Starting phenix.real_space_refine on Wed Nov 19 03:49:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dmw_7967/11_2025/6dmw_7967_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dmw_7967/11_2025/6dmw_7967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dmw_7967/11_2025/6dmw_7967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dmw_7967/11_2025/6dmw_7967.map" model { file = "/net/cci-nas-00/data/ceres_data/6dmw_7967/11_2025/6dmw_7967_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dmw_7967/11_2025/6dmw_7967_neut.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 148 5.16 5 C 13254 2.51 5 N 3476 2.21 5 O 3665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20546 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5076 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 25, 'TRANS': 605} Chain breaks: 2 Chain: "E" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 908 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 2 Chain: "B" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4844 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 24, 'TRANS': 580} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4862 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 24, 'TRANS': 582} Chain breaks: 1 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.06, per 1000 atoms: 0.25 Number of scatterers: 20546 At special positions: 0 Unit cell: (134.2, 133.1, 127.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 148 16.00 O 3665 8.00 N 3476 7.00 C 13254 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: 1.63 Conformation dependent library (CDL) restraints added in 738.5 milliseconds 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4834 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 8 sheets defined 71.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 81 through 90 removed outlier: 3.555A pdb=" N VAL A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.766A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.569A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.919A pdb=" N ASN A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 209 through 222 removed outlier: 3.808A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.760A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 262 removed outlier: 4.487A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.598A pdb=" N ASP A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 285' Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.564A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 removed outlier: 3.984A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.614A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 3.856A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 410 removed outlier: 3.758A pdb=" N VAL A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Proline residue: A 405 - end of helix removed outlier: 3.610A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 422 through 445 removed outlier: 3.693A pdb=" N VAL A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.950A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.724A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 472 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.727A pdb=" N THR A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 488 " --> pdb=" O LYS A 484 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 489 " --> pdb=" O MET A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 513 removed outlier: 4.188A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 removed outlier: 3.729A pdb=" N LEU A 520 " --> pdb=" O ASP A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 4.108A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 567 Processing helix chain 'A' and resid 569 through 586 removed outlier: 3.714A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 581 " --> pdb=" O MET A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 608 removed outlier: 4.163A pdb=" N GLU A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 597 " --> pdb=" O TRP A 593 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.711A pdb=" N LEU A 612 " --> pdb=" O PRO A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 652 removed outlier: 4.086A pdb=" N VAL A 644 " --> pdb=" O ASN A 640 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR A 647 " --> pdb=" O ARG A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 709 removed outlier: 3.549A pdb=" N ILE A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 21 Processing helix chain 'E' and resid 29 through 40 removed outlier: 3.545A pdb=" N VAL E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER E 39 " --> pdb=" O THR E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 75 removed outlier: 3.793A pdb=" N ARG E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 94 removed outlier: 3.537A pdb=" N VAL E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 114 Processing helix chain 'E' and resid 119 through 130 removed outlier: 3.515A pdb=" N ASP E 123 " --> pdb=" O ASP E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 147 removed outlier: 3.523A pdb=" N MET E 145 " --> pdb=" O GLU E 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.613A pdb=" N ARG B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 Processing helix chain 'B' and resid 81 through 90 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.929A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.558A pdb=" N PHE B 169 " --> pdb=" O HIS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.857A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 removed outlier: 3.894A pdb=" N ASN B 197 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 209 through 223 removed outlier: 4.126A pdb=" N CYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 262 removed outlier: 4.077A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.761A pdb=" N SER B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 303 through 308 removed outlier: 3.662A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 324 removed outlier: 3.576A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 removed outlier: 4.004A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 410 removed outlier: 3.518A pdb=" N ASN B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Proline residue: B 405 - end of helix removed outlier: 4.177A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.789A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 removed outlier: 4.166A pdb=" N MET B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.567A pdb=" N LEU B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 471 removed outlier: 3.728A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.860A pdb=" N PHE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP B 489 " --> pdb=" O MET B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 513 removed outlier: 4.286A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.730A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 567 removed outlier: 4.019A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 removed outlier: 3.914A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR B 581 " --> pdb=" O MET B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 608 removed outlier: 4.019A pdb=" N GLU B 591 " --> pdb=" O GLN B 587 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 597 " --> pdb=" O TRP B 593 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 600 " --> pdb=" O GLN B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.745A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.835A pdb=" N GLU C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ALA C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.898A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.516A pdb=" N PHE C 169 " --> pdb=" O HIS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.603A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 removed outlier: 3.771A pdb=" N ASN C 197 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 209 through 223 removed outlier: 3.704A pdb=" N CYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.657A pdb=" N VAL C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.673A pdb=" N SER C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.745A pdb=" N ILE C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 308' Processing helix chain 'C' and resid 310 through 324 Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.522A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 Processing helix chain 'C' and resid 379 through 410 removed outlier: 4.023A pdb=" N ILE C 398 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE C 399 " --> pdb=" O GLY C 395 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU C 400 " --> pdb=" O ALA C 396 " (cutoff:3.500A) Proline residue: C 405 - end of helix removed outlier: 3.900A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.894A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 removed outlier: 3.548A pdb=" N ILE C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 429 " --> pdb=" O PHE C 425 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 431 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET C 440 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.527A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 471 removed outlier: 3.805A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.920A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP C 489 " --> pdb=" O MET C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 512 removed outlier: 4.148A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 521 Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.852A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 567 removed outlier: 4.415A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 586 Processing helix chain 'C' and resid 587 through 608 removed outlier: 4.165A pdb=" N GLU C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.656A pdb=" N ASP D 34 " --> pdb=" O GLU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.869A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.825A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 removed outlier: 3.591A pdb=" N ASN D 197 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 209 through 223 removed outlier: 4.147A pdb=" N CYS D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 263 removed outlier: 4.133A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 4.024A pdb=" N SER D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.933A pdb=" N ARG D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 310 through 324 removed outlier: 3.797A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.635A pdb=" N ILE D 341 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE D 343 " --> pdb=" O TYR D 339 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR D 349 " --> pdb=" O THR D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 Processing helix chain 'D' and resid 379 through 404 removed outlier: 3.521A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE D 398 " --> pdb=" O THR D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 410 removed outlier: 4.228A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 404 through 410' Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 422 through 445 removed outlier: 3.719A pdb=" N ILE D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N MET D 440 " --> pdb=" O VAL D 436 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET D 442 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG D 443 " --> pdb=" O THR D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 463 removed outlier: 3.908A pdb=" N LEU D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS D 463 " --> pdb=" O VAL D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 471 removed outlier: 5.037A pdb=" N TYR D 467 " --> pdb=" O SER D 464 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.871A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 513 removed outlier: 3.669A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 498 " --> pdb=" O CYS D 494 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 521 removed outlier: 3.735A pdb=" N LEU D 520 " --> pdb=" O ASP D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.969A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 586 removed outlier: 4.993A pdb=" N LEU D 568 " --> pdb=" O ILE D 564 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU D 569 " --> pdb=" O ILE D 565 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET D 570 " --> pdb=" O ALA D 566 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 608 removed outlier: 4.259A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA D 599 " --> pdb=" O ALA D 595 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET D 608 " --> pdb=" O LEU D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 removed outlier: 3.519A pdb=" N LEU D 612 " --> pdb=" O PRO D 609 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.807A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.776A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 618 " --> pdb=" O PHE B 630 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.858A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN C 635 " --> pdb=" O THR C 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 353 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.938A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR D 274 " --> pdb=" O ASN D 635 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1110 hydrogen bonds defined for protein. 3216 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.17 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6559 1.34 - 1.46: 4015 1.46 - 1.57: 10187 1.57 - 1.69: 0 1.69 - 1.81: 244 Bond restraints: 21005 Sorted by residual: bond pdb=" CB TRP A 583 " pdb=" CG TRP A 583 " ideal model delta sigma weight residual 1.498 1.440 0.058 3.10e-02 1.04e+03 3.55e+00 bond pdb=" CG1 ILE C 501 " pdb=" CD1 ILE C 501 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.29e+00 bond pdb=" CB TRP A 613 " pdb=" CG TRP A 613 " ideal model delta sigma weight residual 1.498 1.442 0.056 3.10e-02 1.04e+03 3.27e+00 bond pdb=" CB PHE B 508 " pdb=" CG PHE B 508 " ideal model delta sigma weight residual 1.502 1.465 0.037 2.30e-02 1.89e+03 2.58e+00 bond pdb=" C GLY B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 1.331 1.319 0.012 7.90e-03 1.60e+04 2.42e+00 ... (remaining 21000 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 27014 2.04 - 4.07: 1236 4.07 - 6.11: 183 6.11 - 8.14: 44 8.14 - 10.18: 17 Bond angle restraints: 28494 Sorted by residual: angle pdb=" N ILE D 510 " pdb=" CA ILE D 510 " pdb=" C ILE D 510 " ideal model delta sigma weight residual 111.91 106.96 4.95 8.90e-01 1.26e+00 3.10e+01 angle pdb=" C ASN B 127 " pdb=" N GLN B 128 " pdb=" CA GLN B 128 " ideal model delta sigma weight residual 122.08 127.43 -5.35 1.47e+00 4.63e-01 1.33e+01 angle pdb=" N THR C 311 " pdb=" CA THR C 311 " pdb=" C THR C 311 " ideal model delta sigma weight residual 112.75 117.60 -4.85 1.36e+00 5.41e-01 1.27e+01 angle pdb=" N GLY A 476 " pdb=" CA GLY A 476 " pdb=" C GLY A 476 " ideal model delta sigma weight residual 112.34 119.40 -7.06 2.04e+00 2.40e-01 1.20e+01 angle pdb=" C GLY B 521 " pdb=" N GLU B 522 " pdb=" CA GLU B 522 " ideal model delta sigma weight residual 121.54 128.13 -6.59 1.91e+00 2.74e-01 1.19e+01 ... (remaining 28489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 11549 15.07 - 30.13: 708 30.13 - 45.20: 222 45.20 - 60.26: 15 60.26 - 75.33: 15 Dihedral angle restraints: 12509 sinusoidal: 5034 harmonic: 7475 Sorted by residual: dihedral pdb=" CA ASP B 193 " pdb=" C ASP B 193 " pdb=" N SER B 194 " pdb=" CA SER B 194 " ideal model delta harmonic sigma weight residual 180.00 152.06 27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA GLU A 164 " pdb=" C GLU A 164 " pdb=" N HIS A 165 " pdb=" CA HIS A 165 " ideal model delta harmonic sigma weight residual -180.00 -154.35 -25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA GLU D 164 " pdb=" C GLU D 164 " pdb=" N HIS D 165 " pdb=" CA HIS D 165 " ideal model delta harmonic sigma weight residual -180.00 -154.53 -25.47 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 12506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2354 0.056 - 0.112: 704 0.112 - 0.167: 153 0.167 - 0.223: 21 0.223 - 0.279: 4 Chirality restraints: 3236 Sorted by residual: chirality pdb=" CG LEU C 352 " pdb=" CB LEU C 352 " pdb=" CD1 LEU C 352 " pdb=" CD2 LEU C 352 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB ILE D 510 " pdb=" CA ILE D 510 " pdb=" CG1 ILE D 510 " pdb=" CG2 ILE D 510 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE B 183 " pdb=" CA ILE B 183 " pdb=" CG1 ILE B 183 " pdb=" CG2 ILE B 183 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 3233 not shown) Planarity restraints: 3618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 311 " -0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO A 312 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 585 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.87e+00 pdb=" C VAL D 585 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL D 585 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA D 586 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 623 " -0.024 2.00e-02 2.50e+03 1.68e-02 5.65e+00 pdb=" CG TYR D 623 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR D 623 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR D 623 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 623 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 623 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 623 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 623 " -0.001 2.00e-02 2.50e+03 ... (remaining 3615 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5158 2.78 - 3.31: 20475 3.31 - 3.84: 34703 3.84 - 4.37: 38378 4.37 - 4.90: 61439 Nonbonded interactions: 160153 Sorted by model distance: nonbonded pdb=" N VAL B 378 " pdb=" OD2 ASP B 382 " model vdw 2.253 3.120 nonbonded pdb=" OH TYR A 339 " pdb=" O THR A 392 " model vdw 2.268 3.040 nonbonded pdb=" O HIS D 165 " pdb=" OG SER D 168 " model vdw 2.278 3.040 nonbonded pdb=" NH2 ARG A 359 " pdb=" O THR A 366 " model vdw 2.284 3.120 nonbonded pdb=" O ALA A 563 " pdb=" OG1 THR A 567 " model vdw 2.285 3.040 ... (remaining 160148 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 29 through 225 or resid 231 through 638)) selection = chain 'B' selection = (chain 'C' and (resid 29 through 225 or resid 231 through 638)) selection = (chain 'D' and (resid 29 through 225 or resid 231 through 638)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.510 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 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 : 0.006 0.071 21005 Z= 0.308 Angle : 1.017 10.179 28494 Z= 0.548 Chirality : 0.055 0.279 3236 Planarity : 0.007 0.069 3618 Dihedral : 11.364 75.325 7675 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.18 % Allowed : 7.76 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.13), residues: 2538 helix: -2.13 (0.10), residues: 1544 sheet: -3.32 (0.56), residues: 58 loop : -2.08 (0.17), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 615 TYR 0.040 0.003 TYR D 623 PHE 0.037 0.003 PHE A 508 TRP 0.030 0.003 TRP A 613 HIS 0.013 0.003 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00638 (21005) covalent geometry : angle 1.01655 (28494) hydrogen bonds : bond 0.16054 ( 1110) hydrogen bonds : angle 6.65201 ( 3216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 680 time to evaluate : 0.756 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 VAL cc_start: 0.9390 (t) cc_final: 0.9106 (p) REVERT: A 197 ASN cc_start: 0.8779 (m110) cc_final: 0.8469 (t0) REVERT: A 255 MET cc_start: 0.8276 (tpp) cc_final: 0.7782 (tpp) REVERT: A 294 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8282 (pt0) REVERT: A 340 MET cc_start: 0.7812 (tpp) cc_final: 0.7570 (tpp) REVERT: A 445 THR cc_start: 0.5967 (p) cc_final: 0.5730 (p) REVERT: A 447 MET cc_start: 0.4455 (tpt) cc_final: 0.4198 (tpt) REVERT: A 464 SER cc_start: 0.9286 (t) cc_final: 0.8850 (p) REVERT: A 520 LEU cc_start: 0.4410 (pp) cc_final: 0.3617 (pp) REVERT: A 535 GLU cc_start: 0.6710 (mt-10) cc_final: 0.6423 (mt-10) REVERT: A 546 ASN cc_start: 0.7615 (m-40) cc_final: 0.7214 (t0) REVERT: A 553 PHE cc_start: 0.8384 (t80) cc_final: 0.7920 (t80) REVERT: A 577 MET cc_start: 0.8671 (tmm) cc_final: 0.8383 (tmm) REVERT: A 591 GLU cc_start: 0.8281 (tt0) cc_final: 0.7966 (tm-30) REVERT: A 643 ARG cc_start: 0.7416 (mtp180) cc_final: 0.6910 (ptt180) REVERT: E 37 MET cc_start: 0.6491 (mmm) cc_final: 0.5728 (tpt) REVERT: E 76 LYS cc_start: 0.7997 (tppt) cc_final: 0.7794 (tptp) REVERT: E 101 ILE cc_start: 0.5195 (mt) cc_final: 0.4910 (mt) REVERT: E 110 MET cc_start: 0.5985 (tpp) cc_final: 0.5728 (mmt) REVERT: E 125 MET cc_start: 0.7391 (mtp) cc_final: 0.7097 (mmp) REVERT: E 138 ASN cc_start: 0.6462 (p0) cc_final: 0.5890 (p0) REVERT: E 139 TYR cc_start: 0.7530 (t80) cc_final: 0.7267 (t80) REVERT: E 146 MET cc_start: 0.2885 (mmm) cc_final: 0.1894 (mmt) REVERT: B 91 ASN cc_start: 0.6891 (m-40) cc_final: 0.6219 (m110) REVERT: B 162 TYR cc_start: 0.8006 (m-10) cc_final: 0.7805 (m-10) REVERT: B 183 ILE cc_start: 0.7953 (mt) cc_final: 0.7466 (mm) REVERT: B 208 ASN cc_start: 0.8125 (p0) cc_final: 0.7242 (p0) REVERT: B 294 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8840 (pt0) REVERT: B 306 GLN cc_start: 0.7932 (tt0) cc_final: 0.7626 (tp40) REVERT: B 389 GLU cc_start: 0.7558 (tt0) cc_final: 0.7084 (tm-30) REVERT: B 444 LEU cc_start: 0.9018 (mt) cc_final: 0.8711 (mm) REVERT: B 546 ASN cc_start: 0.8349 (m-40) cc_final: 0.7688 (t0) REVERT: B 580 ASP cc_start: 0.5012 (t0) cc_final: 0.3919 (t0) REVERT: B 638 ASP cc_start: 0.6674 (m-30) cc_final: 0.6468 (m-30) REVERT: C 368 LEU cc_start: 0.7994 (tp) cc_final: 0.7585 (tp) REVERT: C 389 GLU cc_start: 0.8503 (tt0) cc_final: 0.8231 (tm-30) REVERT: C 580 ASP cc_start: 0.5755 (t0) cc_final: 0.4874 (t70) REVERT: C 583 TRP cc_start: 0.7621 (t60) cc_final: 0.6996 (t60) REVERT: C 603 MET cc_start: 0.8066 (tmt) cc_final: 0.7852 (tmm) REVERT: D 65 LEU cc_start: 0.9372 (mm) cc_final: 0.9061 (mm) REVERT: D 467 TYR cc_start: 0.6830 (t80) cc_final: 0.6582 (t80) REVERT: D 474 MET cc_start: 0.7380 (ptt) cc_final: 0.7105 (ptm) REVERT: D 499 VAL cc_start: 0.7092 (t) cc_final: 0.6830 (p) REVERT: D 520 LEU cc_start: 0.3932 (pp) cc_final: 0.3410 (pp) REVERT: D 568 LEU cc_start: 0.6685 (pt) cc_final: 0.6485 (pt) outliers start: 4 outliers final: 0 residues processed: 681 average time/residue: 0.1563 time to fit residues: 161.5078 Evaluate side-chains 358 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0370 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 230 GLN A 257 GLN A 426 HIS A 639 GLN B 37 ASN B 513 GLN B 636 HIS C 84 HIS C 206 GLN C 267 GLN C 513 GLN D 84 HIS D 192 GLN D 206 GLN D 636 HIS D 637 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.089525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.076011 restraints weight = 66184.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.077856 restraints weight = 38630.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.079099 restraints weight = 25678.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.079964 restraints weight = 19055.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.080496 restraints weight = 15318.901| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 21005 Z= 0.143 Angle : 0.654 10.308 28494 Z= 0.334 Chirality : 0.039 0.149 3236 Planarity : 0.005 0.053 3618 Dihedral : 5.313 24.765 2792 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.05 % Allowed : 3.11 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.15), residues: 2538 helix: -0.40 (0.12), residues: 1604 sheet: -2.75 (0.57), residues: 61 loop : -1.97 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG D 615 TYR 0.018 0.001 TYR A 547 PHE 0.026 0.002 PHE A 456 TRP 0.048 0.002 TRP B 613 HIS 0.005 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00317 (21005) covalent geometry : angle 0.65398 (28494) hydrogen bonds : bond 0.04715 ( 1110) hydrogen bonds : angle 4.64021 ( 3216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 470 time to evaluate : 0.802 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: symmetry clash REVERT: A 91 ASN cc_start: 0.8790 (m-40) cc_final: 0.8519 (m110) REVERT: A 99 MET cc_start: 0.9003 (mtm) cc_final: 0.8379 (mtp) REVERT: A 340 MET cc_start: 0.9241 (tpp) cc_final: 0.9031 (tpp) REVERT: E 37 MET cc_start: 0.6532 (mmm) cc_final: 0.5183 (tpt) REVERT: E 76 LYS cc_start: 0.9294 (tppt) cc_final: 0.9072 (tppt) REVERT: E 101 ILE cc_start: 0.8023 (mt) cc_final: 0.7775 (mt) REVERT: E 111 THR cc_start: 0.8412 (m) cc_final: 0.8199 (m) REVERT: E 113 LEU cc_start: 0.7392 (tp) cc_final: 0.6644 (tp) REVERT: E 128 GLU cc_start: 0.7308 (tt0) cc_final: 0.7067 (tt0) REVERT: B 216 TYR cc_start: 0.9055 (t80) cc_final: 0.8767 (t80) REVERT: B 261 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8880 (tm-30) REVERT: B 389 GLU cc_start: 0.7974 (tt0) cc_final: 0.7365 (tm-30) REVERT: B 440 MET cc_start: 0.8517 (tmm) cc_final: 0.8178 (tmm) REVERT: B 580 ASP cc_start: 0.6595 (t0) cc_final: 0.6024 (t70) REVERT: C 202 ILE cc_start: 0.9372 (pt) cc_final: 0.9061 (tp) REVERT: C 260 MET cc_start: 0.8922 (tpp) cc_final: 0.8575 (tpp) REVERT: C 340 MET cc_start: 0.8953 (tpp) cc_final: 0.8666 (mmm) REVERT: C 440 MET cc_start: 0.8786 (ppp) cc_final: 0.8545 (ppp) REVERT: C 480 ILE cc_start: 0.9190 (pt) cc_final: 0.8966 (mp) REVERT: D 466 MET cc_start: 0.9474 (mmp) cc_final: 0.9085 (mmt) REVERT: D 497 MET cc_start: 0.8543 (tpt) cc_final: 0.8316 (tpp) REVERT: D 578 MET cc_start: 0.8649 (tpt) cc_final: 0.7883 (tpp) outliers start: 1 outliers final: 0 residues processed: 471 average time/residue: 0.1398 time to fit residues: 103.5481 Evaluate side-chains 288 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 249 optimal weight: 9.9990 chunk 186 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 139 optimal weight: 20.0000 chunk 217 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 201 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 ASN B 158 ASN B 513 GLN C 513 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.082911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.068904 restraints weight = 69097.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.070557 restraints weight = 40878.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.071691 restraints weight = 27794.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.072407 restraints weight = 20988.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.073026 restraints weight = 17247.590| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21005 Z= 0.200 Angle : 0.685 8.039 28494 Z= 0.352 Chirality : 0.041 0.167 3236 Planarity : 0.005 0.065 3618 Dihedral : 4.922 23.155 2792 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.05 % Allowed : 4.38 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.16), residues: 2538 helix: 0.39 (0.12), residues: 1592 sheet: -2.15 (0.55), residues: 65 loop : -1.73 (0.19), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 385 TYR 0.023 0.002 TYR A 547 PHE 0.023 0.002 PHE B 523 TRP 0.029 0.002 TRP D 629 HIS 0.008 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00447 (21005) covalent geometry : angle 0.68466 (28494) hydrogen bonds : bond 0.05012 ( 1110) hydrogen bonds : angle 4.51175 ( 3216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 379 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.8904 (m-40) cc_final: 0.8504 (m110) REVERT: A 99 MET cc_start: 0.9132 (mtm) cc_final: 0.8362 (mtp) REVERT: A 176 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8279 (mm-30) REVERT: A 197 ASN cc_start: 0.7499 (m110) cc_final: 0.7247 (m-40) REVERT: A 368 LEU cc_start: 0.8793 (mm) cc_final: 0.8107 (mm) REVERT: A 442 MET cc_start: 0.8853 (tpp) cc_final: 0.8213 (tmm) REVERT: A 497 MET cc_start: 0.9010 (tpp) cc_final: 0.8559 (tpp) REVERT: A 577 MET cc_start: 0.8259 (tmm) cc_final: 0.8035 (tmm) REVERT: A 578 MET cc_start: 0.8655 (tpt) cc_final: 0.8338 (tpt) REVERT: A 643 ARG cc_start: 0.8279 (ptt180) cc_final: 0.7981 (ptt180) REVERT: E 37 MET cc_start: 0.6628 (mmm) cc_final: 0.5184 (tpt) REVERT: E 90 PHE cc_start: 0.8841 (t80) cc_final: 0.8492 (t80) REVERT: E 110 MET cc_start: 0.8091 (mmt) cc_final: 0.7765 (mmt) REVERT: B 91 ASN cc_start: 0.8306 (m-40) cc_final: 0.8069 (m-40) REVERT: B 389 GLU cc_start: 0.8104 (tt0) cc_final: 0.7432 (tm-30) REVERT: B 466 MET cc_start: 0.8773 (mmp) cc_final: 0.8321 (mmm) REVERT: B 580 ASP cc_start: 0.7780 (t0) cc_final: 0.7287 (t70) REVERT: C 202 ILE cc_start: 0.9394 (pt) cc_final: 0.9137 (tp) REVERT: C 267 GLN cc_start: 0.8950 (tt0) cc_final: 0.8665 (tt0) REVERT: C 302 ARG cc_start: 0.7907 (mtp-110) cc_final: 0.7644 (ptp90) REVERT: C 440 MET cc_start: 0.8884 (ppp) cc_final: 0.8579 (ppp) REVERT: C 480 ILE cc_start: 0.9364 (pt) cc_final: 0.9095 (mm) REVERT: C 537 PHE cc_start: 0.8774 (t80) cc_final: 0.8329 (t80) REVERT: D 340 MET cc_start: 0.9546 (tpp) cc_final: 0.9213 (tpp) REVERT: D 485 MET cc_start: 0.8254 (tpp) cc_final: 0.7859 (tpp) outliers start: 1 outliers final: 0 residues processed: 380 average time/residue: 0.1282 time to fit residues: 78.8530 Evaluate side-chains 259 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 138 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 chunk 231 optimal weight: 0.0770 chunk 149 optimal weight: 10.0000 chunk 157 optimal weight: 0.0970 chunk 235 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 210 optimal weight: 0.0060 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 overall best weight: 0.7954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 708 ASN B 37 ASN B 513 GLN B 636 HIS C 418 GLN C 513 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.086887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.072779 restraints weight = 67245.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.074532 restraints weight = 39674.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.075715 restraints weight = 26649.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.076479 restraints weight = 19898.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.076894 restraints weight = 16221.013| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21005 Z= 0.115 Angle : 0.597 8.113 28494 Z= 0.300 Chirality : 0.038 0.153 3236 Planarity : 0.004 0.051 3618 Dihedral : 4.656 23.081 2792 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.16), residues: 2538 helix: 0.82 (0.13), residues: 1588 sheet: -1.74 (0.55), residues: 65 loop : -1.59 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 707 TYR 0.023 0.001 TYR D 162 PHE 0.025 0.001 PHE C 574 TRP 0.027 0.001 TRP A 583 HIS 0.006 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00236 (21005) covalent geometry : angle 0.59731 (28494) hydrogen bonds : bond 0.04006 ( 1110) hydrogen bonds : angle 4.16595 ( 3216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.8871 (m-40) cc_final: 0.8572 (m110) REVERT: A 99 MET cc_start: 0.9208 (mtm) cc_final: 0.8510 (mtp) REVERT: A 127 ASN cc_start: 0.8458 (m-40) cc_final: 0.7500 (t0) REVERT: A 368 LEU cc_start: 0.8648 (mm) cc_final: 0.7983 (mm) REVERT: A 442 MET cc_start: 0.8855 (tpp) cc_final: 0.8486 (tpp) REVERT: A 577 MET cc_start: 0.8170 (tmm) cc_final: 0.7908 (tmm) REVERT: A 643 ARG cc_start: 0.8227 (ptt180) cc_final: 0.8000 (ptt180) REVERT: E 37 MET cc_start: 0.6348 (mmm) cc_final: 0.4879 (tpt) REVERT: E 90 PHE cc_start: 0.8910 (t80) cc_final: 0.8403 (t80) REVERT: E 92 VAL cc_start: 0.8853 (t) cc_final: 0.8552 (p) REVERT: B 91 ASN cc_start: 0.8120 (m-40) cc_final: 0.7788 (m-40) REVERT: B 389 GLU cc_start: 0.8023 (tt0) cc_final: 0.7479 (tm-30) REVERT: B 466 MET cc_start: 0.8440 (mmp) cc_final: 0.8038 (mmm) REVERT: B 497 MET cc_start: 0.9208 (tpp) cc_final: 0.8931 (tpp) REVERT: B 535 GLU cc_start: 0.8264 (mp0) cc_final: 0.7937 (mp0) REVERT: C 260 MET cc_start: 0.8967 (tpp) cc_final: 0.8584 (tpp) REVERT: C 302 ARG cc_start: 0.7723 (mtp-110) cc_final: 0.7471 (ptp90) REVERT: C 440 MET cc_start: 0.8884 (ppp) cc_final: 0.8554 (ppp) REVERT: C 537 PHE cc_start: 0.8193 (t80) cc_final: 0.7983 (t80) REVERT: C 592 LEU cc_start: 0.9480 (mt) cc_final: 0.9139 (mt) REVERT: D 91 ASN cc_start: 0.8463 (m-40) cc_final: 0.8250 (m-40) REVERT: D 340 MET cc_start: 0.9539 (tpp) cc_final: 0.9277 (tpp) REVERT: D 608 MET cc_start: 0.8961 (mmm) cc_final: 0.8513 (mtp) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.1269 time to fit residues: 79.9925 Evaluate side-chains 269 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 218 optimal weight: 20.0000 chunk 164 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 167 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 HIS B 37 ASN B 513 GLN C 418 GLN C 513 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.084545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.070417 restraints weight = 68051.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.072071 restraints weight = 40312.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.073235 restraints weight = 27370.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.073985 restraints weight = 20555.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.074569 restraints weight = 16821.592| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21005 Z= 0.137 Angle : 0.609 7.811 28494 Z= 0.308 Chirality : 0.039 0.155 3236 Planarity : 0.004 0.036 3618 Dihedral : 4.478 21.204 2792 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.16), residues: 2538 helix: 1.03 (0.13), residues: 1583 sheet: -1.81 (0.56), residues: 63 loop : -1.44 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 606 TYR 0.017 0.001 TYR A 526 PHE 0.026 0.001 PHE E 20 TRP 0.023 0.001 TRP A 583 HIS 0.006 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00310 (21005) covalent geometry : angle 0.60884 (28494) hydrogen bonds : bond 0.04089 ( 1110) hydrogen bonds : angle 4.12102 ( 3216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.8875 (m-40) cc_final: 0.8530 (m110) REVERT: A 99 MET cc_start: 0.9216 (mtm) cc_final: 0.8473 (mtp) REVERT: A 162 TYR cc_start: 0.8192 (m-10) cc_final: 0.7955 (m-10) REVERT: A 368 LEU cc_start: 0.8572 (mm) cc_final: 0.7911 (mm) REVERT: A 577 MET cc_start: 0.8239 (tmm) cc_final: 0.8022 (tmm) REVERT: A 603 MET cc_start: 0.8355 (mmt) cc_final: 0.7814 (tmm) REVERT: A 627 ASP cc_start: 0.8416 (m-30) cc_final: 0.7830 (t0) REVERT: A 643 ARG cc_start: 0.8332 (ptt180) cc_final: 0.7765 (ptt180) REVERT: E 37 MET cc_start: 0.6342 (mmm) cc_final: 0.4987 (tpt) REVERT: E 90 PHE cc_start: 0.8915 (t80) cc_final: 0.8301 (t80) REVERT: E 101 ILE cc_start: 0.8048 (mt) cc_final: 0.7772 (mp) REVERT: B 91 ASN cc_start: 0.8273 (m-40) cc_final: 0.7893 (m-40) REVERT: B 389 GLU cc_start: 0.7961 (tt0) cc_final: 0.7406 (tm-30) REVERT: B 447 MET cc_start: 0.6955 (tpt) cc_final: 0.6409 (ttt) REVERT: B 466 MET cc_start: 0.8625 (mmp) cc_final: 0.8259 (mmm) REVERT: B 497 MET cc_start: 0.9264 (tpp) cc_final: 0.8889 (tpp) REVERT: B 535 GLU cc_start: 0.8313 (mp0) cc_final: 0.7732 (mp0) REVERT: C 202 ILE cc_start: 0.9448 (pt) cc_final: 0.9181 (tt) REVERT: C 302 ARG cc_start: 0.8062 (mtp-110) cc_final: 0.7681 (ptp90) REVERT: C 447 MET cc_start: 0.7173 (mmm) cc_final: 0.6922 (mmm) REVERT: C 570 MET cc_start: 0.8264 (pmm) cc_final: 0.7898 (pmm) REVERT: D 91 ASN cc_start: 0.8402 (m-40) cc_final: 0.8011 (m110) REVERT: D 260 MET cc_start: 0.9045 (tpp) cc_final: 0.8668 (tpp) REVERT: D 340 MET cc_start: 0.9518 (tpp) cc_final: 0.9206 (tpp) REVERT: D 578 MET cc_start: 0.8620 (tpt) cc_final: 0.7393 (tpt) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.1229 time to fit residues: 69.5652 Evaluate side-chains 258 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 187 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 ASN B 513 GLN B 596 GLN C 418 GLN C 513 GLN D 596 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.082858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.068501 restraints weight = 67665.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.070124 restraints weight = 40031.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.071218 restraints weight = 27273.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.071960 restraints weight = 20711.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.072412 restraints weight = 17056.325| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21005 Z= 0.153 Angle : 0.627 7.908 28494 Z= 0.318 Chirality : 0.040 0.160 3236 Planarity : 0.004 0.033 3618 Dihedral : 4.498 22.430 2792 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.16), residues: 2538 helix: 1.14 (0.13), residues: 1570 sheet: -1.97 (0.50), residues: 73 loop : -1.34 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 139 TYR 0.018 0.001 TYR A 526 PHE 0.030 0.001 PHE B 531 TRP 0.022 0.001 TRP A 583 HIS 0.006 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00349 (21005) covalent geometry : angle 0.62669 (28494) hydrogen bonds : bond 0.04380 ( 1110) hydrogen bonds : angle 4.20326 ( 3216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.8907 (m-40) cc_final: 0.8496 (m110) REVERT: A 99 MET cc_start: 0.9221 (mtm) cc_final: 0.8451 (mtp) REVERT: A 368 LEU cc_start: 0.8612 (mm) cc_final: 0.7934 (mm) REVERT: A 442 MET cc_start: 0.8637 (tpp) cc_final: 0.8299 (tpp) REVERT: A 577 MET cc_start: 0.8112 (tmm) cc_final: 0.7849 (tmm) REVERT: A 603 MET cc_start: 0.8470 (mmt) cc_final: 0.7931 (tmm) REVERT: A 627 ASP cc_start: 0.8344 (m-30) cc_final: 0.7909 (t0) REVERT: E 37 MET cc_start: 0.6382 (mmm) cc_final: 0.5024 (tpt) REVERT: E 87 ARG cc_start: 0.8482 (tpp80) cc_final: 0.8281 (tpp-160) REVERT: E 90 PHE cc_start: 0.8903 (t80) cc_final: 0.8433 (t80) REVERT: B 91 ASN cc_start: 0.8257 (m-40) cc_final: 0.7884 (m-40) REVERT: B 389 GLU cc_start: 0.8023 (tt0) cc_final: 0.7426 (tm-30) REVERT: B 403 GLU cc_start: 0.8305 (tp30) cc_final: 0.8051 (tp30) REVERT: B 466 MET cc_start: 0.8652 (mmp) cc_final: 0.8381 (mmm) REVERT: B 497 MET cc_start: 0.9289 (tpp) cc_final: 0.8908 (tpp) REVERT: C 202 ILE cc_start: 0.9507 (pt) cc_final: 0.9221 (tt) REVERT: C 302 ARG cc_start: 0.8164 (mtp-110) cc_final: 0.7482 (ttp-110) REVERT: C 403 GLU cc_start: 0.8615 (tt0) cc_final: 0.8369 (tp30) REVERT: C 447 MET cc_start: 0.7324 (mmm) cc_final: 0.7004 (mmm) REVERT: C 485 MET cc_start: 0.9199 (ttm) cc_final: 0.8601 (ttt) REVERT: C 570 MET cc_start: 0.8144 (pmm) cc_final: 0.7932 (pmm) REVERT: C 608 MET cc_start: 0.8800 (mtm) cc_final: 0.8447 (mtm) REVERT: D 91 ASN cc_start: 0.8555 (m-40) cc_final: 0.8207 (m110) REVERT: D 125 VAL cc_start: 0.9504 (m) cc_final: 0.9277 (p) REVERT: D 260 MET cc_start: 0.9050 (tpp) cc_final: 0.8522 (tpp) REVERT: D 340 MET cc_start: 0.9475 (tpp) cc_final: 0.9140 (tpp) REVERT: D 481 MET cc_start: 0.8923 (ttp) cc_final: 0.8671 (tmm) REVERT: D 578 MET cc_start: 0.8330 (tpt) cc_final: 0.8018 (mmm) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.1270 time to fit residues: 69.5254 Evaluate side-chains 251 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 246 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 224 optimal weight: 8.9990 chunk 202 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 241 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 258 HIS A 267 GLN B 37 ASN B 513 GLN B 582 HIS B 596 GLN B 636 HIS C 418 GLN C 513 GLN ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.079098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.064826 restraints weight = 69098.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.066394 restraints weight = 41017.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.067443 restraints weight = 27762.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.068176 restraints weight = 21029.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.068626 restraints weight = 17301.803| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21005 Z= 0.219 Angle : 0.714 8.710 28494 Z= 0.365 Chirality : 0.043 0.177 3236 Planarity : 0.004 0.035 3618 Dihedral : 4.751 20.586 2792 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.16), residues: 2538 helix: 1.00 (0.13), residues: 1562 sheet: -1.80 (0.50), residues: 75 loop : -1.37 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 470 TYR 0.024 0.002 TYR A 526 PHE 0.044 0.002 PHE B 531 TRP 0.031 0.002 TRP A 702 HIS 0.009 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00501 (21005) covalent geometry : angle 0.71368 (28494) hydrogen bonds : bond 0.05128 ( 1110) hydrogen bonds : angle 4.57381 ( 3216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.8921 (m-40) cc_final: 0.8575 (m110) REVERT: A 99 MET cc_start: 0.9281 (mtm) cc_final: 0.8390 (mtp) REVERT: A 368 LEU cc_start: 0.8750 (mm) cc_final: 0.7911 (mm) REVERT: A 442 MET cc_start: 0.8532 (tpp) cc_final: 0.8319 (tpp) REVERT: A 497 MET cc_start: 0.9089 (tpp) cc_final: 0.8821 (tpp) REVERT: A 577 MET cc_start: 0.8334 (tmm) cc_final: 0.8133 (tmm) REVERT: A 603 MET cc_start: 0.8522 (mmt) cc_final: 0.8084 (tmm) REVERT: A 627 ASP cc_start: 0.8401 (m-30) cc_final: 0.7907 (t0) REVERT: A 643 ARG cc_start: 0.8128 (ptt180) cc_final: 0.7662 (ptt180) REVERT: E 37 MET cc_start: 0.6464 (mmm) cc_final: 0.5097 (tpt) REVERT: E 90 PHE cc_start: 0.8930 (t80) cc_final: 0.8507 (t80) REVERT: B 91 ASN cc_start: 0.8089 (m-40) cc_final: 0.7783 (m-40) REVERT: B 447 MET cc_start: 0.7257 (tpt) cc_final: 0.6564 (ttt) REVERT: C 126 MET cc_start: 0.9541 (ttm) cc_final: 0.9281 (ttm) REVERT: C 202 ILE cc_start: 0.9587 (pt) cc_final: 0.9325 (tt) REVERT: C 302 ARG cc_start: 0.8236 (mtp-110) cc_final: 0.7411 (ttm110) REVERT: C 303 GLU cc_start: 0.7672 (pp20) cc_final: 0.7353 (pp20) REVERT: C 368 LEU cc_start: 0.8830 (mt) cc_final: 0.8473 (mt) REVERT: C 485 MET cc_start: 0.9225 (ttm) cc_final: 0.8673 (ttt) REVERT: C 570 MET cc_start: 0.8157 (pmm) cc_final: 0.7906 (pmm) REVERT: D 55 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8269 (mp0) REVERT: D 91 ASN cc_start: 0.8514 (m-40) cc_final: 0.8081 (m110) REVERT: D 485 MET cc_start: 0.8686 (ttm) cc_final: 0.8228 (ttt) REVERT: D 578 MET cc_start: 0.8336 (tpt) cc_final: 0.8003 (tpp) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.1337 time to fit residues: 66.9765 Evaluate side-chains 232 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 194 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 222 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN B 37 ASN B 513 GLN C 418 GLN C 513 GLN D 582 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.080863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.066469 restraints weight = 67617.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.068078 restraints weight = 39678.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.069170 restraints weight = 26827.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.069908 restraints weight = 20257.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.070365 restraints weight = 16664.609| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21005 Z= 0.150 Angle : 0.658 9.310 28494 Z= 0.330 Chirality : 0.040 0.178 3236 Planarity : 0.004 0.034 3618 Dihedral : 4.636 20.378 2792 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.16), residues: 2538 helix: 1.02 (0.13), residues: 1579 sheet: -1.71 (0.51), residues: 75 loop : -1.41 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 107 TYR 0.044 0.002 TYR C 162 PHE 0.041 0.002 PHE B 531 TRP 0.023 0.001 TRP A 702 HIS 0.007 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00340 (21005) covalent geometry : angle 0.65762 (28494) hydrogen bonds : bond 0.04585 ( 1110) hydrogen bonds : angle 4.33814 ( 3216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8868 (mmp) cc_final: 0.8615 (mmt) REVERT: A 99 MET cc_start: 0.9280 (mtm) cc_final: 0.8429 (mtp) REVERT: A 368 LEU cc_start: 0.8702 (mm) cc_final: 0.8406 (mm) REVERT: A 442 MET cc_start: 0.8584 (tpp) cc_final: 0.8259 (tpp) REVERT: A 497 MET cc_start: 0.9144 (tpp) cc_final: 0.8799 (tpp) REVERT: A 577 MET cc_start: 0.8210 (tmm) cc_final: 0.8004 (tmm) REVERT: A 603 MET cc_start: 0.8506 (mmt) cc_final: 0.8072 (tmm) REVERT: A 627 ASP cc_start: 0.8384 (m-30) cc_final: 0.7921 (t0) REVERT: A 643 ARG cc_start: 0.8171 (ptt180) cc_final: 0.7659 (ptt180) REVERT: E 37 MET cc_start: 0.6454 (mmm) cc_final: 0.5099 (tpt) REVERT: E 90 PHE cc_start: 0.8937 (t80) cc_final: 0.8455 (t80) REVERT: E 101 ILE cc_start: 0.8216 (mt) cc_final: 0.7926 (mp) REVERT: B 91 ASN cc_start: 0.8156 (m-40) cc_final: 0.7784 (m-40) REVERT: B 389 GLU cc_start: 0.8039 (tt0) cc_final: 0.7353 (tm-30) REVERT: C 126 MET cc_start: 0.9576 (ttm) cc_final: 0.9250 (ttm) REVERT: C 129 ASN cc_start: 0.8755 (t0) cc_final: 0.8323 (t0) REVERT: C 132 LEU cc_start: 0.9403 (tp) cc_final: 0.9160 (tp) REVERT: C 202 ILE cc_start: 0.9573 (pt) cc_final: 0.9297 (tt) REVERT: C 302 ARG cc_start: 0.8130 (mtp-110) cc_final: 0.7452 (ttm110) REVERT: C 303 GLU cc_start: 0.7887 (pp20) cc_final: 0.7376 (pp20) REVERT: C 485 MET cc_start: 0.9162 (ttm) cc_final: 0.8848 (ttm) REVERT: C 554 MET cc_start: 0.8059 (ttp) cc_final: 0.6753 (ppp) REVERT: C 570 MET cc_start: 0.8062 (pmm) cc_final: 0.7817 (pmm) REVERT: D 55 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8270 (mp0) REVERT: D 91 ASN cc_start: 0.8610 (m-40) cc_final: 0.8230 (m110) REVERT: D 215 MET cc_start: 0.8227 (mmt) cc_final: 0.7786 (mpp) REVERT: D 260 MET cc_start: 0.9073 (tpp) cc_final: 0.8790 (tpp) REVERT: D 578 MET cc_start: 0.8421 (tpt) cc_final: 0.8108 (tpp) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.1303 time to fit residues: 64.8282 Evaluate side-chains 231 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 93 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 220 optimal weight: 7.9990 chunk 151 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 234 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 708 ASN B 37 ASN B 513 GLN C 418 GLN C 513 GLN D 37 ASN D 582 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.081374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.067078 restraints weight = 66919.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.068690 restraints weight = 39411.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.069779 restraints weight = 26721.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.070545 restraints weight = 20191.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.070994 restraints weight = 16545.544| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.5747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21005 Z= 0.132 Angle : 0.648 8.403 28494 Z= 0.321 Chirality : 0.040 0.155 3236 Planarity : 0.004 0.032 3618 Dihedral : 4.528 19.921 2792 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.17), residues: 2538 helix: 1.14 (0.13), residues: 1576 sheet: -1.30 (0.51), residues: 70 loop : -1.31 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 385 TYR 0.019 0.001 TYR D 547 PHE 0.039 0.001 PHE B 531 TRP 0.024 0.001 TRP A 583 HIS 0.006 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00298 (21005) covalent geometry : angle 0.64755 (28494) hydrogen bonds : bond 0.04218 ( 1110) hydrogen bonds : angle 4.21061 ( 3216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9230 (mtm) cc_final: 0.8501 (mtp) REVERT: A 368 LEU cc_start: 0.8621 (mm) cc_final: 0.8327 (mm) REVERT: A 442 MET cc_start: 0.8535 (tpp) cc_final: 0.8184 (tpp) REVERT: A 497 MET cc_start: 0.9105 (tpp) cc_final: 0.8832 (tpp) REVERT: A 578 MET cc_start: 0.8809 (tpt) cc_final: 0.8587 (tpt) REVERT: A 603 MET cc_start: 0.8484 (mmt) cc_final: 0.8066 (tmm) REVERT: A 627 ASP cc_start: 0.8355 (m-30) cc_final: 0.7903 (t0) REVERT: E 37 MET cc_start: 0.6415 (mmm) cc_final: 0.5081 (tpt) REVERT: E 90 PHE cc_start: 0.8938 (t80) cc_final: 0.8430 (t80) REVERT: E 101 ILE cc_start: 0.8135 (mt) cc_final: 0.7877 (mp) REVERT: B 389 GLU cc_start: 0.8047 (tt0) cc_final: 0.7410 (tm-30) REVERT: B 447 MET cc_start: 0.7194 (tpt) cc_final: 0.6669 (ttt) REVERT: B 493 PHE cc_start: 0.9481 (t80) cc_final: 0.9210 (t80) REVERT: C 126 MET cc_start: 0.9600 (ttm) cc_final: 0.9272 (ttm) REVERT: C 129 ASN cc_start: 0.8710 (t0) cc_final: 0.8277 (t0) REVERT: C 132 LEU cc_start: 0.9399 (tp) cc_final: 0.9198 (tp) REVERT: C 202 ILE cc_start: 0.9584 (pt) cc_final: 0.9268 (tt) REVERT: C 302 ARG cc_start: 0.8169 (mtp-110) cc_final: 0.7527 (ttm110) REVERT: C 303 GLU cc_start: 0.7896 (pp20) cc_final: 0.7392 (pp20) REVERT: C 368 LEU cc_start: 0.8778 (mt) cc_final: 0.8499 (mt) REVERT: C 481 MET cc_start: 0.9107 (tpt) cc_final: 0.8883 (ttp) REVERT: C 485 MET cc_start: 0.9265 (ttm) cc_final: 0.8728 (ttt) REVERT: C 554 MET cc_start: 0.8027 (ttp) cc_final: 0.6707 (ppp) REVERT: C 570 MET cc_start: 0.8045 (pmm) cc_final: 0.7763 (pmm) REVERT: D 91 ASN cc_start: 0.8599 (m-40) cc_final: 0.8228 (m110) REVERT: D 215 MET cc_start: 0.8250 (mmt) cc_final: 0.7957 (mpp) REVERT: D 260 MET cc_start: 0.9049 (tpp) cc_final: 0.8777 (tpp) REVERT: D 385 ARG cc_start: 0.8369 (tmm-80) cc_final: 0.8045 (ttp80) REVERT: D 428 ILE cc_start: 0.9140 (pt) cc_final: 0.8825 (mm) REVERT: D 485 MET cc_start: 0.8668 (ttm) cc_final: 0.8280 (ttt) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.1291 time to fit residues: 64.5608 Evaluate side-chains 243 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 125 optimal weight: 5.9990 chunk 11 optimal weight: 30.0000 chunk 237 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 226 optimal weight: 20.0000 chunk 250 optimal weight: 3.9990 chunk 182 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN B 37 ASN B 513 GLN C 418 GLN C 513 GLN D 37 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.079706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.065335 restraints weight = 68825.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.066921 restraints weight = 40691.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.067996 restraints weight = 27536.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.068741 restraints weight = 20814.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.069240 restraints weight = 17118.773| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21005 Z= 0.183 Angle : 0.695 9.760 28494 Z= 0.350 Chirality : 0.042 0.160 3236 Planarity : 0.004 0.032 3618 Dihedral : 4.625 19.311 2792 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2538 helix: 0.95 (0.13), residues: 1582 sheet: -1.19 (0.52), residues: 70 loop : -1.40 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 107 TYR 0.022 0.002 TYR D 547 PHE 0.041 0.002 PHE B 531 TRP 0.061 0.002 TRP A 702 HIS 0.007 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00422 (21005) covalent geometry : angle 0.69467 (28494) hydrogen bonds : bond 0.04748 ( 1110) hydrogen bonds : angle 4.48966 ( 3216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 99 MET cc_start: 0.9256 (mtm) cc_final: 0.8458 (mtp) REVERT: A 250 GLU cc_start: 0.8039 (tp30) cc_final: 0.7782 (mt-10) REVERT: A 368 LEU cc_start: 0.8672 (mm) cc_final: 0.8426 (mm) REVERT: A 442 MET cc_start: 0.8506 (tpp) cc_final: 0.8203 (tpp) REVERT: A 497 MET cc_start: 0.9139 (tpp) cc_final: 0.8853 (tpp) REVERT: A 603 MET cc_start: 0.8502 (mmt) cc_final: 0.8052 (tmm) REVERT: A 627 ASP cc_start: 0.8368 (m-30) cc_final: 0.7931 (t0) REVERT: A 643 ARG cc_start: 0.7980 (ptt180) cc_final: 0.7587 (ptt180) REVERT: E 37 MET cc_start: 0.6507 (mmm) cc_final: 0.5165 (tpt) REVERT: E 90 PHE cc_start: 0.8993 (t80) cc_final: 0.8422 (t80) REVERT: E 101 ILE cc_start: 0.8238 (mt) cc_final: 0.7978 (mp) REVERT: E 144 GLN cc_start: 0.7906 (tp-100) cc_final: 0.7700 (tp-100) REVERT: B 402 LEU cc_start: 0.8877 (tp) cc_final: 0.8655 (mm) REVERT: B 447 MET cc_start: 0.7241 (tpt) cc_final: 0.6639 (ttt) REVERT: B 466 MET cc_start: 0.8834 (mmp) cc_final: 0.8600 (mmm) REVERT: B 493 PHE cc_start: 0.9511 (t80) cc_final: 0.9231 (t80) REVERT: C 129 ASN cc_start: 0.8806 (t0) cc_final: 0.8339 (t0) REVERT: C 132 LEU cc_start: 0.9436 (tp) cc_final: 0.9183 (tp) REVERT: C 302 ARG cc_start: 0.8408 (mtp-110) cc_final: 0.7560 (ttm110) REVERT: C 340 MET cc_start: 0.8985 (tpp) cc_final: 0.8669 (tpp) REVERT: C 485 MET cc_start: 0.9284 (ttm) cc_final: 0.8798 (ttt) REVERT: C 554 MET cc_start: 0.8034 (ttp) cc_final: 0.6751 (ppp) REVERT: C 570 MET cc_start: 0.8269 (pmm) cc_final: 0.7999 (pmm) REVERT: D 91 ASN cc_start: 0.8551 (m-40) cc_final: 0.8164 (m110) REVERT: D 215 MET cc_start: 0.8249 (mmt) cc_final: 0.7932 (mpp) REVERT: D 260 MET cc_start: 0.9078 (tpp) cc_final: 0.8831 (tpp) REVERT: D 385 ARG cc_start: 0.8492 (tmm-80) cc_final: 0.7771 (ttp80) REVERT: D 520 LEU cc_start: 0.8585 (pp) cc_final: 0.8331 (pp) REVERT: D 570 MET cc_start: 0.8536 (mtp) cc_final: 0.8065 (tpp) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.1249 time to fit residues: 58.4880 Evaluate side-chains 224 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 154 optimal weight: 0.5980 chunk 105 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 238 optimal weight: 0.3980 chunk 161 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 37 ASN B 513 GLN C 513 GLN D 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.083275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.069025 restraints weight = 67506.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.070723 restraints weight = 39087.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.071859 restraints weight = 26065.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.072576 restraints weight = 19497.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.073137 restraints weight = 16040.987| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21005 Z= 0.119 Angle : 0.649 14.812 28494 Z= 0.317 Chirality : 0.039 0.245 3236 Planarity : 0.004 0.036 3618 Dihedral : 4.461 20.876 2792 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.17), residues: 2538 helix: 1.10 (0.13), residues: 1592 sheet: -1.15 (0.51), residues: 70 loop : -1.32 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 615 TYR 0.016 0.001 TYR D 547 PHE 0.038 0.001 PHE B 531 TRP 0.024 0.001 TRP A 583 HIS 0.007 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00257 (21005) covalent geometry : angle 0.64944 (28494) hydrogen bonds : bond 0.03912 ( 1110) hydrogen bonds : angle 4.18781 ( 3216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2857.62 seconds wall clock time: 50 minutes 26.80 seconds (3026.80 seconds total)