Starting phenix.real_space_refine on Fri May 16 03:13:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l0d_62697/05_2025/9l0d_62697.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l0d_62697/05_2025/9l0d_62697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l0d_62697/05_2025/9l0d_62697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l0d_62697/05_2025/9l0d_62697.map" model { file = "/net/cci-nas-00/data/ceres_data/9l0d_62697/05_2025/9l0d_62697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l0d_62697/05_2025/9l0d_62697.cif" } resolution = 3.41 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= 0.001 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 8900 2.51 5 N 2376 2.21 5 O 2549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 186 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13894 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3349 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 400} Chain: "B" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3837 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain: "C" Number of atoms: 5280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5280 Classifications: {'peptide': 657} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 623} Chain: "D" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1428 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Time building chain proxies: 7.47, per 1000 atoms: 0.54 Number of scatterers: 13894 At special positions: 0 Unit cell: (88.62, 117.105, 185.68, 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 69 16.00 O 2549 8.00 N 2376 7.00 C 8900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.6 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 17 sheets defined 40.6% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 237 through 247 removed outlier: 4.525A pdb=" N GLU A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 276 through 290 removed outlier: 6.245A pdb=" N MET A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 344 Processing helix chain 'A' and resid 345 through 356 removed outlier: 4.002A pdb=" N SER A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 356 " --> pdb=" O ILE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.733A pdb=" N ASN A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 382 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 398 through 410 removed outlier: 3.993A pdb=" N ALA A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 452 removed outlier: 3.867A pdb=" N SER A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'A' and resid 499 through 517 removed outlier: 4.391A pdb=" N CYS A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG A 513 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 529 removed outlier: 3.641A pdb=" N ALA A 522 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 538 Processing helix chain 'A' and resid 566 through 584 removed outlier: 3.964A pdb=" N GLU A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 645 removed outlier: 3.827A pdb=" N HIS A 631 " --> pdb=" O VAL A 627 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET A 634 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ASP A 642 " --> pdb=" O ARG A 638 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG A 643 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 644 " --> pdb=" O GLU A 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 43 Processing helix chain 'B' and resid 54 through 73 Processing helix chain 'B' and resid 130 through 150 removed outlier: 3.786A pdb=" N TYR B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 176 removed outlier: 3.769A pdb=" N ALA B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N VAL B 161 " --> pdb=" O GLU B 157 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N LYS B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 185 through 191 removed outlier: 3.707A pdb=" N ILE B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 217 Processing helix chain 'B' and resid 238 through 251 removed outlier: 3.645A pdb=" N ARG B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 244 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 268 through 272 Processing helix chain 'B' and resid 335 through 368 Proline residue: B 348 - end of helix Processing helix chain 'B' and resid 406 through 421 removed outlier: 3.793A pdb=" N THR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 475 Processing helix chain 'C' and resid 2 through 6 removed outlier: 3.536A pdb=" N TYR C 6 " --> pdb=" O GLU C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 321 through 326 removed outlier: 4.334A pdb=" N VAL C 325 " --> pdb=" O PRO C 322 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR C 326 " --> pdb=" O ALA C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.575A pdb=" N LEU C 370 " --> pdb=" O ILE C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 387 through 397 Processing helix chain 'C' and resid 405 through 436 Processing helix chain 'C' and resid 456 through 463 Processing helix chain 'C' and resid 464 through 471 Processing helix chain 'C' and resid 475 through 493 Processing helix chain 'C' and resid 498 through 512 removed outlier: 3.769A pdb=" N HIS C 502 " --> pdb=" O GLN C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 524 Processing helix chain 'C' and resid 530 through 540 Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 544 through 545 No H-bonds generated for 'chain 'C' and resid 544 through 545' Processing helix chain 'C' and resid 546 through 559 removed outlier: 3.676A pdb=" N MET C 554 " --> pdb=" O LEU C 550 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER C 559 " --> pdb=" O LEU C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 572 Processing helix chain 'C' and resid 574 through 586 removed outlier: 3.709A pdb=" N GLY C 584 " --> pdb=" O ARG C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 590 Processing helix chain 'C' and resid 592 through 599 removed outlier: 4.212A pdb=" N PHE C 596 " --> pdb=" O SER C 592 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU C 597 " --> pdb=" O ALA C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 611 Processing helix chain 'C' and resid 612 through 625 removed outlier: 4.179A pdb=" N ASN C 620 " --> pdb=" O PHE C 616 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ARG C 622 " --> pdb=" O GLN C 618 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU C 623 " --> pdb=" O ARG C 619 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG C 624 " --> pdb=" O ASN C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 634 removed outlier: 4.208A pdb=" N GLU C 633 " --> pdb=" O THR C 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 removed outlier: 4.012A pdb=" N GLN D 71 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER D 72 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 78 Processing helix chain 'D' and resid 93 through 98 Processing helix chain 'D' and resid 98 through 110 removed outlier: 3.785A pdb=" N ARG D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 118 removed outlier: 3.576A pdb=" N ASN D 117 " --> pdb=" O ASP D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 146 removed outlier: 3.773A pdb=" N ALA D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 184 Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 267 removed outlier: 6.266A pdb=" N SER A 259 " --> pdb=" O PRO A 264 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS A 305 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ARG A 297 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE B 100 " --> pdb=" O PRO B 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.326A pdb=" N ALA A 390 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 554 " --> pdb=" O SER A 549 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 604 " --> pdb=" O MET A 615 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 605 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 607 " --> pdb=" O LYS A 592 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LYS A 592 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS B 432 " --> pdb=" O LYS A 592 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE A 594 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE B 430 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR A 596 " --> pdb=" O GLU B 428 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU B 428 " --> pdb=" O TYR A 596 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 461 through 464 removed outlier: 4.000A pdb=" N HIS A 478 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 492 " --> pdb=" O HIS A 478 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER A 480 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 490 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 417 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU A 650 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 20 Processing sheet with id=AA5, first strand: chain 'B' and resid 230 through 234 removed outlier: 6.561A pdb=" N PHE B 225 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER B 234 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B 223 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N VAL B 220 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP B 329 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 230 through 234 removed outlier: 6.561A pdb=" N PHE B 225 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER B 234 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B 223 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N VAL B 220 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP B 329 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 393 through 394 Processing sheet with id=AA8, first strand: chain 'C' and resid 8 through 9 Processing sheet with id=AA9, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AB1, first strand: chain 'C' and resid 24 through 29 Processing sheet with id=AB2, first strand: chain 'C' and resid 69 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 113 through 117 removed outlier: 7.193A pdb=" N ILE C 127 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE C 116 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C 125 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE C 132 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER C 149 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE C 134 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 156 through 160 removed outlier: 3.558A pdb=" N TRP C 156 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 156 through 160 removed outlier: 3.558A pdb=" N TRP C 156 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 213 through 218 removed outlier: 6.618A pdb=" N VAL C 241 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE C 257 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU C 243 " --> pdb=" O MET C 255 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 266 through 271 Processing sheet with id=AB8, first strand: chain 'D' and resid 43 through 52 removed outlier: 6.359A pdb=" N LEU D 9 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N TRP D 62 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL D 11 " --> pdb=" O TRP D 62 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N THR D 64 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE D 13 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS D 10 " --> pdb=" O CYS D 83 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL D 85 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE D 12 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL D 87 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU D 14 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N ASP D 89 " --> pdb=" O LEU D 14 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1860 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: 4.80 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3991 1.33 - 1.45: 2300 1.45 - 1.57: 7809 1.57 - 1.69: 0 1.69 - 1.81: 109 Bond restraints: 14209 Sorted by residual: bond pdb=" CA ASN D 22 " pdb=" CB ASN D 22 " ideal model delta sigma weight residual 1.530 1.473 0.057 1.64e-02 3.72e+03 1.21e+01 bond pdb=" C PRO C 545 " pdb=" N PRO C 546 " ideal model delta sigma weight residual 1.336 1.364 -0.028 1.08e-02 8.57e+03 6.64e+00 bond pdb=" CB ASN D 22 " pdb=" CG ASN D 22 " ideal model delta sigma weight residual 1.516 1.456 0.060 2.50e-02 1.60e+03 5.73e+00 bond pdb=" N LYS D 21 " pdb=" CA LYS D 21 " ideal model delta sigma weight residual 1.458 1.428 0.029 1.29e-02 6.01e+03 5.12e+00 bond pdb=" C SER D 23 " pdb=" O SER D 23 " ideal model delta sigma weight residual 1.235 1.220 0.015 7.50e-03 1.78e+04 4.09e+00 ... (remaining 14204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 18881 2.42 - 4.85: 312 4.85 - 7.27: 28 7.27 - 9.69: 6 9.69 - 12.11: 2 Bond angle restraints: 19229 Sorted by residual: angle pdb=" N ILE A 479 " pdb=" CA ILE A 479 " pdb=" C ILE A 479 " ideal model delta sigma weight residual 106.42 114.06 -7.64 1.51e+00 4.39e-01 2.56e+01 angle pdb=" C THR A 278 " pdb=" N MET A 279 " pdb=" CA MET A 279 " ideal model delta sigma weight residual 121.54 130.34 -8.80 1.91e+00 2.74e-01 2.12e+01 angle pdb=" C SER D 34 " pdb=" N ASN D 35 " pdb=" CA ASN D 35 " ideal model delta sigma weight residual 121.90 116.33 5.57 1.26e+00 6.30e-01 1.96e+01 angle pdb=" N LEU A 364 " pdb=" CA LEU A 364 " pdb=" C LEU A 364 " ideal model delta sigma weight residual 112.72 107.18 5.54 1.28e+00 6.10e-01 1.87e+01 angle pdb=" N ILE A 479 " pdb=" CA ILE A 479 " pdb=" CB ILE A 479 " ideal model delta sigma weight residual 112.65 108.35 4.30 1.00e+00 1.00e+00 1.85e+01 ... (remaining 19224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7282 17.99 - 35.98: 989 35.98 - 53.97: 251 53.97 - 71.96: 67 71.96 - 89.95: 27 Dihedral angle restraints: 8616 sinusoidal: 3537 harmonic: 5079 Sorted by residual: dihedral pdb=" CA THR C 611 " pdb=" C THR C 611 " pdb=" N ILE C 612 " pdb=" CA ILE C 612 " ideal model delta harmonic sigma weight residual 180.00 -144.49 -35.51 0 5.00e+00 4.00e-02 5.04e+01 dihedral pdb=" CA GLN C 649 " pdb=" C GLN C 649 " pdb=" N ALA C 650 " pdb=" CA ALA C 650 " ideal model delta harmonic sigma weight residual 180.00 148.74 31.26 0 5.00e+00 4.00e-02 3.91e+01 dihedral pdb=" CA LEU A 275 " pdb=" C LEU A 275 " pdb=" N SER A 276 " pdb=" CA SER A 276 " ideal model delta harmonic sigma weight residual 180.00 148.94 31.06 0 5.00e+00 4.00e-02 3.86e+01 ... (remaining 8613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1844 0.066 - 0.132: 276 0.132 - 0.198: 11 0.198 - 0.264: 2 0.264 - 0.330: 1 Chirality restraints: 2134 Sorted by residual: chirality pdb=" CA ASN D 22 " pdb=" N ASN D 22 " pdb=" C ASN D 22 " pdb=" CB ASN D 22 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CG LEU D 24 " pdb=" CB LEU D 24 " pdb=" CD1 LEU D 24 " pdb=" CD2 LEU D 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CG LEU A 258 " pdb=" CB LEU A 258 " pdb=" CD1 LEU A 258 " pdb=" CD2 LEU A 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2131 not shown) Planarity restraints: 2478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 279 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.84e+00 pdb=" C MET A 279 " -0.054 2.00e-02 2.50e+03 pdb=" O MET A 279 " 0.020 2.00e-02 2.50e+03 pdb=" N GLY A 280 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 276 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C SER A 276 " -0.044 2.00e-02 2.50e+03 pdb=" O SER A 276 " 0.017 2.00e-02 2.50e+03 pdb=" N SER A 277 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 20 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C GLY D 20 " 0.042 2.00e-02 2.50e+03 pdb=" O GLY D 20 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS D 21 " -0.014 2.00e-02 2.50e+03 ... (remaining 2475 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 187 2.58 - 3.16: 11886 3.16 - 3.74: 21298 3.74 - 4.32: 29772 4.32 - 4.90: 49068 Nonbonded interactions: 112211 Sorted by model distance: nonbonded pdb=" O MET C 607 " pdb=" OG1 THR C 611 " model vdw 2.002 3.040 nonbonded pdb=" OG1 THR B 202 " pdb=" OE1 GLN B 360 " model vdw 2.087 3.040 nonbonded pdb=" O PHE D 33 " pdb=" OH TYR D 37 " model vdw 2.113 3.040 nonbonded pdb=" O PHE B 196 " pdb=" OH TYR C 524 " model vdw 2.129 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" O ASN B 89 " model vdw 2.140 3.040 ... (remaining 112206 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.320 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14209 Z= 0.247 Angle : 0.794 12.114 19229 Z= 0.462 Chirality : 0.046 0.330 2134 Planarity : 0.004 0.041 2478 Dihedral : 18.358 89.948 5316 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.55 % Favored : 93.33 % Rotamer: Outliers : 8.00 % Allowed : 20.55 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.75 (0.17), residues: 1710 helix: -2.22 (0.17), residues: 600 sheet: -1.94 (0.24), residues: 385 loop : -2.91 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 461 HIS 0.005 0.001 HIS B 313 PHE 0.017 0.002 PHE B 28 TYR 0.018 0.002 TYR D 37 ARG 0.009 0.001 ARG C 619 Details of bonding type rmsd hydrogen bonds : bond 0.15991 ( 651) hydrogen bonds : angle 7.22473 ( 1860) covalent geometry : bond 0.00532 (14209) covalent geometry : angle 0.79436 (19229) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 302 time to evaluate : 1.436 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 260 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6869 (mt-10) REVERT: A 362 ARG cc_start: 0.7245 (ptm-80) cc_final: 0.6986 (ttp-110) REVERT: A 466 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7696 (mt) REVERT: A 479 ILE cc_start: 0.6328 (OUTLIER) cc_final: 0.6053 (tt) REVERT: A 576 LEU cc_start: 0.8426 (mt) cc_final: 0.7966 (mt) REVERT: A 595 TYR cc_start: 0.8215 (t80) cc_final: 0.7941 (t80) REVERT: A 602 ASN cc_start: 0.8216 (p0) cc_final: 0.7578 (p0) REVERT: B 199 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7831 (p0) REVERT: B 237 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7629 (mm-30) REVERT: B 272 MET cc_start: 0.3994 (mmp) cc_final: 0.3520 (mmm) REVERT: B 376 PHE cc_start: 0.4298 (OUTLIER) cc_final: 0.3909 (p90) REVERT: C 114 LEU cc_start: 0.7356 (mp) cc_final: 0.7108 (mp) REVERT: C 210 GLU cc_start: 0.7999 (mt-10) cc_final: 0.6739 (tm-30) REVERT: C 446 LYS cc_start: 0.7748 (mtpp) cc_final: 0.7530 (mmtm) REVERT: C 619 ARG cc_start: 0.1184 (OUTLIER) cc_final: -0.1496 (mmt180) REVERT: C 622 ARG cc_start: 0.3766 (OUTLIER) cc_final: 0.0642 (mtt90) REVERT: C 628 ASN cc_start: 0.3846 (OUTLIER) cc_final: 0.3260 (t0) outliers start: 123 outliers final: 37 residues processed: 401 average time/residue: 0.2701 time to fit residues: 153.9407 Evaluate side-chains 227 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 chunk 132 optimal weight: 0.6980 chunk 51 optimal weight: 0.0030 chunk 80 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS A 327 GLN A 339 GLN A 358 ASN A 377 GLN A 424 ASN A 520 HIS A 544 HIS B 108 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN B 304 ASN B 417 ASN C 34 GLN C 155 ASN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS C 353 GLN C 476 HIS C 491 ASN ** C 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 HIS C 562 ASN C 602 GLN C 620 ASN D 148 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.231137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.200349 restraints weight = 15370.517| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 2.52 r_work: 0.3731 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14209 Z= 0.160 Angle : 0.697 12.074 19229 Z= 0.361 Chirality : 0.046 0.217 2134 Planarity : 0.005 0.061 2478 Dihedral : 8.152 74.389 1956 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.81 % Allowed : 22.24 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -2.13 (0.19), residues: 1710 helix: -0.44 (0.21), residues: 580 sheet: -1.50 (0.24), residues: 396 loop : -2.09 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 102 HIS 0.013 0.001 HIS C 304 PHE 0.026 0.002 PHE C 641 TYR 0.020 0.002 TYR B 142 ARG 0.004 0.000 ARG C 383 Details of bonding type rmsd hydrogen bonds : bond 0.04970 ( 651) hydrogen bonds : angle 5.52144 ( 1860) covalent geometry : bond 0.00355 (14209) covalent geometry : angle 0.69653 (19229) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 206 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 466 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7686 (mt) REVERT: A 513 ARG cc_start: 0.6140 (ptp-110) cc_final: 0.5831 (ptm160) REVERT: A 576 LEU cc_start: 0.8587 (mt) cc_final: 0.8298 (mt) REVERT: A 602 ASN cc_start: 0.8580 (p0) cc_final: 0.7984 (p0) REVERT: B 272 MET cc_start: 0.4424 (mmp) cc_final: 0.4009 (mmm) REVERT: B 360 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.6581 (tm-30) REVERT: B 376 PHE cc_start: 0.4599 (OUTLIER) cc_final: 0.4176 (p90) REVERT: C 1 MET cc_start: 0.4454 (mtm) cc_final: 0.3986 (mtm) REVERT: C 210 GLU cc_start: 0.7482 (mt-10) cc_final: 0.6894 (tm-30) REVERT: C 474 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6964 (mmm) REVERT: C 619 ARG cc_start: 0.2936 (OUTLIER) cc_final: -0.0954 (mmp-170) REVERT: C 621 GLN cc_start: 0.2820 (OUTLIER) cc_final: 0.1438 (tm-30) REVERT: C 622 ARG cc_start: 0.2316 (OUTLIER) cc_final: -0.0534 (mtt-85) REVERT: C 628 ASN cc_start: 0.4174 (OUTLIER) cc_final: 0.3736 (t0) REVERT: D 9 LEU cc_start: 0.7238 (mt) cc_final: 0.6891 (mt) outliers start: 74 outliers final: 33 residues processed: 264 average time/residue: 0.2471 time to fit residues: 96.2177 Evaluate side-chains 213 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 621 GLN Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 63 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 141 optimal weight: 0.0010 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN A 520 HIS ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 GLN ** C 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.231310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.199489 restraints weight = 15206.272| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 2.58 r_work: 0.3723 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14209 Z= 0.135 Angle : 0.639 12.121 19229 Z= 0.326 Chirality : 0.045 0.222 2134 Planarity : 0.004 0.052 2478 Dihedral : 6.964 69.301 1927 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.36 % Allowed : 24.19 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -1.39 (0.20), residues: 1710 helix: 0.07 (0.21), residues: 611 sheet: -1.05 (0.24), residues: 392 loop : -1.65 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 102 HIS 0.009 0.001 HIS C 150 PHE 0.028 0.002 PHE D 106 TYR 0.018 0.001 TYR B 142 ARG 0.006 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 651) hydrogen bonds : angle 5.08914 ( 1860) covalent geometry : bond 0.00304 (14209) covalent geometry : angle 0.63902 (19229) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 185 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 466 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7652 (mt) REVERT: A 514 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7316 (tp) REVERT: B 252 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7763 (tt) REVERT: B 338 PHE cc_start: 0.7868 (t80) cc_final: 0.7657 (t80) REVERT: B 360 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6467 (tm-30) REVERT: B 376 PHE cc_start: 0.4664 (OUTLIER) cc_final: 0.4275 (p90) REVERT: C 32 ASN cc_start: 0.8059 (m-40) cc_final: 0.7644 (p0) REVERT: C 210 GLU cc_start: 0.7482 (mt-10) cc_final: 0.6862 (tm-30) REVERT: C 597 LEU cc_start: 0.6236 (tt) cc_final: 0.6013 (tt) REVERT: C 621 GLN cc_start: 0.2424 (tp40) cc_final: 0.1209 (tm-30) REVERT: C 622 ARG cc_start: 0.2118 (OUTLIER) cc_final: -0.0561 (mtt-85) outliers start: 67 outliers final: 33 residues processed: 241 average time/residue: 0.2316 time to fit residues: 84.3344 Evaluate side-chains 208 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 106 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 152 optimal weight: 0.0670 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.228794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.192139 restraints weight = 15098.077| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 1.64 r_work: 0.3813 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14209 Z= 0.153 Angle : 0.623 10.223 19229 Z= 0.320 Chirality : 0.045 0.221 2134 Planarity : 0.004 0.054 2478 Dihedral : 6.442 60.993 1913 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.75 % Allowed : 23.73 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -1.10 (0.20), residues: 1710 helix: 0.24 (0.21), residues: 617 sheet: -0.79 (0.25), residues: 378 loop : -1.47 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 102 HIS 0.007 0.001 HIS C 150 PHE 0.020 0.002 PHE C 72 TYR 0.016 0.001 TYR C 102 ARG 0.007 0.000 ARG A 524 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 651) hydrogen bonds : angle 4.96813 ( 1860) covalent geometry : bond 0.00355 (14209) covalent geometry : angle 0.62267 (19229) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 185 time to evaluate : 1.430 Fit side-chains revert: symmetry clash REVERT: A 466 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7627 (mt) REVERT: A 510 PHE cc_start: 0.5210 (OUTLIER) cc_final: 0.4452 (t80) REVERT: A 514 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7212 (tp) REVERT: B 338 PHE cc_start: 0.7755 (t80) cc_final: 0.7396 (t80) REVERT: B 360 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6624 (tm-30) REVERT: B 376 PHE cc_start: 0.4133 (OUTLIER) cc_final: 0.3738 (p90) REVERT: C 17 PHE cc_start: 0.7541 (p90) cc_final: 0.7327 (p90) REVERT: C 32 ASN cc_start: 0.8066 (m-40) cc_final: 0.7775 (p0) REVERT: C 597 LEU cc_start: 0.6258 (tt) cc_final: 0.6043 (tt) REVERT: C 621 GLN cc_start: 0.2612 (tp40) cc_final: 0.1642 (tm-30) REVERT: C 622 ARG cc_start: 0.1583 (OUTLIER) cc_final: -0.0869 (mtt-85) outliers start: 73 outliers final: 47 residues processed: 244 average time/residue: 0.2399 time to fit residues: 88.3747 Evaluate side-chains 222 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 169 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 615 PHE Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 161 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 0.0270 chunk 60 optimal weight: 0.2980 chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN C 269 ASN ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 GLN ** C 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.230107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.198793 restraints weight = 15216.065| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 1.48 r_work: 0.3885 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14209 Z= 0.125 Angle : 0.588 10.051 19229 Z= 0.303 Chirality : 0.044 0.219 2134 Planarity : 0.004 0.052 2478 Dihedral : 6.142 58.445 1911 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.23 % Allowed : 23.99 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.90 (0.20), residues: 1710 helix: 0.37 (0.21), residues: 625 sheet: -0.67 (0.25), residues: 388 loop : -1.35 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 102 HIS 0.008 0.001 HIS C 150 PHE 0.018 0.001 PHE D 106 TYR 0.018 0.001 TYR B 142 ARG 0.009 0.000 ARG A 524 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 651) hydrogen bonds : angle 4.81500 ( 1860) covalent geometry : bond 0.00284 (14209) covalent geometry : angle 0.58811 (19229) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 173 time to evaluate : 1.686 Fit side-chains revert: symmetry clash REVERT: A 466 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7649 (mt) REVERT: A 510 PHE cc_start: 0.4853 (OUTLIER) cc_final: 0.3817 (t80) REVERT: A 641 GLU cc_start: 0.7228 (tt0) cc_final: 0.6802 (tt0) REVERT: B 338 PHE cc_start: 0.7946 (t80) cc_final: 0.7352 (t80) REVERT: B 360 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6421 (tm-30) REVERT: B 376 PHE cc_start: 0.4487 (OUTLIER) cc_final: 0.4092 (p90) REVERT: B 384 MET cc_start: 0.7889 (mtm) cc_final: 0.7438 (mmp) REVERT: C 32 ASN cc_start: 0.8280 (m-40) cc_final: 0.7827 (p0) REVERT: C 75 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7214 (mt-10) REVERT: C 150 HIS cc_start: 0.6070 (t-170) cc_final: 0.5840 (t70) REVERT: C 342 VAL cc_start: 0.7889 (m) cc_final: 0.7615 (p) REVERT: C 556 LYS cc_start: 0.7286 (tttt) cc_final: 0.6904 (tttp) REVERT: C 597 LEU cc_start: 0.6376 (tt) cc_final: 0.6141 (tt) REVERT: C 607 MET cc_start: 0.6185 (tpt) cc_final: 0.5332 (tpt) REVERT: C 621 GLN cc_start: 0.2643 (tp40) cc_final: 0.2409 (tp40) REVERT: C 622 ARG cc_start: 0.2480 (OUTLIER) cc_final: -0.0268 (mtt-85) outliers start: 65 outliers final: 42 residues processed: 227 average time/residue: 0.2394 time to fit residues: 82.2029 Evaluate side-chains 211 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 137 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 141 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 167 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 HIS A 578 GLN C 278 HIS ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.229417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.197663 restraints weight = 15237.478| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 1.48 r_work: 0.3871 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14209 Z= 0.133 Angle : 0.592 10.095 19229 Z= 0.303 Chirality : 0.044 0.207 2134 Planarity : 0.004 0.052 2478 Dihedral : 5.787 53.970 1906 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.16 % Allowed : 24.38 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.74 (0.20), residues: 1710 helix: 0.48 (0.21), residues: 620 sheet: -0.56 (0.25), residues: 394 loop : -1.25 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 102 HIS 0.006 0.001 HIS C 150 PHE 0.016 0.001 PHE C 193 TYR 0.017 0.001 TYR B 247 ARG 0.006 0.000 ARG A 524 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 651) hydrogen bonds : angle 4.78076 ( 1860) covalent geometry : bond 0.00306 (14209) covalent geometry : angle 0.59204 (19229) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 176 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: A 466 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7578 (mt) REVERT: A 510 PHE cc_start: 0.4935 (OUTLIER) cc_final: 0.4134 (t80) REVERT: A 514 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7457 (tp) REVERT: A 641 GLU cc_start: 0.7285 (tt0) cc_final: 0.6826 (tt0) REVERT: B 338 PHE cc_start: 0.8008 (t80) cc_final: 0.7418 (t80) REVERT: B 360 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6424 (tm-30) REVERT: B 376 PHE cc_start: 0.4580 (OUTLIER) cc_final: 0.4352 (p90) REVERT: B 384 MET cc_start: 0.7973 (mtm) cc_final: 0.7524 (mmp) REVERT: C 619 ARG cc_start: 0.3133 (OUTLIER) cc_final: -0.1136 (mmm160) REVERT: C 622 ARG cc_start: 0.2421 (OUTLIER) cc_final: -0.0143 (mtt-85) REVERT: C 649 GLN cc_start: 0.4154 (pt0) cc_final: 0.3043 (mm-40) REVERT: D 67 GLN cc_start: 0.7996 (mp10) cc_final: 0.7747 (mp10) outliers start: 64 outliers final: 45 residues processed: 228 average time/residue: 0.2604 time to fit residues: 90.3397 Evaluate side-chains 221 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 615 PHE Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 91 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 133 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 68 optimal weight: 0.0010 chunk 105 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.229856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.191161 restraints weight = 15181.279| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 1.66 r_work: 0.3821 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14209 Z= 0.127 Angle : 0.591 10.143 19229 Z= 0.301 Chirality : 0.044 0.223 2134 Planarity : 0.004 0.052 2478 Dihedral : 5.712 50.468 1906 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.42 % Allowed : 24.45 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.61 (0.20), residues: 1710 helix: 0.63 (0.22), residues: 619 sheet: -0.43 (0.26), residues: 376 loop : -1.24 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 102 HIS 0.004 0.001 HIS B 313 PHE 0.013 0.001 PHE B 148 TYR 0.016 0.001 TYR B 142 ARG 0.009 0.000 ARG A 524 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 651) hydrogen bonds : angle 4.72516 ( 1860) covalent geometry : bond 0.00295 (14209) covalent geometry : angle 0.59051 (19229) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 167 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 MET cc_start: 0.8232 (tpp) cc_final: 0.8032 (tpt) REVERT: A 466 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7497 (mt) REVERT: A 510 PHE cc_start: 0.5153 (OUTLIER) cc_final: 0.4264 (t80) REVERT: A 517 ARG cc_start: 0.5527 (tpp80) cc_final: 0.5003 (tpp-160) REVERT: A 641 GLU cc_start: 0.6931 (tt0) cc_final: 0.6455 (tt0) REVERT: B 338 PHE cc_start: 0.7842 (t80) cc_final: 0.7344 (t80) REVERT: B 360 GLN cc_start: 0.6883 (OUTLIER) cc_final: 0.6543 (tm-30) REVERT: B 384 MET cc_start: 0.7672 (mtm) cc_final: 0.7337 (mmp) REVERT: C 619 ARG cc_start: 0.2963 (OUTLIER) cc_final: 0.1764 (ppt170) REVERT: C 622 ARG cc_start: 0.1290 (OUTLIER) cc_final: -0.0791 (mtt-85) REVERT: C 649 GLN cc_start: 0.3985 (pt0) cc_final: 0.3174 (mm-40) outliers start: 68 outliers final: 51 residues processed: 222 average time/residue: 0.2444 time to fit residues: 81.3341 Evaluate side-chains 210 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 154 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 45 PHE Chi-restraints excluded: chain D residue 99 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 8 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 162 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 101 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 HIS ** C 279 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 = 0.4569 r_free = 0.4569 target = 0.229700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.200963 restraints weight = 15143.383| |-----------------------------------------------------------------------------| r_work (start): 0.4307 rms_B_bonded: 1.36 r_work: 0.3908 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14209 Z= 0.140 Angle : 0.611 10.182 19229 Z= 0.313 Chirality : 0.045 0.223 2134 Planarity : 0.004 0.052 2478 Dihedral : 5.532 49.597 1902 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.36 % Allowed : 24.97 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1710 helix: 0.65 (0.22), residues: 619 sheet: -0.40 (0.26), residues: 376 loop : -1.14 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 102 HIS 0.004 0.001 HIS A 300 PHE 0.035 0.002 PHE C 180 TYR 0.016 0.001 TYR B 142 ARG 0.008 0.000 ARG A 524 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 651) hydrogen bonds : angle 4.76631 ( 1860) covalent geometry : bond 0.00328 (14209) covalent geometry : angle 0.61065 (19229) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 162 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 ARG cc_start: 0.6569 (ptm160) cc_final: 0.5918 (mtm110) REVERT: A 387 MET cc_start: 0.8286 (tpp) cc_final: 0.8030 (tpt) REVERT: A 466 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7642 (mt) REVERT: A 510 PHE cc_start: 0.5019 (OUTLIER) cc_final: 0.4058 (t80) REVERT: B 55 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7074 (tttp) REVERT: B 360 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6512 (tm-30) REVERT: B 384 MET cc_start: 0.7872 (mtm) cc_final: 0.7475 (mmp) REVERT: C 329 SER cc_start: 0.4049 (OUTLIER) cc_final: 0.3267 (m) REVERT: C 556 LYS cc_start: 0.7349 (tttt) cc_final: 0.7004 (tttm) REVERT: C 619 ARG cc_start: 0.2892 (OUTLIER) cc_final: 0.1756 (ppt170) REVERT: C 622 ARG cc_start: 0.1788 (OUTLIER) cc_final: -0.0655 (mtt-85) REVERT: C 649 GLN cc_start: 0.4561 (pt0) cc_final: 0.3380 (mm-40) outliers start: 67 outliers final: 51 residues processed: 217 average time/residue: 0.2294 time to fit residues: 75.0326 Evaluate side-chains 212 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 154 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 615 PHE Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 168 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 131 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 140 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 120 optimal weight: 0.0370 chunk 159 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 HIS ** C 279 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 = 0.4568 r_free = 0.4568 target = 0.229431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.189705 restraints weight = 15058.142| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 1.63 r_work: 0.3795 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14209 Z= 0.130 Angle : 0.604 9.584 19229 Z= 0.307 Chirality : 0.044 0.224 2134 Planarity : 0.004 0.052 2478 Dihedral : 5.430 49.224 1900 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.84 % Allowed : 25.42 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.43 (0.20), residues: 1710 helix: 0.67 (0.21), residues: 621 sheet: -0.21 (0.26), residues: 371 loop : -1.11 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 102 HIS 0.004 0.001 HIS B 313 PHE 0.034 0.001 PHE C 180 TYR 0.025 0.001 TYR B 247 ARG 0.007 0.000 ARG A 524 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 651) hydrogen bonds : angle 4.73626 ( 1860) covalent geometry : bond 0.00304 (14209) covalent geometry : angle 0.60394 (19229) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 162 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 ARG cc_start: 0.6561 (ptm160) cc_final: 0.5891 (mtm110) REVERT: A 387 MET cc_start: 0.8318 (tpp) cc_final: 0.8103 (tpt) REVERT: A 466 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7675 (mt) REVERT: A 510 PHE cc_start: 0.5014 (OUTLIER) cc_final: 0.4063 (t80) REVERT: B 55 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6927 (tttp) REVERT: B 360 GLN cc_start: 0.6981 (OUTLIER) cc_final: 0.6528 (tm-30) REVERT: B 384 MET cc_start: 0.7997 (mtm) cc_final: 0.7500 (mmp) REVERT: C 145 LYS cc_start: 0.7684 (mtmm) cc_final: 0.7065 (pttm) REVERT: C 474 MET cc_start: 0.7432 (mmm) cc_final: 0.7093 (mmp) REVERT: C 556 LYS cc_start: 0.7394 (tttt) cc_final: 0.7009 (tttm) REVERT: C 622 ARG cc_start: 0.1826 (OUTLIER) cc_final: 0.0076 (mtm180) REVERT: C 649 GLN cc_start: 0.4318 (pt0) cc_final: 0.3245 (mm-40) outliers start: 59 outliers final: 47 residues processed: 210 average time/residue: 0.2384 time to fit residues: 76.5995 Evaluate side-chains 209 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 157 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 45 PHE Chi-restraints excluded: chain D residue 168 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 63 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 HIS ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 GLN ** 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 = 0.4575 r_free = 0.4575 target = 0.230342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.196825 restraints weight = 15051.633| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 1.59 r_work: 0.3859 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14209 Z= 0.123 Angle : 0.600 9.312 19229 Z= 0.306 Chirality : 0.044 0.214 2134 Planarity : 0.004 0.051 2478 Dihedral : 5.335 48.888 1898 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.51 % Allowed : 25.81 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 (0.20), residues: 1710 helix: 0.73 (0.22), residues: 622 sheet: -0.19 (0.26), residues: 371 loop : -1.04 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 102 HIS 0.004 0.001 HIS B 313 PHE 0.029 0.001 PHE C 180 TYR 0.025 0.001 TYR B 247 ARG 0.007 0.000 ARG A 524 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 651) hydrogen bonds : angle 4.69550 ( 1860) covalent geometry : bond 0.00285 (14209) covalent geometry : angle 0.59958 (19229) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 161 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 ARG cc_start: 0.6544 (ptm160) cc_final: 0.6042 (mtm110) REVERT: A 466 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7598 (mt) REVERT: A 510 PHE cc_start: 0.5125 (OUTLIER) cc_final: 0.4392 (t80) REVERT: B 55 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6786 (tttp) REVERT: B 384 MET cc_start: 0.7742 (mtm) cc_final: 0.7391 (mmp) REVERT: C 136 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.6898 (mp10) REVERT: C 145 LYS cc_start: 0.7059 (mtmm) cc_final: 0.6692 (pttm) REVERT: C 474 MET cc_start: 0.7147 (mmm) cc_final: 0.6800 (mmp) REVERT: C 556 LYS cc_start: 0.7207 (tttt) cc_final: 0.6755 (tttp) REVERT: C 619 ARG cc_start: 0.2605 (OUTLIER) cc_final: -0.1195 (mmm160) REVERT: C 622 ARG cc_start: 0.0793 (OUTLIER) cc_final: -0.1058 (mtm180) REVERT: C 649 GLN cc_start: 0.3806 (pt0) cc_final: 0.3397 (mm-40) outliers start: 54 outliers final: 43 residues processed: 205 average time/residue: 0.2377 time to fit residues: 73.3890 Evaluate side-chains 207 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 45 PHE Chi-restraints excluded: chain D residue 168 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.6078 > 50: distance: 25 - 95: 29.684 distance: 28 - 92: 25.666 distance: 61 - 68: 33.877 distance: 68 - 69: 41.960 distance: 69 - 70: 52.567 distance: 69 - 72: 32.906 distance: 70 - 76: 29.687 distance: 72 - 73: 35.628 distance: 73 - 74: 49.096 distance: 73 - 75: 35.018 distance: 76 - 77: 11.225 distance: 76 - 82: 39.763 distance: 77 - 78: 42.366 distance: 77 - 80: 53.652 distance: 78 - 79: 36.853 distance: 78 - 83: 57.435 distance: 80 - 81: 43.593 distance: 81 - 82: 48.963 distance: 83 - 84: 6.256 distance: 84 - 85: 26.536 distance: 84 - 87: 18.771 distance: 85 - 86: 34.498 distance: 85 - 92: 20.406 distance: 87 - 88: 12.129 distance: 88 - 89: 40.159 distance: 89 - 90: 50.272 distance: 90 - 91: 18.968 distance: 92 - 93: 25.223 distance: 93 - 94: 27.391 distance: 93 - 96: 27.599 distance: 94 - 95: 43.007 distance: 94 - 103: 56.996 distance: 96 - 97: 32.751 distance: 97 - 98: 14.540 distance: 97 - 99: 17.229 distance: 98 - 100: 10.987 distance: 99 - 101: 15.644 distance: 100 - 102: 21.164 distance: 101 - 102: 27.318 distance: 103 - 104: 11.724 distance: 104 - 105: 27.252 distance: 104 - 107: 38.004 distance: 105 - 106: 14.740 distance: 105 - 112: 11.784 distance: 107 - 108: 41.297 distance: 108 - 109: 42.033 distance: 109 - 110: 12.235 distance: 109 - 111: 39.251 distance: 112 - 113: 6.395 distance: 113 - 114: 9.470 distance: 113 - 116: 14.640 distance: 114 - 115: 29.744 distance: 114 - 120: 29.592 distance: 116 - 117: 23.953 distance: 116 - 118: 20.917 distance: 120 - 121: 11.273 distance: 121 - 122: 26.544 distance: 121 - 124: 16.304 distance: 122 - 129: 40.433 distance: 124 - 125: 9.585 distance: 125 - 126: 18.244 distance: 126 - 127: 6.558 distance: 126 - 128: 26.840 distance: 129 - 130: 32.660 distance: 130 - 131: 56.658 distance: 130 - 133: 38.475 distance: 131 - 132: 23.108 distance: 131 - 137: 43.168 distance: 133 - 134: 44.864 distance: 134 - 135: 29.412 distance: 134 - 136: 18.260 distance: 137 - 138: 15.326 distance: 137 - 143: 10.448 distance: 138 - 139: 34.059 distance: 138 - 141: 34.311 distance: 139 - 140: 32.191 distance: 139 - 144: 51.740 distance: 141 - 142: 18.414 distance: 142 - 143: 41.785 distance: 144 - 145: 51.014 distance: 145 - 146: 32.180 distance: 145 - 148: 47.006 distance: 146 - 147: 26.608 distance: 146 - 149: 21.474