Starting phenix.real_space_refine on Mon May 12 16:42:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yj2_33869/05_2025/7yj2_33869.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yj2_33869/05_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_33869/05_2025/7yj2_33869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yj2_33869/05_2025/7yj2_33869.map" model { file = "/net/cci-nas-00/data/ceres_data/7yj2_33869/05_2025/7yj2_33869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yj2_33869/05_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-5687/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: 6.26, per 1000 atoms: 0.69 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: 2.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.03 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: 2.59 Time building geometry restraints manager: 3.21 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.910 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.257 9325 Z= 0.501 Angle : 1.029 10.177 12622 Z= 0.629 Chirality : 0.065 0.289 1413 Planarity : 0.006 0.051 1602 Dihedral : 17.033 89.539 3434 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.08 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 Details of bonding type rmsd hydrogen bonds : bond 0.27372 ( 361) hydrogen bonds : angle 8.33695 ( 1017) covalent geometry : bond 0.00963 ( 9324) covalent geometry : angle 1.02948 (12622) Misc. bond : bond 0.25676 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 129 time to evaluate : 0.998 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: 1.4182 time to fit residues: 292.1414 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 : 1.023 ------------------------------------------------------------------------------- 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 = 0.120604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.097705 restraints weight = 11861.546| |-----------------------------------------------------------------------------| 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: 0.2767 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- 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: 0.8441 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 9325 Z= 0.123 Angle : 0.609 12.174 12622 Z= 0.316 Chirality : 0.044 0.224 1413 Planarity : 0.005 0.039 1602 Dihedral : 10.456 89.751 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 Details of bonding type rmsd hydrogen bonds : bond 0.04897 ( 361) hydrogen bonds : angle 4.87769 ( 1017) covalent geometry : bond 0.00268 ( 9324) covalent geometry : angle 0.60888 (12622) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 1.044 Fit side-chains REVERT: B 130 ILE cc_start: 0.8847 (pt) cc_final: 0.8563 (pt) REVERT: B 161 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8153 (mttm) REVERT: B 290 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8139 (ttpp) REVERT: E 37 ARG cc_start: 0.7454 (tpt170) cc_final: 0.7202 (tmt90) REVERT: D 15 ARG cc_start: 0.7332 (mtp180) cc_final: 0.6160 (mtp85) REVERT: D 17 MET cc_start: 0.7295 (tpt) cc_final: 0.6993 (mmt) REVERT: C 11 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.6636 (mppt) REVERT: A 62 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8106 (tm-30) REVERT: A 229 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7848 (mt0) REVERT: A 239 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8398 (mtt180) outliers start: 40 outliers final: 15 residues processed: 154 average time/residue: 1.3021 time to fit residues: 213.9130 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 : 1.103 ------------------------------------------------------------------------------- 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: 3.9990 chunk 89 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3270 r_free = 0.3270 target = 0.116644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.093831 restraints weight = 11981.587| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.80 r_work: 0.2824 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 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 = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9325 Z= 0.253 Angle : 0.709 10.882 12622 Z= 0.363 Chirality : 0.050 0.225 1413 Planarity : 0.005 0.050 1602 Dihedral : 7.376 74.853 1303 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.03 % Favored : 93.88 % Rotamer: Outliers : 4.42 % Allowed : 16.24 % Favored : 79.34 % 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: -1.71 (0.24), residues: 1144 helix: -0.47 (0.23), residues: 528 sheet: -0.67 (0.46), residues: 126 loop : -1.95 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 32 HIS 0.006 0.001 HIS E 24 PHE 0.024 0.002 PHE D 42 TYR 0.018 0.002 TYR B 342 ARG 0.004 0.001 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.06172 ( 361) hydrogen bonds : angle 4.83338 ( 1017) covalent geometry : bond 0.00634 ( 9324) covalent geometry : angle 0.70890 (12622) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 110 time to evaluate : 1.033 Fit side-chains REVERT: B 57 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7696 (mtp-110) REVERT: B 124 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8658 (ptt-90) REVERT: B 161 LYS cc_start: 0.8547 (ttpp) cc_final: 0.8075 (mttm) REVERT: B 209 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8412 (mt-10) REVERT: B 290 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8145 (ttpp) REVERT: B 475 MET cc_start: 0.9364 (OUTLIER) cc_final: 0.8433 (mtt) REVERT: E 37 ARG cc_start: 0.7584 (tpt170) cc_final: 0.7287 (tmt90) REVERT: D 15 ARG cc_start: 0.7354 (mtp180) cc_final: 0.6239 (mtp85) REVERT: D 17 MET cc_start: 0.7375 (tpt) cc_final: 0.7102 (mmt) REVERT: D 132 MET cc_start: 0.8779 (tpp) cc_final: 0.8239 (mmt) REVERT: C 11 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.6707 (mppt) REVERT: A 62 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: A 99 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6911 (mm-30) REVERT: A 229 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7195 (mp10) REVERT: A 239 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8429 (mtt180) outliers start: 43 outliers final: 19 residues processed: 142 average time/residue: 1.4010 time to fit residues: 211.0841 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 : 1.051 ------------------------------------------------------------------------------- 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 13 MET 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 402 THR 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: 1.9990 chunk 16 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3283 r_free = 0.3283 target = 0.117790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.094903 restraints weight = 11953.988| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.84 r_work: 0.2834 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9325 Z= 0.151 Angle : 0.598 8.101 12622 Z= 0.311 Chirality : 0.046 0.195 1413 Planarity : 0.004 0.045 1602 Dihedral : 6.947 71.199 1299 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.76 % Rotamer: Outliers : 4.93 % Allowed : 15.72 % Favored : 79.34 % 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: -1.36 (0.25), residues: 1144 helix: -0.07 (0.24), residues: 527 sheet: -0.63 (0.46), residues: 128 loop : -1.89 (0.26), residues: 489 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 0.014 0.002 TYR B 342 ARG 0.003 0.000 ARG B 271 Details of bonding type rmsd hydrogen bonds : bond 0.04783 ( 361) hydrogen bonds : angle 4.53959 ( 1017) covalent geometry : bond 0.00369 ( 9324) covalent geometry : angle 0.59765 (12622) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 111 time to evaluate : 1.072 Fit side-chains REVERT: B 117 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8149 (t0) REVERT: B 124 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8587 (ptt-90) REVERT: B 161 LYS cc_start: 0.8545 (ttpp) cc_final: 0.8063 (mmtm) REVERT: B 244 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.9028 (mtp) REVERT: B 290 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8152 (ttpp) REVERT: B 475 MET cc_start: 0.9318 (OUTLIER) cc_final: 0.8355 (mtt) REVERT: E 37 ARG cc_start: 0.7592 (tpt170) cc_final: 0.7334 (tmt90) REVERT: D 15 ARG cc_start: 0.7336 (mtp180) cc_final: 0.6165 (mtp85) REVERT: D 17 MET cc_start: 0.7421 (tpt) cc_final: 0.7129 (mmt) REVERT: D 132 MET cc_start: 0.8759 (tpp) cc_final: 0.8231 (mmt) REVERT: C 11 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6707 (mppt) REVERT: A 99 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6863 (mm-30) REVERT: A 150 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8290 (m-30) REVERT: A 229 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7048 (mp10) REVERT: A 239 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8355 (mtt180) outliers start: 48 outliers final: 19 residues processed: 145 average time/residue: 1.3555 time to fit residues: 209.0196 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 : 1.062 ------------------------------------------------------------------------------- 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 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 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 141 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 158 THR 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 435 GLU 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: 0.9990 chunk 110 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3264 r_free = 0.3264 target = 0.116635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.094635 restraints weight = 12031.933| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.69 r_work: 0.2842 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9325 Z= 0.186 Angle : 0.625 8.753 12622 Z= 0.323 Chirality : 0.047 0.199 1413 Planarity : 0.005 0.050 1602 Dihedral : 6.685 70.694 1289 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.68 % Favored : 94.23 % Rotamer: Outliers : 5.24 % Allowed : 15.72 % 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: -1.24 (0.25), residues: 1144 helix: 0.07 (0.24), residues: 521 sheet: -0.48 (0.47), residues: 126 loop : -1.87 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 32 HIS 0.005 0.001 HIS E 24 PHE 0.031 0.002 PHE D 42 TYR 0.016 0.002 TYR B 342 ARG 0.004 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.05127 ( 361) hydrogen bonds : angle 4.56206 ( 1017) covalent geometry : bond 0.00464 ( 9324) covalent geometry : angle 0.62454 (12622) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 108 time to evaluate : 1.047 Fit side-chains REVERT: B 117 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8173 (t0) REVERT: B 124 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8660 (ptt-90) REVERT: B 161 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8174 (mtpp) REVERT: B 209 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8369 (mt-10) REVERT: B 290 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8076 (ttpp) REVERT: B 436 LYS cc_start: 0.7672 (ttmm) cc_final: 0.7345 (ttmm) REVERT: B 475 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.8378 (mtt) REVERT: B 490 ASN cc_start: 0.9006 (OUTLIER) cc_final: 0.8724 (m-40) REVERT: E 37 ARG cc_start: 0.7654 (tpt170) cc_final: 0.7394 (tmt90) REVERT: D 15 ARG cc_start: 0.7275 (mtp180) cc_final: 0.6222 (mtp85) REVERT: D 17 MET cc_start: 0.7495 (tpt) cc_final: 0.7196 (mmt) REVERT: D 132 MET cc_start: 0.8714 (tpp) cc_final: 0.8226 (mmt) REVERT: C 11 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.6724 (mppt) REVERT: C 40 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7567 (mtp) REVERT: A 99 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6799 (mm-30) REVERT: A 150 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8292 (m-30) REVERT: A 229 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7038 (mp10) REVERT: A 411 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8344 (tt) REVERT: A 428 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8448 (mt0) outliers start: 51 outliers final: 24 residues processed: 147 average time/residue: 1.2474 time to fit residues: 195.4025 Evaluate side-chains 143 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 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 B residue 490 ASN Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 46 LEU 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 C residue 14 SER Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 47 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3299 r_free = 0.3299 target = 0.119308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.097405 restraints weight = 11894.050| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.68 r_work: 0.2877 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9325 Z= 0.124 Angle : 0.546 7.622 12622 Z= 0.285 Chirality : 0.044 0.215 1413 Planarity : 0.004 0.043 1602 Dihedral : 6.372 64.535 1289 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.52 % Allowed : 16.55 % 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: -0.92 (0.25), residues: 1144 helix: 0.29 (0.24), residues: 532 sheet: -0.30 (0.46), residues: 124 loop : -1.68 (0.27), residues: 488 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 0.012 0.001 TYR B 342 ARG 0.004 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 361) hydrogen bonds : angle 4.35668 ( 1017) covalent geometry : bond 0.00297 ( 9324) covalent geometry : angle 0.54612 (12622) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 113 time to evaluate : 0.981 Fit side-chains REVERT: B 117 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8135 (t0) REVERT: B 124 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8602 (ptt-90) REVERT: B 161 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8170 (mttm) REVERT: B 244 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.9025 (mtt) REVERT: B 436 LYS cc_start: 0.7651 (ttmm) cc_final: 0.7316 (ttmm) REVERT: B 475 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8370 (mtt) REVERT: B 490 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8564 (m-40) REVERT: E 37 ARG cc_start: 0.7607 (tpt170) cc_final: 0.7363 (tmt90) REVERT: D 15 ARG cc_start: 0.7255 (mtp180) cc_final: 0.6207 (mtp85) REVERT: D 17 MET cc_start: 0.7444 (tpt) cc_final: 0.7206 (mmt) REVERT: D 132 MET cc_start: 0.8685 (tpp) cc_final: 0.8182 (mmt) REVERT: C 40 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7653 (mtp) REVERT: A 62 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8144 (tm-30) REVERT: A 184 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8900 (mm) REVERT: A 229 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7114 (mp10) REVERT: A 239 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8337 (mtt180) REVERT: A 411 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8290 (tt) outliers start: 44 outliers final: 20 residues processed: 146 average time/residue: 1.2624 time to fit residues: 197.0459 Evaluate side-chains 142 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 244 MET Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 490 ASN 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 134 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 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 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 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: 0.0670 chunk 64 optimal weight: 4.9990 chunk 109 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.0670 chunk 52 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.122666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.101402 restraints weight = 11962.858| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.58 r_work: 0.2913 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 9325 Z= 0.103 Angle : 0.512 8.666 12622 Z= 0.268 Chirality : 0.043 0.209 1413 Planarity : 0.004 0.039 1602 Dihedral : 5.734 64.969 1281 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.01 % Allowed : 16.96 % 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: -0.58 (0.25), residues: 1144 helix: 0.57 (0.24), residues: 531 sheet: -0.21 (0.46), residues: 124 loop : -1.48 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 32 HIS 0.004 0.000 HIS B 47 PHE 0.008 0.001 PHE C 55 TYR 0.010 0.001 TYR D 110 ARG 0.006 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 361) hydrogen bonds : angle 4.22599 ( 1017) covalent geometry : bond 0.00242 ( 9324) covalent geometry : angle 0.51169 (12622) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.958 Fit side-chains REVERT: B 89 ASP cc_start: 0.8321 (m-30) cc_final: 0.7245 (m-30) REVERT: B 120 ASN cc_start: 0.8182 (p0) cc_final: 0.7652 (p0) REVERT: B 124 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7844 (ptt90) REVERT: B 161 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8200 (mttm) REVERT: B 189 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7263 (mp10) REVERT: B 244 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8899 (mtp) REVERT: B 436 LYS cc_start: 0.7523 (ttmm) cc_final: 0.7140 (ttmm) REVERT: B 475 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8342 (mtt) REVERT: B 490 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8462 (m-40) REVERT: B 530 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7980 (mt-10) REVERT: E 37 ARG cc_start: 0.7504 (tpt170) cc_final: 0.7262 (tmt90) REVERT: D 15 ARG cc_start: 0.7232 (mtp180) cc_final: 0.6174 (mtp85) REVERT: D 132 MET cc_start: 0.8738 (tpp) cc_final: 0.8322 (mmt) REVERT: C 40 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7619 (mtp) REVERT: A 62 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8000 (tm-30) REVERT: A 99 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6754 (mm-30) REVERT: A 184 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8892 (mm) REVERT: A 229 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7555 (mt0) REVERT: A 239 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8261 (mtt180) REVERT: A 284 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: A 411 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8223 (tt) outliers start: 39 outliers final: 15 residues processed: 149 average time/residue: 1.3520 time to fit residues: 213.9679 Evaluate side-chains 137 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 490 ASN Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 2 optimal weight: 0.9980 chunk 109 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3312 r_free = 0.3312 target = 0.120262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.098110 restraints weight = 12034.067| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.72 r_work: 0.2873 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9325 Z= 0.117 Angle : 0.537 9.010 12622 Z= 0.279 Chirality : 0.044 0.225 1413 Planarity : 0.004 0.040 1602 Dihedral : 5.574 65.355 1276 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.01 % Allowed : 17.57 % Favored : 78.42 % 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: 0.54 (0.24), residues: 540 sheet: -0.17 (0.46), residues: 124 loop : -1.40 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.003 0.001 HIS B 47 PHE 0.011 0.001 PHE B 280 TYR 0.012 0.001 TYR B 342 ARG 0.005 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 361) hydrogen bonds : angle 4.24193 ( 1017) covalent geometry : bond 0.00282 ( 9324) covalent geometry : angle 0.53659 (12622) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: B 89 ASP cc_start: 0.8405 (m-30) cc_final: 0.7333 (m-30) REVERT: B 120 ASN cc_start: 0.8261 (p0) cc_final: 0.7745 (p0) REVERT: B 124 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7782 (ptt90) REVERT: B 161 LYS cc_start: 0.8629 (ttpp) cc_final: 0.8226 (mttm) REVERT: B 189 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7297 (mp10) REVERT: B 244 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.8910 (mtp) REVERT: B 436 LYS cc_start: 0.7549 (ttmm) cc_final: 0.7154 (ttmm) REVERT: B 475 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8406 (mtt) REVERT: B 490 ASN cc_start: 0.8974 (OUTLIER) cc_final: 0.8502 (m-40) REVERT: B 530 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8014 (mt-10) REVERT: E 37 ARG cc_start: 0.7579 (tpt170) cc_final: 0.7320 (tmt90) REVERT: D 15 ARG cc_start: 0.7279 (mtp180) cc_final: 0.6223 (mtp85) REVERT: D 132 MET cc_start: 0.8839 (tpp) cc_final: 0.8254 (mmt) REVERT: C 40 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7709 (mtp) REVERT: A 62 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8070 (tm-30) REVERT: A 99 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6840 (mm-30) REVERT: A 184 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8918 (mm) REVERT: A 203 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.6920 (mmt-90) REVERT: A 229 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7587 (mt0) REVERT: A 239 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8306 (mtt180) REVERT: A 284 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8071 (tm-30) outliers start: 39 outliers final: 16 residues processed: 145 average time/residue: 1.3196 time to fit residues: 203.3124 Evaluate side-chains 141 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 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 B residue 542 HIS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 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 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 443 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 92 optimal weight: 0.0070 chunk 33 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN B 440 GLN A 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.096752 restraints weight = 11923.094| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.68 r_work: 0.2858 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9325 Z= 0.145 Angle : 0.566 9.453 12622 Z= 0.295 Chirality : 0.045 0.252 1413 Planarity : 0.004 0.042 1602 Dihedral : 5.617 64.108 1275 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % 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: -0.58 (0.25), residues: 1144 helix: 0.54 (0.24), residues: 535 sheet: -0.31 (0.46), residues: 128 loop : -1.43 (0.28), 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 0.014 0.001 PHE B 280 TYR 0.014 0.001 TYR B 342 ARG 0.005 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 361) hydrogen bonds : angle 4.31210 ( 1017) covalent geometry : bond 0.00357 ( 9324) covalent geometry : angle 0.56614 (12622) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.958 Fit side-chains REVERT: B 124 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8570 (ptt-90) REVERT: B 161 LYS cc_start: 0.8636 (ttpp) cc_final: 0.8249 (mttm) REVERT: B 189 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7332 (mp10) REVERT: B 244 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.9011 (mtp) REVERT: B 290 LYS cc_start: 0.8698 (tmmm) cc_final: 0.8228 (ttpp) REVERT: B 436 LYS cc_start: 0.7557 (ttmm) cc_final: 0.7191 (ttmm) REVERT: B 475 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8386 (mtt) REVERT: B 490 ASN cc_start: 0.8991 (OUTLIER) cc_final: 0.8548 (m-40) REVERT: B 530 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8016 (mt-10) REVERT: E 37 ARG cc_start: 0.7573 (tpt170) cc_final: 0.7291 (tmt90) REVERT: D 15 ARG cc_start: 0.7265 (mtp180) cc_final: 0.6240 (mtp85) REVERT: D 66 THR cc_start: 0.8878 (m) cc_final: 0.8673 (m) REVERT: D 132 MET cc_start: 0.8804 (tpp) cc_final: 0.8230 (mmt) REVERT: C 40 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7745 (mtp) REVERT: A 62 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8134 (tm-30) REVERT: A 99 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6778 (mm-30) REVERT: A 150 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8296 (m-30) REVERT: A 184 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8927 (mm) REVERT: A 203 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7002 (mmt-90) REVERT: A 229 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: A 239 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8311 (mtt180) REVERT: A 284 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: A 411 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8243 (tt) outliers start: 39 outliers final: 18 residues processed: 143 average time/residue: 1.3584 time to fit residues: 206.0928 Evaluate side-chains 147 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 490 ASN Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 47 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 181 ARG 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 411 LEU Chi-restraints excluded: chain A residue 435 GLU 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 104 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN B 440 GLN A 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.119416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.097091 restraints weight = 12071.101| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.73 r_work: 0.2858 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9325 Z= 0.137 Angle : 0.558 9.393 12622 Z= 0.291 Chirality : 0.045 0.265 1413 Planarity : 0.004 0.041 1602 Dihedral : 5.571 63.750 1275 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.80 % Allowed : 17.78 % Favored : 78.42 % 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: -0.52 (0.25), residues: 1144 helix: 0.57 (0.24), residues: 535 sheet: -0.08 (0.47), residues: 124 loop : -1.43 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 361) hydrogen bonds : angle 4.31093 ( 1017) covalent geometry : bond 0.00337 ( 9324) covalent geometry : angle 0.55848 (12622) Misc. bond : bond 0.00009 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: B 124 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8581 (ptt-90) REVERT: B 161 LYS cc_start: 0.8620 (ttpp) cc_final: 0.8238 (mttm) REVERT: B 189 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7321 (mp10) REVERT: B 244 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.9025 (mtp) REVERT: B 290 LYS cc_start: 0.8673 (tmmm) cc_final: 0.8197 (ttpp) REVERT: B 436 LYS cc_start: 0.7545 (ttmm) cc_final: 0.7178 (ttmm) REVERT: B 475 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8399 (mtt) REVERT: B 490 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8514 (m-40) REVERT: B 530 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7995 (mt-10) REVERT: E 37 ARG cc_start: 0.7602 (tpt170) cc_final: 0.7326 (tmt90) REVERT: D 15 ARG cc_start: 0.7250 (mtp180) cc_final: 0.6219 (mtp85) REVERT: D 132 MET cc_start: 0.8803 (tpp) cc_final: 0.8233 (mmt) REVERT: C 40 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7684 (mtm) REVERT: A 62 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8130 (tm-30) REVERT: A 99 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6771 (mm-30) REVERT: A 184 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8926 (mm) REVERT: A 203 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.6997 (mmt-90) REVERT: A 229 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7044 (mp10) REVERT: A 239 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8307 (mtt180) REVERT: A 284 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: A 411 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8231 (tt) outliers start: 37 outliers final: 19 residues processed: 145 average time/residue: 1.3528 time to fit residues: 208.0654 Evaluate side-chains 146 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 490 ASN Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 47 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 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 411 LEU Chi-restraints excluded: chain A residue 435 GLU 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: 4.9990 chunk 5 optimal weight: 0.0040 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 chunk 90 optimal weight: 0.0370 chunk 53 optimal weight: 3.9990 overall best weight: 1.0212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN B 440 GLN A 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.098026 restraints weight = 11942.369| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.72 r_work: 0.2881 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9325 Z= 0.117 Angle : 0.534 9.267 12622 Z= 0.279 Chirality : 0.044 0.265 1413 Planarity : 0.004 0.040 1602 Dihedral : 5.433 64.547 1275 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.91 % Allowed : 17.88 % 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: -0.40 (0.26), residues: 1144 helix: 0.63 (0.24), residues: 543 sheet: -0.05 (0.47), residues: 124 loop : -1.35 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.004 0.001 HIS B 47 PHE 0.011 0.001 PHE B 280 TYR 0.012 0.001 TYR B 342 ARG 0.006 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 361) hydrogen bonds : angle 4.22919 ( 1017) covalent geometry : bond 0.00284 ( 9324) covalent geometry : angle 0.53370 (12622) Misc. bond : bond 0.00010 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6450.33 seconds wall clock time: 112 minutes 3.58 seconds (6723.58 seconds total)