Starting phenix.real_space_refine on Thu Mar 13 19:11:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yj2_33869/03_2025/7yj2_33869.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yj2_33869/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yj2_33869/03_2025/7yj2_33869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yj2_33869/03_2025/7yj2_33869.map" model { file = "/net/cci-nas-00/data/ceres_data/7yj2_33869/03_2025/7yj2_33869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yj2_33869/03_2025/7yj2_33869.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP: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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: 5.32, per 1000 atoms: 0.58 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: 2.15 Conformation dependent library (CDL) restraints added in 991.8 milliseconds 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: 1.05 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: 2.48 Time building geometry restraints manager: 2.57 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: 1.150 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.540 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.860 ------------------------------------------------------------------------------- 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 0.094 9324 Z= 0.630 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 : 9.08 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.002 TRP C 32 HIS 0.008 0.002 HIS D 65 PHE 0.044 0.003 PHE B 111 TYR 0.029 0.003 TYR B 93 ARG 0.007 0.001 ARG B 450 *********************** 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 : 0.949 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: 1.5097 time to fit residues: 310.7632 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 : 1.020 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.0040 chunk 102 optimal weight: 0.8980 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 229 GLN A 428 GLN A 469 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.120597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.097698 restraints weight = 11861.880| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.85 r_work: 0.2888 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- 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 = 0.80 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 = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9324 Z= 0.179 Angle : 0.609 12.179 12622 Z= 0.316 Chirality : 0.044 0.224 1413 Planarity : 0.005 0.039 1602 Dihedral : 10.456 89.746 1395 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.93 % Rotamer: Outliers : 4.11 % Allowed : 12.85 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.24), residues: 1144 helix: -0.73 (0.23), residues: 528 sheet: -0.67 (0.47), residues: 124 loop : -2.05 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 32 HIS 0.004 0.001 HIS E 24 PHE 0.046 0.001 PHE D 42 TYR 0.019 0.001 TYR E 44 ARG 0.006 0.000 ARG A 233 *********************** 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 164 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 1.113 Fit side-chains REVERT: B 130 ILE cc_start: 0.8846 (pt) cc_final: 0.8563 (pt) REVERT: B 161 LYS cc_start: 0.8575 (ttpp) cc_final: 0.8148 (mttm) REVERT: B 290 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8137 (ttpp) REVERT: E 37 ARG cc_start: 0.7451 (tpt170) cc_final: 0.7198 (tmt90) REVERT: D 15 ARG cc_start: 0.7329 (mtp180) cc_final: 0.6154 (mtp85) REVERT: D 17 MET cc_start: 0.7295 (tpt) cc_final: 0.6993 (mmt) REVERT: C 11 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.6630 (mppt) REVERT: A 62 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8102 (tm-30) REVERT: A 229 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7846 (mt0) REVERT: A 239 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8395 (mtt180) outliers start: 40 outliers final: 15 residues processed: 154 average time/residue: 1.8894 time to fit residues: 310.9013 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 : 1.285 ------------------------------------------------------------------------------- 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 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 229 GLN 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 43 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3275 r_free = 0.3275 target = 0.117026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.094231 restraints weight = 11982.773| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.80 r_work: 0.2822 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9324 Z= 0.378 Angle : 0.690 10.973 12622 Z= 0.354 Chirality : 0.049 0.223 1413 Planarity : 0.005 0.049 1602 Dihedral : 7.304 74.144 1303 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.03 % Favored : 93.88 % Rotamer: Outliers : 4.32 % Allowed : 16.03 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.24), residues: 1144 helix: -0.42 (0.23), residues: 528 sheet: -0.67 (0.46), residues: 126 loop : -1.93 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 32 HIS 0.006 0.001 HIS E 24 PHE 0.025 0.002 PHE D 42 TYR 0.017 0.002 TYR B 342 ARG 0.004 0.001 ARG A 405 *********************** 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 152 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 1.134 Fit side-chains REVERT: B 57 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7698 (mtp-110) REVERT: B 124 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8653 (ptt-90) REVERT: B 161 LYS cc_start: 0.8541 (ttpp) cc_final: 0.8067 (mttm) REVERT: B 209 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8425 (mt-10) REVERT: B 290 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8116 (ttpp) REVERT: B 475 MET cc_start: 0.9359 (OUTLIER) cc_final: 0.8426 (mtt) REVERT: E 37 ARG cc_start: 0.7580 (tpt170) cc_final: 0.7288 (tmt90) REVERT: D 15 ARG cc_start: 0.7359 (mtp180) cc_final: 0.6246 (mtp85) REVERT: D 17 MET cc_start: 0.7419 (tpt) cc_final: 0.7147 (mmt) REVERT: D 132 MET cc_start: 0.8776 (tpp) cc_final: 0.8231 (mmt) REVERT: C 11 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.6741 (mppt) REVERT: A 62 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8178 (tm-30) REVERT: A 99 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6913 (mm-30) REVERT: A 229 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7159 (mp10) REVERT: A 239 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8409 (mtt180) outliers start: 42 outliers final: 17 residues processed: 141 average time/residue: 1.4466 time to fit residues: 215.8429 Evaluate side-chains 135 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 124 ARG 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 B residue 475 MET Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain D residue 25 SER 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 11 LYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain A residue 62 GLU 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 181 ARG Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 301 ASP 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 99 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 14 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.3289 r_free = 0.3289 target = 0.118043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.095254 restraints weight = 11905.856| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.80 r_work: 0.2828 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9324 Z= 0.287 Angle : 0.625 8.396 12622 Z= 0.324 Chirality : 0.047 0.200 1413 Planarity : 0.005 0.047 1602 Dihedral : 7.008 72.176 1298 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 5.04 % Allowed : 15.83 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.24), residues: 1144 helix: -0.08 (0.24), residues: 519 sheet: -0.52 (0.46), residues: 126 loop : -1.90 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 32 HIS 0.005 0.001 HIS E 24 PHE 0.030 0.002 PHE D 42 TYR 0.015 0.002 TYR B 342 ARG 0.003 0.000 ARG B 271 *********************** 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 158 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 109 time to evaluate : 0.995 Fit side-chains REVERT: B 117 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8161 (t0) REVERT: B 124 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8619 (ptt-90) REVERT: B 161 LYS cc_start: 0.8548 (ttpp) cc_final: 0.8127 (mtpp) REVERT: B 290 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8153 (ttpp) REVERT: B 475 MET cc_start: 0.9319 (OUTLIER) cc_final: 0.8384 (mtt) REVERT: E 37 ARG cc_start: 0.7624 (tpt170) cc_final: 0.7359 (tmt90) REVERT: D 15 ARG cc_start: 0.7357 (mtp180) cc_final: 0.6198 (mtp85) REVERT: D 17 MET cc_start: 0.7442 (tpt) cc_final: 0.7162 (mmt) REVERT: D 132 MET cc_start: 0.8779 (tpp) cc_final: 0.8267 (mmt) REVERT: C 11 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.6727 (mppt) REVERT: A 99 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.6855 (mm-30) REVERT: A 150 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8290 (m-30) REVERT: A 229 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7117 (mp10) REVERT: A 239 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8365 (mtt180) outliers start: 49 outliers final: 20 residues processed: 145 average time/residue: 1.4276 time to fit residues: 219.7450 Evaluate side-chains 135 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 117 ASP Chi-restraints excluded: chain B residue 124 ARG 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 542 HIS 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 133 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 147 ILE 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 150 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 443 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 99 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 58 optimal weight: 0.0030 chunk 78 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.121130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.099894 restraints weight = 11922.862| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.57 r_work: 0.2897 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 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 = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9324 Z= 0.177 Angle : 0.536 7.597 12622 Z= 0.280 Chirality : 0.044 0.197 1413 Planarity : 0.004 0.041 1602 Dihedral : 6.305 65.254 1289 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.90 % Favored : 95.02 % Rotamer: Outliers : 4.32 % Allowed : 16.65 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.25), residues: 1144 helix: 0.20 (0.24), residues: 533 sheet: -0.28 (0.46), residues: 124 loop : -1.70 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 32 HIS 0.004 0.001 HIS B 47 PHE 0.032 0.001 PHE D 42 TYR 0.011 0.001 TYR B 342 ARG 0.005 0.000 ARG A 233 *********************** 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 155 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 1.088 Fit side-chains REVERT: B 124 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8570 (ptt-90) REVERT: B 161 LYS cc_start: 0.8579 (ttpp) cc_final: 0.8106 (mmtm) REVERT: B 244 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.9019 (mtp) REVERT: B 436 LYS cc_start: 0.7579 (ttmm) cc_final: 0.7225 (ttmm) REVERT: B 475 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8372 (mtt) REVERT: B 490 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8513 (m-40) REVERT: E 37 ARG cc_start: 0.7541 (tpt170) cc_final: 0.7319 (tmt90) REVERT: D 15 ARG cc_start: 0.7246 (mtp180) cc_final: 0.6154 (mtp85) REVERT: D 17 MET cc_start: 0.7351 (tpt) cc_final: 0.7115 (mmt) REVERT: C 40 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7553 (mtp) REVERT: A 62 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8084 (tm-30) REVERT: A 229 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.6969 (mp10) REVERT: A 239 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8310 (mtt180) REVERT: A 411 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8264 (tt) REVERT: A 428 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8352 (mt0) outliers start: 42 outliers final: 16 residues processed: 147 average time/residue: 1.3437 time to fit residues: 210.5943 Evaluate side-chains 137 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 124 ARG 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 490 ASN 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 134 VAL Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain A residue 90 SER 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 229 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN 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 = 0.3260 r_free = 0.3260 target = 0.116352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.094376 restraints weight = 11953.077| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.68 r_work: 0.2833 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9324 Z= 0.372 Angle : 0.661 9.635 12622 Z= 0.342 Chirality : 0.049 0.217 1413 Planarity : 0.005 0.051 1602 Dihedral : 6.442 66.521 1281 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.34 % Allowed : 15.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.25), residues: 1144 helix: 0.08 (0.23), residues: 526 sheet: -0.44 (0.46), residues: 128 loop : -1.80 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 32 HIS 0.004 0.001 HIS B 47 PHE 0.019 0.002 PHE B 280 TYR 0.018 0.002 TYR B 342 ARG 0.004 0.001 ARG B 57 *********************** 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 159 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 107 time to evaluate : 1.048 Fit side-chains REVERT: B 124 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8694 (ptt-90) REVERT: B 161 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8154 (mttm) REVERT: B 209 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8416 (mt-10) REVERT: B 244 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8962 (mtp) REVERT: B 290 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8180 (ttpp) REVERT: B 429 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7536 (mt0) REVERT: B 436 LYS cc_start: 0.7730 (ttmm) cc_final: 0.7417 (ttmm) REVERT: B 475 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.8401 (mtt) REVERT: E 37 ARG cc_start: 0.7694 (tpt170) cc_final: 0.7401 (tmt90) REVERT: D 15 ARG cc_start: 0.7293 (mtp180) cc_final: 0.6243 (mtp85) REVERT: D 17 MET cc_start: 0.7495 (tpt) cc_final: 0.7218 (mmt) REVERT: D 132 MET cc_start: 0.8714 (tpp) cc_final: 0.8176 (mmt) REVERT: C 40 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7644 (mtp) REVERT: A 99 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.6794 (mm-30) REVERT: A 150 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8278 (m-30) REVERT: A 184 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8956 (mm) REVERT: A 229 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7018 (mp10) REVERT: A 411 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8354 (tt) REVERT: A 428 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8454 (mt0) outliers start: 52 outliers final: 23 residues processed: 146 average time/residue: 1.3655 time to fit residues: 211.8805 Evaluate side-chains 141 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 124 ARG Chi-restraints excluded: chain B residue 141 VAL 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 244 MET Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 44 TYR 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 133 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 14 SER 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 150 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 VAL 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 411 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 443 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 0.0170 chunk 52 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN 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 = 0.3313 r_free = 0.3313 target = 0.120210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.098885 restraints weight = 12009.287| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.58 r_work: 0.2885 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- 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 = 0.79 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 = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9324 Z= 0.205 Angle : 0.552 8.457 12622 Z= 0.289 Chirality : 0.045 0.219 1413 Planarity : 0.004 0.043 1602 Dihedral : 6.116 62.449 1281 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.21 % Allowed : 16.75 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.25), residues: 1144 helix: 0.37 (0.24), residues: 526 sheet: -0.24 (0.46), residues: 124 loop : -1.67 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 32 HIS 0.004 0.001 HIS B 47 PHE 0.011 0.001 PHE B 280 TYR 0.013 0.001 TYR D 110 ARG 0.005 0.000 ARG A 233 *********************** 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 154 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 0.943 Fit side-chains REVERT: B 124 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8554 (ptt-90) REVERT: B 161 LYS cc_start: 0.8563 (ttpp) cc_final: 0.8108 (mttm) REVERT: B 244 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8982 (mtp) REVERT: B 290 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8140 (ttpp) REVERT: B 436 LYS cc_start: 0.7610 (ttmm) cc_final: 0.7283 (ttmm) REVERT: B 475 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8351 (mtt) REVERT: B 530 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7930 (mt-10) REVERT: E 37 ARG cc_start: 0.7543 (tpt170) cc_final: 0.7289 (tmt90) REVERT: D 15 ARG cc_start: 0.7228 (mtp180) cc_final: 0.6211 (mtp85) REVERT: C 40 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7617 (mtp) REVERT: A 62 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8099 (tm-30) REVERT: A 99 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6771 (mm-30) REVERT: A 184 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8899 (mm) REVERT: A 203 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7208 (mmt-90) REVERT: A 229 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.6998 (mp10) REVERT: A 239 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8311 (mtt180) REVERT: A 411 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8239 (tt) outliers start: 41 outliers final: 22 residues processed: 144 average time/residue: 1.3569 time to fit residues: 207.6184 Evaluate side-chains 141 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 124 ARG 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 293 LYS Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 44 TYR 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 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 158 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 VAL 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 239 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 402 THR 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 2 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 77 optimal weight: 0.0040 chunk 22 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 = 0.3347 r_free = 0.3347 target = 0.122866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.101600 restraints weight = 11986.927| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.58 r_work: 0.2926 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 9324 Z= 0.151 Angle : 0.504 8.935 12622 Z= 0.263 Chirality : 0.043 0.219 1413 Planarity : 0.004 0.041 1602 Dihedral : 5.627 65.212 1281 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.39 % Allowed : 17.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.25), residues: 1144 helix: 0.55 (0.24), residues: 540 sheet: -0.19 (0.46), residues: 124 loop : -1.41 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 32 HIS 0.003 0.000 HIS B 47 PHE 0.008 0.001 PHE C 55 TYR 0.010 0.001 TYR B 235 ARG 0.006 0.000 ARG A 233 *********************** 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 146 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: B 89 ASP cc_start: 0.8318 (m-30) cc_final: 0.7240 (m-30) REVERT: B 120 ASN cc_start: 0.8077 (p0) cc_final: 0.7610 (p0) REVERT: B 124 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.7869 (ptt90) REVERT: B 161 LYS cc_start: 0.8590 (ttpp) cc_final: 0.8190 (mttm) REVERT: B 189 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7248 (mp10) REVERT: B 244 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8892 (mtp) REVERT: B 436 LYS cc_start: 0.7505 (ttmm) cc_final: 0.7116 (ttmm) REVERT: B 475 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8358 (mtt) REVERT: B 530 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7903 (mt-10) REVERT: E 37 ARG cc_start: 0.7521 (tpt170) cc_final: 0.7276 (tmt90) REVERT: D 15 ARG cc_start: 0.7215 (mtp180) cc_final: 0.6129 (mtp85) REVERT: D 17 MET cc_start: 0.7221 (tpt) cc_final: 0.6922 (mmt) REVERT: D 25 SER cc_start: 0.9008 (t) cc_final: 0.8780 (p) REVERT: C 40 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7583 (mtm) REVERT: A 62 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8002 (tm-30) REVERT: A 99 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6738 (mm-30) REVERT: A 203 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7177 (mmt-90) REVERT: A 229 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7562 (mt0) REVERT: A 239 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8340 (mtt180) REVERT: A 284 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7986 (tm-30) outliers start: 33 outliers final: 13 residues processed: 138 average time/residue: 1.3951 time to fit residues: 204.3875 Evaluate side-chains 131 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 141 VAL 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 475 MET 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 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 158 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 284 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 92 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 72 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- 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 = 0.3287 r_free = 0.3287 target = 0.118337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.096171 restraints weight = 11928.212| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.71 r_work: 0.2839 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9324 Z= 0.304 Angle : 0.611 10.028 12622 Z= 0.316 Chirality : 0.047 0.236 1413 Planarity : 0.004 0.046 1602 Dihedral : 5.858 63.115 1276 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.01 % Allowed : 17.68 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.25), residues: 1144 helix: 0.37 (0.23), residues: 535 sheet: -0.39 (0.46), residues: 128 loop : -1.49 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.004 0.001 HIS B 47 PHE 0.016 0.002 PHE B 280 TYR 0.017 0.002 TYR D 110 ARG 0.005 0.000 ARG A 233 *********************** 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 148 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 1.362 Fit side-chains REVERT: B 124 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8595 (ptt-90) REVERT: B 161 LYS cc_start: 0.8607 (ttpp) cc_final: 0.8193 (mttm) REVERT: B 189 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7323 (mp10) REVERT: B 244 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8991 (mtp) REVERT: B 290 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8211 (ttpp) REVERT: B 436 LYS cc_start: 0.7625 (ttmm) cc_final: 0.7277 (ttmm) REVERT: B 475 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.8365 (mtt) REVERT: B 530 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8015 (mt-10) REVERT: E 37 ARG cc_start: 0.7631 (tpt170) cc_final: 0.7345 (tmt90) REVERT: D 15 ARG cc_start: 0.7249 (mtp180) cc_final: 0.6254 (mtp85) REVERT: D 132 MET cc_start: 0.8861 (mpp) cc_final: 0.8297 (mmt) REVERT: C 40 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7803 (mtp) REVERT: A 62 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8151 (tm-30) REVERT: A 99 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6772 (mm-30) REVERT: A 150 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8268 (m-30) REVERT: A 229 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.6999 (mp10) REVERT: A 239 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8348 (mtt180) REVERT: A 284 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8078 (tm-30) REVERT: A 411 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8243 (tt) REVERT: A 428 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8496 (mt0) outliers start: 39 outliers final: 15 residues processed: 140 average time/residue: 1.3692 time to fit residues: 204.0969 Evaluate side-chains 137 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 141 VAL 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 B residue 475 MET 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 134 VAL Chi-restraints excluded: chain C residue 23 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 150 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 428 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 104 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3312 r_free = 0.3312 target = 0.120199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.098772 restraints weight = 12055.188| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.59 r_work: 0.2879 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9324 Z= 0.227 Angle : 0.569 9.805 12622 Z= 0.295 Chirality : 0.045 0.256 1413 Planarity : 0.004 0.043 1602 Dihedral : 5.726 63.140 1276 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.08 % Allowed : 18.71 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1144 helix: 0.48 (0.24), residues: 535 sheet: -0.18 (0.46), residues: 124 loop : -1.49 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 32 HIS 0.004 0.001 HIS B 47 PHE 0.012 0.001 PHE B 280 TYR 0.014 0.001 TYR B 342 ARG 0.006 0.000 ARG A 233 ********************** 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 146 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 1.031 Fit side-chains REVERT: B 124 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8571 (ptt-90) REVERT: B 161 LYS cc_start: 0.8577 (ttpp) cc_final: 0.8164 (mttm) REVERT: B 189 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: B 244 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.9009 (mtp) REVERT: B 290 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8105 (ttpp) REVERT: B 436 LYS cc_start: 0.7580 (ttmm) cc_final: 0.7215 (ttmm) REVERT: B 440 GLN cc_start: 0.8408 (mt0) cc_final: 0.7782 (mt0) REVERT: B 444 GLU cc_start: 0.8015 (mp0) cc_final: 0.7645 (mp0) REVERT: B 475 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8419 (mtt) REVERT: B 530 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7995 (mt-10) REVERT: E 37 ARG cc_start: 0.7564 (tpt170) cc_final: 0.7283 (tmt90) REVERT: D 15 ARG cc_start: 0.7196 (mtp180) cc_final: 0.6196 (mtp85) REVERT: D 132 MET cc_start: 0.8823 (mpp) cc_final: 0.8274 (mmt) REVERT: C 40 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7770 (mtp) REVERT: A 62 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8115 (tm-30) REVERT: A 99 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6701 (mm-30) REVERT: A 203 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.6955 (mmt-90) REVERT: A 229 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.6939 (mp10) REVERT: A 239 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8302 (mtt180) REVERT: A 284 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8045 (tm-30) REVERT: A 411 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8195 (tt) outliers start: 30 outliers final: 16 residues processed: 138 average time/residue: 1.5551 time to fit residues: 227.3361 Evaluate side-chains 139 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 141 VAL 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 B residue 475 MET 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 134 VAL Chi-restraints excluded: chain C residue 23 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 158 THR Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 187 VAL 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 239 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 443 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 79 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 90 optimal weight: 0.3980 chunk 53 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN 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 = 0.3325 r_free = 0.3325 target = 0.121507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.100445 restraints weight = 12000.218| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.52 r_work: 0.2924 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 9324 Z= 0.166 Angle : 0.520 9.379 12622 Z= 0.272 Chirality : 0.043 0.252 1413 Planarity : 0.004 0.041 1602 Dihedral : 5.424 64.988 1275 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.98 % Allowed : 19.32 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.26), residues: 1144 helix: 0.64 (0.24), residues: 541 sheet: -0.10 (0.46), residues: 124 loop : -1.34 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 32 HIS 0.003 0.000 HIS B 47 PHE 0.009 0.001 PHE B 280 TYR 0.010 0.001 TYR D 110 ARG 0.006 0.000 ARG A 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7263.52 seconds wall clock time: 128 minutes 35.46 seconds (7715.46 seconds total)