Starting phenix.real_space_refine on Sat Feb 7 08:52:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wi0_65981/02_2026/9wi0_65981.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wi0_65981/02_2026/9wi0_65981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wi0_65981/02_2026/9wi0_65981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wi0_65981/02_2026/9wi0_65981.map" model { file = "/net/cci-nas-00/data/ceres_data/9wi0_65981/02_2026/9wi0_65981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wi0_65981/02_2026/9wi0_65981.cif" } resolution = 2.89 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= -0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 19944 2.51 5 N 5562 2.21 5 O 5658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31284 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5214 Classifications: {'peptide': 656} Link IDs: {'PCIS': 3, 'PTRANS': 31, 'TRANS': 621} Chain: "B" Number of atoms: 5214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5214 Classifications: {'peptide': 656} Link IDs: {'PCIS': 3, 'PTRANS': 31, 'TRANS': 621} Chain: "C" Number of atoms: 5214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5214 Classifications: {'peptide': 656} Link IDs: {'PCIS': 3, 'PTRANS': 31, 'TRANS': 621} Chain: "D" Number of atoms: 5214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5214 Classifications: {'peptide': 656} Link IDs: {'PCIS': 3, 'PTRANS': 31, 'TRANS': 621} Chain: "E" Number of atoms: 5214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5214 Classifications: {'peptide': 656} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 621} Chain: "F" Number of atoms: 5214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5214 Classifications: {'peptide': 656} Link IDs: {'PCIS': 3, 'PTRANS': 31, 'TRANS': 621} Time building chain proxies: 7.77, per 1000 atoms: 0.25 Number of scatterers: 31284 At special positions: 0 Unit cell: (123, 163.18, 173.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5658 8.00 N 5562 7.00 C 19944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 629 " distance=2.03 Simple disulfide: pdb=" SG CYS B 558 " - pdb=" SG CYS B 629 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.4 seconds 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7296 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 41 sheets defined 37.1% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 157 through 175 removed outlier: 3.643A pdb=" N GLN A 175 " --> pdb=" O GLN A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 182 Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 202 through 207 removed outlier: 3.689A pdb=" N PHE A 207 " --> pdb=" O ASP A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 removed outlier: 3.672A pdb=" N VAL A 224 " --> pdb=" O MET A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 Processing helix chain 'A' and resid 311 through 315 removed outlier: 4.001A pdb=" N ARG A 315 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.619A pdb=" N ASN A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.529A pdb=" N LYS A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 400 Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.773A pdb=" N GLU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 408' Processing helix chain 'A' and resid 409 through 423 removed outlier: 3.684A pdb=" N ASN A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 437 removed outlier: 3.743A pdb=" N VAL A 435 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR A 436 " --> pdb=" O SER A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 461 through 481 removed outlier: 3.677A pdb=" N ASP A 471 " --> pdb=" O LYS A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 512 through 519 Processing helix chain 'A' and resid 527 through 532 removed outlier: 4.055A pdb=" N LYS A 532 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 552 removed outlier: 3.701A pdb=" N ARG A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 removed outlier: 3.572A pdb=" N GLU A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 653 removed outlier: 4.027A pdb=" N ILE A 642 " --> pdb=" O MET A 638 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP A 647 " --> pdb=" O ASP A 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 23 removed outlier: 3.717A pdb=" N CYS B 13 " --> pdb=" O HIS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 removed outlier: 3.711A pdb=" N LEU B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 75 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.788A pdb=" N TRP B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN B 123 " --> pdb=" O TRP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 182 Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 213 through 224 Processing helix chain 'B' and resid 289 through 297 Processing helix chain 'B' and resid 325 through 336 removed outlier: 3.715A pdb=" N HIS B 330 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.574A pdb=" N LEU B 357 " --> pdb=" O SER B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.597A pdb=" N ASN B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.544A pdb=" N GLU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 408' Processing helix chain 'B' and resid 409 through 423 removed outlier: 3.572A pdb=" N ASN B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.580A pdb=" N VAL B 435 " --> pdb=" O THR B 432 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR B 436 " --> pdb=" O SER B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 460 No H-bonds generated for 'chain 'B' and resid 458 through 460' Processing helix chain 'B' and resid 461 through 481 removed outlier: 3.632A pdb=" N ASP B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 522 Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 540 through 552 removed outlier: 3.752A pdb=" N GLU B 545 " --> pdb=" O ARG B 541 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 546 " --> pdb=" O ASP B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 557 removed outlier: 3.849A pdb=" N ARG B 557 " --> pdb=" O ALA B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 578 Processing helix chain 'B' and resid 607 through 611 Processing helix chain 'B' and resid 639 through 652 Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 46 through 52 Processing helix chain 'C' and resid 64 through 74 removed outlier: 4.030A pdb=" N LEU C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 96 removed outlier: 3.850A pdb=" N GLN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA C 96 " --> pdb=" O ILE C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 123 removed outlier: 3.993A pdb=" N TRP C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN C 123 " --> pdb=" O TRP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 182 Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 213 through 224 removed outlier: 3.611A pdb=" N LEU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 327 through 336 removed outlier: 3.671A pdb=" N GLU C 333 " --> pdb=" O ASN C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 383 removed outlier: 3.883A pdb=" N ILE C 376 " --> pdb=" O HIS C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 401 through 410 removed outlier: 3.909A pdb=" N VAL C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 423 removed outlier: 3.579A pdb=" N ARG C 415 " --> pdb=" O GLU C 411 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS C 422 " --> pdb=" O ARG C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 437 removed outlier: 3.706A pdb=" N VAL C 435 " --> pdb=" O THR C 432 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR C 436 " --> pdb=" O SER C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 461 through 478 Processing helix chain 'C' and resid 510 through 521 removed outlier: 3.981A pdb=" N GLU C 521 " --> pdb=" O LEU C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 553 Processing helix chain 'C' and resid 573 through 587 removed outlier: 3.596A pdb=" N LYS C 587 " --> pdb=" O ALA C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 630 Processing helix chain 'C' and resid 637 through 653 removed outlier: 3.524A pdb=" N THR C 641 " --> pdb=" O ASP C 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 44 through 53 removed outlier: 3.604A pdb=" N LEU D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 74 Processing helix chain 'D' and resid 115 through 123 Processing helix chain 'D' and resid 157 through 176 removed outlier: 3.944A pdb=" N GLN D 175 " --> pdb=" O GLN D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 removed outlier: 3.805A pdb=" N GLY D 183 " --> pdb=" O ALA D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 224 Processing helix chain 'D' and resid 289 through 297 Processing helix chain 'D' and resid 325 through 336 removed outlier: 3.777A pdb=" N ARG D 334 " --> pdb=" O HIS D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 removed outlier: 3.945A pdb=" N ILE D 376 " --> pdb=" O HIS D 372 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS D 381 " --> pdb=" O GLU D 377 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS D 383 " --> pdb=" O HIS D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 410 through 423 removed outlier: 3.590A pdb=" N CYS D 420 " --> pdb=" O ILE D 416 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS D 422 " --> pdb=" O ARG D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 482 removed outlier: 3.515A pdb=" N GLY D 482 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 509 removed outlier: 4.123A pdb=" N SER D 508 " --> pdb=" O ARG D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 521 removed outlier: 3.665A pdb=" N GLN D 514 " --> pdb=" O ARG D 510 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE D 516 " --> pdb=" O ILE D 512 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU D 519 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL D 520 " --> pdb=" O ILE D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 533 removed outlier: 4.254A pdb=" N LYS D 532 " --> pdb=" O ASP D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 553 Processing helix chain 'D' and resid 573 through 585 removed outlier: 4.080A pdb=" N LEU D 577 " --> pdb=" O SER D 573 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N MET D 580 " --> pdb=" O GLU D 576 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 630 Processing helix chain 'D' and resid 637 through 652 removed outlier: 3.722A pdb=" N THR D 641 " --> pdb=" O ASP D 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 23 Processing helix chain 'E' and resid 44 through 52 Processing helix chain 'E' and resid 64 through 73 Processing helix chain 'E' and resid 89 through 94 removed outlier: 3.932A pdb=" N LEU E 93 " --> pdb=" O TYR E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 123 Processing helix chain 'E' and resid 157 through 175 Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 191 through 195 removed outlier: 3.916A pdb=" N GLU E 194 " --> pdb=" O ARG E 191 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA E 195 " --> pdb=" O GLU E 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 191 through 195' Processing helix chain 'E' and resid 202 through 207 removed outlier: 3.507A pdb=" N PHE E 207 " --> pdb=" O ASP E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 224 Processing helix chain 'E' and resid 288 through 297 Processing helix chain 'E' and resid 327 through 336 removed outlier: 3.930A pdb=" N GLU E 333 " --> pdb=" O ASN E 329 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG E 334 " --> pdb=" O HIS E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 383 Processing helix chain 'E' and resid 394 through 400 Processing helix chain 'E' and resid 410 through 423 Processing helix chain 'E' and resid 461 through 478 removed outlier: 3.721A pdb=" N ASP E 471 " --> pdb=" O LYS E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 520 removed outlier: 3.586A pdb=" N VAL E 520 " --> pdb=" O ILE E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 553 removed outlier: 3.733A pdb=" N GLU E 545 " --> pdb=" O ARG E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 585 Processing helix chain 'E' and resid 624 through 631 Processing helix chain 'E' and resid 637 through 653 removed outlier: 4.142A pdb=" N THR E 652 " --> pdb=" O PHE E 648 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL E 653 " --> pdb=" O PHE E 649 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 20 Processing helix chain 'F' and resid 45 through 53 Processing helix chain 'F' and resid 68 through 74 removed outlier: 3.519A pdb=" N ALA F 72 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU F 74 " --> pdb=" O ARG F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 94 removed outlier: 3.693A pdb=" N LEU F 93 " --> pdb=" O TYR F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 124 removed outlier: 3.664A pdb=" N TRP F 119 " --> pdb=" O ALA F 115 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN F 123 " --> pdb=" O TRP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 183 Proline residue: F 178 - end of helix Processing helix chain 'F' and resid 191 through 195 Processing helix chain 'F' and resid 213 through 224 removed outlier: 3.544A pdb=" N VAL F 224 " --> pdb=" O MET F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 297 Processing helix chain 'F' and resid 325 through 336 removed outlier: 3.856A pdb=" N ASN F 329 " --> pdb=" O GLY F 325 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS F 330 " --> pdb=" O PHE F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 383 Processing helix chain 'F' and resid 394 through 400 removed outlier: 4.032A pdb=" N THR F 399 " --> pdb=" O PRO F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 410 removed outlier: 4.091A pdb=" N VAL F 405 " --> pdb=" O ASN F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 423 removed outlier: 3.601A pdb=" N VAL F 421 " --> pdb=" O ILE F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 436 removed outlier: 3.567A pdb=" N VAL F 435 " --> pdb=" O THR F 432 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR F 436 " --> pdb=" O SER F 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 432 through 436' Processing helix chain 'F' and resid 461 through 481 Processing helix chain 'F' and resid 510 through 521 removed outlier: 3.679A pdb=" N GLN F 514 " --> pdb=" O ARG F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 553 Processing helix chain 'F' and resid 554 through 557 removed outlier: 3.723A pdb=" N ARG F 557 " --> pdb=" O ALA F 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 554 through 557' Processing helix chain 'F' and resid 573 through 587 Processing helix chain 'F' and resid 637 through 653 removed outlier: 3.518A pdb=" N THR F 641 " --> pdb=" O ASP F 637 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL F 653 " --> pdb=" O PHE F 649 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 removed outlier: 8.443A pdb=" N TYR A 57 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE A 29 " --> pdb=" O TYR A 57 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N THR A 3 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A 29 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A 5 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU A 132 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113 removed outlier: 5.501A pdb=" N ARG A 112 " --> pdb=" O PHE A 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 128 Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 235 removed outlier: 6.225A pdb=" N THR A 278 " --> pdb=" O TRP A 243 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER A 245 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE A 276 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL A 247 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU A 274 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 279 " --> pdb=" O MET A 287 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 362 through 366 removed outlier: 3.673A pdb=" N ASP A 347 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL A 318 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LEU A 346 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE A 320 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 386 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AA7, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AA8, first strand: chain 'A' and resid 535 through 536 Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.860A pdb=" N THR B 3 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE B 29 " --> pdb=" O THR B 3 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL B 5 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL B 78 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B 101 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU B 103 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B 132 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 128 removed outlier: 3.598A pdb=" N THR B 128 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE B 150 " --> pdb=" O THR B 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 233 through 235 removed outlier: 6.850A pdb=" N VAL B 242 " --> pdb=" O GLY B 279 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY B 279 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SER B 244 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA B 268 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL B 259 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 233 through 235 removed outlier: 6.850A pdb=" N VAL B 242 " --> pdb=" O GLY B 279 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY B 279 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SER B 244 " --> pdb=" O VAL B 277 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 362 through 366 removed outlier: 7.238A pdb=" N VAL B 343 " --> pdb=" O HIS B 363 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL B 365 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY B 345 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 451 through 453 Processing sheet with id=AB6, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AB7, first strand: chain 'C' and resid 29 through 30 removed outlier: 7.090A pdb=" N VAL C 5 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL C 4 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE C 82 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE C 6 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE C 79 " --> pdb=" O PHE C 101 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU C 103 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N SER C 81 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 259 through 261 removed outlier: 4.005A pdb=" N SER C 261 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 278 through 280 Processing sheet with id=AC1, first strand: chain 'C' and resid 341 through 343 removed outlier: 6.535A pdb=" N THR C 316 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 443 through 444 Processing sheet with id=AC3, first strand: chain 'C' and resid 486 through 490 Processing sheet with id=AC4, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AC5, first strand: chain 'C' and resid 535 through 536 Processing sheet with id=AC6, first strand: chain 'D' and resid 4 through 6 removed outlier: 6.295A pdb=" N VAL D 4 " --> pdb=" O PHE D 80 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N PHE D 82 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE D 6 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE D 79 " --> pdb=" O PHE D 101 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU D 103 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER D 81 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA D 100 " --> pdb=" O MET D 135 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 29 through 30 removed outlier: 7.081A pdb=" N ILE D 29 " --> pdb=" O TYR D 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 233 through 235 removed outlier: 5.966A pdb=" N VAL D 242 " --> pdb=" O GLN D 280 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLN D 280 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ARG D 246 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ILE D 276 " --> pdb=" O ARG D 246 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.873A pdb=" N LEU D 319 " --> pdb=" O LEU D 387 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 451 through 453 Processing sheet with id=AD2, first strand: chain 'D' and resid 489 through 490 removed outlier: 6.251A pdb=" N ARG D 489 " --> pdb=" O ILE D 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 493 through 494 Processing sheet with id=AD4, first strand: chain 'E' and resid 78 through 82 removed outlier: 6.438A pdb=" N ILE E 79 " --> pdb=" O PHE E 101 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU E 103 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER E 81 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU E 132 " --> pdb=" O VAL E 145 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 231 through 234 removed outlier: 3.624A pdb=" N ALA E 231 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR E 278 " --> pdb=" O TRP E 243 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N SER E 245 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ILE E 276 " --> pdb=" O SER E 245 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 342 through 343 removed outlier: 6.354A pdb=" N GLU E 342 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE E 320 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL E 386 " --> pdb=" O ILE E 428 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE E 427 " --> pdb=" O THR E 486 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 489 through 490 removed outlier: 6.373A pdb=" N ARG E 489 " --> pdb=" O ILE E 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AD9, first strand: chain 'E' and resid 535 through 536 Processing sheet with id=AE1, first strand: chain 'F' and resid 28 through 30 removed outlier: 4.630A pdb=" N VAL F 5 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE F 30 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE F 80 " --> pdb=" O VAL F 4 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N SER F 81 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 231 through 235 removed outlier: 6.463A pdb=" N PHE F 240 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA F 281 " --> pdb=" O PHE F 240 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL F 242 " --> pdb=" O GLY F 279 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLY F 279 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N SER F 244 " --> pdb=" O VAL F 277 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL F 277 " --> pdb=" O SER F 244 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 365 through 366 removed outlier: 6.227A pdb=" N THR F 316 " --> pdb=" O GLU F 342 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N TYR F 344 " --> pdb=" O THR F 316 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL F 318 " --> pdb=" O TYR F 344 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU F 346 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE F 320 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL F 386 " --> pdb=" O ILE F 428 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N ILE F 563 " --> pdb=" O PHE F 485 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU F 487 " --> pdb=" O ILE F 563 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ILE F 565 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG F 489 " --> pdb=" O ILE F 565 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 443 through 444 Processing sheet with id=AE5, first strand: chain 'F' and resid 493 through 494 1007 hydrogen bonds defined for protein. 2817 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: 6.07 Time building geometry restraints manager: 3.75 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: 10468 1.34 - 1.46: 7208 1.46 - 1.58: 14220 1.58 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 32070 Sorted by residual: bond pdb=" C HIS C 211 " pdb=" N LYS C 212 " ideal model delta sigma weight residual 1.330 1.360 -0.030 1.47e-02 4.63e+03 4.23e+00 bond pdb=" C ASN C 35 " pdb=" N PRO C 36 " ideal model delta sigma weight residual 1.337 1.355 -0.018 9.80e-03 1.04e+04 3.39e+00 bond pdb=" C LEU D 177 " pdb=" N PRO D 178 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.36e-02 5.41e+03 3.11e+00 bond pdb=" C LEU B 177 " pdb=" N PRO B 178 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.28e-02 6.10e+03 2.98e+00 bond pdb=" C LEU E 177 " pdb=" N PRO E 178 " ideal model delta sigma weight residual 1.335 1.359 -0.023 1.36e-02 5.41e+03 2.97e+00 ... (remaining 32065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 42262 1.93 - 3.87: 1139 3.87 - 5.80: 121 5.80 - 7.73: 22 7.73 - 9.66: 4 Bond angle restraints: 43548 Sorted by residual: angle pdb=" N VAL D 380 " pdb=" CA VAL D 380 " pdb=" C VAL D 380 " ideal model delta sigma weight residual 111.91 106.28 5.63 8.90e-01 1.26e+00 4.00e+01 angle pdb=" N MET A 638 " pdb=" CA MET A 638 " pdb=" C MET A 638 " ideal model delta sigma weight residual 113.38 106.10 7.28 1.23e+00 6.61e-01 3.50e+01 angle pdb=" N VAL D 653 " pdb=" CA VAL D 653 " pdb=" C VAL D 653 " ideal model delta sigma weight residual 113.10 108.13 4.97 9.70e-01 1.06e+00 2.62e+01 angle pdb=" C ARG D 191 " pdb=" CA ARG D 191 " pdb=" CB ARG D 191 " ideal model delta sigma weight residual 116.54 111.06 5.48 1.15e+00 7.56e-01 2.27e+01 angle pdb=" N VAL A 405 " pdb=" CA VAL A 405 " pdb=" C VAL A 405 " ideal model delta sigma weight residual 112.80 107.46 5.34 1.15e+00 7.56e-01 2.16e+01 ... (remaining 43543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16313 17.99 - 35.98: 1989 35.98 - 53.97: 622 53.97 - 71.96: 97 71.96 - 89.96: 53 Dihedral angle restraints: 19074 sinusoidal: 7710 harmonic: 11364 Sorted by residual: dihedral pdb=" CA ASP E 226 " pdb=" C ASP E 226 " pdb=" N PRO E 227 " pdb=" CA PRO E 227 " ideal model delta harmonic sigma weight residual 180.00 -140.71 -39.29 0 5.00e+00 4.00e-02 6.17e+01 dihedral pdb=" CB CYS B 558 " pdb=" SG CYS B 558 " pdb=" SG CYS B 629 " pdb=" CB CYS B 629 " ideal model delta sinusoidal sigma weight residual -86.00 -43.48 -42.52 1 1.00e+01 1.00e-02 2.52e+01 dihedral pdb=" CA ARG B 628 " pdb=" C ARG B 628 " pdb=" N CYS B 629 " pdb=" CA CYS B 629 " ideal model delta harmonic sigma weight residual 180.00 157.01 22.99 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 19071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3561 0.045 - 0.089: 933 0.089 - 0.134: 247 0.134 - 0.178: 8 0.178 - 0.223: 3 Chirality restraints: 4752 Sorted by residual: chirality pdb=" CB THR C 3 " pdb=" CA THR C 3 " pdb=" OG1 THR C 3 " pdb=" CG2 THR C 3 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB ILE A 636 " pdb=" CA ILE A 636 " pdb=" CG1 ILE A 636 " pdb=" CG2 ILE A 636 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ASN F 401 " pdb=" N ASN F 401 " pdb=" C ASN F 401 " pdb=" CB ASN F 401 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 4749 not shown) Planarity restraints: 5682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 359 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.28e+00 pdb=" N PRO E 360 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 360 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 360 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 594 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.80e+00 pdb=" N PRO B 595 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 595 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 595 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 228 " -0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO D 229 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 229 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 229 " -0.030 5.00e-02 4.00e+02 ... (remaining 5679 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 765 2.70 - 3.25: 29652 3.25 - 3.80: 46436 3.80 - 4.35: 61170 4.35 - 4.90: 100169 Nonbonded interactions: 238192 Sorted by model distance: nonbonded pdb=" O PHE F 648 " pdb=" OG1 THR F 652 " model vdw 2.144 3.040 nonbonded pdb=" O GLN C 291 " pdb=" OG1 THR C 295 " model vdw 2.146 3.040 nonbonded pdb=" O GLY D 531 " pdb=" OH TYR D 609 " model vdw 2.182 3.040 nonbonded pdb=" O LEU E 172 " pdb=" OG1 THR E 176 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR B 202 " pdb=" OD1 ASP B 205 " model vdw 2.213 3.040 ... (remaining 238187 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.040 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: 0.060 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 29.510 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 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:7.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32072 Z= 0.160 Angle : 0.727 9.663 43552 Z= 0.453 Chirality : 0.042 0.223 4752 Planarity : 0.005 0.057 5682 Dihedral : 17.623 89.955 11772 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.08 % Favored : 91.26 % Rotamer: Outliers : 1.17 % Allowed : 25.14 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -1.99 (0.13), residues: 3924 helix: -0.04 (0.15), residues: 1334 sheet: -1.44 (0.25), residues: 433 loop : -2.21 (0.12), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 315 TYR 0.019 0.001 TYR C 398 PHE 0.031 0.001 PHE B 594 TRP 0.009 0.001 TRP A 228 HIS 0.015 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00280 (32070) covalent geometry : angle 0.72722 (43548) SS BOND : bond 0.00125 ( 2) SS BOND : angle 1.53035 ( 4) hydrogen bonds : bond 0.17911 ( 998) hydrogen bonds : angle 7.32343 ( 2817) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASN cc_start: 0.8567 (m110) cc_final: 0.8336 (m-40) REVERT: A 220 MET cc_start: 0.8194 (tpp) cc_final: 0.7958 (tpt) REVERT: C 434 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7288 (tt0) REVERT: E 471 ASP cc_start: 0.7307 (m-30) cc_final: 0.6893 (m-30) REVERT: F 1 MET cc_start: 0.1151 (ppp) cc_final: 0.0801 (tmt) outliers start: 39 outliers final: 18 residues processed: 244 average time/residue: 0.6998 time to fit residues: 202.4919 Evaluate side-chains 177 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 620 LYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 536 CYS Chi-restraints excluded: chain F residue 453 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 197 optimal weight: 40.0000 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.0020 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 overall best weight: 1.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS A 379 HIS B 218 HIS B 567 ASN C 294 GLN ** C 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 HIS D 618 HIS E 61 ASN F 102 ASN F 133 HIS F 492 ASN F 533 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5119 r_free = 0.5119 target = 0.282607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.196031 restraints weight = 34151.291| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 2.03 r_work: 0.3953 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3808 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32072 Z= 0.153 Angle : 0.588 10.572 43552 Z= 0.304 Chirality : 0.043 0.171 4752 Planarity : 0.005 0.056 5682 Dihedral : 4.798 58.087 4369 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.82 % Favored : 91.54 % Rotamer: Outliers : 3.45 % Allowed : 24.50 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -1.80 (0.13), residues: 3924 helix: 0.13 (0.15), residues: 1344 sheet: -1.16 (0.26), residues: 427 loop : -2.16 (0.12), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 505 TYR 0.019 0.001 TYR C 398 PHE 0.026 0.001 PHE B 594 TRP 0.010 0.001 TRP E 475 HIS 0.012 0.001 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00360 (32070) covalent geometry : angle 0.58765 (43548) SS BOND : bond 0.00049 ( 2) SS BOND : angle 2.41123 ( 4) hydrogen bonds : bond 0.04140 ( 998) hydrogen bonds : angle 5.37406 ( 2817) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 172 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7097 (tm-30) REVERT: A 220 MET cc_start: 0.8207 (tpp) cc_final: 0.7830 (tpp) REVERT: A 275 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6398 (tm-30) REVERT: A 534 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8307 (mtpt) REVERT: B 220 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.6347 (ptp) REVERT: B 387 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8580 (mt) REVERT: B 469 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8124 (mt) REVERT: B 535 ARG cc_start: 0.6518 (mmm160) cc_final: 0.6266 (tpt170) REVERT: B 644 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6696 (mp0) REVERT: C 339 ASP cc_start: 0.7724 (m-30) cc_final: 0.7456 (m-30) REVERT: C 434 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7836 (tt0) REVERT: C 533 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6975 (tm-30) REVERT: C 619 ARG cc_start: 0.6605 (tpt-90) cc_final: 0.6265 (mmm160) REVERT: C 633 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7500 (tp30) REVERT: D 409 ASP cc_start: 0.7700 (m-30) cc_final: 0.7458 (m-30) REVERT: D 445 ASP cc_start: 0.8169 (t0) cc_final: 0.7955 (t0) REVERT: D 650 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.5951 (pp) REVERT: E 387 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7921 (mt) REVERT: E 441 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7801 (t0) REVERT: E 644 GLU cc_start: 0.8214 (mp0) cc_final: 0.7953 (mp0) REVERT: F 1 MET cc_start: 0.1714 (ppp) cc_final: 0.0942 (tmt) REVERT: F 494 MET cc_start: 0.8346 (ptt) cc_final: 0.8129 (ppp) REVERT: F 577 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6852 (mp) REVERT: F 580 MET cc_start: 0.7277 (ptp) cc_final: 0.6776 (ptp) outliers start: 115 outliers final: 37 residues processed: 265 average time/residue: 0.6055 time to fit residues: 193.6749 Evaluate side-chains 207 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 404 ARG Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 620 LYS Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 HIS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 558 CYS Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 460 ARG Chi-restraints excluded: chain F residue 577 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 62 optimal weight: 0.0270 chunk 246 optimal weight: 5.9990 chunk 320 optimal weight: 0.0770 chunk 127 optimal weight: 0.3980 chunk 186 optimal weight: 1.9990 chunk 366 optimal weight: 1.9990 chunk 66 optimal weight: 30.0000 chunk 165 optimal weight: 0.0870 chunk 109 optimal weight: 1.9990 chunk 310 optimal weight: 8.9990 chunk 236 optimal weight: 0.9980 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 ASN B 218 HIS C 514 GLN D 618 HIS E 219 ASN E 361 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5144 r_free = 0.5144 target = 0.285359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.191803 restraints weight = 34319.915| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 3.70 r_work: 0.3929 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32072 Z= 0.101 Angle : 0.537 10.616 43552 Z= 0.273 Chirality : 0.042 0.153 4752 Planarity : 0.004 0.055 5682 Dihedral : 4.381 58.841 4358 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.29 % Favored : 92.10 % Rotamer: Outliers : 2.55 % Allowed : 25.23 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -1.53 (0.13), residues: 3924 helix: 0.40 (0.15), residues: 1348 sheet: -0.95 (0.26), residues: 426 loop : -2.05 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 424 TYR 0.021 0.001 TYR C 398 PHE 0.021 0.001 PHE B 594 TRP 0.007 0.001 TRP D 243 HIS 0.008 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00213 (32070) covalent geometry : angle 0.53697 (43548) SS BOND : bond 0.00783 ( 2) SS BOND : angle 1.36415 ( 4) hydrogen bonds : bond 0.03007 ( 998) hydrogen bonds : angle 4.87318 ( 2817) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 183 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.7021 (tm-30) REVERT: A 220 MET cc_start: 0.8139 (tpp) cc_final: 0.7552 (tpt) REVERT: A 261 SER cc_start: 0.7313 (t) cc_final: 0.6871 (p) REVERT: A 275 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6362 (tm-30) REVERT: A 534 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8270 (mtpt) REVERT: B 387 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8568 (mt) REVERT: B 404 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7610 (mmp80) REVERT: B 469 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8188 (mt) REVERT: B 633 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7582 (tp30) REVERT: B 644 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: C 192 GLU cc_start: 0.2464 (OUTLIER) cc_final: 0.1489 (pm20) REVERT: C 407 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8031 (mp0) REVERT: C 434 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7942 (tt0) REVERT: C 533 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6936 (tm-30) REVERT: C 619 ARG cc_start: 0.6594 (tpt-90) cc_final: 0.6221 (tpt90) REVERT: D 135 MET cc_start: 0.2662 (ttt) cc_final: 0.2398 (ttp) REVERT: D 404 ARG cc_start: 0.6775 (mmp80) cc_final: 0.6484 (mmm160) REVERT: D 409 ASP cc_start: 0.7752 (m-30) cc_final: 0.7479 (m-30) REVERT: D 445 ASP cc_start: 0.8166 (t0) cc_final: 0.7903 (t0) REVERT: D 517 LEU cc_start: 0.7149 (tt) cc_final: 0.6941 (pp) REVERT: E 316 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8528 (t) REVERT: E 329 ASN cc_start: 0.9300 (OUTLIER) cc_final: 0.8775 (p0) REVERT: E 355 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7499 (ptt-90) REVERT: E 387 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7893 (mt) REVERT: E 618 HIS cc_start: 0.4642 (OUTLIER) cc_final: 0.1984 (p-80) REVERT: F 1 MET cc_start: 0.1931 (ppp) cc_final: 0.1122 (tmt) REVERT: F 135 MET cc_start: 0.2099 (pmt) cc_final: 0.1196 (mtt) REVERT: F 438 MET cc_start: 0.7917 (mtt) cc_final: 0.7588 (mtt) REVERT: F 577 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6885 (mp) REVERT: F 623 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7791 (mt) outliers start: 85 outliers final: 27 residues processed: 251 average time/residue: 0.5769 time to fit residues: 176.4297 Evaluate side-chains 205 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 404 ARG Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 620 LYS Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain E residue 355 ARG Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 558 CYS Chi-restraints excluded: chain E residue 569 GLU Chi-restraints excluded: chain E residue 618 HIS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 623 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 274 optimal weight: 50.0000 chunk 1 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 357 optimal weight: 3.9990 chunk 239 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 232 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 333 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS B 564 ASN ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN D 248 HIS D 618 HIS ** E 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS F 340 HIS F 518 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5109 r_free = 0.5109 target = 0.281200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.195252 restraints weight = 33880.060| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 2.29 r_work: 0.3918 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32072 Z= 0.164 Angle : 0.574 10.142 43552 Z= 0.295 Chirality : 0.044 0.196 4752 Planarity : 0.004 0.054 5682 Dihedral : 4.432 56.488 4352 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.59 % Allowed : 8.00 % Favored : 91.41 % Rotamer: Outliers : 3.48 % Allowed : 25.41 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -1.56 (0.13), residues: 3924 helix: 0.26 (0.15), residues: 1359 sheet: -1.01 (0.26), residues: 436 loop : -1.98 (0.13), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 489 TYR 0.017 0.001 TYR C 398 PHE 0.024 0.001 PHE B 491 TRP 0.010 0.001 TRP E 475 HIS 0.008 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00396 (32070) covalent geometry : angle 0.57401 (43548) SS BOND : bond 0.00997 ( 2) SS BOND : angle 2.30936 ( 4) hydrogen bonds : bond 0.03545 ( 998) hydrogen bonds : angle 4.82854 ( 2817) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 168 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: A 220 MET cc_start: 0.8260 (tpp) cc_final: 0.7646 (tpt) REVERT: A 275 GLU cc_start: 0.7430 (tm-30) cc_final: 0.6654 (tm-30) REVERT: A 329 ASN cc_start: 0.9234 (OUTLIER) cc_final: 0.8956 (p0) REVERT: A 635 LYS cc_start: 0.7265 (mtmm) cc_final: 0.6704 (mptt) REVERT: B 135 MET cc_start: 0.4868 (mmp) cc_final: 0.4526 (mpm) REVERT: B 220 MET cc_start: 0.6809 (tmm) cc_final: 0.6468 (ptp) REVERT: B 387 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8637 (mt) REVERT: B 469 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8098 (mt) REVERT: B 535 ARG cc_start: 0.6772 (mmm160) cc_final: 0.6353 (mmt-90) REVERT: B 564 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8234 (t0) REVERT: B 644 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6644 (mp0) REVERT: C 192 GLU cc_start: 0.2485 (OUTLIER) cc_final: 0.1391 (pm20) REVERT: C 226 ASP cc_start: 0.3110 (OUTLIER) cc_final: 0.2359 (p0) REVERT: C 287 MET cc_start: 0.1264 (OUTLIER) cc_final: 0.0837 (tmt) REVERT: C 333 GLU cc_start: 0.8033 (tt0) cc_final: 0.7555 (tp30) REVERT: C 339 ASP cc_start: 0.7827 (m-30) cc_final: 0.7614 (m-30) REVERT: C 407 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8093 (mp0) REVERT: C 434 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8064 (mt-10) REVERT: C 533 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: C 619 ARG cc_start: 0.6671 (tpt-90) cc_final: 0.6365 (tpt90) REVERT: D 135 MET cc_start: 0.2863 (ttt) cc_final: 0.2507 (ttp) REVERT: D 445 ASP cc_start: 0.8292 (t0) cc_final: 0.8009 (t0) REVERT: D 650 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6019 (pp) REVERT: E 387 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8029 (mp) REVERT: E 409 ASP cc_start: 0.7956 (m-30) cc_final: 0.7569 (t0) REVERT: E 618 HIS cc_start: 0.4345 (OUTLIER) cc_final: 0.4042 (t70) REVERT: F 1 MET cc_start: 0.1534 (ppp) cc_final: 0.0861 (tmt) REVERT: F 387 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8500 (mp) REVERT: F 438 MET cc_start: 0.8011 (mtt) cc_final: 0.7681 (mtt) REVERT: F 623 ILE cc_start: 0.8135 (mm) cc_final: 0.7919 (mt) outliers start: 116 outliers final: 51 residues processed: 258 average time/residue: 0.5958 time to fit residues: 186.7679 Evaluate side-chains 217 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 152 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 404 ARG Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 620 LYS Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 618 HIS Chi-restraints excluded: chain C residue 620 LYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 255 GLN Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 438 MET Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 569 GLU Chi-restraints excluded: chain E residue 618 HIS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 460 ARG Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 622 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 74 optimal weight: 0.4980 chunk 117 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 375 optimal weight: 20.0000 chunk 166 optimal weight: 0.7980 chunk 22 optimal weight: 0.0000 chunk 128 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 HIS B 218 HIS B 564 ASN C 102 ASN C 280 GLN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN D 618 HIS E 361 HIS E 588 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.283105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.196517 restraints weight = 34106.230| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 2.24 r_work: 0.3967 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 32072 Z= 0.103 Angle : 0.529 10.038 43552 Z= 0.270 Chirality : 0.042 0.170 4752 Planarity : 0.004 0.058 5682 Dihedral : 4.245 54.732 4352 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.21 % Favored : 92.23 % Rotamer: Outliers : 3.09 % Allowed : 25.98 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -1.41 (0.14), residues: 3924 helix: 0.42 (0.15), residues: 1359 sheet: -0.87 (0.27), residues: 435 loop : -1.93 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 355 TYR 0.020 0.001 TYR C 398 PHE 0.021 0.001 PHE B 594 TRP 0.012 0.001 TRP C 228 HIS 0.013 0.001 HIS E 588 Details of bonding type rmsd covalent geometry : bond 0.00235 (32070) covalent geometry : angle 0.52881 (43548) SS BOND : bond 0.00399 ( 2) SS BOND : angle 1.48038 ( 4) hydrogen bonds : bond 0.02860 ( 998) hydrogen bonds : angle 4.66077 ( 2817) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 171 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.7132 (tm-30) REVERT: A 185 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7610 (mm) REVERT: A 220 MET cc_start: 0.8276 (tpp) cc_final: 0.7674 (tpt) REVERT: A 261 SER cc_start: 0.7790 (t) cc_final: 0.7344 (p) REVERT: A 275 GLU cc_start: 0.7417 (tm-30) cc_final: 0.6581 (tm-30) REVERT: A 534 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8240 (mtpt) REVERT: A 635 LYS cc_start: 0.7170 (mtmm) cc_final: 0.6646 (mptt) REVERT: B 135 MET cc_start: 0.4735 (mmp) cc_final: 0.4509 (mpm) REVERT: B 241 THR cc_start: 0.6712 (m) cc_final: 0.6507 (t) REVERT: B 283 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6794 (t0) REVERT: B 387 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8565 (mt) REVERT: B 469 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8062 (mt) REVERT: B 644 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: C 192 GLU cc_start: 0.2372 (OUTLIER) cc_final: 0.1313 (pm20) REVERT: C 226 ASP cc_start: 0.3348 (OUTLIER) cc_final: 0.2674 (p0) REVERT: C 287 MET cc_start: 0.1389 (OUTLIER) cc_final: 0.0924 (tmt) REVERT: C 333 GLU cc_start: 0.7935 (tt0) cc_final: 0.7597 (tp30) REVERT: C 434 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7817 (tt0) REVERT: C 533 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: C 619 ARG cc_start: 0.6405 (tpt-90) cc_final: 0.5996 (mmm160) REVERT: D 80 PHE cc_start: 0.3216 (OUTLIER) cc_final: 0.2716 (t80) REVERT: D 135 MET cc_start: 0.2813 (ttt) cc_final: 0.2490 (ttp) REVERT: D 445 ASP cc_start: 0.8135 (t0) cc_final: 0.7878 (t0) REVERT: D 650 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.5981 (pp) REVERT: E 38 GLU cc_start: 0.1655 (OUTLIER) cc_final: 0.1330 (mp0) REVERT: E 329 ASN cc_start: 0.9372 (OUTLIER) cc_final: 0.9020 (p0) REVERT: E 387 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7886 (mt) REVERT: E 618 HIS cc_start: 0.4368 (OUTLIER) cc_final: 0.4101 (t70) REVERT: E 644 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: F 1 MET cc_start: 0.1555 (ppp) cc_final: 0.0869 (tmt) REVERT: F 135 MET cc_start: 0.2003 (pmt) cc_final: 0.0677 (mtt) REVERT: F 400 ARG cc_start: 0.7154 (ttt-90) cc_final: 0.6935 (ttt-90) REVERT: F 438 MET cc_start: 0.7958 (mtt) cc_final: 0.7650 (mtt) REVERT: F 494 MET cc_start: 0.8228 (ppp) cc_final: 0.7791 (pp-130) REVERT: F 577 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7143 (mp) outliers start: 103 outliers final: 44 residues processed: 255 average time/residue: 0.5802 time to fit residues: 180.0086 Evaluate side-chains 221 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 158 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 404 ARG Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 620 LYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 558 CYS Chi-restraints excluded: chain E residue 569 GLU Chi-restraints excluded: chain E residue 618 HIS Chi-restraints excluded: chain E residue 644 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 351 ASP Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 460 ARG Chi-restraints excluded: chain F residue 577 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 176 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 300 optimal weight: 0.8980 chunk 262 optimal weight: 40.0000 chunk 49 optimal weight: 2.9990 chunk 224 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 328 optimal weight: 0.4980 chunk 76 optimal weight: 0.0770 chunk 68 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 HIS ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 HIS B 218 HIS ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN D 618 HIS E 288 GLN E 361 HIS F 448 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5112 r_free = 0.5112 target = 0.282474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.196452 restraints weight = 34002.802| |-----------------------------------------------------------------------------| r_work (start): 0.4491 rms_B_bonded: 2.02 r_work: 0.4179 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4063 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 32072 Z= 0.106 Angle : 0.536 12.447 43552 Z= 0.273 Chirality : 0.042 0.185 4752 Planarity : 0.004 0.059 5682 Dihedral : 4.111 54.028 4348 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.52 % Favored : 91.97 % Rotamer: Outliers : 2.79 % Allowed : 26.34 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -1.34 (0.14), residues: 3924 helix: 0.52 (0.15), residues: 1354 sheet: -0.92 (0.26), residues: 440 loop : -1.89 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 314 TYR 0.019 0.001 TYR C 398 PHE 0.021 0.001 PHE B 594 TRP 0.017 0.001 TRP D 67 HIS 0.007 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00244 (32070) covalent geometry : angle 0.53563 (43548) SS BOND : bond 0.00403 ( 2) SS BOND : angle 1.44333 ( 4) hydrogen bonds : bond 0.02811 ( 998) hydrogen bonds : angle 4.58951 ( 2817) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 169 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.8671 (tpp) cc_final: 0.8155 (tpt) REVERT: A 261 SER cc_start: 0.8064 (t) cc_final: 0.7629 (p) REVERT: A 275 GLU cc_start: 0.7600 (tm-30) cc_final: 0.6950 (tm-30) REVERT: A 580 MET cc_start: 0.5743 (mmm) cc_final: 0.5520 (mmm) REVERT: B 11 MET cc_start: 0.5888 (OUTLIER) cc_final: 0.5544 (pmm) REVERT: B 220 MET cc_start: 0.6999 (tmm) cc_final: 0.6486 (ptp) REVERT: B 283 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6214 (t70) REVERT: B 469 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8004 (mt) REVERT: B 471 ASP cc_start: 0.7857 (m-30) cc_final: 0.7627 (m-30) REVERT: B 644 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: C 192 GLU cc_start: 0.2510 (OUTLIER) cc_final: 0.1368 (pm20) REVERT: C 226 ASP cc_start: 0.2982 (OUTLIER) cc_final: 0.2470 (p0) REVERT: C 434 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7826 (tt0) REVERT: C 533 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.6971 (tt0) REVERT: C 619 ARG cc_start: 0.6100 (tpt-90) cc_final: 0.5850 (mmm160) REVERT: D 135 MET cc_start: 0.3230 (ttt) cc_final: 0.2840 (ttp) REVERT: D 650 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.5834 (pp) REVERT: E 38 GLU cc_start: 0.1401 (OUTLIER) cc_final: 0.1161 (mp0) REVERT: E 329 ASN cc_start: 0.9246 (OUTLIER) cc_final: 0.8866 (p0) REVERT: E 361 HIS cc_start: 0.8239 (OUTLIER) cc_final: 0.7494 (p-80) REVERT: E 387 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7734 (mt) REVERT: E 499 ASP cc_start: 0.3830 (OUTLIER) cc_final: 0.3551 (m-30) REVERT: F 1 MET cc_start: 0.1274 (ppp) cc_final: 0.0651 (tmt) REVERT: F 135 MET cc_start: 0.1791 (pmt) cc_final: 0.0393 (mtt) REVERT: F 438 MET cc_start: 0.8053 (mtt) cc_final: 0.7745 (mtt) REVERT: F 494 MET cc_start: 0.8384 (ppp) cc_final: 0.8040 (pp-130) REVERT: F 577 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7313 (mp) outliers start: 93 outliers final: 50 residues processed: 244 average time/residue: 0.6250 time to fit residues: 184.4836 Evaluate side-chains 217 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 153 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 620 LYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain E residue 361 HIS Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 569 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 351 ASP Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 577 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 333 optimal weight: 3.9990 chunk 358 optimal weight: 0.0970 chunk 229 optimal weight: 3.9990 chunk 334 optimal weight: 20.0000 chunk 270 optimal weight: 20.0000 chunk 154 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 340 optimal weight: 40.0000 chunk 193 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN C 238 GLN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN D 618 HIS E 361 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5121 r_free = 0.5121 target = 0.281131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.197145 restraints weight = 33349.814| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 3.11 r_work: 0.3834 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32072 Z= 0.151 Angle : 0.569 11.960 43552 Z= 0.288 Chirality : 0.043 0.236 4752 Planarity : 0.004 0.062 5682 Dihedral : 4.240 59.762 4348 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.18 % Favored : 91.31 % Rotamer: Outliers : 3.06 % Allowed : 26.22 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -1.36 (0.14), residues: 3924 helix: 0.48 (0.15), residues: 1349 sheet: -0.99 (0.26), residues: 441 loop : -1.87 (0.13), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 497 TYR 0.017 0.001 TYR C 398 PHE 0.021 0.001 PHE B 594 TRP 0.012 0.001 TRP D 67 HIS 0.021 0.001 HIS E 361 Details of bonding type rmsd covalent geometry : bond 0.00364 (32070) covalent geometry : angle 0.56882 (43548) SS BOND : bond 0.00711 ( 2) SS BOND : angle 1.86335 ( 4) hydrogen bonds : bond 0.03127 ( 998) hydrogen bonds : angle 4.62237 ( 2817) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 161 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.8255 (tpp) cc_final: 0.7631 (tpt) REVERT: A 275 GLU cc_start: 0.7492 (tm-30) cc_final: 0.6687 (tm-30) REVERT: A 329 ASN cc_start: 0.9216 (OUTLIER) cc_final: 0.8947 (p0) REVERT: A 580 MET cc_start: 0.5926 (mmm) cc_final: 0.5651 (mmm) REVERT: A 635 LYS cc_start: 0.7335 (mtmm) cc_final: 0.6700 (mptt) REVERT: B 11 MET cc_start: 0.5843 (OUTLIER) cc_final: 0.5578 (pmm) REVERT: B 135 MET cc_start: 0.4989 (mpm) cc_final: 0.4066 (tmm) REVERT: B 283 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.6406 (t70) REVERT: B 469 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8113 (mt) REVERT: B 471 ASP cc_start: 0.8510 (m-30) cc_final: 0.8286 (m-30) REVERT: B 571 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: B 644 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: C 192 GLU cc_start: 0.2397 (OUTLIER) cc_final: 0.1337 (pm20) REVERT: C 434 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8186 (mt-10) REVERT: C 494 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8533 (tpt) REVERT: C 533 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7090 (tt0) REVERT: C 619 ARG cc_start: 0.6546 (tpt-90) cc_final: 0.6073 (mmm160) REVERT: D 135 MET cc_start: 0.2638 (ttt) cc_final: 0.2356 (ttp) REVERT: D 445 ASP cc_start: 0.8495 (t0) cc_final: 0.8273 (t0) REVERT: D 517 LEU cc_start: 0.7303 (tm) cc_final: 0.6786 (pp) REVERT: E 38 GLU cc_start: 0.1488 (OUTLIER) cc_final: 0.1044 (mp0) REVERT: E 135 MET cc_start: 0.4516 (OUTLIER) cc_final: 0.4120 (mpp) REVERT: E 315 ARG cc_start: 0.7154 (mmt90) cc_final: 0.6869 (tpt170) REVERT: E 329 ASN cc_start: 0.9483 (OUTLIER) cc_final: 0.9226 (p0) REVERT: E 361 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.8273 (p-80) REVERT: E 387 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8070 (mp) REVERT: E 499 ASP cc_start: 0.3850 (OUTLIER) cc_final: 0.3531 (m-30) REVERT: F 1 MET cc_start: 0.1552 (ppp) cc_final: 0.0835 (tmt) REVERT: F 135 MET cc_start: 0.2104 (pmt) cc_final: 0.0831 (mtt) REVERT: F 438 MET cc_start: 0.8063 (mtt) cc_final: 0.7768 (mtt) outliers start: 102 outliers final: 57 residues processed: 242 average time/residue: 0.6067 time to fit residues: 179.0863 Evaluate side-chains 230 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 158 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 404 ARG Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 571 GLU Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 618 HIS Chi-restraints excluded: chain C residue 620 LYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain E residue 361 HIS Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 569 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 85 ARG Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 460 ARG Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 622 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 227 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 133 optimal weight: 20.0000 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 36 optimal weight: 0.0980 chunk 321 optimal weight: 20.0000 chunk 317 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN D 618 HIS E 64 HIS E 361 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5125 r_free = 0.5125 target = 0.281750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.197509 restraints weight = 33296.401| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 2.93 r_work: 0.3859 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32072 Z= 0.119 Angle : 0.557 13.742 43552 Z= 0.281 Chirality : 0.043 0.233 4752 Planarity : 0.004 0.065 5682 Dihedral : 4.207 59.638 4348 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.59 % Favored : 91.90 % Rotamer: Outliers : 2.82 % Allowed : 26.37 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -1.33 (0.14), residues: 3924 helix: 0.51 (0.15), residues: 1359 sheet: -0.95 (0.27), residues: 433 loop : -1.87 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 497 TYR 0.019 0.001 TYR C 398 PHE 0.021 0.001 PHE B 594 TRP 0.010 0.001 TRP D 67 HIS 0.026 0.001 HIS E 361 Details of bonding type rmsd covalent geometry : bond 0.00283 (32070) covalent geometry : angle 0.55714 (43548) SS BOND : bond 0.00538 ( 2) SS BOND : angle 1.62261 ( 4) hydrogen bonds : bond 0.02913 ( 998) hydrogen bonds : angle 4.59723 ( 2817) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 166 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.8243 (tpp) cc_final: 0.7733 (tpt) REVERT: A 275 GLU cc_start: 0.7450 (tm-30) cc_final: 0.6557 (tm-30) REVERT: A 329 ASN cc_start: 0.9168 (OUTLIER) cc_final: 0.8908 (p0) REVERT: A 635 LYS cc_start: 0.7324 (mtmm) cc_final: 0.6700 (mptt) REVERT: B 11 MET cc_start: 0.5794 (OUTLIER) cc_final: 0.5529 (pmm) REVERT: B 220 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6405 (ptp) REVERT: B 469 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8094 (mt) REVERT: B 471 ASP cc_start: 0.8502 (m-30) cc_final: 0.8268 (m-30) REVERT: B 644 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6514 (mp0) REVERT: C 192 GLU cc_start: 0.2423 (OUTLIER) cc_final: 0.1345 (pm20) REVERT: C 220 MET cc_start: 0.6500 (pmm) cc_final: 0.6238 (tmt) REVERT: C 226 ASP cc_start: 0.3475 (OUTLIER) cc_final: 0.2708 (p0) REVERT: C 434 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8140 (mt-10) REVERT: C 494 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8513 (tpt) REVERT: C 533 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7089 (tt0) REVERT: C 619 ARG cc_start: 0.6483 (tpt-90) cc_final: 0.5994 (mmm160) REVERT: D 135 MET cc_start: 0.2625 (ttt) cc_final: 0.2350 (ttp) REVERT: D 445 ASP cc_start: 0.8454 (t0) cc_final: 0.8225 (t0) REVERT: E 38 GLU cc_start: 0.1366 (OUTLIER) cc_final: 0.0901 (mp0) REVERT: E 135 MET cc_start: 0.4506 (OUTLIER) cc_final: 0.4123 (mpp) REVERT: E 315 ARG cc_start: 0.6886 (mmt90) cc_final: 0.6369 (tpt170) REVERT: E 329 ASN cc_start: 0.9441 (OUTLIER) cc_final: 0.9110 (p0) REVERT: E 387 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8101 (mp) REVERT: E 499 ASP cc_start: 0.3935 (OUTLIER) cc_final: 0.3610 (m-30) REVERT: E 643 ASP cc_start: 0.8165 (t0) cc_final: 0.7866 (t0) REVERT: F 1 MET cc_start: 0.1597 (ppp) cc_final: 0.0853 (tmt) REVERT: F 135 MET cc_start: 0.2177 (pmt) cc_final: 0.0961 (mtt) REVERT: F 438 MET cc_start: 0.8069 (mtt) cc_final: 0.7759 (mtt) REVERT: F 481 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: F 494 MET cc_start: 0.8225 (ppp) cc_final: 0.7849 (pp-130) outliers start: 94 outliers final: 61 residues processed: 239 average time/residue: 0.5940 time to fit residues: 171.8378 Evaluate side-chains 232 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 156 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 404 ARG Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 618 HIS Chi-restraints excluded: chain C residue 620 LYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 569 GLU Chi-restraints excluded: chain E residue 585 PHE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 85 ARG Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 460 ARG Chi-restraints excluded: chain F residue 481 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 92 optimal weight: 5.9990 chunk 264 optimal weight: 7.9990 chunk 250 optimal weight: 1.9990 chunk 362 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 126 optimal weight: 0.5980 chunk 205 optimal weight: 50.0000 chunk 61 optimal weight: 4.9990 chunk 163 optimal weight: 0.5980 chunk 326 optimal weight: 20.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN C 238 GLN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN D 618 HIS E 330 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5108 r_free = 0.5108 target = 0.279510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.195481 restraints weight = 33232.062| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 3.20 r_work: 0.3769 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 32072 Z= 0.199 Angle : 0.627 13.557 43552 Z= 0.318 Chirality : 0.045 0.226 4752 Planarity : 0.005 0.067 5682 Dihedral : 4.458 51.826 4348 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.49 % Favored : 91.00 % Rotamer: Outliers : 2.94 % Allowed : 26.19 % Favored : 70.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -1.46 (0.13), residues: 3924 helix: 0.33 (0.15), residues: 1361 sheet: -0.97 (0.27), residues: 426 loop : -1.90 (0.13), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 497 TYR 0.015 0.001 TYR C 398 PHE 0.020 0.001 PHE B 594 TRP 0.011 0.001 TRP E 475 HIS 0.008 0.001 HIS B 627 Details of bonding type rmsd covalent geometry : bond 0.00488 (32070) covalent geometry : angle 0.62627 (43548) SS BOND : bond 0.01152 ( 2) SS BOND : angle 2.38888 ( 4) hydrogen bonds : bond 0.03591 ( 998) hydrogen bonds : angle 4.71737 ( 2817) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 160 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.8170 (tpp) cc_final: 0.7545 (tpt) REVERT: A 261 SER cc_start: 0.7855 (t) cc_final: 0.7390 (p) REVERT: A 275 GLU cc_start: 0.7455 (tm-30) cc_final: 0.6541 (tm-30) REVERT: A 635 LYS cc_start: 0.7427 (mtmm) cc_final: 0.6915 (mptt) REVERT: B 220 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.6455 (ptp) REVERT: B 469 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8203 (mt) REVERT: B 644 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6428 (mp0) REVERT: C 192 GLU cc_start: 0.2428 (OUTLIER) cc_final: -0.0259 (pt0) REVERT: C 434 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8171 (mt-10) REVERT: C 494 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8501 (tpt) REVERT: C 533 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7205 (tt0) REVERT: C 619 ARG cc_start: 0.6609 (tpt-90) cc_final: 0.6101 (mmm160) REVERT: C 620 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8171 (mtpt) REVERT: C 630 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8303 (mt) REVERT: D 135 MET cc_start: 0.2590 (ttt) cc_final: 0.2318 (ttp) REVERT: D 220 MET cc_start: -0.0356 (pp-130) cc_final: -0.0622 (ppp) REVERT: D 445 ASP cc_start: 0.8539 (t0) cc_final: 0.8270 (t0) REVERT: D 517 LEU cc_start: 0.7307 (tm) cc_final: 0.6824 (pp) REVERT: E 315 ARG cc_start: 0.7351 (mmt90) cc_final: 0.6899 (tpt170) REVERT: E 387 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8188 (mp) REVERT: E 404 ARG cc_start: 0.8784 (mmm160) cc_final: 0.8539 (mmp80) REVERT: E 409 ASP cc_start: 0.8025 (m-30) cc_final: 0.7560 (t0) REVERT: E 499 ASP cc_start: 0.3987 (OUTLIER) cc_final: 0.3606 (m-30) REVERT: E 535 ARG cc_start: 0.5840 (mmm160) cc_final: 0.5225 (mmt90) REVERT: F 1 MET cc_start: 0.1786 (ppp) cc_final: 0.1103 (tmt) REVERT: F 438 MET cc_start: 0.8073 (mtt) cc_final: 0.7800 (mtt) REVERT: F 481 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: F 494 MET cc_start: 0.8160 (ppp) cc_final: 0.7767 (pp-130) outliers start: 98 outliers final: 54 residues processed: 238 average time/residue: 0.5894 time to fit residues: 170.0495 Evaluate side-chains 217 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 152 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 404 ARG Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 618 HIS Chi-restraints excluded: chain C residue 620 LYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 569 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 85 ARG Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 317 ARG Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 460 ARG Chi-restraints excluded: chain F residue 481 GLU Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 622 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 248 optimal weight: 8.9990 chunk 339 optimal weight: 5.9990 chunk 244 optimal weight: 0.0870 chunk 265 optimal weight: 0.9980 chunk 319 optimal weight: 0.0370 chunk 14 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 233 optimal weight: 0.9990 chunk 140 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 overall best weight: 1.2240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 GLN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 HIS E 361 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5095 r_free = 0.5095 target = 0.280410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.192590 restraints weight = 33872.619| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 2.19 r_work: 0.3909 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32072 Z= 0.142 Angle : 0.589 17.825 43552 Z= 0.297 Chirality : 0.043 0.221 4752 Planarity : 0.004 0.069 5682 Dihedral : 4.355 52.745 4348 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.93 % Favored : 91.56 % Rotamer: Outliers : 2.22 % Allowed : 26.88 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -1.37 (0.14), residues: 3924 helix: 0.43 (0.15), residues: 1358 sheet: -0.90 (0.27), residues: 427 loop : -1.86 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 497 TYR 0.018 0.001 TYR C 398 PHE 0.026 0.001 PHE B 594 TRP 0.009 0.001 TRP E 475 HIS 0.009 0.001 HIS E 361 Details of bonding type rmsd covalent geometry : bond 0.00343 (32070) covalent geometry : angle 0.58810 (43548) SS BOND : bond 0.00680 ( 2) SS BOND : angle 2.41908 ( 4) hydrogen bonds : bond 0.03096 ( 998) hydrogen bonds : angle 4.65755 ( 2817) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 160 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.8269 (tpp) cc_final: 0.7752 (tpt) REVERT: A 245 SER cc_start: 0.8216 (OUTLIER) cc_final: 0.7815 (m) REVERT: A 261 SER cc_start: 0.7951 (t) cc_final: 0.7484 (p) REVERT: A 275 GLU cc_start: 0.7456 (tm-30) cc_final: 0.6479 (tm-30) REVERT: A 635 LYS cc_start: 0.7387 (mtmm) cc_final: 0.6938 (mptt) REVERT: B 135 MET cc_start: 0.5221 (mpp) cc_final: 0.4554 (mmp) REVERT: B 220 MET cc_start: 0.6873 (OUTLIER) cc_final: 0.6464 (ptp) REVERT: B 469 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8095 (mt) REVERT: B 471 ASP cc_start: 0.8282 (m-30) cc_final: 0.7969 (m-30) REVERT: B 644 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6457 (mp0) REVERT: C 192 GLU cc_start: 0.2463 (OUTLIER) cc_final: -0.0265 (pt0) REVERT: C 434 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8057 (mt-10) REVERT: C 494 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8436 (tpt) REVERT: C 533 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7144 (tt0) REVERT: C 619 ARG cc_start: 0.6258 (tpt-90) cc_final: 0.5855 (mmm160) REVERT: C 630 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8230 (mt) REVERT: D 135 MET cc_start: 0.2692 (ttt) cc_final: 0.2360 (ttp) REVERT: D 220 MET cc_start: -0.0368 (pp-130) cc_final: -0.0660 (ppp) REVERT: D 404 ARG cc_start: 0.7058 (mmp80) cc_final: 0.6829 (mmp80) REVERT: D 445 ASP cc_start: 0.8284 (t0) cc_final: 0.8046 (t0) REVERT: E 315 ARG cc_start: 0.7148 (mmt90) cc_final: 0.6909 (tpt170) REVERT: E 329 ASN cc_start: 0.9455 (OUTLIER) cc_final: 0.9239 (p0) REVERT: E 387 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8019 (mp) REVERT: E 404 ARG cc_start: 0.8622 (mmm160) cc_final: 0.8365 (mmp80) REVERT: E 499 ASP cc_start: 0.3754 (OUTLIER) cc_final: 0.3379 (m-30) REVERT: E 535 ARG cc_start: 0.5942 (mmm160) cc_final: 0.5428 (mmt90) REVERT: E 643 ASP cc_start: 0.8112 (t0) cc_final: 0.7869 (t0) REVERT: F 1 MET cc_start: 0.1683 (ppp) cc_final: 0.1001 (tmt) REVERT: F 135 MET cc_start: 0.1895 (pmt) cc_final: 0.0495 (mtt) REVERT: F 400 ARG cc_start: 0.7220 (ttt-90) cc_final: 0.6969 (ttt-90) REVERT: F 438 MET cc_start: 0.8084 (mtt) cc_final: 0.7807 (mtt) REVERT: F 481 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7859 (mp0) outliers start: 74 outliers final: 51 residues processed: 221 average time/residue: 0.6710 time to fit residues: 177.8049 Evaluate side-chains 213 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 150 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 404 ARG Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 620 LYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain E residue 361 HIS Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 569 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 85 ARG Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 317 ARG Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 460 ARG Chi-restraints excluded: chain F residue 481 GLU Chi-restraints excluded: chain F residue 622 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 204 optimal weight: 30.0000 chunk 381 optimal weight: 3.9990 chunk 276 optimal weight: 9.9990 chunk 373 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 342 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 289 optimal weight: 0.0170 chunk 1 optimal weight: 1.9990 chunk 283 optimal weight: 20.0000 chunk 162 optimal weight: 0.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5098 r_free = 0.5098 target = 0.280783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.195782 restraints weight = 33993.714| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 2.47 r_work: 0.3882 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32072 Z= 0.126 Angle : 0.582 16.741 43552 Z= 0.292 Chirality : 0.043 0.219 4752 Planarity : 0.004 0.069 5682 Dihedral : 4.325 53.046 4348 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.98 % Favored : 91.54 % Rotamer: Outliers : 2.28 % Allowed : 26.91 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -1.33 (0.14), residues: 3924 helix: 0.46 (0.15), residues: 1359 sheet: -0.88 (0.27), residues: 427 loop : -1.84 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 314 TYR 0.018 0.001 TYR C 398 PHE 0.026 0.001 PHE B 594 TRP 0.009 0.001 TRP E 475 HIS 0.013 0.001 HIS E 361 Details of bonding type rmsd covalent geometry : bond 0.00300 (32070) covalent geometry : angle 0.58170 (43548) SS BOND : bond 0.00595 ( 2) SS BOND : angle 2.29857 ( 4) hydrogen bonds : bond 0.03014 ( 998) hydrogen bonds : angle 4.61928 ( 2817) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15589.30 seconds wall clock time: 265 minutes 5.85 seconds (15905.85 seconds total)