Starting phenix.real_space_refine on Sun Sep 13 07:36:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q5b_13831/09_2026/7q5b_13831.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q5b_13831/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7q5b_13831/09_2026/7q5b_13831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q5b_13831/09_2026/7q5b_13831.map" model { file = "/net/cci-nas-00/data/ceres_data/7q5b_13831/09_2026/7q5b_13831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q5b_13831/09_2026/7q5b_13831.cif" } 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-2.2.1-6174/lib/python3.11/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: 5.41, 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: 1.61 Conformation dependent library (CDL) restraints added in 799.4 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: 2.59 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: 4.01 Time building geometry restraints manager: 2.35 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=" C3' DA S 30 " pdb=" O3' DA S 30 " ideal model delta sigma weight residual 1.435 1.486 -0.051 1.30e-02 5.92e+03 1.57e+01 bond pdb=" C3' DC S 23 " pdb=" C2' DC S 23 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.54e+01 ... (remaining 22546 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 30883 3.76 - 7.52: 304 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: 3176 0.091 - 0.182: 307 0.182 - 0.272: 29 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.530 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6040 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 : 0.005 0.077 22552 Z= 0.378 Angle : 0.961 18.793 31218 Z= 0.644 Chirality : 0.056 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/Z covalent geometry : bond 0.00494 / 0.38 (22551) covalent geometry : angle 0.96138 / 0.64 (31216) SS BOND : bond 0.00232 / 0.12 ( 1) SS BOND : angle 0.57827 / 0.96 ( 2) hydrogen bonds : bond 0.16869 / 18.60 ( 816) hydrogen bonds : angle 6.68761 / 8.67 ( 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 : 0.598 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: 0.5300 (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: 0.4582 (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: 0.6892 (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: 0.7300 (tp) REVERT: Y 131 ASP cc_start: 0.8210 (m-30) cc_final: 0.7926 (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: 0.3319 (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: 0.5573 (t0) REVERT: Z 494 PHE cc_start: 0.4215 (t80) cc_final: 0.2628 (m-80) outliers start: 2 outliers final: 1 residues processed: 380 average time/residue: 0.1659 time to fit residues: 95.9390 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 : 0.778 ------------------------------------------------------------------------------- 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: 5.9990 chunk 227 optimal weight: 0.0670 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 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: 10.0000 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 ASN A 278 ASN B 84 GLN B 394 GLN ** 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 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 207 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.114820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.095422 restraints weight = 86500.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.094932 restraints weight = 62579.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.095587 restraints weight = 48491.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.095892 restraints weight = 40576.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.096006 restraints weight = 35454.161| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22552 Z= 0.205 Angle : 0.804 13.948 31218 Z= 0.435 Chirality : 0.050 0.386 3516 Planarity : 0.007 0.084 3379 Dihedral : 24.282 176.315 4372 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.81 % Favored : 86.10 % Rotamer: Outliers : 1.44 % Allowed : 11.74 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.30 (0.17), residues: 848 sheet: -1.58 (0.45), residues: 107 loop : -2.90 (0.16), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 401 TYR 0.030 0.002 TYR C 389 PHE 0.032 0.002 PHE A 213 TRP 0.028 0.003 TRP Z 213 HIS 0.014 0.002 HIS C 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.21 (22551) covalent geometry : angle 0.80352 / 0.43 (31216) SS BOND : bond 0.00049 / 0.02 ( 1) SS BOND : angle 1.10866 / 1.85 ( 2) hydrogen bonds : bond 0.05622 / 6.14 ( 816) hydrogen bonds : angle 5.54720 / 7.43 ( 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 263 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7393 (mmp) cc_final: 0.6155 (mtp) REVERT: B 57 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6967 (tp) REVERT: B 283 HIS cc_start: 0.6972 (p-80) cc_final: 0.6483 (p-80) REVERT: B 310 LEU cc_start: 0.8426 (mp) cc_final: 0.8021 (mp) REVERT: B 330 PHE cc_start: 0.5077 (p90) cc_final: 0.4497 (p90) REVERT: B 390 MET cc_start: 0.6412 (ptt) cc_final: 0.5742 (mtt) REVERT: C 90 ARG cc_start: 0.6383 (tpt-90) cc_final: 0.6019 (tpp-160) REVERT: C 272 ARG cc_start: 0.7082 (ttt180) cc_final: 0.6652 (tpp80) REVERT: C 274 TYR cc_start: 0.5651 (t80) cc_final: 0.4820 (t80) REVERT: D 117 TRP cc_start: 0.6682 (OUTLIER) cc_final: 0.6366 (t60) REVERT: D 215 TYR cc_start: 0.6445 (m-10) cc_final: 0.5509 (m-10) REVERT: D 235 TYR cc_start: 0.6368 (t80) cc_final: 0.6128 (t80) REVERT: Y 131 ASP cc_start: 0.8368 (m-30) cc_final: 0.8061 (m-30) REVERT: Y 240 MET cc_start: 0.5271 (mtm) cc_final: 0.3506 (tpp) REVERT: Z 460 ASP cc_start: 0.6150 (m-30) cc_final: 0.5770 (t0) REVERT: Z 494 PHE cc_start: 0.4801 (t80) cc_final: 0.3422 (m-80) outliers start: 29 outliers final: 21 residues processed: 248 average time/residue: 0.1620 time to fit residues: 62.4485 Evaluate side-chains 212 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 57 LEU 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 230 MET Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 473 CYS Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 349 GLN 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 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: 20.0000 chunk 105 optimal weight: 0.0270 chunk 229 optimal weight: 1.9990 chunk 125 optimal weight: 0.4980 chunk 183 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 114 ASN Z 141 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.116113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.096638 restraints weight = 86065.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.097768 restraints weight = 55896.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.098227 restraints weight = 40562.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.098014 restraints weight = 33808.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.098156 restraints weight = 31862.091| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22552 Z= 0.150 Angle : 0.717 11.365 31218 Z= 0.391 Chirality : 0.048 0.399 3516 Planarity : 0.005 0.077 3379 Dihedral : 24.223 177.330 4372 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.05 % Favored : 86.86 % Rotamer: Outliers : 1.64 % Allowed : 14.88 % Favored : 83.48 % 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: -2.41 (0.17), residues: 2223 helix: -0.05 (0.18), residues: 854 sheet: -1.98 (0.47), residues: 96 loop : -2.84 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG Y 171 TYR 0.021 0.002 TYR B 435 PHE 0.047 0.002 PHE C 506 TRP 0.026 0.002 TRP Z 213 HIS 0.008 0.001 HIS C 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (22551) covalent geometry : angle 0.71696 / 0.39 (31216) SS BOND : bond 0.00107 / 0.05 ( 1) SS BOND : angle 1.06579 / 1.78 ( 2) hydrogen bonds : bond 0.05007 / 5.47 ( 816) hydrogen bonds : angle 5.19685 / 7.01 ( 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 248 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 0.768 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: B 57 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6881 (tp) REVERT: B 283 HIS cc_start: 0.6865 (p-80) cc_final: 0.6359 (p-80) REVERT: B 330 PHE cc_start: 0.4988 (p90) cc_final: 0.4433 (p90) REVERT: B 390 MET cc_start: 0.6137 (ptt) cc_final: 0.5541 (mtt) REVERT: C 90 ARG cc_start: 0.6228 (tpt-90) cc_final: 0.5864 (tpp-160) REVERT: C 272 ARG cc_start: 0.7018 (ttt180) cc_final: 0.6688 (tpp80) REVERT: D 117 TRP cc_start: 0.6717 (OUTLIER) cc_final: 0.6414 (t60) REVERT: D 128 ILE cc_start: 0.7278 (mm) cc_final: 0.6965 (pt) REVERT: D 215 TYR cc_start: 0.6391 (m-10) cc_final: 0.5583 (m-10) REVERT: Y 131 ASP cc_start: 0.8338 (m-30) cc_final: 0.8039 (m-30) REVERT: Y 240 MET cc_start: 0.5341 (mtm) cc_final: 0.3485 (tpp) REVERT: Z 460 ASP cc_start: 0.6079 (m-30) cc_final: 0.5698 (t0) REVERT: Z 494 PHE cc_start: 0.4361 (t80) cc_final: 0.2985 (m-80) outliers start: 33 outliers final: 21 residues processed: 236 average time/residue: 0.1554 time to fit residues: 58.0039 Evaluate side-chains 211 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 132 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 397 VAL Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 349 GLN 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 198 THR Chi-restraints excluded: chain D residue 213 PHE 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: 2.9990 chunk 37 optimal weight: 0.9990 chunk 188 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 59 optimal weight: 0.9990 chunk 197 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 ASN C 203 GLN C 294 ASN ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS Z 114 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.116153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.097164 restraints weight = 86093.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.098116 restraints weight = 55330.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.098721 restraints weight = 39158.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.098736 restraints weight = 31549.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.098781 restraints weight = 30959.856| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6304 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22552 Z= 0.142 Angle : 0.699 11.115 31218 Z= 0.382 Chirality : 0.047 0.389 3516 Planarity : 0.005 0.091 3379 Dihedral : 24.233 177.451 4372 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.96 % Favored : 86.95 % Rotamer: Outliers : 2.34 % Allowed : 16.97 % Favored : 80.70 % 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: -2.31 (0.17), residues: 2223 helix: 0.11 (0.18), residues: 846 sheet: -2.12 (0.46), residues: 96 loop : -2.80 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 98 TYR 0.027 0.002 TYR Y 139 PHE 0.026 0.002 PHE A 192 TRP 0.018 0.002 TRP D 117 HIS 0.008 0.001 HIS D 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (22551) covalent geometry : angle 0.69897 / 0.38 (31216) SS BOND : bond 0.00086 / 0.04 ( 1) SS BOND : angle 0.84832 / 1.41 ( 2) hydrogen bonds : bond 0.04662 / 5.08 ( 816) hydrogen bonds : angle 5.03172 / 6.84 ( 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 251 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 204 time to evaluate : 0.786 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: A 45 MET cc_start: 0.6715 (mmp) cc_final: 0.5825 (mtp) REVERT: B 283 HIS cc_start: 0.6907 (p-80) cc_final: 0.6383 (p-80) REVERT: B 310 LEU cc_start: 0.8354 (mp) cc_final: 0.8001 (mp) REVERT: B 330 PHE cc_start: 0.4904 (p90) cc_final: 0.4335 (p90) REVERT: B 390 MET cc_start: 0.6116 (ptt) cc_final: 0.5498 (mtt) REVERT: B 485 GLU cc_start: 0.6241 (mp0) cc_final: 0.5635 (pt0) REVERT: C 90 ARG cc_start: 0.6373 (tpt-90) cc_final: 0.6041 (tpp-160) REVERT: C 272 ARG cc_start: 0.7180 (ttt180) cc_final: 0.6856 (tpp80) REVERT: D 128 ILE cc_start: 0.7267 (mm) cc_final: 0.6991 (pt) REVERT: D 215 TYR cc_start: 0.6322 (m-10) cc_final: 0.5509 (m-10) REVERT: Y 105 ARG cc_start: 0.5208 (tpm170) cc_final: 0.4739 (tpp-160) REVERT: Y 121 MET cc_start: 0.5176 (tpt) cc_final: 0.4901 (tpp) REVERT: Y 131 ASP cc_start: 0.8268 (m-30) cc_final: 0.7983 (m-30) REVERT: Y 240 MET cc_start: 0.5310 (mtm) cc_final: 0.3489 (tpp) REVERT: Z 114 ASN cc_start: 0.6910 (OUTLIER) cc_final: 0.6617 (t0) REVERT: Z 460 ASP cc_start: 0.6062 (m-30) cc_final: 0.5668 (t0) REVERT: Z 494 PHE cc_start: 0.4479 (t80) cc_final: 0.3280 (m-80) outliers start: 47 outliers final: 35 residues processed: 235 average time/residue: 0.1590 time to fit residues: 59.0305 Evaluate side-chains 223 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 397 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 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 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 41 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 163 MET 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 Y residue 84 THR Chi-restraints excluded: chain Y residue 188 GLU Chi-restraints excluded: chain Y residue 189 LEU Chi-restraints excluded: chain Z residue 114 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 169 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 94 optimal weight: 0.0970 chunk 178 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.0970 chunk 100 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.116886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.098266 restraints weight = 85409.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.099020 restraints weight = 54279.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.099724 restraints weight = 38360.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.099906 restraints weight = 31808.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.099998 restraints weight = 31388.013| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22552 Z= 0.134 Angle : 0.679 10.260 31218 Z= 0.372 Chirality : 0.046 0.382 3516 Planarity : 0.005 0.087 3379 Dihedral : 24.223 177.862 4372 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.91 % Favored : 87.00 % Rotamer: Outliers : 2.24 % Allowed : 18.26 % Favored : 79.50 % 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: -2.26 (0.17), residues: 2223 helix: 0.16 (0.18), residues: 849 sheet: -2.18 (0.47), residues: 96 loop : -2.77 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 269 TYR 0.020 0.001 TYR B 435 PHE 0.031 0.002 PHE D 291 TRP 0.018 0.002 TRP D 117 HIS 0.005 0.001 HIS D 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 (22551) covalent geometry : angle 0.67876 / 0.37 (31216) SS BOND : bond 0.00075 / 0.04 ( 1) SS BOND : angle 0.76984 / 1.28 ( 2) hydrogen bonds : bond 0.04491 / 4.93 ( 816) hydrogen bonds : angle 4.90209 / 6.68 ( 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 253 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 208 time to evaluate : 0.727 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: B 98 PHE cc_start: 0.6269 (m-80) cc_final: 0.5995 (m-80) REVERT: B 283 HIS cc_start: 0.6866 (p-80) cc_final: 0.6310 (p-80) REVERT: B 330 PHE cc_start: 0.4801 (p90) cc_final: 0.4270 (p90) REVERT: B 390 MET cc_start: 0.6116 (ptt) cc_final: 0.5569 (mtt) REVERT: C 71 MET cc_start: 0.4178 (mmm) cc_final: 0.3704 (mmt) REVERT: C 90 ARG cc_start: 0.6356 (tpt-90) cc_final: 0.6037 (tpp-160) REVERT: C 272 ARG cc_start: 0.7141 (ttt180) cc_final: 0.6845 (tpp80) REVERT: D 31 HIS cc_start: 0.5165 (OUTLIER) cc_final: 0.4886 (t-90) REVERT: D 128 ILE cc_start: 0.7242 (mm) cc_final: 0.7016 (pt) REVERT: D 215 TYR cc_start: 0.6271 (m-10) cc_final: 0.5408 (m-10) REVERT: Y 105 ARG cc_start: 0.5157 (tpm170) cc_final: 0.4558 (tpp-160) REVERT: Y 121 MET cc_start: 0.5186 (tpt) cc_final: 0.4951 (tpp) REVERT: Y 131 ASP cc_start: 0.8260 (m-30) cc_final: 0.7968 (m-30) REVERT: Y 240 MET cc_start: 0.5293 (mtm) cc_final: 0.3486 (tpp) REVERT: Z 460 ASP cc_start: 0.6081 (m-30) cc_final: 0.5703 (t0) REVERT: Z 494 PHE cc_start: 0.4446 (t80) cc_final: 0.3264 (m-80) outliers start: 45 outliers final: 33 residues processed: 238 average time/residue: 0.1529 time to fit residues: 58.5396 Evaluate side-chains 223 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 208 LEU 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 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 31 HIS Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain D residue 137 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 D residue 346 THR Chi-restraints excluded: chain X residue 442 ILE Chi-restraints excluded: chain Y residue 189 LEU Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 157 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 191 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 229 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 214 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 119 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 16 optimal weight: 0.4980 chunk 163 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS Z 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.116637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.097677 restraints weight = 85551.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.098345 restraints weight = 54708.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.099027 restraints weight = 39436.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.099428 restraints weight = 32881.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.099483 restraints weight = 32215.154| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22552 Z= 0.135 Angle : 0.676 9.912 31218 Z= 0.369 Chirality : 0.046 0.376 3516 Planarity : 0.005 0.092 3379 Dihedral : 24.226 177.933 4372 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.00 % Favored : 86.91 % Rotamer: Outliers : 3.03 % Allowed : 18.61 % Favored : 78.36 % 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: -2.22 (0.18), residues: 2223 helix: 0.18 (0.18), residues: 849 sheet: -2.19 (0.47), residues: 96 loop : -2.74 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 269 TYR 0.019 0.001 TYR B 435 PHE 0.023 0.002 PHE D 291 TRP 0.015 0.001 TRP D 117 HIS 0.008 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (22551) covalent geometry : angle 0.67552 / 0.37 (31216) SS BOND : bond 0.00072 / 0.04 ( 1) SS BOND : angle 0.66154 / 1.10 ( 2) hydrogen bonds : bond 0.04385 / 4.78 ( 816) hydrogen bonds : angle 4.85211 / 6.62 ( 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 262 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 201 time to evaluate : 0.823 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: 0.6728 (mmp) cc_final: 0.5858 (mtp) REVERT: B 31 HIS cc_start: 0.5661 (OUTLIER) cc_final: 0.4657 (t-90) REVERT: B 98 PHE cc_start: 0.6465 (m-80) cc_final: 0.6186 (m-80) REVERT: B 161 ILE cc_start: 0.5131 (OUTLIER) cc_final: 0.4892 (tt) REVERT: B 283 HIS cc_start: 0.6892 (p-80) cc_final: 0.6351 (p-80) REVERT: B 328 ARG cc_start: 0.5972 (tpt-90) cc_final: 0.4629 (tpt90) REVERT: B 351 GLU cc_start: 0.7534 (mp0) cc_final: 0.7014 (tp30) REVERT: B 390 MET cc_start: 0.6139 (ptt) cc_final: 0.5557 (mtt) REVERT: B 485 GLU cc_start: 0.6208 (mp0) cc_final: 0.5500 (pt0) REVERT: C 71 MET cc_start: 0.3968 (mmm) cc_final: 0.3355 (mmt) REVERT: C 90 ARG cc_start: 0.6385 (tpt-90) cc_final: 0.6045 (tpp-160) REVERT: C 272 ARG cc_start: 0.7212 (ttt180) cc_final: 0.6915 (tpp80) REVERT: D 31 HIS cc_start: 0.5110 (OUTLIER) cc_final: 0.4644 (t-90) REVERT: D 117 TRP cc_start: 0.6674 (OUTLIER) cc_final: 0.5634 (t60) REVERT: D 128 ILE cc_start: 0.7181 (mm) cc_final: 0.6628 (tp) REVERT: D 169 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7090 (mt) REVERT: D 215 TYR cc_start: 0.6392 (m-10) cc_final: 0.5538 (m-10) REVERT: Y 105 ARG cc_start: 0.5089 (tpm170) cc_final: 0.4568 (tpp-160) REVERT: Y 121 MET cc_start: 0.5234 (tpt) cc_final: 0.5029 (tpp) REVERT: Y 131 ASP cc_start: 0.8289 (m-30) cc_final: 0.8008 (m-30) REVERT: Y 240 MET cc_start: 0.5328 (mtm) cc_final: 0.3488 (tpp) REVERT: Z 460 ASP cc_start: 0.6042 (m-30) cc_final: 0.5662 (t0) REVERT: Z 494 PHE cc_start: 0.4442 (t80) cc_final: 0.3287 (m-80) outliers start: 61 outliers final: 41 residues processed: 244 average time/residue: 0.1533 time to fit residues: 59.4948 Evaluate side-chains 233 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 325 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 108 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 208 LEU Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 490 GLU 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 319 ILE Chi-restraints excluded: chain C residue 395 ILE 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 163 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 62 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 114 optimal weight: 0.0020 chunk 215 optimal weight: 0.9980 chunk 229 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 31 HIS C 416 ASN ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.116652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.097731 restraints weight = 85357.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.098619 restraints weight = 55171.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.099003 restraints weight = 43809.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.099225 restraints weight = 34695.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.099299 restraints weight = 32457.928| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22552 Z= 0.135 Angle : 0.682 9.355 31218 Z= 0.370 Chirality : 0.046 0.371 3516 Planarity : 0.005 0.064 3379 Dihedral : 24.244 177.963 4372 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.36 % Favored : 86.55 % Rotamer: Outliers : 2.74 % Allowed : 18.86 % Favored : 78.41 % 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: -2.18 (0.18), residues: 2223 helix: 0.21 (0.18), residues: 849 sheet: -2.20 (0.46), residues: 96 loop : -2.72 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 328 TYR 0.019 0.001 TYR C 435 PHE 0.021 0.002 PHE D 291 TRP 0.013 0.002 TRP D 117 HIS 0.005 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (22551) covalent geometry : angle 0.68151 / 0.37 (31216) SS BOND : bond 0.00074 / 0.04 ( 1) SS BOND : angle 0.59986 / 1.00 ( 2) hydrogen bonds : bond 0.04332 / 4.74 ( 816) hydrogen bonds : angle 4.79363 / 6.57 ( 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 254 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 199 time to evaluate : 0.809 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: A 45 MET cc_start: 0.6654 (mmp) cc_final: 0.5782 (mtp) REVERT: B 98 PHE cc_start: 0.6384 (m-80) cc_final: 0.6104 (m-80) REVERT: B 161 ILE cc_start: 0.5127 (OUTLIER) cc_final: 0.4924 (tt) REVERT: B 163 MET cc_start: 0.7027 (ptt) cc_final: 0.6771 (ptt) REVERT: B 283 HIS cc_start: 0.6928 (p-80) cc_final: 0.6376 (p-80) REVERT: B 351 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6909 (tp30) REVERT: B 390 MET cc_start: 0.6151 (ptt) cc_final: 0.5588 (mtt) REVERT: C 71 MET cc_start: 0.3722 (mmm) cc_final: 0.3232 (mmt) REVERT: C 90 ARG cc_start: 0.6392 (tpt-90) cc_final: 0.6043 (tpp-160) REVERT: C 272 ARG cc_start: 0.7044 (ttt180) cc_final: 0.6786 (tpp80) REVERT: C 425 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7421 (tp) REVERT: D 31 HIS cc_start: 0.5116 (OUTLIER) cc_final: 0.4661 (t-90) REVERT: D 117 TRP cc_start: 0.6792 (OUTLIER) cc_final: 0.5804 (t60) REVERT: D 128 ILE cc_start: 0.7257 (mm) cc_final: 0.6660 (tp) REVERT: D 169 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7231 (mt) REVERT: D 215 TYR cc_start: 0.6309 (m-10) cc_final: 0.5434 (m-10) REVERT: Y 121 MET cc_start: 0.5157 (tpt) cc_final: 0.4955 (tpp) REVERT: Y 131 ASP cc_start: 0.8267 (m-30) cc_final: 0.7998 (m-30) REVERT: Y 240 MET cc_start: 0.5303 (mtm) cc_final: 0.3502 (tpp) REVERT: Z 460 ASP cc_start: 0.5953 (m-30) cc_final: 0.5566 (t0) REVERT: Z 494 PHE cc_start: 0.4392 (t80) cc_final: 0.3266 (m-80) outliers start: 55 outliers final: 37 residues processed: 242 average time/residue: 0.1487 time to fit residues: 58.3577 Evaluate side-chains 227 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 325 VAL Chi-restraints excluded: chain A residue 385 LYS 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 108 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 208 LEU Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 215 TYR 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 319 ILE Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 425 ILE 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 137 ILE Chi-restraints excluded: chain D residue 163 MET 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 Y residue 84 THR Chi-restraints excluded: chain Y residue 189 LEU Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 157 ILE Chi-restraints excluded: chain Z residue 199 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 178 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 37 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 176 optimal weight: 0.0000 chunk 11 optimal weight: 0.9980 chunk 137 optimal weight: 0.0010 chunk 223 optimal weight: 4.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 31 HIS C 175 ASN ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 95 ASN Z 114 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.117014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.098137 restraints weight = 84776.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.098961 restraints weight = 55384.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.099445 restraints weight = 42326.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.099613 restraints weight = 34993.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.099689 restraints weight = 33389.413| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22552 Z= 0.131 Angle : 0.685 14.842 31218 Z= 0.368 Chirality : 0.046 0.367 3516 Planarity : 0.004 0.061 3379 Dihedral : 24.202 177.979 4370 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.87 % Favored : 87.09 % Rotamer: Outliers : 2.64 % Allowed : 19.35 % Favored : 78.01 % 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: -2.20 (0.18), residues: 2223 helix: 0.19 (0.18), residues: 854 sheet: -2.32 (0.46), residues: 96 loop : -2.73 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 262 TYR 0.032 0.001 TYR Y 139 PHE 0.022 0.001 PHE B 209 TRP 0.010 0.001 TRP D 117 HIS 0.016 0.001 HIS Z 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 (22551) covalent geometry : angle 0.68529 / 0.37 (31216) SS BOND : bond 0.00055 / 0.03 ( 1) SS BOND : angle 0.60608 / 1.01 ( 2) hydrogen bonds : bond 0.04216 / 4.63 ( 816) hydrogen bonds : angle 4.72960 / 6.49 ( 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 246 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 193 time to evaluate : 0.772 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: 0.6644 (mmp) cc_final: 0.5765 (mtp) REVERT: A 240 LYS cc_start: 0.7363 (mmtp) cc_final: 0.7071 (tppt) REVERT: B 98 PHE cc_start: 0.6302 (m-80) cc_final: 0.6048 (m-80) REVERT: B 283 HIS cc_start: 0.6922 (p-80) cc_final: 0.6364 (p-80) REVERT: B 351 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7000 (tp30) REVERT: B 390 MET cc_start: 0.6115 (ptt) cc_final: 0.5551 (mtt) REVERT: B 485 GLU cc_start: 0.6171 (mp0) cc_final: 0.5481 (pt0) REVERT: C 71 MET cc_start: 0.3711 (mmm) cc_final: 0.3163 (mmt) REVERT: C 90 ARG cc_start: 0.6422 (tpt-90) cc_final: 0.6073 (tpp-160) REVERT: C 272 ARG cc_start: 0.7286 (ttt180) cc_final: 0.6982 (tpp80) REVERT: C 425 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7244 (tp) REVERT: D 31 HIS cc_start: 0.5216 (OUTLIER) cc_final: 0.4769 (t-90) REVERT: D 117 TRP cc_start: 0.6854 (OUTLIER) cc_final: 0.5804 (t60) REVERT: D 169 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7112 (mt) REVERT: D 204 LEU cc_start: 0.8527 (mt) cc_final: 0.7445 (tt) REVERT: D 215 TYR cc_start: 0.6308 (m-10) cc_final: 0.5411 (m-10) REVERT: Y 131 ASP cc_start: 0.8298 (m-30) cc_final: 0.8024 (m-30) REVERT: Y 240 MET cc_start: 0.5331 (mtm) cc_final: 0.3518 (tpp) REVERT: Z 112 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7183 (mt) REVERT: Z 155 TYR cc_start: 0.6497 (OUTLIER) cc_final: 0.6147 (m-80) REVERT: Z 460 ASP cc_start: 0.6106 (m-30) cc_final: 0.5720 (t0) REVERT: Z 494 PHE cc_start: 0.4534 (t80) cc_final: 0.3383 (m-80) outliers start: 53 outliers final: 36 residues processed: 233 average time/residue: 0.1445 time to fit residues: 55.0127 Evaluate side-chains 220 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 325 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 215 TYR 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 319 ILE Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 425 ILE 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 137 ILE Chi-restraints excluded: chain D residue 163 MET 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 Y residue 189 LEU Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 155 TYR 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: 0.3980 chunk 175 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 195 optimal weight: 0.9990 chunk 230 optimal weight: 5.9990 chunk 132 optimal weight: 0.0170 chunk 73 optimal weight: 0.9990 chunk 4 optimal weight: 30.0000 chunk 71 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 31 HIS C 259 GLN C 265 GLN ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 114 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.116790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.097828 restraints weight = 85236.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.098606 restraints weight = 56948.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.099154 restraints weight = 43492.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.099198 restraints weight = 35552.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.099326 restraints weight = 33038.621| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22552 Z= 0.134 Angle : 0.688 13.087 31218 Z= 0.370 Chirality : 0.047 0.366 3516 Planarity : 0.005 0.073 3379 Dihedral : 24.213 177.566 4370 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.18 % Favored : 86.77 % Rotamer: Outliers : 2.49 % Allowed : 20.15 % Favored : 77.36 % 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: -2.16 (0.18), residues: 2223 helix: 0.19 (0.18), residues: 851 sheet: -2.17 (0.46), residues: 102 loop : -2.68 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 171 TYR 0.029 0.001 TYR C 435 PHE 0.046 0.002 PHE Y 99 TRP 0.009 0.001 TRP B 158 HIS 0.014 0.001 HIS Z 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (22551) covalent geometry : angle 0.68758 / 0.37 (31216) SS BOND : bond 0.00047 / 0.02 ( 1) SS BOND : angle 0.55075 / 0.92 ( 2) hydrogen bonds : bond 0.04213 / 4.61 ( 816) hydrogen bonds : angle 4.75121 / 6.50 ( 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 235 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 185 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.6717 (mmp) cc_final: 0.5863 (mtp) REVERT: A 207 LEU cc_start: 0.6650 (mp) cc_final: 0.6404 (mt) REVERT: A 240 LYS cc_start: 0.7382 (mmtp) cc_final: 0.7087 (tppt) REVERT: B 62 ARG cc_start: 0.7327 (ptt90) cc_final: 0.7122 (ptt180) REVERT: B 98 PHE cc_start: 0.6273 (m-80) cc_final: 0.5991 (m-80) REVERT: B 283 HIS cc_start: 0.6979 (p-80) cc_final: 0.6411 (p-80) REVERT: B 351 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6966 (tp30) REVERT: B 390 MET cc_start: 0.6179 (ptt) cc_final: 0.5594 (mtt) REVERT: C 71 MET cc_start: 0.3525 (mmm) cc_final: 0.2978 (mmt) REVERT: C 90 ARG cc_start: 0.6393 (tpt-90) cc_final: 0.6076 (tpp-160) REVERT: C 272 ARG cc_start: 0.7150 (ttt180) cc_final: 0.6864 (tpp80) REVERT: C 425 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7254 (tp) REVERT: D 31 HIS cc_start: 0.5104 (OUTLIER) cc_final: 0.4648 (t-90) REVERT: D 117 TRP cc_start: 0.6935 (OUTLIER) cc_final: 0.5962 (t60) REVERT: D 128 ILE cc_start: 0.7409 (pt) cc_final: 0.6945 (tp) REVERT: D 169 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7228 (mt) REVERT: D 204 LEU cc_start: 0.8574 (mt) cc_final: 0.7434 (tt) REVERT: D 215 TYR cc_start: 0.6215 (m-10) cc_final: 0.5353 (m-10) REVERT: Y 131 ASP cc_start: 0.8317 (m-30) cc_final: 0.8009 (m-30) REVERT: Y 240 MET cc_start: 0.5444 (mtm) cc_final: 0.3570 (tpp) REVERT: Z 112 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7188 (mt) REVERT: Z 155 TYR cc_start: 0.6415 (OUTLIER) cc_final: 0.5999 (m-80) REVERT: Z 460 ASP cc_start: 0.5960 (m-30) cc_final: 0.5548 (t0) REVERT: Z 494 PHE cc_start: 0.4431 (t80) cc_final: 0.3304 (m-80) outliers start: 50 outliers final: 36 residues processed: 222 average time/residue: 0.1499 time to fit residues: 54.0947 Evaluate side-chains 220 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 325 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 215 TYR 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 319 ILE Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 425 ILE 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 163 MET 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 Y residue 189 LEU Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 114 ASN Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 155 TYR 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: 0.5980 chunk 187 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 177 optimal weight: 0.0070 chunk 134 optimal weight: 0.7980 chunk 222 optimal weight: 0.8980 chunk 180 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 31 HIS ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.116685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.097772 restraints weight = 85906.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.098375 restraints weight = 54370.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.099087 restraints weight = 39504.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.099496 restraints weight = 33103.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.099551 restraints weight = 32342.996| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.151 22552 Z= 0.168 Angle : 0.812 59.168 31218 Z= 0.460 Chirality : 0.047 0.366 3516 Planarity : 0.005 0.071 3379 Dihedral : 24.215 177.567 4370 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.14 % Favored : 86.82 % Rotamer: Outliers : 2.19 % Allowed : 20.50 % Favored : 77.31 % Cbeta Deviations : 0.05 % 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: -2.19 (0.18), residues: 2223 helix: 0.14 (0.18), residues: 857 sheet: -2.14 (0.47), residues: 102 loop : -2.69 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 328 TYR 0.019 0.001 TYR B 435 PHE 0.042 0.002 PHE Y 99 TRP 0.009 0.001 TRP B 158 HIS 0.015 0.001 HIS C 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (22551) covalent geometry : angle 0.81227 / 0.46 (31216) SS BOND : bond 0.00059 / 0.03 ( 1) SS BOND : angle 0.53671 / 0.89 ( 2) hydrogen bonds : bond 0.04231 / 4.63 ( 816) hydrogen bonds : angle 4.78997 / 6.53 ( 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 222 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.6686 (mmp) cc_final: 0.5816 (mtp) REVERT: A 207 LEU cc_start: 0.6643 (mp) cc_final: 0.6390 (mt) REVERT: A 240 LYS cc_start: 0.7384 (mmtp) cc_final: 0.7089 (tppt) REVERT: B 98 PHE cc_start: 0.6266 (m-80) cc_final: 0.5988 (m-80) REVERT: B 283 HIS cc_start: 0.6966 (p-80) cc_final: 0.6391 (p-80) REVERT: B 351 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6989 (tp30) REVERT: B 390 MET cc_start: 0.6132 (ptt) cc_final: 0.5570 (mtt) REVERT: C 71 MET cc_start: 0.3519 (mmm) cc_final: 0.2972 (mmt) REVERT: C 90 ARG cc_start: 0.6380 (tpt-90) cc_final: 0.6072 (tpp-160) REVERT: C 272 ARG cc_start: 0.7148 (ttt180) cc_final: 0.6866 (tpp80) REVERT: C 425 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7237 (tp) REVERT: D 31 HIS cc_start: 0.5101 (OUTLIER) cc_final: 0.4646 (t-90) REVERT: D 117 TRP cc_start: 0.6937 (OUTLIER) cc_final: 0.5954 (t60) REVERT: D 128 ILE cc_start: 0.7412 (pt) cc_final: 0.6943 (tp) REVERT: D 169 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7216 (mt) REVERT: D 204 LEU cc_start: 0.8575 (mt) cc_final: 0.7435 (tt) REVERT: D 215 TYR cc_start: 0.6243 (m-10) cc_final: 0.5365 (m-10) REVERT: Y 131 ASP cc_start: 0.8331 (m-30) cc_final: 0.8021 (m-30) REVERT: Y 240 MET cc_start: 0.5415 (mtm) cc_final: 0.3551 (tpp) REVERT: Z 112 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7177 (mt) REVERT: Z 155 TYR cc_start: 0.6418 (OUTLIER) cc_final: 0.5998 (m-80) REVERT: Z 460 ASP cc_start: 0.5960 (m-30) cc_final: 0.5551 (t0) REVERT: Z 494 PHE cc_start: 0.4456 (t80) cc_final: 0.3318 (m-80) outliers start: 44 outliers final: 35 residues processed: 209 average time/residue: 0.1493 time to fit residues: 50.5968 Evaluate side-chains 217 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 325 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 215 TYR 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 319 ILE Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 425 ILE 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 163 MET 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 Y residue 189 LEU Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 155 TYR 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: 6.9990 chunk 196 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 103 optimal weight: 0.0970 chunk 82 optimal weight: 0.4980 chunk 211 optimal weight: 0.9990 chunk 26 optimal weight: 0.0000 chunk 18 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 chunk 134 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 31 HIS ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.116679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.097782 restraints weight = 85410.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.098720 restraints weight = 55043.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.099077 restraints weight = 43438.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.099285 restraints weight = 34644.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.099361 restraints weight = 32260.719| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.151 22552 Z= 0.168 Angle : 0.812 59.168 31218 Z= 0.460 Chirality : 0.047 0.366 3516 Planarity : 0.005 0.071 3379 Dihedral : 24.215 177.567 4370 Min Nonbonded Distance : 1.368 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.14 % Favored : 86.82 % Rotamer: Outliers : 2.09 % Allowed : 20.55 % Favored : 77.36 % Cbeta Deviations : 0.05 % 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: -2.19 (0.18), residues: 2223 helix: 0.14 (0.18), residues: 857 sheet: -2.14 (0.47), residues: 102 loop : -2.69 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 328 TYR 0.019 0.001 TYR B 435 PHE 0.042 0.002 PHE Y 99 TRP 0.009 0.001 TRP B 158 HIS 0.015 0.001 HIS C 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (22551) covalent geometry : angle 0.81227 / 0.46 (31216) SS BOND : bond 0.00059 / 0.03 ( 1) SS BOND : angle 0.53671 / 0.89 ( 2) hydrogen bonds : bond 0.04231 / 4.63 ( 816) hydrogen bonds : angle 4.78997 / 6.53 ( 2197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3417.62 seconds wall clock time: 60 minutes 36.72 seconds (3636.72 seconds total)