Starting phenix.real_space_refine on Thu Sep 26 00:39:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owt_20217/09_2024/6owt_20217.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owt_20217/09_2024/6owt_20217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owt_20217/09_2024/6owt_20217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owt_20217/09_2024/6owt_20217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owt_20217/09_2024/6owt_20217.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owt_20217/09_2024/6owt_20217.cif" } resolution = 3.8 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= 0.003 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 32 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 7498 2.51 5 N 1975 2.21 5 O 2130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11649 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4255 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 22, 'TRANS': 567} Unresolved non-hydrogen bonds: 418 Unresolved non-hydrogen angles: 512 Unresolved non-hydrogen dihedrals: 344 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 234 Chain: "B" Number of atoms: 4242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4242 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 26, 'TRANS': 551} Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 421 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 17, 'TYR:plan': 1, 'ASN:plan1': 11, 'HIS:plan': 2, 'GLU:plan': 16, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 202 Chain: "M" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 932 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 121} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 61 Chain: "T" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 74 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1047 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "S" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1099 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 139} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 60 Time building chain proxies: 7.40, per 1000 atoms: 0.64 Number of scatterers: 11649 At special positions: 0 Unit cell: (98.814, 105.708, 127.539, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 2130 8.00 N 1975 7.00 C 7498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS N 193 " - pdb=" SG CYS S 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.7 seconds 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 4 sheets defined 68.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 51 through 68 Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 82 through 85 removed outlier: 3.677A pdb=" N SER A 85 " --> pdb=" O LEU A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 106 through 122 Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 149 through 156 removed outlier: 3.748A pdb=" N LYS A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 179 removed outlier: 3.814A pdb=" N LYS A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.764A pdb=" N THR A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 222 through 238 removed outlier: 3.749A pdb=" N VAL A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER A 227 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.622A pdb=" N CYS A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 293 Processing helix chain 'A' and resid 299 through 321 removed outlier: 4.264A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 removed outlier: 3.556A pdb=" N ARG A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 352 removed outlier: 4.311A pdb=" N LEU A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.533A pdb=" N SER A 358 " --> pdb=" O CYS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 382 through 397 Processing helix chain 'A' and resid 401 through 414 Processing helix chain 'A' and resid 420 through 435 removed outlier: 3.840A pdb=" N ILE A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 452 removed outlier: 4.115A pdb=" N TYR A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 removed outlier: 4.104A pdb=" N TRP A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 509 through 512 removed outlier: 3.593A pdb=" N ALA A 512 " --> pdb=" O ASN A 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 512' Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 531 removed outlier: 3.913A pdb=" N LEU A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.585A pdb=" N LEU A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 565 removed outlier: 3.684A pdb=" N ILE A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 573 through 587 Processing helix chain 'A' and resid 591 through 599 Processing helix chain 'A' and resid 610 through 620 Processing helix chain 'B' and resid 17 through 24 removed outlier: 3.705A pdb=" N GLU B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 44 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 62 through 76 Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 87 through 93 Processing helix chain 'B' and resid 99 through 111 Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 122 through 128 Processing helix chain 'B' and resid 134 through 149 removed outlier: 3.671A pdb=" N ARG B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 170 removed outlier: 3.961A pdb=" N ALA B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 188 Processing helix chain 'B' and resid 199 through 213 removed outlier: 4.927A pdb=" N ASN B 205 " --> pdb=" O PRO B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 228 removed outlier: 4.221A pdb=" N PHE B 221 " --> pdb=" O TRP B 217 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 245 Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 274 through 291 removed outlier: 3.572A pdb=" N ASN B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Proline residue: B 286 - end of helix Processing helix chain 'B' and resid 295 through 313 removed outlier: 3.746A pdb=" N LEU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.872A pdb=" N PHE B 325 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.654A pdb=" N LEU B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 361 removed outlier: 3.793A pdb=" N ALA B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU B 357 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 366 through 384 removed outlier: 4.104A pdb=" N GLY B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.830A pdb=" N GLN B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 413 " --> pdb=" O GLU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 436 removed outlier: 4.228A pdb=" N GLU B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 436 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 454 Processing helix chain 'B' and resid 461 through 472 removed outlier: 4.121A pdb=" N LEU B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 490 through 495 Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.686A pdb=" N GLN B 512 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 531 removed outlier: 3.745A pdb=" N SER B 531 " --> pdb=" O TRP B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 Processing helix chain 'B' and resid 556 through 566 removed outlier: 4.082A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS B 566 " --> pdb=" O GLU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 575 removed outlier: 4.079A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 581 removed outlier: 4.008A pdb=" N PHE B 581 " --> pdb=" O PRO B 578 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 36 removed outlier: 3.980A pdb=" N PHE M 32 " --> pdb=" O ALA M 28 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG M 33 " --> pdb=" O VAL M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 removed outlier: 3.945A pdb=" N VAL M 78 " --> pdb=" O ASN M 74 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE M 79 " --> pdb=" O ALA M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 104 through 116 removed outlier: 3.577A pdb=" N TYR M 109 " --> pdb=" O PHE M 105 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU M 114 " --> pdb=" O GLU M 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU M 116 " --> pdb=" O LEU M 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 22 Processing helix chain 'N' and resid 112 through 127 Processing helix chain 'N' and resid 135 through 150 Processing helix chain 'N' and resid 217 through 221 removed outlier: 3.589A pdb=" N TYR N 221 " --> pdb=" O LYS N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 224 through 229 removed outlier: 3.583A pdb=" N TYR N 229 " --> pdb=" O ALA N 225 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 40 removed outlier: 3.598A pdb=" N ILE S 32 " --> pdb=" O LYS S 28 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU S 33 " --> pdb=" O GLN S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 95 removed outlier: 4.084A pdb=" N PHE S 95 " --> pdb=" O LEU S 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 106 Processing helix chain 'S' and resid 106 through 117 removed outlier: 3.534A pdb=" N THR S 112 " --> pdb=" O TYR S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 138 Processing sheet with id=AA1, first strand: chain 'B' and resid 8 through 9 removed outlier: 6.423A pdb=" N THR B 8 " --> pdb=" O ASN N 181 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL N 178 " --> pdb=" O ALA N 212 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA N 212 " --> pdb=" O VAL N 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 14 through 16 removed outlier: 6.801A pdb=" N ILE M 7 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.525A pdb=" N ILE S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE S 5 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TRP S 19 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ARG S 3 " --> pdb=" O TRP S 19 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE S 4 " --> pdb=" O CYS S 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 118 through 119 677 hydrogen bonds defined for protein. 2001 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: 3.72 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3820 1.34 - 1.46: 2333 1.46 - 1.58: 5653 1.58 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 11872 Sorted by residual: bond pdb=" C THR B 245 " pdb=" N PRO B 246 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.92e+00 bond pdb=" C PRO B 286 " pdb=" N PRO B 287 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.20e-02 6.94e+03 2.11e+00 bond pdb=" C GLU B 124 " pdb=" N PRO B 125 " ideal model delta sigma weight residual 1.336 1.352 -0.016 1.25e-02 6.40e+03 1.71e+00 bond pdb=" CA THR B 245 " pdb=" C THR B 245 " ideal model delta sigma weight residual 1.522 1.538 -0.016 1.26e-02 6.30e+03 1.70e+00 bond pdb=" C ILE A 151 " pdb=" N PRO A 152 " ideal model delta sigma weight residual 1.336 1.352 -0.016 1.23e-02 6.61e+03 1.69e+00 ... (remaining 11867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 16042 2.29 - 4.58: 167 4.58 - 6.87: 12 6.87 - 9.16: 6 9.16 - 11.45: 1 Bond angle restraints: 16228 Sorted by residual: angle pdb=" C ARG M 60 " pdb=" N SER M 61 " pdb=" CA SER M 61 " ideal model delta sigma weight residual 121.54 128.54 -7.00 1.91e+00 2.74e-01 1.34e+01 angle pdb=" N ASN B 200 " pdb=" CA ASN B 200 " pdb=" C ASN B 200 " ideal model delta sigma weight residual 109.81 117.66 -7.85 2.21e+00 2.05e-01 1.26e+01 angle pdb=" CA PRO B 286 " pdb=" C PRO B 286 " pdb=" N PRO B 287 " ideal model delta sigma weight residual 117.93 121.99 -4.06 1.20e+00 6.94e-01 1.15e+01 angle pdb=" CA LEU B 482 " pdb=" CB LEU B 482 " pdb=" CG LEU B 482 " ideal model delta sigma weight residual 116.30 127.75 -11.45 3.50e+00 8.16e-02 1.07e+01 angle pdb=" CA ALA B 285 " pdb=" C ALA B 285 " pdb=" N PRO B 286 " ideal model delta sigma weight residual 118.44 123.05 -4.61 1.59e+00 3.96e-01 8.39e+00 ... (remaining 16223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 6658 17.86 - 35.71: 364 35.71 - 53.57: 89 53.57 - 71.42: 9 71.42 - 89.28: 7 Dihedral angle restraints: 7127 sinusoidal: 2450 harmonic: 4677 Sorted by residual: dihedral pdb=" CB CYS N 193 " pdb=" SG CYS N 193 " pdb=" SG CYS S 97 " pdb=" CB CYS S 97 " ideal model delta sinusoidal sigma weight residual 93.00 137.83 -44.83 1 1.00e+01 1.00e-02 2.79e+01 dihedral pdb=" CA ILE B 488 " pdb=" C ILE B 488 " pdb=" N VAL B 489 " pdb=" CA VAL B 489 " ideal model delta harmonic sigma weight residual 180.00 154.93 25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA ASN B 62 " pdb=" C ASN B 62 " pdb=" N LEU B 63 " pdb=" CA LEU B 63 " ideal model delta harmonic sigma weight residual -180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 7124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1360 0.039 - 0.077: 479 0.077 - 0.116: 109 0.116 - 0.155: 20 0.155 - 0.193: 1 Chirality restraints: 1969 Sorted by residual: chirality pdb=" CB VAL A 555 " pdb=" CA VAL A 555 " pdb=" CG1 VAL A 555 " pdb=" CG2 VAL A 555 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA ASN B 200 " pdb=" N ASN B 200 " pdb=" C ASN B 200 " pdb=" CB ASN B 200 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA THR B 245 " pdb=" N THR B 245 " pdb=" C THR B 245 " pdb=" CB THR B 245 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 1966 not shown) Planarity restraints: 2071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 285 " 0.044 5.00e-02 4.00e+02 6.58e-02 6.92e+00 pdb=" N PRO B 286 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 286 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 286 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 576 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO B 577 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 577 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 577 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS N 196 " 0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO N 197 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO N 197 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO N 197 " 0.028 5.00e-02 4.00e+02 ... (remaining 2068 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3690 2.82 - 3.34: 10608 3.34 - 3.86: 19388 3.86 - 4.38: 20741 4.38 - 4.90: 36282 Nonbonded interactions: 90709 Sorted by model distance: nonbonded pdb=" O SER A 234 " pdb=" OG1 THR A 238 " model vdw 2.304 3.040 nonbonded pdb=" O VAL A 204 " pdb=" OG1 THR A 208 " model vdw 2.305 3.040 nonbonded pdb=" OD2 ASP A 382 " pdb=" OG SER A 384 " model vdw 2.317 3.040 nonbonded pdb=" O HIS S 36 " pdb=" OG1 THR S 40 " model vdw 2.320 3.040 nonbonded pdb=" O TYR A 478 " pdb=" OG1 THR A 482 " model vdw 2.320 3.040 ... (remaining 90704 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.620 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 0.003 0.049 11872 Z= 0.213 Angle : 0.613 11.446 16228 Z= 0.349 Chirality : 0.041 0.193 1969 Planarity : 0.006 0.066 2071 Dihedral : 12.403 89.277 4076 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.31 % Allowed : 9.78 % Favored : 87.91 % 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: -3.98 (0.15), residues: 1561 helix: -2.32 (0.11), residues: 978 sheet: -1.54 (0.67), residues: 54 loop : -3.10 (0.22), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 462 HIS 0.005 0.001 HIS S 85 PHE 0.019 0.002 PHE B 492 TYR 0.011 0.001 TYR B 405 ARG 0.003 0.000 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 332 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8306 (m-80) cc_final: 0.8040 (m-10) REVERT: A 409 MET cc_start: 0.9127 (mmt) cc_final: 0.8523 (mmt) REVERT: B 139 LYS cc_start: 0.7987 (tppp) cc_final: 0.7783 (tppp) REVERT: B 140 THR cc_start: 0.8391 (p) cc_final: 0.8096 (t) REVERT: B 312 LYS cc_start: 0.8626 (tptt) cc_final: 0.7754 (mttt) REVERT: B 527 TRP cc_start: 0.8049 (t60) cc_final: 0.7003 (t60) REVERT: B 558 THR cc_start: 0.8304 (p) cc_final: 0.8034 (t) REVERT: M 18 ARG cc_start: 0.8030 (tpp80) cc_final: 0.7712 (mtp85) REVERT: M 60 ARG cc_start: 0.7044 (mmm160) cc_final: 0.6797 (mmm160) REVERT: M 93 PHE cc_start: 0.7072 (p90) cc_final: 0.6832 (p90) REVERT: M 100 ASN cc_start: 0.8371 (m110) cc_final: 0.8040 (m110) REVERT: M 122 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7501 (mm-40) REVERT: N 157 GLN cc_start: 0.8094 (tt0) cc_final: 0.7770 (tt0) REVERT: N 209 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7351 (mt-10) REVERT: N 223 TYR cc_start: 0.6687 (OUTLIER) cc_final: 0.4042 (t80) REVERT: S 9 ASN cc_start: 0.7818 (p0) cc_final: 0.7368 (p0) REVERT: S 61 ARG cc_start: 0.8355 (ttt-90) cc_final: 0.6811 (ptm-80) REVERT: S 122 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7784 (mp0) outliers start: 26 outliers final: 8 residues processed: 350 average time/residue: 0.2668 time to fit residues: 127.6539 Evaluate side-chains 222 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 213 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain N residue 223 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 79 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 216 GLN A 266 GLN A 333 GLN A 387 GLN A 488 GLN ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN B 278 ASN B 504 GLN B 505 GLN M 35 ASN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 121 HIS ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 202 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11872 Z= 0.220 Angle : 0.595 8.224 16228 Z= 0.302 Chirality : 0.041 0.225 1969 Planarity : 0.004 0.047 2071 Dihedral : 5.316 59.622 1701 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.20 % Allowed : 15.47 % Favored : 81.33 % 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: -1.68 (0.20), residues: 1561 helix: -0.32 (0.15), residues: 988 sheet: -1.17 (0.68), residues: 54 loop : -2.59 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 462 HIS 0.007 0.001 HIS A 527 PHE 0.027 0.002 PHE B 492 TYR 0.022 0.001 TYR A 88 ARG 0.008 0.001 ARG M 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 248 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8342 (m-80) cc_final: 0.7890 (m-80) REVERT: A 409 MET cc_start: 0.9183 (mmt) cc_final: 0.8549 (mmt) REVERT: A 474 ASP cc_start: 0.7434 (m-30) cc_final: 0.7101 (m-30) REVERT: A 602 MET cc_start: 0.7645 (mmp) cc_final: 0.7303 (mmm) REVERT: B 139 LYS cc_start: 0.8469 (tppp) cc_final: 0.7995 (tppt) REVERT: B 140 THR cc_start: 0.8414 (p) cc_final: 0.8193 (t) REVERT: B 175 MET cc_start: 0.8235 (mmm) cc_final: 0.7704 (mmt) REVERT: B 312 LYS cc_start: 0.8628 (tptt) cc_final: 0.7879 (mttt) REVERT: B 479 GLN cc_start: 0.7421 (mp10) cc_final: 0.6820 (mt0) REVERT: B 527 TRP cc_start: 0.7887 (t60) cc_final: 0.6760 (t60) REVERT: B 558 THR cc_start: 0.8359 (p) cc_final: 0.8144 (t) REVERT: M 1 MET cc_start: 0.7428 (mtm) cc_final: 0.7104 (ttm) REVERT: M 18 ARG cc_start: 0.7877 (tpp80) cc_final: 0.7657 (mtp85) REVERT: M 84 LYS cc_start: 0.8233 (tmtt) cc_final: 0.7989 (tppp) REVERT: N 185 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7834 (tp30) REVERT: N 223 TYR cc_start: 0.6405 (OUTLIER) cc_final: 0.3966 (t80) REVERT: S 21 MET cc_start: 0.7783 (mmp) cc_final: 0.7522 (mmm) REVERT: S 61 ARG cc_start: 0.8273 (ttt-90) cc_final: 0.6864 (ptm-80) REVERT: S 122 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7538 (mm-30) REVERT: S 124 ARG cc_start: 0.7812 (ttt-90) cc_final: 0.7534 (ttp80) outliers start: 36 outliers final: 21 residues processed: 269 average time/residue: 0.2512 time to fit residues: 93.9280 Evaluate side-chains 225 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 203 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 108 ILE Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 213 TRP Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain S residue 126 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 141 optimal weight: 5.9990 chunk 153 optimal weight: 0.4980 chunk 126 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 48 optimal weight: 0.0980 chunk 113 optimal weight: 0.0060 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11872 Z= 0.170 Angle : 0.574 13.267 16228 Z= 0.286 Chirality : 0.041 0.291 1969 Planarity : 0.004 0.062 2071 Dihedral : 5.086 53.213 1700 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.93 % Allowed : 17.07 % Favored : 80.00 % 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: -0.77 (0.21), residues: 1561 helix: 0.45 (0.16), residues: 981 sheet: -0.74 (0.70), residues: 54 loop : -2.31 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 462 HIS 0.004 0.001 HIS A 527 PHE 0.024 0.001 PHE B 492 TYR 0.018 0.001 TYR M 83 ARG 0.005 0.001 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 218 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8363 (m-80) cc_final: 0.7754 (m-80) REVERT: A 166 GLN cc_start: 0.7857 (pt0) cc_final: 0.7644 (pt0) REVERT: A 409 MET cc_start: 0.9141 (mmt) cc_final: 0.8553 (mmt) REVERT: A 504 LEU cc_start: 0.8315 (mt) cc_final: 0.8068 (mt) REVERT: A 584 LEU cc_start: 0.9075 (tp) cc_final: 0.8851 (tp) REVERT: A 602 MET cc_start: 0.7611 (mmp) cc_final: 0.7349 (mmm) REVERT: B 139 LYS cc_start: 0.8555 (tppp) cc_final: 0.8138 (tppp) REVERT: B 140 THR cc_start: 0.8418 (p) cc_final: 0.8172 (t) REVERT: B 175 MET cc_start: 0.8244 (mmm) cc_final: 0.7749 (mmt) REVERT: B 312 LYS cc_start: 0.8630 (tptt) cc_final: 0.7915 (mttt) REVERT: B 527 TRP cc_start: 0.7891 (t60) cc_final: 0.6786 (t60) REVERT: B 558 THR cc_start: 0.8380 (p) cc_final: 0.8146 (t) REVERT: B 562 GLU cc_start: 0.7335 (tp30) cc_final: 0.6927 (tp30) REVERT: M 84 LYS cc_start: 0.8165 (tmtt) cc_final: 0.7911 (tppp) REVERT: N 24 ARG cc_start: 0.7873 (mtm180) cc_final: 0.7641 (mtm-85) REVERT: N 223 TYR cc_start: 0.6160 (OUTLIER) cc_final: 0.3518 (t80) REVERT: S 61 ARG cc_start: 0.8242 (ttt-90) cc_final: 0.6802 (ptm-80) REVERT: S 122 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7534 (mp0) REVERT: S 124 ARG cc_start: 0.7727 (ttt-90) cc_final: 0.7492 (ttp80) outliers start: 33 outliers final: 20 residues processed: 239 average time/residue: 0.2496 time to fit residues: 84.0810 Evaluate side-chains 219 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 198 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain S residue 38 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A 527 HIS A 531 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11872 Z= 0.211 Angle : 0.574 9.820 16228 Z= 0.287 Chirality : 0.041 0.271 1969 Planarity : 0.003 0.042 2071 Dihedral : 4.980 49.828 1700 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.38 % Allowed : 17.60 % Favored : 79.02 % 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: -0.28 (0.22), residues: 1561 helix: 0.83 (0.17), residues: 987 sheet: -0.31 (0.74), residues: 54 loop : -2.17 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP N 173 HIS 0.005 0.001 HIS S 85 PHE 0.020 0.001 PHE B 492 TYR 0.013 0.001 TYR N 167 ARG 0.012 0.001 ARG S 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 215 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8259 (m-80) cc_final: 0.7990 (m-10) REVERT: A 409 MET cc_start: 0.9189 (mmt) cc_final: 0.8611 (mmt) REVERT: A 602 MET cc_start: 0.7819 (mmp) cc_final: 0.7594 (mmm) REVERT: B 139 LYS cc_start: 0.8605 (tppp) cc_final: 0.8141 (tppp) REVERT: B 140 THR cc_start: 0.8438 (p) cc_final: 0.8198 (t) REVERT: B 175 MET cc_start: 0.8259 (mmm) cc_final: 0.7714 (mmm) REVERT: B 312 LYS cc_start: 0.8660 (tptt) cc_final: 0.7917 (mttt) REVERT: B 448 MET cc_start: 0.8484 (mmm) cc_final: 0.7689 (tpt) REVERT: B 527 TRP cc_start: 0.7915 (t60) cc_final: 0.6771 (t60) REVERT: B 558 THR cc_start: 0.8393 (p) cc_final: 0.8191 (t) REVERT: M 1 MET cc_start: 0.7318 (mtm) cc_final: 0.6965 (ttm) REVERT: M 84 LYS cc_start: 0.8219 (tmtt) cc_final: 0.7974 (tppp) REVERT: N 24 ARG cc_start: 0.7895 (mtm180) cc_final: 0.7650 (mtm-85) REVERT: N 223 TYR cc_start: 0.6062 (OUTLIER) cc_final: 0.3415 (t80) REVERT: S 15 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7983 (mmm-85) REVERT: S 61 ARG cc_start: 0.8234 (ttt-90) cc_final: 0.6714 (ptm-80) REVERT: S 100 GLU cc_start: 0.6467 (tp30) cc_final: 0.5667 (tp30) REVERT: S 122 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7553 (mp0) REVERT: S 124 ARG cc_start: 0.7754 (ttt180) cc_final: 0.7097 (ttp80) REVERT: S 138 LEU cc_start: 0.9202 (mt) cc_final: 0.8989 (mt) outliers start: 38 outliers final: 28 residues processed: 240 average time/residue: 0.2345 time to fit residues: 80.7350 Evaluate side-chains 226 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 196 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 158 ASN Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 126 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN B 179 ASN ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN M 122 GLN ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11872 Z= 0.316 Angle : 0.667 17.070 16228 Z= 0.328 Chirality : 0.043 0.281 1969 Planarity : 0.004 0.045 2071 Dihedral : 5.079 52.190 1698 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.82 % Allowed : 19.38 % Favored : 76.80 % 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: -0.19 (0.22), residues: 1561 helix: 0.86 (0.17), residues: 987 sheet: -0.40 (0.75), residues: 54 loop : -2.03 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 173 HIS 0.008 0.001 HIS S 85 PHE 0.020 0.002 PHE B 492 TYR 0.017 0.002 TYR B 300 ARG 0.005 0.001 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 206 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 TYR cc_start: 0.8497 (t80) cc_final: 0.8062 (t80) REVERT: A 396 MET cc_start: 0.7462 (mmm) cc_final: 0.6873 (tpp) REVERT: A 409 MET cc_start: 0.9209 (mmt) cc_final: 0.8635 (mmt) REVERT: A 418 TYR cc_start: 0.7452 (m-80) cc_final: 0.7227 (m-10) REVERT: B 139 LYS cc_start: 0.8692 (tppp) cc_final: 0.8255 (tppp) REVERT: B 140 THR cc_start: 0.8488 (p) cc_final: 0.8238 (t) REVERT: B 175 MET cc_start: 0.8298 (mmm) cc_final: 0.7676 (mmm) REVERT: B 527 TRP cc_start: 0.8046 (t60) cc_final: 0.6831 (t60) REVERT: B 528 ARG cc_start: 0.7727 (mtt180) cc_final: 0.7263 (mtm-85) REVERT: B 558 THR cc_start: 0.8495 (p) cc_final: 0.8291 (t) REVERT: M 84 LYS cc_start: 0.8269 (tmtt) cc_final: 0.8020 (tppp) REVERT: N 24 ARG cc_start: 0.7990 (mtm180) cc_final: 0.7719 (mtm-85) REVERT: N 157 GLN cc_start: 0.7664 (mt0) cc_final: 0.6882 (mp10) REVERT: N 202 GLN cc_start: 0.8870 (tt0) cc_final: 0.8666 (tt0) REVERT: N 223 TYR cc_start: 0.6351 (OUTLIER) cc_final: 0.3757 (t80) REVERT: S 61 ARG cc_start: 0.8270 (ttt-90) cc_final: 0.6769 (ptm-80) REVERT: S 122 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7287 (mm-30) REVERT: S 138 LEU cc_start: 0.9224 (mt) cc_final: 0.8946 (mt) outliers start: 43 outliers final: 30 residues processed: 234 average time/residue: 0.2356 time to fit residues: 78.8921 Evaluate side-chains 232 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 201 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 158 ASN Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 38 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11872 Z= 0.239 Angle : 0.606 12.101 16228 Z= 0.303 Chirality : 0.042 0.292 1969 Planarity : 0.004 0.041 2071 Dihedral : 5.001 52.545 1696 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.02 % Allowed : 20.71 % Favored : 76.27 % 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: -0.04 (0.22), residues: 1561 helix: 1.02 (0.17), residues: 987 sheet: -0.48 (0.74), residues: 54 loop : -2.05 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 207 HIS 0.005 0.001 HIS S 85 PHE 0.031 0.002 PHE A 66 TYR 0.013 0.001 TYR N 145 ARG 0.004 0.000 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 211 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.9198 (mmt) cc_final: 0.8627 (mmt) REVERT: B 139 LYS cc_start: 0.8639 (tppp) cc_final: 0.8191 (tppp) REVERT: B 140 THR cc_start: 0.8407 (p) cc_final: 0.8183 (t) REVERT: B 175 MET cc_start: 0.8339 (mmm) cc_final: 0.7805 (mmt) REVERT: B 448 MET cc_start: 0.8509 (tpt) cc_final: 0.7860 (tpt) REVERT: B 527 TRP cc_start: 0.7948 (t60) cc_final: 0.6758 (t60) REVERT: M 84 LYS cc_start: 0.8230 (tmtt) cc_final: 0.7963 (tppp) REVERT: M 93 PHE cc_start: 0.7537 (p90) cc_final: 0.6789 (p90) REVERT: N 24 ARG cc_start: 0.8010 (mtm180) cc_final: 0.7732 (mtm-85) REVERT: N 195 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8583 (m) REVERT: N 223 TYR cc_start: 0.6279 (OUTLIER) cc_final: 0.3683 (t80) REVERT: S 15 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7870 (mmm-85) REVERT: S 18 LYS cc_start: 0.8244 (mmmm) cc_final: 0.8000 (ttmt) REVERT: S 61 ARG cc_start: 0.8311 (ttt-90) cc_final: 0.6745 (ptm-80) REVERT: S 122 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7239 (mm-30) REVERT: S 124 ARG cc_start: 0.7944 (ttt180) cc_final: 0.7051 (ttp80) outliers start: 34 outliers final: 27 residues processed: 234 average time/residue: 0.2456 time to fit residues: 81.7662 Evaluate side-chains 230 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 200 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 158 ASN Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 195 VAL Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 38 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 110 optimal weight: 0.0170 chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 150 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11872 Z= 0.194 Angle : 0.596 13.062 16228 Z= 0.295 Chirality : 0.041 0.314 1969 Planarity : 0.004 0.062 2071 Dihedral : 4.959 56.030 1696 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.02 % Allowed : 21.87 % Favored : 75.11 % 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: 0.10 (0.22), residues: 1561 helix: 1.11 (0.17), residues: 986 sheet: -0.42 (0.75), residues: 54 loop : -1.95 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 462 HIS 0.004 0.001 HIS S 85 PHE 0.018 0.001 PHE B 492 TYR 0.020 0.001 TYR A 418 ARG 0.006 0.001 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 219 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 MET cc_start: 0.7142 (tpp) cc_final: 0.6907 (tpp) REVERT: A 409 MET cc_start: 0.9198 (mmt) cc_final: 0.8598 (mmt) REVERT: A 504 LEU cc_start: 0.8313 (mt) cc_final: 0.8046 (mt) REVERT: B 139 LYS cc_start: 0.8633 (tppp) cc_final: 0.8156 (tppp) REVERT: B 140 THR cc_start: 0.8408 (p) cc_final: 0.8164 (t) REVERT: B 175 MET cc_start: 0.8286 (mmm) cc_final: 0.7722 (mmt) REVERT: B 527 TRP cc_start: 0.7912 (t60) cc_final: 0.6741 (t60) REVERT: M 70 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8246 (mtmm) REVERT: M 84 LYS cc_start: 0.8174 (tmtt) cc_final: 0.7920 (tppp) REVERT: M 93 PHE cc_start: 0.7587 (p90) cc_final: 0.7081 (p90) REVERT: T 7 ASP cc_start: 0.7296 (t70) cc_final: 0.6714 (t70) REVERT: N 24 ARG cc_start: 0.7987 (mtm180) cc_final: 0.7726 (mtm-85) REVERT: N 223 TYR cc_start: 0.6160 (OUTLIER) cc_final: 0.3537 (t80) REVERT: S 61 ARG cc_start: 0.8300 (ttt-90) cc_final: 0.6705 (ptm-80) REVERT: S 122 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7435 (mm-30) REVERT: S 124 ARG cc_start: 0.7879 (ttt180) cc_final: 0.7002 (ttp80) outliers start: 34 outliers final: 28 residues processed: 241 average time/residue: 0.2317 time to fit residues: 80.0760 Evaluate side-chains 234 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 204 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 70 LYS Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 158 ASN Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 38 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 45 optimal weight: 0.0050 chunk 29 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 74 optimal weight: 0.0970 chunk 14 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11872 Z= 0.172 Angle : 0.594 12.626 16228 Z= 0.293 Chirality : 0.041 0.316 1969 Planarity : 0.004 0.057 2071 Dihedral : 4.897 52.444 1696 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.20 % Allowed : 22.13 % Favored : 74.67 % 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: 0.22 (0.22), residues: 1561 helix: 1.20 (0.17), residues: 985 sheet: -0.48 (0.74), residues: 54 loop : -1.88 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 462 HIS 0.003 0.001 HIS S 85 PHE 0.036 0.001 PHE A 66 TYR 0.021 0.001 TYR A 88 ARG 0.008 0.001 ARG S 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 217 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 MET cc_start: 0.7200 (tpp) cc_final: 0.6823 (tpp) REVERT: A 409 MET cc_start: 0.9199 (mmt) cc_final: 0.8607 (mmt) REVERT: A 504 LEU cc_start: 0.8278 (mt) cc_final: 0.8046 (mt) REVERT: A 551 LEU cc_start: 0.7107 (tp) cc_final: 0.6806 (tp) REVERT: B 139 LYS cc_start: 0.8630 (tppp) cc_final: 0.8149 (tppp) REVERT: B 140 THR cc_start: 0.8404 (p) cc_final: 0.8137 (t) REVERT: B 175 MET cc_start: 0.8236 (mmm) cc_final: 0.7674 (mmt) REVERT: B 257 LEU cc_start: 0.8182 (mt) cc_final: 0.7748 (tt) REVERT: B 448 MET cc_start: 0.8668 (tpt) cc_final: 0.7957 (tpt) REVERT: B 527 TRP cc_start: 0.7843 (t60) cc_final: 0.6706 (t60) REVERT: B 562 GLU cc_start: 0.7293 (tp30) cc_final: 0.7031 (tt0) REVERT: M 70 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8227 (mtmm) REVERT: M 84 LYS cc_start: 0.8201 (tmtt) cc_final: 0.7903 (tppp) REVERT: T 7 ASP cc_start: 0.7333 (t70) cc_final: 0.6797 (t70) REVERT: N 24 ARG cc_start: 0.7965 (mtm180) cc_final: 0.7697 (mtm-85) REVERT: N 223 TYR cc_start: 0.6074 (OUTLIER) cc_final: 0.3381 (t80) REVERT: S 61 ARG cc_start: 0.8277 (ttt-90) cc_final: 0.6672 (ptm-80) REVERT: S 122 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7485 (mp0) REVERT: S 124 ARG cc_start: 0.7873 (ttt180) cc_final: 0.6995 (ttp80) outliers start: 36 outliers final: 29 residues processed: 244 average time/residue: 0.2532 time to fit residues: 88.7526 Evaluate side-chains 234 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 203 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 70 LYS Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 213 TRP Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain S residue 38 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11872 Z= 0.212 Angle : 0.626 13.732 16228 Z= 0.306 Chirality : 0.042 0.334 1969 Planarity : 0.004 0.056 2071 Dihedral : 4.916 51.701 1696 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.84 % Allowed : 23.29 % Favored : 73.87 % 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: 0.25 (0.22), residues: 1561 helix: 1.21 (0.17), residues: 986 sheet: -0.67 (0.73), residues: 56 loop : -1.81 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 213 HIS 0.004 0.001 HIS S 85 PHE 0.019 0.001 PHE M 93 TYR 0.013 0.001 TYR B 277 ARG 0.008 0.001 ARG S 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 202 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8356 (m-80) cc_final: 0.8094 (m-10) REVERT: A 396 MET cc_start: 0.7268 (tpp) cc_final: 0.6865 (tpp) REVERT: A 409 MET cc_start: 0.9216 (mmt) cc_final: 0.8624 (mmt) REVERT: A 504 LEU cc_start: 0.8343 (mt) cc_final: 0.8097 (mt) REVERT: A 551 LEU cc_start: 0.7126 (tp) cc_final: 0.6838 (tp) REVERT: B 139 LYS cc_start: 0.8651 (tppp) cc_final: 0.8170 (tppp) REVERT: B 140 THR cc_start: 0.8436 (p) cc_final: 0.8178 (t) REVERT: B 175 MET cc_start: 0.8240 (mmm) cc_final: 0.7712 (mmt) REVERT: B 257 LEU cc_start: 0.8176 (mt) cc_final: 0.7703 (tt) REVERT: B 448 MET cc_start: 0.8688 (tpt) cc_final: 0.7971 (tpt) REVERT: B 527 TRP cc_start: 0.7861 (t60) cc_final: 0.6701 (t60) REVERT: M 70 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8233 (mtmm) REVERT: M 84 LYS cc_start: 0.8210 (tmtt) cc_final: 0.7940 (tppp) REVERT: M 85 MET cc_start: 0.8047 (tpp) cc_final: 0.7739 (tmm) REVERT: M 89 MET cc_start: 0.7802 (tpp) cc_final: 0.7570 (tpp) REVERT: T 7 ASP cc_start: 0.7368 (t70) cc_final: 0.6958 (t70) REVERT: N 24 ARG cc_start: 0.8025 (mtm180) cc_final: 0.7729 (mtm-85) REVERT: N 223 TYR cc_start: 0.6121 (OUTLIER) cc_final: 0.3419 (t80) REVERT: S 18 LYS cc_start: 0.8555 (ttpt) cc_final: 0.7933 (ttmt) REVERT: S 61 ARG cc_start: 0.8281 (ttt-90) cc_final: 0.6667 (ptm-80) REVERT: S 122 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7514 (mp0) REVERT: S 124 ARG cc_start: 0.7842 (ttt180) cc_final: 0.6987 (ttp80) outliers start: 32 outliers final: 26 residues processed: 225 average time/residue: 0.2350 time to fit residues: 75.4788 Evaluate side-chains 227 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 70 LYS Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain S residue 38 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 70 optimal weight: 0.0670 chunk 102 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 143 optimal weight: 0.0870 chunk 123 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 95 optimal weight: 0.0980 chunk 75 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 ASN ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11872 Z= 0.163 Angle : 0.612 13.687 16228 Z= 0.296 Chirality : 0.041 0.331 1969 Planarity : 0.004 0.053 2071 Dihedral : 4.812 50.040 1696 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.58 % Allowed : 23.56 % Favored : 73.87 % 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: 0.34 (0.22), residues: 1561 helix: 1.29 (0.17), residues: 985 sheet: -0.40 (0.74), residues: 54 loop : -1.80 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP N 213 HIS 0.004 0.001 HIS S 85 PHE 0.038 0.001 PHE A 66 TYR 0.051 0.001 TYR A 88 ARG 0.007 0.001 ARG S 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 211 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLN cc_start: 0.7919 (pt0) cc_final: 0.7399 (mt0) REVERT: A 396 MET cc_start: 0.7248 (tpp) cc_final: 0.6858 (tpp) REVERT: A 409 MET cc_start: 0.9181 (mmt) cc_final: 0.8563 (mmt) REVERT: A 504 LEU cc_start: 0.8268 (mt) cc_final: 0.8044 (mt) REVERT: A 551 LEU cc_start: 0.7203 (tp) cc_final: 0.6924 (tp) REVERT: B 139 LYS cc_start: 0.8632 (tppp) cc_final: 0.8166 (tppp) REVERT: B 140 THR cc_start: 0.8385 (p) cc_final: 0.8103 (t) REVERT: B 175 MET cc_start: 0.8186 (mmm) cc_final: 0.7630 (mmt) REVERT: B 257 LEU cc_start: 0.8044 (mt) cc_final: 0.7438 (tt) REVERT: B 448 MET cc_start: 0.8640 (tpt) cc_final: 0.7936 (tpt) REVERT: B 527 TRP cc_start: 0.7785 (t60) cc_final: 0.6659 (t60) REVERT: B 528 ARG cc_start: 0.7707 (mtt180) cc_final: 0.7191 (mtm-85) REVERT: B 562 GLU cc_start: 0.7236 (tp30) cc_final: 0.7019 (tt0) REVERT: M 21 ARG cc_start: 0.7526 (mtt90) cc_final: 0.7102 (mpt-90) REVERT: M 70 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8258 (mttp) REVERT: M 77 MET cc_start: 0.7200 (ttt) cc_final: 0.6954 (ttt) REVERT: M 84 LYS cc_start: 0.8195 (tmtt) cc_final: 0.7911 (tppp) REVERT: T 7 ASP cc_start: 0.7312 (t70) cc_final: 0.6862 (t70) REVERT: N 24 ARG cc_start: 0.7962 (mtm180) cc_final: 0.7650 (mtm-85) REVERT: N 167 TYR cc_start: 0.5522 (m-10) cc_final: 0.5157 (m-10) REVERT: N 223 TYR cc_start: 0.6070 (OUTLIER) cc_final: 0.4095 (t80) REVERT: S 18 LYS cc_start: 0.8598 (ttpt) cc_final: 0.7819 (ttmt) REVERT: S 21 MET cc_start: 0.6670 (mmm) cc_final: 0.6350 (mmt) REVERT: S 61 ARG cc_start: 0.8236 (ttt-90) cc_final: 0.6670 (ptm-80) REVERT: S 80 TYR cc_start: 0.8294 (m-80) cc_final: 0.8090 (m-80) REVERT: S 122 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7343 (mm-30) REVERT: S 124 ARG cc_start: 0.7833 (ttt180) cc_final: 0.6767 (ttp80) outliers start: 29 outliers final: 23 residues processed: 230 average time/residue: 0.2421 time to fit residues: 79.8409 Evaluate side-chains 225 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 200 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 70 LYS Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain S residue 38 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 114 optimal weight: 0.0070 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 108 optimal weight: 0.0060 overall best weight: 0.3414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.159777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.130025 restraints weight = 20123.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.131700 restraints weight = 14331.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133101 restraints weight = 10646.757| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11872 Z= 0.172 Angle : 0.624 13.431 16228 Z= 0.301 Chirality : 0.042 0.328 1969 Planarity : 0.004 0.052 2071 Dihedral : 4.729 50.890 1696 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.67 % Allowed : 23.73 % Favored : 73.60 % 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: 0.36 (0.22), residues: 1561 helix: 1.29 (0.17), residues: 988 sheet: -0.53 (0.72), residues: 56 loop : -1.76 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 462 HIS 0.003 0.001 HIS S 85 PHE 0.018 0.001 PHE M 93 TYR 0.013 0.001 TYR B 277 ARG 0.008 0.001 ARG S 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2523.01 seconds wall clock time: 49 minutes 53.67 seconds (2993.67 seconds total)