mm) cc_final: 0.6816 (tp) REVERT: Y 105 ARG cc_start: 0.4827 (tpm170) cc_final: 0.4019 (tpp-160) REVERT: Y 131 ASP cc_start: 0.8189 (m-30) cc_final: 0.7873 (m-30) REVERT: Y 240 MET cc_start: 0.5209 (mtm) cc_final: 0.3587 (tpp) REVERT: Z 112 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7113 (mt) REVERT: Z 116 PHE cc_start: 0.6159 (OUTLIER) cc_final: 0.5684 (t80) REVERT: Z 185 PHE cc_start: 0.4597 (OUTLIER) cc_final: 0.3562 (m-80) REVERT: Z 213 TRP cc_start: 0.2852 (m-10) cc_final: 0.2370 (m-10) REVERT: Z 460 ASP cc_start: 0.6055 (m-30) cc_final: 0.5663 (t0) REVERT: Z 494 PHE cc_start: 0.4759 (t80) cc_final: 0.3647 (m-80) outliers start: 63 outliers final: 43 residues processed: 233 average time/residue: 0.1399 time to fit residues: 52.9372 Evaluate side-chains 234 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 182 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 31 HIS Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain X residue 437 THR Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 116 PHE Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 157 ILE Chi-restraints excluded: chain Z residue 185 PHE Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain Z residue 199 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 106 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 HIS ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.113416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.093974 restraints weight = 85592.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.094828 restraints weight = 56275.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.095243 restraints weight = 38465.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.095906 restraints weight = 33426.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.095820 restraints weight = 31337.308| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22552 Z= 0.170 Angle : 0.710 14.463 31218 Z= 0.377 Chirality : 0.044 0.207 3516 Planarity : 0.005 0.074 3379 Dihedral : 24.155 179.511 4370 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 14.62 % Favored : 85.34 % Rotamer: Outliers : 3.08 % Allowed : 21.00 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.17), residues: 2223 helix: 0.02 (0.18), residues: 851 sheet: -2.03 (0.47), residues: 99 loop : -2.77 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 262 TYR 0.025 0.002 TYR C 435 PHE 0.022 0.002 PHE B 209 TRP 0.016 0.002 TRP C 117 HIS 0.010 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00378 (22551) covalent geometry : angle 0.71020 (31216) SS BOND : bond 0.00068 ( 1) SS BOND : angle 1.11371 ( 2) hydrogen bonds : bond 0.04402 ( 816) hydrogen bonds : angle 4.84780 ( 2197) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 182 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.5897 (t80) cc_final: 0.5637 (t80) REVERT: B 57 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6470 (tp) REVERT: B 89 MET cc_start: 0.7131 (ptp) cc_final: 0.6228 (ptp) REVERT: B 98 PHE cc_start: 0.6421 (m-80) cc_final: 0.6039 (m-80) REVERT: B 161 ILE cc_start: 0.5103 (OUTLIER) cc_final: 0.4746 (tt) REVERT: B 235 TYR cc_start: 0.7696 (t80) cc_final: 0.7394 (t80) REVERT: B 310 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8078 (mp) REVERT: B 390 MET cc_start: 0.6115 (ptt) cc_final: 0.5744 (mtt) REVERT: C 69 ASP cc_start: 0.4828 (t0) cc_final: 0.4504 (t0) REVERT: C 425 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7362 (tp) REVERT: C 475 MET cc_start: 0.6505 (mmm) cc_final: 0.6110 (mmm) REVERT: D 31 HIS cc_start: 0.5217 (OUTLIER) cc_final: 0.4705 (t-90) REVERT: D 117 TRP cc_start: 0.6985 (OUTLIER) cc_final: 0.6368 (t60) REVERT: D 128 ILE cc_start: 0.7075 (mm) cc_final: 0.6525 (tp) REVERT: Y 105 ARG cc_start: 0.4749 (tpm170) cc_final: 0.3948 (tpp-160) REVERT: Y 131 ASP cc_start: 0.8096 (m-30) cc_final: 0.7778 (m-30) REVERT: Y 240 MET cc_start: 0.5114 (mtm) cc_final: 0.3580 (tpp) REVERT: Z 112 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7126 (mt) REVERT: Z 116 PHE cc_start: 0.6193 (OUTLIER) cc_final: 0.5696 (t80) REVERT: Z 185 PHE cc_start: 0.4547 (OUTLIER) cc_final: 0.3629 (m-80) REVERT: Z 213 TRP cc_start: 0.3078 (m-10) cc_final: 0.2577 (m-10) REVERT: Z 460 ASP cc_start: 0.5991 (m-30) cc_final: 0.5588 (t0) REVERT: Z 494 PHE cc_start: 0.4610 (t80) cc_final: 0.3574 (m-80) outliers start: 62 outliers final: 45 residues processed: 228 average time/residue: 0.1463 time to fit residues: 53.8606 Evaluate side-chains 232 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 178 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 31 HIS Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain X residue 437 THR Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 116 PHE Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 157 ILE Chi-restraints excluded: chain Z residue 185 PHE Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain Z residue 199 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 99 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 204 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 177 optimal weight: 0.0020 chunk 134 optimal weight: 0.2980 chunk 222 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 HIS ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 379 HIS C 265 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.115386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.095970 restraints weight = 85933.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.096756 restraints weight = 55301.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.097332 restraints weight = 38741.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.097618 restraints weight = 32144.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.097628 restraints weight = 31960.654| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22552 Z= 0.141 Angle : 0.688 15.170 31218 Z= 0.364 Chirality : 0.042 0.206 3516 Planarity : 0.005 0.069 3379 Dihedral : 24.096 179.968 4370 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.77 % Favored : 86.19 % Rotamer: Outliers : 2.74 % Allowed : 21.04 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.18), residues: 2223 helix: 0.09 (0.18), residues: 851 sheet: -2.39 (0.44), residues: 111 loop : -2.74 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 258 TYR 0.019 0.001 TYR C 274 PHE 0.036 0.002 PHE D 291 TRP 0.009 0.002 TRP A 282 HIS 0.008 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00311 (22551) covalent geometry : angle 0.68775 (31216) SS BOND : bond 0.00024 ( 1) SS BOND : angle 1.08202 ( 2) hydrogen bonds : bond 0.04075 ( 816) hydrogen bonds : angle 4.72850 ( 2197) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 196 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7523 (mmm) cc_final: 0.6832 (mtp) REVERT: A 74 TYR cc_start: 0.5797 (t80) cc_final: 0.5533 (t80) REVERT: B 57 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6459 (tp) REVERT: B 98 PHE cc_start: 0.6264 (m-80) cc_final: 0.6051 (m-80) REVERT: B 161 ILE cc_start: 0.4987 (OUTLIER) cc_final: 0.4692 (tt) REVERT: B 235 TYR cc_start: 0.7614 (t80) cc_final: 0.7301 (t80) REVERT: B 310 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7897 (mp) REVERT: B 390 MET cc_start: 0.6014 (ptt) cc_final: 0.5671 (mtt) REVERT: C 290 GLU cc_start: 0.5930 (pt0) cc_final: 0.5626 (tt0) REVERT: C 425 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7165 (tp) REVERT: C 475 MET cc_start: 0.6456 (mmm) cc_final: 0.6097 (mmm) REVERT: D 31 HIS cc_start: 0.5035 (OUTLIER) cc_final: 0.4437 (t-90) REVERT: D 117 TRP cc_start: 0.6999 (OUTLIER) cc_final: 0.6512 (t60) REVERT: D 128 ILE cc_start: 0.7126 (mm) cc_final: 0.6624 (tp) REVERT: Y 97 LYS cc_start: 0.5857 (mttt) cc_final: 0.5002 (pttm) REVERT: Y 131 ASP cc_start: 0.8127 (m-30) cc_final: 0.7809 (m-30) REVERT: Y 240 MET cc_start: 0.5138 (mtm) cc_final: 0.3558 (tpp) REVERT: Z 74 GLU cc_start: 0.6739 (mt-10) cc_final: 0.6517 (tm-30) REVERT: Z 112 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7091 (mt) REVERT: Z 116 PHE cc_start: 0.6265 (OUTLIER) cc_final: 0.5781 (t80) REVERT: Z 213 TRP cc_start: 0.3111 (m-10) cc_final: 0.2436 (m-10) REVERT: Z 460 ASP cc_start: 0.5995 (m-30) cc_final: 0.5580 (t0) REVERT: Z 494 PHE cc_start: 0.4709 (t80) cc_final: 0.3190 (m-80) outliers start: 55 outliers final: 41 residues processed: 238 average time/residue: 0.1381 time to fit residues: 53.1229 Evaluate side-chains 230 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 181 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 379 HIS Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 31 HIS Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 116 PHE Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 157 ILE Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain Z residue 199 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 166 optimal weight: 2.9990 chunk 196 optimal weight: 0.6980 chunk 122 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 211 optimal weight: 3.9990 chunk 26 optimal weight: 0.0980 chunk 18 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 chunk 134 optimal weight: 0.5980 chunk 169 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 HIS B 135 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.115191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.096064 restraints weight = 85905.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.096980 restraints weight = 55742.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.097430 restraints weight = 37762.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.098148 restraints weight = 33211.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.098182 restraints weight = 29668.473| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22552 Z= 0.141 Angle : 0.693 14.506 31218 Z= 0.366 Chirality : 0.043 0.203 3516 Planarity : 0.005 0.071 3379 Dihedral : 24.080 179.971 4370 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.95 % Favored : 86.01 % Rotamer: Outliers : 2.79 % Allowed : 21.34 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.17), residues: 2223 helix: 0.09 (0.18), residues: 857 sheet: -2.37 (0.44), residues: 110 loop : -2.74 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 380 TYR 0.025 0.001 TYR C 435 PHE 0.039 0.002 PHE D 291 TRP 0.009 0.002 TRP A 282 HIS 0.008 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00312 (22551) covalent geometry : angle 0.69287 (31216) SS BOND : bond 0.00025 ( 1) SS BOND : angle 1.13724 ( 2) hydrogen bonds : bond 0.04071 ( 816) hydrogen bonds : angle 4.71763 ( 2197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3334.73 seconds wall clock time: 58 minutes 54.77 seconds (3534.77 seconds total)