Starting phenix.real_space_refine on Sat Aug 23 02:27:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yj2_33869/08_2025/7yj2_33869.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yj2_33869/08_2025/7yj2_33869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yj2_33869/08_2025/7yj2_33869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yj2_33869/08_2025/7yj2_33869.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yj2_33869/08_2025/7yj2_33869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yj2_33869/08_2025/7yj2_33869.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 50 5.16 5 C 5878 2.51 5 N 1542 2.21 5 O 1653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9124 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3953 Classifications: {'peptide': 502} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 18, 'TRANS': 483} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 298 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1162 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "C" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 411 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "A" Number of atoms: 3285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3285 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.05, per 1000 atoms: 0.22 Number of scatterers: 9124 At special positions: 0 Unit cell: (93.96, 86.4, 124.2, 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 50 16.00 P 1 15.00 O 1653 8.00 N 1542 7.00 C 5878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 237.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 9 sheets defined 50.2% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'B' and resid 67 through 95 removed outlier: 3.612A pdb=" N TYR B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL B 76 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 82 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TRP B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.569A pdb=" N ARG B 124 " --> pdb=" O ASN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 130 Processing helix chain 'B' and resid 177 through 181 removed outlier: 4.077A pdb=" N PHE B 181 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.797A pdb=" N GLU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 removed outlier: 4.091A pdb=" N ASN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 243 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 284 through 294 removed outlier: 3.629A pdb=" N GLU B 289 " --> pdb=" O MET B 285 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 335 Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 391 through 402 removed outlier: 3.722A pdb=" N ILE B 395 " --> pdb=" O LYS B 391 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR B 400 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 408 removed outlier: 3.570A pdb=" N VAL B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 433 through 457 removed outlier: 3.631A pdb=" N LEU B 442 " --> pdb=" O CYS B 438 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 488 removed outlier: 3.595A pdb=" N ILE B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 487 " --> pdb=" O GLY B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 501 Processing helix chain 'B' and resid 517 through 536 removed outlier: 3.819A pdb=" N GLU B 530 " --> pdb=" O LYS B 526 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 18 removed outlier: 3.580A pdb=" N LEU E 17 " --> pdb=" O MET E 13 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR E 18 " --> pdb=" O VAL E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 26 removed outlier: 3.907A pdb=" N LEU E 25 " --> pdb=" O PRO E 21 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE E 26 " --> pdb=" O ALA E 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 21 through 26' Processing helix chain 'E' and resid 26 through 39 removed outlier: 3.763A pdb=" N ILE E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 19 Processing helix chain 'D' and resid 21 through 37 removed outlier: 3.593A pdb=" N ALA D 29 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 30 " --> pdb=" O TYR D 26 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 33 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 66 removed outlier: 3.566A pdb=" N ASN D 53 " --> pdb=" O TRP D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 96 through 116 removed outlier: 3.675A pdb=" N LEU D 102 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) Proline residue: D 106 - end of helix removed outlier: 3.705A pdb=" N LEU D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE D 115 " --> pdb=" O PHE D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 136 removed outlier: 3.971A pdb=" N VAL D 129 " --> pdb=" O VAL D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 removed outlier: 3.523A pdb=" N HIS D 143 " --> pdb=" O PRO D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.715A pdb=" N PHE C 16 " --> pdb=" O GLN C 12 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR C 17 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 50 removed outlier: 3.630A pdb=" N ILE C 44 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 55 removed outlier: 3.831A pdb=" N PHE C 55 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 64 removed outlier: 3.580A pdb=" N TRP A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.512A pdb=" N ALA A 119 " --> pdb=" O PRO A 115 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.810A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 175 removed outlier: 3.691A pdb=" N ALA A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 213 through 227 removed outlier: 3.740A pdb=" N LEU A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.687A pdb=" N ARG A 236 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.675A pdb=" N LEU A 260 " --> pdb=" O PRO A 256 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 294 removed outlier: 3.764A pdb=" N HIS A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.719A pdb=" N ILE A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 330 removed outlier: 3.580A pdb=" N LEU A 330 " --> pdb=" O HIS A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 359 removed outlier: 3.560A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 369 removed outlier: 3.573A pdb=" N VAL A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 removed outlier: 4.177A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS A 374 " --> pdb=" O CYS A 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 369 through 374' Processing helix chain 'A' and resid 404 through 420 removed outlier: 3.981A pdb=" N GLU A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 removed outlier: 3.673A pdb=" N ALA A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA3, first strand: chain 'B' and resid 146 through 152 removed outlier: 5.371A pdb=" N VAL B 146 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY B 169 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ASN B 165 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N GLN B 152 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR B 163 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.626A pdb=" N ALA B 231 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 310 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B 255 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU B 313 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU B 257 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N GLU B 315 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N ASP B 259 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 317 through 318 removed outlier: 3.612A pdb=" N SER B 323 " --> pdb=" O TYR B 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.965A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 85 through 86 removed outlier: 4.435A pdb=" N VAL A 94 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA A 425 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.604A pdb=" N GLY A 316 " --> pdb=" O TYR A 164 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP A 188 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 383 through 386 removed outlier: 4.310A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) 361 hydrogen bonds defined for protein. 1017 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2853 1.33 - 1.45: 1327 1.45 - 1.57: 5060 1.57 - 1.69: 1 1.69 - 1.81: 83 Bond restraints: 9324 Sorted by residual: bond pdb=" C2 PLP B 601 " pdb=" C3 PLP B 601 " ideal model delta sigma weight residual 1.390 1.484 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C4 PLP B 601 " pdb=" C5 PLP B 601 " ideal model delta sigma weight residual 1.390 1.482 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C3 PLP B 601 " pdb=" C4 PLP B 601 " ideal model delta sigma weight residual 1.390 1.480 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C VAL B 469 " pdb=" N PRO B 470 " ideal model delta sigma weight residual 1.335 1.319 0.016 8.70e-03 1.32e+04 3.26e+00 bond pdb=" C6 PLP B 601 " pdb=" N1 PLP B 601 " ideal model delta sigma weight residual 1.380 1.345 0.035 2.00e-02 2.50e+03 3.15e+00 ... (remaining 9319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 11952 2.04 - 4.07: 558 4.07 - 6.11: 86 6.11 - 8.14: 19 8.14 - 10.18: 7 Bond angle restraints: 12622 Sorted by residual: angle pdb=" N ILE A 300 " pdb=" CA ILE A 300 " pdb=" C ILE A 300 " ideal model delta sigma weight residual 111.91 118.22 -6.31 8.90e-01 1.26e+00 5.03e+01 angle pdb=" N PRO A 78 " pdb=" CA PRO A 78 " pdb=" CB PRO A 78 " ideal model delta sigma weight residual 103.25 109.64 -6.39 1.05e+00 9.07e-01 3.71e+01 angle pdb=" CA PRO A 135 " pdb=" C PRO A 135 " pdb=" N ARG A 136 " ideal model delta sigma weight residual 116.45 121.20 -4.75 8.50e-01 1.38e+00 3.13e+01 angle pdb=" CA PRO A 135 " pdb=" C PRO A 135 " pdb=" O PRO A 135 " ideal model delta sigma weight residual 121.38 117.36 4.02 7.70e-01 1.69e+00 2.72e+01 angle pdb=" N ASP B 117 " pdb=" CA ASP B 117 " pdb=" C ASP B 117 " ideal model delta sigma weight residual 111.75 118.21 -6.46 1.28e+00 6.10e-01 2.54e+01 ... (remaining 12617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4874 17.91 - 35.82: 475 35.82 - 53.72: 169 53.72 - 71.63: 42 71.63 - 89.54: 12 Dihedral angle restraints: 5572 sinusoidal: 2230 harmonic: 3342 Sorted by residual: dihedral pdb=" CA LEU B 473 " pdb=" C LEU B 473 " pdb=" N TYR B 474 " pdb=" CA TYR B 474 " ideal model delta harmonic sigma weight residual -180.00 -156.42 -23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA PRO A 135 " pdb=" C PRO A 135 " pdb=" N ARG A 136 " pdb=" CA ARG A 136 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA TYR B 461 " pdb=" C TYR B 461 " pdb=" N GLY B 462 " pdb=" CA GLY B 462 " ideal model delta harmonic sigma weight residual 180.00 162.17 17.83 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 5569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 960 0.058 - 0.116: 352 0.116 - 0.174: 71 0.174 - 0.231: 23 0.231 - 0.289: 7 Chirality restraints: 1413 Sorted by residual: chirality pdb=" CA GLU A 400 " pdb=" N GLU A 400 " pdb=" C GLU A 400 " pdb=" CB GLU A 400 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA ARG A 181 " pdb=" N ARG A 181 " pdb=" C ARG A 181 " pdb=" CB ARG A 181 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA ASP B 117 " pdb=" N ASP B 117 " pdb=" C ASP B 117 " pdb=" CB ASP B 117 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1410 not shown) Planarity restraints: 1602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 111 " -0.011 2.00e-02 2.50e+03 2.06e-02 7.43e+00 pdb=" CG PHE B 111 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE B 111 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE B 111 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 111 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE B 111 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 116 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C GLN B 116 " 0.042 2.00e-02 2.50e+03 pdb=" O GLN B 116 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP B 117 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 413 " -0.010 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C GLN A 413 " 0.037 2.00e-02 2.50e+03 pdb=" O GLN A 413 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU A 414 " -0.013 2.00e-02 2.50e+03 ... (remaining 1599 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 219 2.67 - 3.23: 8104 3.23 - 3.79: 12975 3.79 - 4.34: 18649 4.34 - 4.90: 31173 Nonbonded interactions: 71120 Sorted by model distance: nonbonded pdb=" O THR B 66 " pdb=" NH1 ARG D 20 " model vdw 2.119 3.120 nonbonded pdb=" O TRP B 134 " pdb=" O GLY A 137 " model vdw 2.131 3.040 nonbonded pdb=" OH TYR A 178 " pdb=" O VAL A 324 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR A 53 " pdb=" OE1 GLU A 56 " model vdw 2.206 3.040 nonbonded pdb=" OD2 ASP B 132 " pdb=" ND2 ASN B 157 " model vdw 2.212 3.120 ... (remaining 71115 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.80 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.290 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 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 : 0.010 0.257 9325 Z= 0.501 Angle : 1.029 10.177 12622 Z= 0.629 Chirality : 0.065 0.289 1413 Planarity : 0.006 0.051 1602 Dihedral : 17.033 89.539 3434 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.08 % Favored : 92.31 % Rotamer: Outliers : 8.32 % Allowed : 4.93 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.30 (0.22), residues: 1144 helix: -2.04 (0.21), residues: 524 sheet: -1.36 (0.45), residues: 125 loop : -2.47 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 450 TYR 0.029 0.003 TYR B 93 PHE 0.044 0.003 PHE B 111 TRP 0.014 0.002 TRP C 32 HIS 0.008 0.002 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00963 ( 9324) covalent geometry : angle 1.02948 (12622) hydrogen bonds : bond 0.27372 ( 361) hydrogen bonds : angle 8.33695 ( 1017) Misc. bond : bond 0.25676 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 129 time to evaluate : 0.404 Fit side-chains REVERT: B 68 MET cc_start: 0.8554 (tpp) cc_final: 0.8325 (tpt) REVERT: B 92 ARG cc_start: 0.7234 (ttp-110) cc_final: 0.7015 (ttp-110) REVERT: B 117 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7755 (t0) REVERT: B 161 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8082 (mttm) REVERT: B 183 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7890 (ptm160) REVERT: B 209 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8030 (mt-10) REVERT: E 42 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7373 (mtpp) REVERT: D 15 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6329 (mtp85) REVERT: D 17 MET cc_start: 0.7093 (tpt) cc_final: 0.6860 (mmt) REVERT: D 132 MET cc_start: 0.8513 (mmp) cc_final: 0.8144 (mmp) REVERT: D 141 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8608 (mm-40) REVERT: C 11 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.6519 (tmmt) REVERT: C 12 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: A 62 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: A 428 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8197 (tt0) outliers start: 81 outliers final: 39 residues processed: 195 average time/residue: 0.7172 time to fit residues: 147.5466 Evaluate side-chains 158 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 108 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 465 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN B 440 GLN B 441 GLN D 18 ASN A 224 GLN A 428 GLN A 469 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.119820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.096836 restraints weight = 11934.429| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.86 r_work: 0.2883 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9325 Z= 0.129 Angle : 0.620 12.041 12622 Z= 0.321 Chirality : 0.045 0.228 1413 Planarity : 0.005 0.039 1602 Dihedral : 10.553 89.833 1395 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.93 % Rotamer: Outliers : 4.21 % Allowed : 13.26 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.24), residues: 1144 helix: -0.73 (0.23), residues: 527 sheet: -0.67 (0.47), residues: 124 loop : -2.07 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 233 TYR 0.019 0.001 TYR E 44 PHE 0.045 0.002 PHE D 42 TRP 0.014 0.001 TRP C 32 HIS 0.005 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9324) covalent geometry : angle 0.61977 (12622) hydrogen bonds : bond 0.04873 ( 361) hydrogen bonds : angle 4.87899 ( 1017) Misc. bond : bond 0.00119 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.364 Fit side-chains REVERT: B 130 ILE cc_start: 0.8860 (pt) cc_final: 0.8572 (pt) REVERT: B 161 LYS cc_start: 0.8594 (ttpp) cc_final: 0.8156 (mttm) REVERT: B 209 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8338 (mt-10) REVERT: B 290 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8164 (ttpp) REVERT: E 37 ARG cc_start: 0.7496 (tpt170) cc_final: 0.7238 (tmt90) REVERT: D 15 ARG cc_start: 0.7305 (mtp180) cc_final: 0.6126 (mtp85) REVERT: D 17 MET cc_start: 0.7309 (tpt) cc_final: 0.6992 (mmt) REVERT: C 11 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6648 (mppt) REVERT: A 62 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: A 239 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8439 (mtt180) outliers start: 41 outliers final: 16 residues processed: 153 average time/residue: 0.6101 time to fit residues: 99.2551 Evaluate side-chains 132 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 402 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 chunk 58 optimal weight: 0.0470 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 ASN A 229 GLN A 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.121102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.098137 restraints weight = 11944.000| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.85 r_work: 0.2900 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9325 Z= 0.108 Angle : 0.548 10.774 12622 Z= 0.282 Chirality : 0.043 0.188 1413 Planarity : 0.004 0.036 1602 Dihedral : 6.486 66.405 1305 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.24 % Favored : 94.67 % Rotamer: Outliers : 3.19 % Allowed : 15.52 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.25), residues: 1144 helix: 0.04 (0.24), residues: 522 sheet: -0.58 (0.47), residues: 124 loop : -1.79 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 271 TYR 0.010 0.001 TYR E 44 PHE 0.031 0.001 PHE D 42 TRP 0.011 0.001 TRP C 32 HIS 0.003 0.000 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9324) covalent geometry : angle 0.54772 (12622) hydrogen bonds : bond 0.04124 ( 361) hydrogen bonds : angle 4.42893 ( 1017) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.390 Fit side-chains REVERT: B 130 ILE cc_start: 0.8762 (pt) cc_final: 0.8495 (pt) REVERT: B 161 LYS cc_start: 0.8510 (ttpp) cc_final: 0.8107 (mttm) REVERT: B 475 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8338 (mtt) REVERT: E 37 ARG cc_start: 0.7478 (tpt170) cc_final: 0.7235 (tmt90) REVERT: D 15 ARG cc_start: 0.7290 (mtp180) cc_final: 0.6135 (mtp85) REVERT: D 17 MET cc_start: 0.7328 (tpt) cc_final: 0.7125 (mmt) REVERT: D 132 MET cc_start: 0.8840 (tpp) cc_final: 0.8399 (mmt) REVERT: C 11 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.6647 (mppt) REVERT: A 62 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: A 239 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8385 (mtt180) REVERT: A 284 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7990 (tm-30) outliers start: 31 outliers final: 9 residues processed: 134 average time/residue: 0.7059 time to fit residues: 99.9535 Evaluate side-chains 121 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 102 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 65 optimal weight: 0.4980 chunk 12 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.121103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.099046 restraints weight = 12092.539| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.73 r_work: 0.2896 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9325 Z= 0.110 Angle : 0.538 7.646 12622 Z= 0.279 Chirality : 0.043 0.184 1413 Planarity : 0.004 0.038 1602 Dihedral : 5.740 59.968 1284 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % Rotamer: Outliers : 3.08 % Allowed : 16.03 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.25), residues: 1144 helix: 0.38 (0.24), residues: 522 sheet: -0.40 (0.46), residues: 124 loop : -1.67 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 271 TYR 0.011 0.001 TYR B 342 PHE 0.029 0.001 PHE D 42 TRP 0.010 0.001 TRP C 32 HIS 0.004 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9324) covalent geometry : angle 0.53839 (12622) hydrogen bonds : bond 0.03861 ( 361) hydrogen bonds : angle 4.30800 ( 1017) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.302 Fit side-chains REVERT: B 130 ILE cc_start: 0.8829 (pt) cc_final: 0.8551 (pt) REVERT: B 161 LYS cc_start: 0.8508 (ttpp) cc_final: 0.8124 (mttm) REVERT: B 165 ASN cc_start: 0.8466 (m-40) cc_final: 0.8243 (m-40) REVERT: B 290 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8155 (ttpp) REVERT: B 436 LYS cc_start: 0.7503 (ttmm) cc_final: 0.7130 (ttmm) REVERT: B 475 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8419 (mtt) REVERT: B 530 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7919 (mt-10) REVERT: E 37 ARG cc_start: 0.7543 (tpt170) cc_final: 0.7306 (tmt90) REVERT: D 15 ARG cc_start: 0.7239 (mtp180) cc_final: 0.6170 (mtp85) REVERT: D 17 MET cc_start: 0.7428 (tpt) cc_final: 0.7123 (mmt) REVERT: D 132 MET cc_start: 0.8825 (tpp) cc_final: 0.8218 (mmt) REVERT: C 40 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7498 (mtp) REVERT: A 62 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8054 (tm-30) REVERT: A 99 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6883 (mm-30) REVERT: A 239 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8360 (mtt180) REVERT: A 284 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7925 (tm-30) outliers start: 30 outliers final: 14 residues processed: 135 average time/residue: 0.6348 time to fit residues: 90.9516 Evaluate side-chains 129 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 HIS D 18 ASN A 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.119169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.097034 restraints weight = 11946.122| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.71 r_work: 0.2861 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9325 Z= 0.159 Angle : 0.588 8.274 12622 Z= 0.304 Chirality : 0.046 0.196 1413 Planarity : 0.004 0.039 1602 Dihedral : 5.530 59.767 1277 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.91 % Allowed : 16.34 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.25), residues: 1144 helix: 0.32 (0.24), residues: 527 sheet: -0.49 (0.46), residues: 128 loop : -1.62 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 405 TYR 0.015 0.002 TYR B 342 PHE 0.031 0.002 PHE D 42 TRP 0.010 0.001 TRP C 32 HIS 0.005 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9324) covalent geometry : angle 0.58755 (12622) hydrogen bonds : bond 0.04659 ( 361) hydrogen bonds : angle 4.40767 ( 1017) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.378 Fit side-chains REVERT: B 161 LYS cc_start: 0.8559 (ttpp) cc_final: 0.8168 (mttm) REVERT: B 165 ASN cc_start: 0.8450 (m-40) cc_final: 0.8227 (m110) REVERT: B 290 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8148 (ttpp) REVERT: B 436 LYS cc_start: 0.7673 (ttmm) cc_final: 0.7350 (ttmm) REVERT: B 475 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.8384 (mtt) REVERT: E 37 ARG cc_start: 0.7642 (tpt170) cc_final: 0.7396 (tmt90) REVERT: D 15 ARG cc_start: 0.7281 (mtp180) cc_final: 0.6232 (mtp85) REVERT: D 17 MET cc_start: 0.7391 (tpt) cc_final: 0.7072 (mmt) REVERT: D 132 MET cc_start: 0.8791 (tpp) cc_final: 0.8217 (mmt) REVERT: C 40 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7606 (mtp) REVERT: A 62 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8121 (tm-30) REVERT: A 99 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6876 (mm-30) REVERT: A 239 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8352 (mtt180) REVERT: A 284 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: A 428 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8456 (mt0) outliers start: 38 outliers final: 20 residues processed: 138 average time/residue: 0.6612 time to fit residues: 97.1075 Evaluate side-chains 132 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 48 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.120743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.098635 restraints weight = 12063.114| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.73 r_work: 0.2888 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9325 Z= 0.107 Angle : 0.525 7.575 12622 Z= 0.274 Chirality : 0.043 0.208 1413 Planarity : 0.004 0.038 1602 Dihedral : 5.208 59.339 1277 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.70 % Allowed : 16.75 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.25), residues: 1144 helix: 0.47 (0.24), residues: 537 sheet: -0.28 (0.46), residues: 124 loop : -1.46 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 271 TYR 0.011 0.001 TYR B 342 PHE 0.030 0.001 PHE D 42 TRP 0.012 0.001 TRP C 32 HIS 0.004 0.000 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9324) covalent geometry : angle 0.52522 (12622) hydrogen bonds : bond 0.03782 ( 361) hydrogen bonds : angle 4.25200 ( 1017) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.364 Fit side-chains REVERT: B 161 LYS cc_start: 0.8569 (ttpp) cc_final: 0.8213 (mttp) REVERT: B 165 ASN cc_start: 0.8434 (m-40) cc_final: 0.8220 (m-40) REVERT: B 244 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.9068 (mtp) REVERT: B 290 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8139 (ttpp) REVERT: B 436 LYS cc_start: 0.7592 (ttmm) cc_final: 0.7251 (ttmm) REVERT: B 475 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8383 (mtt) REVERT: B 530 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8030 (mt-10) REVERT: E 37 ARG cc_start: 0.7584 (tpt170) cc_final: 0.7357 (tmt90) REVERT: D 15 ARG cc_start: 0.7247 (mtp180) cc_final: 0.6188 (mtp85) REVERT: D 17 MET cc_start: 0.7330 (tpt) cc_final: 0.7103 (mmt) REVERT: D 132 MET cc_start: 0.8763 (tpp) cc_final: 0.8184 (mmt) REVERT: C 40 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7607 (mtm) REVERT: A 62 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8097 (tm-30) REVERT: A 99 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6874 (mm-30) REVERT: A 239 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8374 (mtt180) REVERT: A 284 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7958 (tm-30) outliers start: 36 outliers final: 16 residues processed: 141 average time/residue: 0.6015 time to fit residues: 90.1886 Evaluate side-chains 133 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 109 optimal weight: 0.0670 chunk 51 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 0.0470 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.122718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.101484 restraints weight = 12015.595| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.58 r_work: 0.2922 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 9325 Z= 0.101 Angle : 0.513 8.183 12622 Z= 0.266 Chirality : 0.043 0.217 1413 Planarity : 0.004 0.038 1602 Dihedral : 4.883 59.480 1272 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.70 % Allowed : 16.86 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.25), residues: 1144 helix: 0.65 (0.24), residues: 535 sheet: -0.23 (0.47), residues: 124 loop : -1.36 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 271 TYR 0.010 0.001 TYR B 342 PHE 0.009 0.001 PHE B 280 TRP 0.011 0.001 TRP C 32 HIS 0.003 0.000 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 9324) covalent geometry : angle 0.51290 (12622) hydrogen bonds : bond 0.03532 ( 361) hydrogen bonds : angle 4.16939 ( 1017) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.321 Fit side-chains REVERT: B 161 LYS cc_start: 0.8538 (ttpp) cc_final: 0.8184 (mttm) REVERT: B 165 ASN cc_start: 0.8412 (m-40) cc_final: 0.8195 (m110) REVERT: B 244 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8922 (mtp) REVERT: B 436 LYS cc_start: 0.7509 (ttmm) cc_final: 0.7129 (ttmm) REVERT: B 475 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8420 (mtt) REVERT: B 530 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7867 (mt-10) REVERT: E 37 ARG cc_start: 0.7486 (tpt170) cc_final: 0.7244 (tmt90) REVERT: D 15 ARG cc_start: 0.7205 (mtp180) cc_final: 0.6134 (mtp85) REVERT: D 17 MET cc_start: 0.7214 (tpt) cc_final: 0.6906 (mmt) REVERT: D 132 MET cc_start: 0.8735 (tpp) cc_final: 0.8175 (mmt) REVERT: A 62 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8008 (tm-30) REVERT: A 99 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6806 (mm-30) REVERT: A 239 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8312 (mtt180) REVERT: A 284 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: A 411 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8156 (tt) outliers start: 36 outliers final: 16 residues processed: 144 average time/residue: 0.6337 time to fit residues: 97.1498 Evaluate side-chains 131 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.118369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.096339 restraints weight = 11986.912| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.68 r_work: 0.2858 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9325 Z= 0.166 Angle : 0.590 9.017 12622 Z= 0.306 Chirality : 0.046 0.239 1413 Planarity : 0.004 0.041 1602 Dihedral : 5.162 59.955 1272 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.60 % Allowed : 17.47 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.25), residues: 1144 helix: 0.52 (0.24), residues: 531 sheet: -0.36 (0.47), residues: 128 loop : -1.44 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 181 TYR 0.016 0.002 TYR B 342 PHE 0.016 0.002 PHE B 280 TRP 0.009 0.001 TRP C 32 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 9324) covalent geometry : angle 0.58957 (12622) hydrogen bonds : bond 0.04631 ( 361) hydrogen bonds : angle 4.35239 ( 1017) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.247 Fit side-chains REVERT: B 161 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8253 (mttm) REVERT: B 165 ASN cc_start: 0.8463 (m-40) cc_final: 0.8252 (m110) REVERT: B 244 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.8903 (mtp) REVERT: B 290 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8185 (ttpp) REVERT: B 436 LYS cc_start: 0.7632 (ttmm) cc_final: 0.7294 (ttmm) REVERT: B 475 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.8418 (mtt) REVERT: B 530 GLU cc_start: 0.8265 (mt-10) cc_final: 0.8021 (mt-10) REVERT: E 37 ARG cc_start: 0.7628 (tpt170) cc_final: 0.7352 (tmt90) REVERT: D 15 ARG cc_start: 0.7251 (mtp180) cc_final: 0.6196 (mtp85) REVERT: D 17 MET cc_start: 0.7349 (tpt) cc_final: 0.7116 (mmt) REVERT: D 132 MET cc_start: 0.8758 (tpp) cc_final: 0.8168 (mmt) REVERT: C 11 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.6725 (mptt) REVERT: A 62 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8138 (tm-30) REVERT: A 99 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6808 (mm-30) REVERT: A 239 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8317 (mtt180) REVERT: A 284 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7926 (tm-30) REVERT: A 411 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8245 (tt) REVERT: A 428 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8493 (mt0) outliers start: 35 outliers final: 17 residues processed: 137 average time/residue: 0.5925 time to fit residues: 86.1440 Evaluate side-chains 134 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 23 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 73 optimal weight: 0.0980 chunk 38 optimal weight: 0.0010 chunk 95 optimal weight: 0.2980 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.0670 chunk 106 optimal weight: 3.9990 overall best weight: 0.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 ASN A 407 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.124351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.103202 restraints weight = 11914.844| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.58 r_work: 0.2956 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 9325 Z= 0.090 Angle : 0.488 8.514 12622 Z= 0.255 Chirality : 0.042 0.234 1413 Planarity : 0.003 0.036 1602 Dihedral : 4.640 58.169 1272 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.67 % Allowed : 18.50 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.26), residues: 1144 helix: 0.82 (0.24), residues: 540 sheet: -0.01 (0.47), residues: 124 loop : -1.23 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 271 TYR 0.007 0.001 TYR B 235 PHE 0.006 0.001 PHE B 280 TRP 0.014 0.001 TRP C 32 HIS 0.003 0.000 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 9324) covalent geometry : angle 0.48768 (12622) hydrogen bonds : bond 0.02972 ( 361) hydrogen bonds : angle 4.08179 ( 1017) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.399 Fit side-chains REVERT: B 109 LYS cc_start: 0.9021 (pmtt) cc_final: 0.8338 (mtmt) REVERT: B 161 LYS cc_start: 0.8571 (ttpp) cc_final: 0.8182 (mttm) REVERT: B 165 ASN cc_start: 0.8403 (m-40) cc_final: 0.8200 (m110) REVERT: B 189 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7257 (mp10) REVERT: B 244 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8910 (mtp) REVERT: B 290 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8092 (ttpp) REVERT: B 530 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7864 (mt-10) REVERT: E 37 ARG cc_start: 0.7409 (tpt170) cc_final: 0.7066 (tmt90) REVERT: D 15 ARG cc_start: 0.7150 (mtp180) cc_final: 0.6099 (mtp85) REVERT: D 25 SER cc_start: 0.8963 (t) cc_final: 0.8729 (p) REVERT: D 116 TYR cc_start: 0.8969 (m-80) cc_final: 0.8359 (m-80) REVERT: D 132 MET cc_start: 0.8723 (tpp) cc_final: 0.8202 (mmt) REVERT: C 11 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6662 (mptt) REVERT: A 62 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7984 (tm-30) REVERT: A 99 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6523 (mm-30) REVERT: A 239 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8265 (mtt180) REVERT: A 284 GLU cc_start: 0.8040 (pt0) cc_final: 0.7776 (tm-30) outliers start: 26 outliers final: 10 residues processed: 133 average time/residue: 0.6645 time to fit residues: 93.8956 Evaluate side-chains 124 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 105 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 407 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.098407 restraints weight = 12097.806| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.75 r_work: 0.2888 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9325 Z= 0.120 Angle : 0.541 9.084 12622 Z= 0.283 Chirality : 0.044 0.255 1413 Planarity : 0.004 0.039 1602 Dihedral : 4.567 59.512 1269 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.26 % Allowed : 19.22 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.26), residues: 1144 helix: 0.81 (0.24), residues: 540 sheet: -0.00 (0.48), residues: 124 loop : -1.18 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.012 0.001 TYR B 342 PHE 0.011 0.001 PHE A 209 TRP 0.010 0.001 TRP C 32 HIS 0.003 0.000 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9324) covalent geometry : angle 0.54082 (12622) hydrogen bonds : bond 0.03724 ( 361) hydrogen bonds : angle 4.14393 ( 1017) Misc. bond : bond 0.00006 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.353 Fit side-chains REVERT: B 109 LYS cc_start: 0.9026 (pmtt) cc_final: 0.8349 (mtmt) REVERT: B 161 LYS cc_start: 0.8610 (ttpp) cc_final: 0.8241 (mttm) REVERT: B 165 ASN cc_start: 0.8448 (m-40) cc_final: 0.8230 (m110) REVERT: B 244 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.8940 (mtp) REVERT: B 290 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8189 (ttpp) REVERT: B 436 LYS cc_start: 0.7506 (ttmm) cc_final: 0.7138 (ttmm) REVERT: B 490 ASN cc_start: 0.8955 (OUTLIER) cc_final: 0.8486 (m-40) REVERT: B 530 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7995 (mt-10) REVERT: E 37 ARG cc_start: 0.7588 (tpt170) cc_final: 0.7324 (tmt90) REVERT: D 15 ARG cc_start: 0.7209 (mtp180) cc_final: 0.6143 (mtp85) REVERT: D 116 TYR cc_start: 0.8912 (m-80) cc_final: 0.8335 (m-80) REVERT: D 132 MET cc_start: 0.8751 (tpp) cc_final: 0.8370 (mmt) REVERT: C 11 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6588 (mptt) REVERT: A 62 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8054 (tm-30) REVERT: A 99 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6686 (mm-30) REVERT: A 107 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.8037 (p0) REVERT: A 284 GLU cc_start: 0.8071 (pt0) cc_final: 0.7804 (tm-30) outliers start: 22 outliers final: 11 residues processed: 128 average time/residue: 0.6044 time to fit residues: 82.2045 Evaluate side-chains 126 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 96 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 407 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.120723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.098782 restraints weight = 11889.505| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.68 r_work: 0.2891 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9325 Z= 0.123 Angle : 0.543 9.165 12622 Z= 0.284 Chirality : 0.044 0.278 1413 Planarity : 0.004 0.039 1602 Dihedral : 4.614 59.327 1269 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.36 % Allowed : 19.12 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.26), residues: 1144 helix: 0.80 (0.24), residues: 540 sheet: 0.01 (0.48), residues: 124 loop : -1.20 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 271 TYR 0.012 0.001 TYR D 110 PHE 0.011 0.001 PHE B 280 TRP 0.010 0.001 TRP C 32 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9324) covalent geometry : angle 0.54326 (12622) hydrogen bonds : bond 0.03802 ( 361) hydrogen bonds : angle 4.15462 ( 1017) Misc. bond : bond 0.00009 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3259.03 seconds wall clock time: 56 minutes 11.18 seconds (3371.18 seconds total)