Starting phenix.real_space_refine on Fri Feb 6 13:15:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nm1_49528/02_2026/9nm1_49528.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nm1_49528/02_2026/9nm1_49528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nm1_49528/02_2026/9nm1_49528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nm1_49528/02_2026/9nm1_49528.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nm1_49528/02_2026/9nm1_49528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nm1_49528/02_2026/9nm1_49528.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 108 5.16 5 C 15525 2.51 5 N 4319 2.21 5 O 4931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 24914 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3908 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 482} Chain breaks: 2 Chain: "B" Number of atoms: 4147 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 532, 4136 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 509} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 532, 4136 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 509} Chain breaks: 1 bond proxies already assigned to first conformer: 4181 Chain: "C" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4206 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 519} Chain: "D" Number of atoms: 4197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4197 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 518} Chain: "E" Number of atoms: 4120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4120 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 509} Chain: "F" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3816 Classifications: {'peptide': 490} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 469} Chain breaks: 4 Chain: "K" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 90 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG B 396 " occ=0.43 ... (20 atoms not shown) pdb=" NH2BARG B 396 " occ=0.57 Time building chain proxies: 6.91, per 1000 atoms: 0.28 Number of scatterers: 24914 At special positions: 0 Unit cell: (147.96, 143.576, 151.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 P 31 15.00 O 4931 8.00 N 4319 7.00 C 15525 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5886 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 12 sheets defined 54.3% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 245 through 256 Processing helix chain 'A' and resid 262 through 270 removed outlier: 3.561A pdb=" N ILE A 266 " --> pdb=" O PRO A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 298 removed outlier: 3.532A pdb=" N ILE A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 320 through 325 Processing helix chain 'A' and resid 327 through 337 Processing helix chain 'A' and resid 367 through 380 removed outlier: 3.557A pdb=" N LYS A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 446 through 454 Processing helix chain 'A' and resid 460 through 478 Processing helix chain 'A' and resid 498 through 509 removed outlier: 3.670A pdb=" N PHE A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 523 removed outlier: 3.718A pdb=" N LEU A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 552 removed outlier: 3.588A pdb=" N SER A 537 " --> pdb=" O GLU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 580 Processing helix chain 'A' and resid 590 through 595 removed outlier: 3.640A pdb=" N LEU A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 612 removed outlier: 3.715A pdb=" N PHE A 610 " --> pdb=" O ILE A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 651 removed outlier: 3.545A pdb=" N LEU A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 677 Processing helix chain 'A' and resid 694 through 705 Processing helix chain 'A' and resid 708 through 723 Processing helix chain 'A' and resid 729 through 743 Processing helix chain 'A' and resid 745 through 758 removed outlier: 3.830A pdb=" N GLU A 749 " --> pdb=" O ASP A 745 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLU A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 245 through 255 Processing helix chain 'B' and resid 262 through 270 removed outlier: 3.541A pdb=" N GLY B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 removed outlier: 3.540A pdb=" N GLY B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 327 through 337 removed outlier: 3.616A pdb=" N ALA B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.932A pdb=" N VAL B 354 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 380 removed outlier: 3.554A pdb=" N ASP B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.551A pdb=" N LEU B 399 " --> pdb=" O AARG B 396 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 400 " --> pdb=" O LYS B 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 400' Processing helix chain 'B' and resid 402 through 406 removed outlier: 3.634A pdb=" N LEU B 405 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG B 406 " --> pdb=" O ALA B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 402 through 406' Processing helix chain 'B' and resid 420 through 432 Processing helix chain 'B' and resid 433 through 438 removed outlier: 3.614A pdb=" N ASN B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 454 removed outlier: 3.538A pdb=" N LEU B 450 " --> pdb=" O ASN B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 478 Processing helix chain 'B' and resid 490 through 495 removed outlier: 3.630A pdb=" N ALA B 493 " --> pdb=" O LYS B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 506 removed outlier: 3.518A pdb=" N PHE B 502 " --> pdb=" O THR B 498 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 506 " --> pdb=" O PHE B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 523 removed outlier: 3.556A pdb=" N CYS B 523 " --> pdb=" O ASP B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 551 removed outlier: 4.097A pdb=" N ASN B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 580 removed outlier: 3.917A pdb=" N LEU B 573 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B 580 " --> pdb=" O GLU B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 613 Processing helix chain 'B' and resid 640 through 651 removed outlier: 3.827A pdb=" N LEU B 644 " --> pdb=" O SER B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 Processing helix chain 'B' and resid 678 through 682 removed outlier: 3.717A pdb=" N CYS B 681 " --> pdb=" O ILE B 678 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE B 682 " --> pdb=" O LEU B 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 678 through 682' Processing helix chain 'B' and resid 693 through 705 removed outlier: 3.725A pdb=" N LEU B 697 " --> pdb=" O ASN B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 723 removed outlier: 3.837A pdb=" N ARG B 721 " --> pdb=" O ASN B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 743 removed outlier: 3.974A pdb=" N HIS B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 758 removed outlier: 4.410A pdb=" N LEU B 750 " --> pdb=" O PRO B 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 255 removed outlier: 3.541A pdb=" N THR C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 269 removed outlier: 3.522A pdb=" N ILE C 266 " --> pdb=" O PRO C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 Processing helix chain 'C' and resid 318 through 325 Processing helix chain 'C' and resid 327 through 337 Processing helix chain 'C' and resid 350 through 354 removed outlier: 4.044A pdb=" N VAL C 354 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.543A pdb=" N ASP C 380 " --> pdb=" O LEU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 446 through 454 Processing helix chain 'C' and resid 458 through 476 removed outlier: 3.580A pdb=" N ILE C 462 " --> pdb=" O SER C 458 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU C 463 " --> pdb=" O GLY C 459 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 506 removed outlier: 3.607A pdb=" N PHE C 502 " --> pdb=" O THR C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 523 removed outlier: 3.666A pdb=" N ASP C 519 " --> pdb=" O ILE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 552 removed outlier: 3.730A pdb=" N SER C 537 " --> pdb=" O GLU C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 582 removed outlier: 3.908A pdb=" N LEU C 573 " --> pdb=" O GLY C 569 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY C 582 " --> pdb=" O ALA C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 595 Processing helix chain 'C' and resid 598 through 613 removed outlier: 3.647A pdb=" N ALA C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 640 through 651 removed outlier: 3.501A pdb=" N LEU C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 676 Processing helix chain 'C' and resid 694 through 705 removed outlier: 3.548A pdb=" N ASN C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 722 removed outlier: 3.955A pdb=" N ARG C 721 " --> pdb=" O ASN C 717 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER C 722 " --> pdb=" O GLU C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 744 removed outlier: 3.611A pdb=" N THR C 735 " --> pdb=" O LYS C 731 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N HIS C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU C 744 " --> pdb=" O ALA C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 758 removed outlier: 4.283A pdb=" N LEU C 750 " --> pdb=" O PRO C 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 246 through 255 Processing helix chain 'D' and resid 262 through 270 Processing helix chain 'D' and resid 288 through 297 Processing helix chain 'D' and resid 318 through 323 removed outlier: 3.793A pdb=" N ILE D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 337 removed outlier: 3.951A pdb=" N ALA D 336 " --> pdb=" O ALA D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 341 removed outlier: 3.998A pdb=" N SER D 341 " --> pdb=" O GLY D 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 338 through 341' Processing helix chain 'D' and resid 350 through 354 removed outlier: 3.561A pdb=" N VAL D 354 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 380 removed outlier: 3.772A pdb=" N ASP D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.764A pdb=" N ARG D 406 " --> pdb=" O ALA D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 432 Processing helix chain 'D' and resid 433 through 438 Processing helix chain 'D' and resid 446 through 454 Processing helix chain 'D' and resid 458 through 479 removed outlier: 4.040A pdb=" N ILE D 462 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU D 463 " --> pdb=" O GLY D 459 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY D 464 " --> pdb=" O ALA D 460 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS D 476 " --> pdb=" O PHE D 472 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N THR D 477 " --> pdb=" O ALA D 473 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL D 478 " --> pdb=" O ILE D 474 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN D 479 " --> pdb=" O ASN D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 493 Processing helix chain 'D' and resid 498 through 506 removed outlier: 4.185A pdb=" N PHE D 502 " --> pdb=" O THR D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 524 removed outlier: 3.962A pdb=" N VAL D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 552 Processing helix chain 'D' and resid 569 through 580 removed outlier: 3.912A pdb=" N LEU D 573 " --> pdb=" O GLY D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 595 removed outlier: 3.849A pdb=" N LEU D 594 " --> pdb=" O SER D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 612 Processing helix chain 'D' and resid 625 through 630 removed outlier: 3.711A pdb=" N VAL D 630 " --> pdb=" O LEU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 651 removed outlier: 3.654A pdb=" N LEU D 644 " --> pdb=" O SER D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 677 Processing helix chain 'D' and resid 678 through 682 removed outlier: 3.907A pdb=" N CYS D 681 " --> pdb=" O ILE D 678 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE D 682 " --> pdb=" O LEU D 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 678 through 682' Processing helix chain 'D' and resid 693 through 705 removed outlier: 3.886A pdb=" N LEU D 697 " --> pdb=" O ASN D 693 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU D 703 " --> pdb=" O ASN D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 722 Processing helix chain 'D' and resid 729 through 744 removed outlier: 4.298A pdb=" N HIS D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP D 743 " --> pdb=" O THR D 739 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU D 744 " --> pdb=" O ALA D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 758 removed outlier: 4.473A pdb=" N LEU D 750 " --> pdb=" O PRO D 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 256 removed outlier: 3.504A pdb=" N PHE E 256 " --> pdb=" O PHE E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 260 Processing helix chain 'E' and resid 262 through 270 removed outlier: 4.411A pdb=" N ILE E 266 " --> pdb=" O PRO E 262 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU E 267 " --> pdb=" O PRO E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 298 removed outlier: 4.285A pdb=" N GLY E 295 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N THR E 296 " --> pdb=" O ARG E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 317 through 324 Processing helix chain 'E' and resid 327 through 338 Processing helix chain 'E' and resid 339 through 341 No H-bonds generated for 'chain 'E' and resid 339 through 341' Processing helix chain 'E' and resid 351 through 354 removed outlier: 3.851A pdb=" N VAL E 354 " --> pdb=" O LEU E 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 351 through 354' Processing helix chain 'E' and resid 366 through 381 removed outlier: 3.928A pdb=" N VAL E 371 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL E 372 " --> pdb=" O GLY E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 400 removed outlier: 3.574A pdb=" N LEU E 399 " --> pdb=" O ARG E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 405 Processing helix chain 'E' and resid 420 through 438 removed outlier: 5.002A pdb=" N LYS E 434 " --> pdb=" O ILE E 430 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N MET E 435 " --> pdb=" O GLN E 431 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN E 438 " --> pdb=" O LYS E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 454 removed outlier: 3.502A pdb=" N LEU E 450 " --> pdb=" O ASN E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 475 removed outlier: 3.559A pdb=" N PHE E 472 " --> pdb=" O SER E 468 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA E 473 " --> pdb=" O ALA E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 509 removed outlier: 3.556A pdb=" N PHE E 502 " --> pdb=" O THR E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 524 removed outlier: 3.576A pdb=" N VAL E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 552 removed outlier: 4.176A pdb=" N ASN E 536 " --> pdb=" O SER E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 582 removed outlier: 3.765A pdb=" N GLY E 582 " --> pdb=" O ALA E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 595 removed outlier: 3.796A pdb=" N LEU E 594 " --> pdb=" O SER E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 614 Processing helix chain 'E' and resid 625 through 630 removed outlier: 3.641A pdb=" N VAL E 630 " --> pdb=" O LEU E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 640 through 651 removed outlier: 3.568A pdb=" N LEU E 644 " --> pdb=" O SER E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 669 through 677 Processing helix chain 'E' and resid 678 through 682 removed outlier: 3.776A pdb=" N CYS E 681 " --> pdb=" O ILE E 678 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE E 682 " --> pdb=" O LEU E 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 678 through 682' Processing helix chain 'E' and resid 693 through 705 removed outlier: 3.583A pdb=" N LEU E 697 " --> pdb=" O ASN E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 708 through 723 removed outlier: 3.708A pdb=" N ARG E 721 " --> pdb=" O ASN E 717 " (cutoff:3.500A) Processing helix chain 'E' and resid 730 through 744 Processing helix chain 'E' and resid 746 through 758 removed outlier: 3.962A pdb=" N LEU E 750 " --> pdb=" O PRO E 746 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU E 752 " --> pdb=" O ASN E 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 246 No H-bonds generated for 'chain 'F' and resid 245 through 246' Processing helix chain 'F' and resid 248 through 248 No H-bonds generated for 'chain 'F' and resid 248 through 248' Processing helix chain 'F' and resid 249 through 255 Processing helix chain 'F' and resid 257 through 261 Processing helix chain 'F' and resid 262 through 270 removed outlier: 3.751A pdb=" N ILE F 266 " --> pdb=" O PRO F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 298 removed outlier: 3.750A pdb=" N GLY F 295 " --> pdb=" O ALA F 291 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR F 296 " --> pdb=" O ARG F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 317 through 327 removed outlier: 4.067A pdb=" N PHE F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 337 Processing helix chain 'F' and resid 350 through 355 removed outlier: 4.100A pdb=" N VAL F 354 " --> pdb=" O GLU F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 380 removed outlier: 3.986A pdb=" N VAL F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP F 380 " --> pdb=" O LEU F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 400 removed outlier: 3.633A pdb=" N LEU F 399 " --> pdb=" O ARG F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 438 removed outlier: 5.036A pdb=" N LYS F 434 " --> pdb=" O ILE F 430 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N MET F 435 " --> pdb=" O GLN F 431 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN F 438 " --> pdb=" O LYS F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 454 Processing helix chain 'F' and resid 458 through 478 removed outlier: 3.565A pdb=" N THR F 477 " --> pdb=" O ALA F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 491 through 495 Processing helix chain 'F' and resid 498 through 506 removed outlier: 3.618A pdb=" N PHE F 502 " --> pdb=" O THR F 498 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU F 506 " --> pdb=" O PHE F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 523 removed outlier: 3.652A pdb=" N CYS F 523 " --> pdb=" O ASP F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 552 removed outlier: 4.032A pdb=" N ASN F 536 " --> pdb=" O SER F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 582 removed outlier: 3.881A pdb=" N GLY F 582 " --> pdb=" O ALA F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 590 through 595 removed outlier: 3.947A pdb=" N LEU F 594 " --> pdb=" O SER F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 612 removed outlier: 3.719A pdb=" N ALA F 604 " --> pdb=" O SER F 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 630 removed outlier: 3.696A pdb=" N VAL F 630 " --> pdb=" O LEU F 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 651 removed outlier: 3.599A pdb=" N LEU F 644 " --> pdb=" O SER F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 669 through 676 Processing helix chain 'F' and resid 677 through 682 removed outlier: 4.119A pdb=" N SER F 680 " --> pdb=" O ASP F 677 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE F 682 " --> pdb=" O LEU F 679 " (cutoff:3.500A) Processing helix chain 'F' and resid 693 through 704 removed outlier: 3.638A pdb=" N LEU F 697 " --> pdb=" O ASN F 693 " (cutoff:3.500A) Processing helix chain 'F' and resid 708 through 721 removed outlier: 4.175A pdb=" N ILE F 716 " --> pdb=" O ARG F 712 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN F 717 " --> pdb=" O VAL F 713 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG F 721 " --> pdb=" O ASN F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 744 removed outlier: 4.370A pdb=" N HIS F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU F 744 " --> pdb=" O ALA F 740 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 757 Processing sheet with id=AA1, first strand: chain 'A' and resid 304 through 307 removed outlier: 6.249A pdb=" N LYS A 304 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASP A 349 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL A 306 " --> pdb=" O ASP A 349 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU A 277 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR A 394 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 279 " --> pdb=" O THR A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 586 through 589 removed outlier: 6.559A pdb=" N ARG A 587 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL A 558 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N THR A 665 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A 560 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N THR A 667 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ILE A 562 " --> pdb=" O THR A 667 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN A 684 " --> pdb=" O SER A 559 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 304 through 307 removed outlier: 3.606A pdb=" N MET B 393 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 277 " --> pdb=" O GLY B 392 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N THR B 394 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 279 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU B 278 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 585 through 589 removed outlier: 6.635A pdb=" N PHE B 585 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL B 622 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ARG B 587 " --> pdb=" O VAL B 622 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 561 " --> pdb=" O ILE B 686 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 344 through 348 removed outlier: 3.568A pdb=" N MET C 393 " --> pdb=" O PHE C 348 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU C 277 " --> pdb=" O GLY C 392 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N THR C 394 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU C 279 " --> pdb=" O THR C 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 586 through 589 removed outlier: 6.575A pdb=" N LEU C 621 " --> pdb=" O MET C 664 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N THR C 666 " --> pdb=" O LEU C 621 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE C 623 " --> pdb=" O THR C 666 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN C 684 " --> pdb=" O SER C 559 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 304 through 306 removed outlier: 3.705A pdb=" N MET D 393 " --> pdb=" O PHE D 348 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU D 277 " --> pdb=" O GLY D 392 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N THR D 394 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU D 279 " --> pdb=" O THR D 394 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU D 278 " --> pdb=" O VAL D 414 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 585 through 589 removed outlier: 3.946A pdb=" N PHE D 585 " --> pdb=" O LEU D 618 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL D 558 " --> pdb=" O ILE D 663 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N THR D 665 " --> pdb=" O VAL D 558 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU D 560 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR D 667 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE D 562 " --> pdb=" O THR D 667 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN D 684 " --> pdb=" O SER D 559 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 304 through 307 removed outlier: 6.194A pdb=" N LYS E 304 " --> pdb=" O ILE E 347 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP E 349 " --> pdb=" O LYS E 304 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL E 306 " --> pdb=" O ASP E 349 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU E 389 " --> pdb=" O HIS E 344 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE E 346 " --> pdb=" O LEU E 389 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET E 393 " --> pdb=" O PHE E 348 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU E 277 " --> pdb=" O GLY E 392 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N THR E 394 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU E 279 " --> pdb=" O THR E 394 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY E 276 " --> pdb=" O VAL E 412 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N VAL E 414 " --> pdb=" O GLY E 276 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU E 278 " --> pdb=" O VAL E 414 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 585 through 589 removed outlier: 3.609A pdb=" N ARG E 587 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL E 558 " --> pdb=" O ILE E 663 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N THR E 665 " --> pdb=" O VAL E 558 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU E 560 " --> pdb=" O THR E 665 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR E 667 " --> pdb=" O LEU E 560 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE E 562 " --> pdb=" O THR E 667 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN E 684 " --> pdb=" O SER E 559 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 276 through 280 removed outlier: 6.645A pdb=" N LEU F 277 " --> pdb=" O GLY F 392 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N THR F 394 " --> pdb=" O LEU F 277 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU F 279 " --> pdb=" O THR F 394 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N HIS F 344 " --> pdb=" O LEU F 389 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE F 391 " --> pdb=" O HIS F 344 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE F 346 " --> pdb=" O ILE F 391 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N MET F 393 " --> pdb=" O ILE F 346 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE F 348 " --> pdb=" O MET F 393 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS F 304 " --> pdb=" O ILE F 347 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASP F 349 " --> pdb=" O LYS F 304 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL F 306 " --> pdb=" O ASP F 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 585 through 589 removed outlier: 4.132A pdb=" N PHE F 585 " --> pdb=" O LEU F 618 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL F 558 " --> pdb=" O ILE F 663 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR F 665 " --> pdb=" O VAL F 558 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU F 560 " --> pdb=" O THR F 665 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N THR F 667 " --> pdb=" O LEU F 560 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE F 562 " --> pdb=" O THR F 667 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN F 684 " --> pdb=" O SER F 559 " (cutoff:3.500A) 1038 hydrogen bonds defined for protein. 3027 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.20 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4268 1.31 - 1.43: 5815 1.43 - 1.56: 14839 1.56 - 1.69: 51 1.69 - 1.82: 198 Bond restraints: 25171 Sorted by residual: bond pdb=" C ALA A 300 " pdb=" N LYS A 301 " ideal model delta sigma weight residual 1.330 1.394 -0.063 1.37e-02 5.33e+03 2.12e+01 bond pdb=" C ARG E 424 " pdb=" O ARG E 424 " ideal model delta sigma weight residual 1.236 1.181 0.056 1.29e-02 6.01e+03 1.86e+01 bond pdb=" C SER A 616 " pdb=" O SER A 616 " ideal model delta sigma weight residual 1.236 1.199 0.037 8.90e-03 1.26e+04 1.75e+01 bond pdb=" C ARG B 424 " pdb=" O ARG B 424 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.26e-02 6.30e+03 1.71e+01 bond pdb=" CA SER A 616 " pdb=" CB SER A 616 " ideal model delta sigma weight residual 1.535 1.486 0.049 1.21e-02 6.83e+03 1.64e+01 ... (remaining 25166 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 33154 1.77 - 3.55: 704 3.55 - 5.32: 106 5.32 - 7.10: 36 7.10 - 8.87: 9 Bond angle restraints: 34009 Sorted by residual: angle pdb=" O ALA A 300 " pdb=" C ALA A 300 " pdb=" N LYS A 301 " ideal model delta sigma weight residual 122.59 127.38 -4.79 1.33e+00 5.65e-01 1.29e+01 angle pdb=" C3' ATP C 801 " pdb=" C4' ATP C 801 " pdb=" O4' ATP C 801 " ideal model delta sigma weight residual 105.22 100.82 4.40 1.30e+00 5.94e-01 1.15e+01 angle pdb=" C3' ATP B 801 " pdb=" C4' ATP B 801 " pdb=" O4' ATP B 801 " ideal model delta sigma weight residual 105.22 100.86 4.36 1.30e+00 5.94e-01 1.13e+01 angle pdb=" N ARG E 424 " pdb=" CA ARG E 424 " pdb=" CB ARG E 424 " ideal model delta sigma weight residual 110.30 115.12 -4.82 1.54e+00 4.22e-01 9.80e+00 angle pdb=" C3' ATP F 801 " pdb=" C4' ATP F 801 " pdb=" O4' ATP F 801 " ideal model delta sigma weight residual 105.22 101.35 3.87 1.30e+00 5.94e-01 8.88e+00 ... (remaining 34004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.51: 14785 29.51 - 59.03: 877 59.03 - 88.54: 86 88.54 - 118.05: 4 118.05 - 147.56: 1 Dihedral angle restraints: 15753 sinusoidal: 6680 harmonic: 9073 Sorted by residual: dihedral pdb=" C2' ADP E 801 " pdb=" C1' ADP E 801 " pdb=" N9 ADP E 801 " pdb=" C4 ADP E 801 " ideal model delta sinusoidal sigma weight residual 91.55 -120.89 -147.56 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" O1B ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PB ADP E 801 " pdb=" PA ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 38.97 -98.97 1 2.00e+01 2.50e-03 2.77e+01 dihedral pdb=" CA ALA D 228 " pdb=" C ALA D 228 " pdb=" N VAL D 229 " pdb=" CA VAL D 229 " ideal model delta harmonic sigma weight residual -180.00 -155.57 -24.43 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 15750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3399 0.062 - 0.123: 451 0.123 - 0.185: 53 0.185 - 0.247: 5 0.247 - 0.308: 22 Chirality restraints: 3930 Sorted by residual: chirality pdb=" C2' ATP D 802 " pdb=" C1' ATP D 802 " pdb=" C3' ATP D 802 " pdb=" O2' ATP D 802 " both_signs ideal model delta sigma weight residual False -2.68 -2.99 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C2' ATP C 801 " pdb=" C1' ATP C 801 " pdb=" C3' ATP C 801 " pdb=" O2' ATP C 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.99 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C2' ATP B 801 " pdb=" C1' ATP B 801 " pdb=" C3' ATP B 801 " pdb=" O2' ATP B 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 3927 not shown) Planarity restraints: 4368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 603 " 0.016 2.00e-02 2.50e+03 3.16e-02 1.00e+01 pdb=" C ILE F 603 " -0.055 2.00e-02 2.50e+03 pdb=" O ILE F 603 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA F 604 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 392 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.21e+00 pdb=" C GLY D 392 " 0.046 2.00e-02 2.50e+03 pdb=" O GLY D 392 " -0.018 2.00e-02 2.50e+03 pdb=" N MET D 393 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 560 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C LEU C 560 " 0.046 2.00e-02 2.50e+03 pdb=" O LEU C 560 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU C 561 " -0.015 2.00e-02 2.50e+03 ... (remaining 4365 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 440 2.68 - 3.23: 23901 3.23 - 3.79: 34146 3.79 - 4.34: 44380 4.34 - 4.90: 77432 Nonbonded interactions: 180299 Sorted by model distance: nonbonded pdb=" N GLN F 657 " pdb=" OE1 GLN F 657 " model vdw 2.125 3.120 nonbonded pdb=" O GLY C 308 " pdb=" O HOH C 901 " model vdw 2.197 3.040 nonbonded pdb=" O SER E 722 " pdb=" O HOH E 901 " model vdw 2.203 3.040 nonbonded pdb=" OE2 GLU F 421 " pdb=" NZ LYS F 455 " model vdw 2.217 3.120 nonbonded pdb=" OD1 ASP F 352 " pdb=" OG1 THR F 394 " model vdw 2.228 3.040 ... (remaining 180294 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 245 through 246 or resid 248 through 357 or resid 366 thro \ ugh 395 or resid 397 through 413 or resid 419 through 758)) selection = (chain 'B' and (resid 245 through 246 or resid 248 through 357 or resid 366 thro \ ugh 395 or resid 397 through 413 or resid 419 through 478 or resid 491 through 7 \ 58)) selection = (chain 'C' and (resid 245 through 246 or resid 248 through 357 or resid 366 thro \ ugh 395 or resid 397 through 413 or resid 419 through 478 or resid 491 through 7 \ 58)) selection = (chain 'D' and (resid 245 through 246 or resid 248 through 357 or resid 366 thro \ ugh 395 or resid 397 through 413 or resid 419 through 478 or resid 491 through 7 \ 58)) selection = (chain 'E' and (resid 245 through 246 or resid 248 through 357 or resid 366 thro \ ugh 395 or resid 397 through 413 or resid 419 through 478 or resid 491 through 7 \ 58)) selection = (chain 'F' and (resid 245 through 395 or resid 397 through 478 or resid 491 thro \ ugh 758)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.290 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25171 Z= 0.223 Angle : 0.678 8.870 34009 Z= 0.360 Chirality : 0.048 0.308 3930 Planarity : 0.005 0.075 4368 Dihedral : 17.598 147.563 9867 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.03 % Favored : 94.81 % Rotamer: Outliers : 0.66 % Allowed : 15.61 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.15), residues: 3126 helix: 1.15 (0.15), residues: 1420 sheet: 0.30 (0.24), residues: 401 loop : -1.73 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 231 TYR 0.013 0.002 TYR E 614 PHE 0.022 0.002 PHE D 261 TRP 0.009 0.001 TRP B 632 HIS 0.003 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00497 (25171) covalent geometry : angle 0.67801 (34009) hydrogen bonds : bond 0.15959 ( 1038) hydrogen bonds : angle 5.32735 ( 3027) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 514 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8393 (m-40) REVERT: B 424 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8404 (mtm-85) REVERT: D 608 ASN cc_start: 0.8133 (m-40) cc_final: 0.7888 (m-40) REVERT: E 297 MET cc_start: 0.6925 (ttp) cc_final: 0.6549 (ttp) REVERT: E 328 LYS cc_start: 0.8437 (ptpt) cc_final: 0.8216 (ptpp) REVERT: E 334 TYR cc_start: 0.9026 (t80) cc_final: 0.8585 (t80) REVERT: E 398 ASP cc_start: 0.8636 (p0) cc_final: 0.8412 (p0) REVERT: F 660 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7304 (mtt180) outliers start: 18 outliers final: 4 residues processed: 527 average time/residue: 0.1921 time to fit residues: 152.4946 Evaluate side-chains 360 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 353 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain B residue 424 ARG Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain F residue 660 ARG Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 174 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.0000 chunk 298 optimal weight: 0.5980 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 756 GLN B 273 HIS B 386 ASN B 684 ASN B 742 HIS C 619 ASN C 657 GLN C 717 ASN E 373 ASN E 374 GLN E 657 GLN F 344 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.095945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.066815 restraints weight = 92220.343| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 5.05 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25171 Z= 0.125 Angle : 0.638 11.160 34009 Z= 0.325 Chirality : 0.041 0.166 3930 Planarity : 0.005 0.087 4368 Dihedral : 10.586 135.775 3708 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.48 % Favored : 95.36 % Rotamer: Outliers : 2.08 % Allowed : 18.75 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.16), residues: 3126 helix: 1.29 (0.14), residues: 1490 sheet: 0.49 (0.24), residues: 419 loop : -1.57 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 712 TYR 0.030 0.001 TYR E 334 PHE 0.021 0.001 PHE A 726 TRP 0.007 0.000 TRP B 632 HIS 0.007 0.001 HIS E 742 Details of bonding type rmsd covalent geometry : bond 0.00270 (25171) covalent geometry : angle 0.63789 (34009) hydrogen bonds : bond 0.03949 ( 1038) hydrogen bonds : angle 4.13756 ( 3027) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 388 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.9438 (tm-30) cc_final: 0.9041 (pp20) REVERT: A 321 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7917 (tm-30) REVERT: A 420 ASP cc_start: 0.8304 (t0) cc_final: 0.8062 (t0) REVERT: A 590 SER cc_start: 0.9251 (OUTLIER) cc_final: 0.8744 (t) REVERT: A 593 GLU cc_start: 0.8736 (mp0) cc_final: 0.8505 (mp0) REVERT: B 356 LYS cc_start: 0.9278 (mttm) cc_final: 0.8914 (mttm) REVERT: B 424 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8551 (mtm-85) REVERT: B 435 MET cc_start: 0.9759 (ptp) cc_final: 0.9549 (ptm) REVERT: B 627 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8312 (pm20) REVERT: B 707 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6242 (pp) REVERT: C 331 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8609 (mt-10) REVERT: C 385 LEU cc_start: 0.8724 (tt) cc_final: 0.8427 (tp) REVERT: C 441 MET cc_start: 0.9341 (ttp) cc_final: 0.9039 (ttp) REVERT: C 463 GLU cc_start: 0.8654 (tt0) cc_final: 0.8423 (mm-30) REVERT: C 597 MET cc_start: 0.8481 (mtp) cc_final: 0.8053 (mtp) REVERT: C 627 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8559 (pt0) REVERT: C 749 GLU cc_start: 0.8986 (tp30) cc_final: 0.8482 (tp30) REVERT: D 401 ASP cc_start: 0.8907 (t70) cc_final: 0.8682 (t0) REVERT: D 593 GLU cc_start: 0.9270 (mp0) cc_final: 0.8890 (mp0) REVERT: D 608 ASN cc_start: 0.9520 (m-40) cc_final: 0.9286 (m-40) REVERT: E 320 GLU cc_start: 0.9215 (mt-10) cc_final: 0.9005 (mp0) REVERT: E 331 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8866 (mt-10) REVERT: E 384 GLN cc_start: 0.9416 (mp10) cc_final: 0.9133 (mp10) REVERT: E 593 GLU cc_start: 0.9281 (mp0) cc_final: 0.8985 (pm20) REVERT: E 597 MET cc_start: 0.9231 (mtm) cc_final: 0.8850 (mtm) REVERT: F 267 GLU cc_start: 0.9509 (tm-30) cc_final: 0.9293 (pp20) REVERT: F 301 LYS cc_start: 0.9344 (tptt) cc_final: 0.9046 (ttpp) REVERT: F 627 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8620 (pm20) REVERT: F 701 MET cc_start: 0.9601 (mmm) cc_final: 0.9290 (tpt) outliers start: 57 outliers final: 31 residues processed: 431 average time/residue: 0.1645 time to fit residues: 112.6880 Evaluate side-chains 386 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 349 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 424 ARG Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 598 SER Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 598 SER Chi-restraints excluded: chain F residue 600 SER Chi-restraints excluded: chain F residue 627 GLU Chi-restraints excluded: chain F residue 660 ARG Chi-restraints excluded: chain F residue 756 GLN Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 179 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 267 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 196 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 282 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 284 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 GLN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 HIS B 756 GLN ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.092402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.062344 restraints weight = 142399.803| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 6.17 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25171 Z= 0.201 Angle : 0.625 13.105 34009 Z= 0.319 Chirality : 0.042 0.163 3930 Planarity : 0.004 0.067 4368 Dihedral : 10.106 125.320 3703 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.74 % Favored : 95.10 % Rotamer: Outliers : 2.89 % Allowed : 18.71 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.16), residues: 3126 helix: 1.44 (0.14), residues: 1495 sheet: 0.69 (0.24), residues: 407 loop : -1.38 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 712 TYR 0.013 0.001 TYR E 334 PHE 0.019 0.001 PHE A 726 TRP 0.005 0.001 TRP B 632 HIS 0.008 0.001 HIS E 742 Details of bonding type rmsd covalent geometry : bond 0.00467 (25171) covalent geometry : angle 0.62548 (34009) hydrogen bonds : bond 0.04164 ( 1038) hydrogen bonds : angle 4.14929 ( 3027) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 340 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.9486 (tm-30) cc_final: 0.9198 (pp20) REVERT: A 321 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8031 (tm-30) REVERT: A 353 SER cc_start: 0.9537 (m) cc_final: 0.9272 (p) REVERT: A 356 LYS cc_start: 0.8896 (mtmm) cc_final: 0.8552 (mtmm) REVERT: B 356 LYS cc_start: 0.9321 (mttm) cc_final: 0.8946 (mttm) REVERT: B 424 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8812 (mtm-85) REVERT: B 519 ASP cc_start: 0.9334 (m-30) cc_final: 0.9081 (m-30) REVERT: B 627 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8438 (pm20) REVERT: B 676 MET cc_start: 0.9478 (mtm) cc_final: 0.9180 (mtm) REVERT: B 754 MET cc_start: 0.9430 (mmm) cc_final: 0.9202 (mmm) REVERT: C 331 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8599 (mt-10) REVERT: C 441 MET cc_start: 0.9286 (ttp) cc_final: 0.8970 (ttp) REVERT: C 463 GLU cc_start: 0.8645 (tt0) cc_final: 0.8370 (mm-30) REVERT: C 597 MET cc_start: 0.8683 (mtp) cc_final: 0.8261 (mtp) REVERT: C 614 TYR cc_start: 0.9096 (m-80) cc_final: 0.7779 (m-80) REVERT: C 640 SER cc_start: 0.9581 (m) cc_final: 0.9163 (t) REVERT: C 678 ILE cc_start: 0.9444 (tt) cc_final: 0.9193 (tp) REVERT: C 749 GLU cc_start: 0.9103 (tp30) cc_final: 0.8618 (tp30) REVERT: D 521 LYS cc_start: 0.9672 (ttmm) cc_final: 0.9241 (mtmm) REVERT: D 593 GLU cc_start: 0.9349 (mp0) cc_final: 0.8919 (mp0) REVERT: D 608 ASN cc_start: 0.9576 (m-40) cc_final: 0.9333 (m-40) REVERT: E 320 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8994 (mp0) REVERT: E 646 MET cc_start: 0.8825 (tmm) cc_final: 0.8400 (tmm) REVERT: E 701 MET cc_start: 0.9403 (tpp) cc_final: 0.9155 (tpp) REVERT: F 267 GLU cc_start: 0.9554 (tm-30) cc_final: 0.9134 (pt0) REVERT: F 297 MET cc_start: 0.8525 (tmm) cc_final: 0.8299 (ppp) REVERT: F 593 GLU cc_start: 0.9257 (mp0) cc_final: 0.9022 (mp0) REVERT: F 701 MET cc_start: 0.9594 (mmm) cc_final: 0.9325 (mmm) outliers start: 79 outliers final: 44 residues processed: 398 average time/residue: 0.1623 time to fit residues: 103.2979 Evaluate side-chains 365 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 319 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 424 ARG Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 726 PHE Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 417 HIS Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 SER Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain E residue 737 ILE Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 660 ARG Chi-restraints excluded: chain F residue 756 GLN Chi-restraints excluded: chain K residue 172 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 178 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 250 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 239 optimal weight: 10.0000 chunk 252 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN A 657 GLN B 413 GLN B 742 HIS C 384 GLN C 536 ASN ** E 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.089061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.060279 restraints weight = 128195.047| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 5.93 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25171 Z= 0.146 Angle : 0.604 13.909 34009 Z= 0.307 Chirality : 0.041 0.181 3930 Planarity : 0.004 0.067 4368 Dihedral : 9.762 116.821 3703 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.51 % Favored : 95.36 % Rotamer: Outliers : 2.41 % Allowed : 19.81 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.16), residues: 3126 helix: 1.60 (0.14), residues: 1492 sheet: 0.68 (0.24), residues: 412 loop : -1.29 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 253 TYR 0.012 0.001 TYR E 531 PHE 0.019 0.001 PHE A 256 TRP 0.005 0.001 TRP B 632 HIS 0.009 0.001 HIS E 742 Details of bonding type rmsd covalent geometry : bond 0.00341 (25171) covalent geometry : angle 0.60358 (34009) hydrogen bonds : bond 0.03626 ( 1038) hydrogen bonds : angle 3.93511 ( 3027) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 330 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.9457 (tm-30) cc_final: 0.9154 (pp20) REVERT: A 321 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7946 (tm-30) REVERT: A 353 SER cc_start: 0.9515 (m) cc_final: 0.9231 (p) REVERT: A 356 LYS cc_start: 0.8940 (mtmm) cc_final: 0.8661 (mtmm) REVERT: A 590 SER cc_start: 0.9356 (OUTLIER) cc_final: 0.9055 (t) REVERT: A 593 GLU cc_start: 0.8896 (mp0) cc_final: 0.8656 (mp0) REVERT: A 627 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8221 (mp0) REVERT: B 356 LYS cc_start: 0.9332 (mttm) cc_final: 0.8954 (mttm) REVERT: B 424 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8772 (mtm-85) REVERT: B 519 ASP cc_start: 0.9299 (m-30) cc_final: 0.9014 (m-30) REVERT: B 627 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8402 (pm20) REVERT: B 676 MET cc_start: 0.9415 (mtm) cc_final: 0.9106 (mtm) REVERT: B 754 MET cc_start: 0.9417 (mmm) cc_final: 0.9180 (mmm) REVERT: C 245 ASP cc_start: 0.9428 (OUTLIER) cc_final: 0.9165 (m-30) REVERT: C 441 MET cc_start: 0.9279 (ttp) cc_final: 0.8876 (ttp) REVERT: C 463 GLU cc_start: 0.8608 (tt0) cc_final: 0.8336 (mm-30) REVERT: C 597 MET cc_start: 0.8669 (mtp) cc_final: 0.8243 (mtp) REVERT: C 614 TYR cc_start: 0.9071 (m-80) cc_final: 0.7674 (m-80) REVERT: C 627 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8456 (pm20) REVERT: C 640 SER cc_start: 0.9612 (m) cc_final: 0.9183 (t) REVERT: C 678 ILE cc_start: 0.9478 (tt) cc_final: 0.9187 (tp) REVERT: C 749 GLU cc_start: 0.9008 (tp30) cc_final: 0.8605 (tp30) REVERT: D 521 LYS cc_start: 0.9680 (ttmm) cc_final: 0.9249 (mtmm) REVERT: D 608 ASN cc_start: 0.9584 (m-40) cc_final: 0.9334 (m-40) REVERT: E 320 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8995 (mp0) REVERT: E 413 GLN cc_start: 0.9580 (mt0) cc_final: 0.8968 (mp10) REVERT: E 593 GLU cc_start: 0.9249 (mp0) cc_final: 0.9026 (mp0) REVERT: E 646 MET cc_start: 0.8971 (tmm) cc_final: 0.8689 (tmm) REVERT: E 691 MET cc_start: 0.7338 (ptp) cc_final: 0.6941 (ptp) REVERT: E 701 MET cc_start: 0.9426 (tpp) cc_final: 0.9128 (tpp) REVERT: F 267 GLU cc_start: 0.9551 (tm-30) cc_final: 0.9160 (pt0) REVERT: F 593 GLU cc_start: 0.9273 (mp0) cc_final: 0.9044 (mp0) REVERT: F 701 MET cc_start: 0.9596 (mmm) cc_final: 0.9333 (mmm) outliers start: 66 outliers final: 40 residues processed: 380 average time/residue: 0.1688 time to fit residues: 101.8666 Evaluate side-chains 352 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 306 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 424 ARG Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 726 PHE Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain E residue 248 PHE Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 417 HIS Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 SER Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain F residue 293 LYS Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 660 ARG Chi-restraints excluded: chain F residue 756 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 66 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 200 optimal weight: 0.4980 chunk 201 optimal weight: 9.9990 chunk 246 optimal weight: 7.9990 chunk 307 optimal weight: 0.9980 chunk 159 optimal weight: 0.2980 chunk 124 optimal weight: 3.9990 chunk 265 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 HIS C 384 GLN E 507 ASN F 344 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.090197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.062311 restraints weight = 94902.797| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 5.07 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25171 Z= 0.101 Angle : 0.572 14.081 34009 Z= 0.289 Chirality : 0.040 0.163 3930 Planarity : 0.004 0.067 4368 Dihedral : 9.238 107.927 3701 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.58 % Favored : 95.33 % Rotamer: Outliers : 2.60 % Allowed : 19.77 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.16), residues: 3126 helix: 1.75 (0.14), residues: 1483 sheet: 0.79 (0.24), residues: 410 loop : -1.18 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 335 TYR 0.014 0.001 TYR E 531 PHE 0.022 0.001 PHE A 256 TRP 0.004 0.000 TRP B 632 HIS 0.015 0.001 HIS E 742 Details of bonding type rmsd covalent geometry : bond 0.00221 (25171) covalent geometry : angle 0.57203 (34009) hydrogen bonds : bond 0.02908 ( 1038) hydrogen bonds : angle 3.67452 ( 3027) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 350 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.9435 (tm-30) cc_final: 0.9125 (pp20) REVERT: A 321 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7940 (tm-30) REVERT: A 353 SER cc_start: 0.9517 (m) cc_final: 0.9268 (p) REVERT: A 548 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8346 (tm-30) REVERT: A 590 SER cc_start: 0.9376 (OUTLIER) cc_final: 0.8732 (t) REVERT: A 593 GLU cc_start: 0.8967 (mp0) cc_final: 0.8561 (pm20) REVERT: A 597 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.8996 (ptp) REVERT: B 356 LYS cc_start: 0.9330 (mttm) cc_final: 0.8974 (mttm) REVERT: B 424 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8656 (mtm-85) REVERT: B 519 ASP cc_start: 0.9300 (m-30) cc_final: 0.8995 (m-30) REVERT: B 528 MET cc_start: 0.8717 (tpp) cc_final: 0.8443 (tpp) REVERT: B 627 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: B 752 GLU cc_start: 0.9495 (OUTLIER) cc_final: 0.9070 (pt0) REVERT: B 754 MET cc_start: 0.9415 (mmm) cc_final: 0.9168 (mmm) REVERT: C 331 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8501 (mt-10) REVERT: C 441 MET cc_start: 0.9341 (ttp) cc_final: 0.8923 (ttp) REVERT: C 463 GLU cc_start: 0.8560 (tt0) cc_final: 0.8260 (mm-30) REVERT: C 597 MET cc_start: 0.8498 (mtp) cc_final: 0.8059 (mtp) REVERT: C 614 TYR cc_start: 0.9006 (m-80) cc_final: 0.7581 (m-80) REVERT: C 627 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8573 (pm20) REVERT: C 631 ASP cc_start: 0.9136 (m-30) cc_final: 0.8927 (m-30) REVERT: C 640 SER cc_start: 0.9578 (m) cc_final: 0.9125 (t) REVERT: C 678 ILE cc_start: 0.9421 (tt) cc_final: 0.9098 (tp) REVERT: C 749 GLU cc_start: 0.8967 (tp30) cc_final: 0.8640 (tp30) REVERT: D 321 GLU cc_start: 0.9108 (tp30) cc_final: 0.8781 (tp30) REVERT: D 521 LYS cc_start: 0.9675 (ttmm) cc_final: 0.9333 (mtmm) REVERT: D 608 ASN cc_start: 0.9563 (m-40) cc_final: 0.9298 (m-40) REVERT: E 320 GLU cc_start: 0.9227 (mt-10) cc_final: 0.9024 (mp0) REVERT: E 413 GLN cc_start: 0.9583 (mt0) cc_final: 0.8970 (mp-120) REVERT: E 593 GLU cc_start: 0.9225 (mp0) cc_final: 0.8942 (pm20) REVERT: E 605 TYR cc_start: 0.9556 (t80) cc_final: 0.9316 (t80) REVERT: E 646 MET cc_start: 0.9064 (tmm) cc_final: 0.8401 (tmm) REVERT: E 691 MET cc_start: 0.7122 (ptp) cc_final: 0.6741 (ptp) REVERT: E 701 MET cc_start: 0.9463 (tpp) cc_final: 0.9137 (tpp) REVERT: F 267 GLU cc_start: 0.9534 (tm-30) cc_final: 0.9137 (pt0) REVERT: F 349 ASP cc_start: 0.9556 (t0) cc_final: 0.9279 (p0) REVERT: F 440 MET cc_start: 0.8715 (ptp) cc_final: 0.8493 (pmm) REVERT: F 593 GLU cc_start: 0.9273 (mp0) cc_final: 0.9045 (mp0) REVERT: F 608 ASN cc_start: 0.9626 (m-40) cc_final: 0.9253 (m-40) REVERT: F 701 MET cc_start: 0.9581 (mmm) cc_final: 0.9188 (tpp) outliers start: 71 outliers final: 38 residues processed: 403 average time/residue: 0.1600 time to fit residues: 103.3545 Evaluate side-chains 366 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 322 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 424 ARG Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 597 MET Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 248 PHE Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 417 HIS Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 SER Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 688 VAL Chi-restraints excluded: chain F residue 756 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 50 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 256 optimal weight: 8.9990 chunk 209 optimal weight: 7.9990 chunk 307 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN A 657 GLN A 756 GLN B 742 HIS C 344 HIS C 748 ASN D 541 ASN F 344 HIS ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.090624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.061524 restraints weight = 115247.542| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 5.46 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25171 Z= 0.225 Angle : 0.641 12.199 34009 Z= 0.325 Chirality : 0.042 0.162 3930 Planarity : 0.005 0.098 4368 Dihedral : 9.189 109.221 3697 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.28 % Favored : 94.62 % Rotamer: Outliers : 2.74 % Allowed : 20.07 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.16), residues: 3126 helix: 1.71 (0.14), residues: 1490 sheet: 0.72 (0.24), residues: 419 loop : -1.14 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 611 TYR 0.015 0.001 TYR E 531 PHE 0.025 0.001 PHE A 256 TRP 0.004 0.001 TRP C 632 HIS 0.010 0.001 HIS E 742 Details of bonding type rmsd covalent geometry : bond 0.00524 (25171) covalent geometry : angle 0.64109 (34009) hydrogen bonds : bond 0.04091 ( 1038) hydrogen bonds : angle 4.02528 ( 3027) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 310 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8565 (tm-30) REVERT: A 321 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8036 (tm-30) REVERT: A 353 SER cc_start: 0.9525 (m) cc_final: 0.9308 (p) REVERT: A 398 ASP cc_start: 0.8907 (p0) cc_final: 0.8674 (p0) REVERT: A 415 GLU cc_start: 0.8875 (tt0) cc_final: 0.8638 (tm-30) REVERT: A 590 SER cc_start: 0.9306 (OUTLIER) cc_final: 0.8562 (t) REVERT: A 593 GLU cc_start: 0.9042 (mp0) cc_final: 0.8563 (pm20) REVERT: A 676 MET cc_start: 0.9345 (mtm) cc_final: 0.8909 (mtm) REVERT: B 356 LYS cc_start: 0.9353 (mttm) cc_final: 0.8982 (mttm) REVERT: B 424 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8836 (mtm-85) REVERT: B 517 GLU cc_start: 0.9127 (tp30) cc_final: 0.8307 (tp30) REVERT: B 519 ASP cc_start: 0.9371 (m-30) cc_final: 0.9068 (m-30) REVERT: B 528 MET cc_start: 0.8794 (tpp) cc_final: 0.8548 (tpp) REVERT: B 627 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8399 (pm20) REVERT: B 752 GLU cc_start: 0.9493 (OUTLIER) cc_final: 0.9060 (pt0) REVERT: B 754 MET cc_start: 0.9464 (mmm) cc_final: 0.9186 (mmm) REVERT: C 331 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8599 (mt-10) REVERT: C 597 MET cc_start: 0.8655 (mtp) cc_final: 0.8311 (mtp) REVERT: C 614 TYR cc_start: 0.9097 (m-80) cc_final: 0.7604 (m-80) REVERT: C 627 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: C 640 SER cc_start: 0.9673 (m) cc_final: 0.9282 (t) REVERT: C 678 ILE cc_start: 0.9463 (tt) cc_final: 0.9097 (tp) REVERT: D 521 LYS cc_start: 0.9681 (ttmm) cc_final: 0.9358 (mtmm) REVERT: D 608 ASN cc_start: 0.9613 (m-40) cc_final: 0.9351 (m-40) REVERT: D 701 MET cc_start: 0.9468 (ptp) cc_final: 0.8871 (tmm) REVERT: E 320 GLU cc_start: 0.9242 (mt-10) cc_final: 0.9025 (mp0) REVERT: E 413 GLN cc_start: 0.9640 (mt0) cc_final: 0.8955 (mp-120) REVERT: E 605 TYR cc_start: 0.9596 (t80) cc_final: 0.9361 (t80) REVERT: E 646 MET cc_start: 0.9070 (tmm) cc_final: 0.8470 (tmm) REVERT: E 691 MET cc_start: 0.7546 (ptp) cc_final: 0.7329 (ptp) REVERT: E 701 MET cc_start: 0.9454 (tpp) cc_final: 0.9116 (tpp) REVERT: E 726 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7979 (t80) REVERT: F 267 GLU cc_start: 0.9554 (tm-30) cc_final: 0.9125 (pt0) REVERT: F 349 ASP cc_start: 0.9536 (t0) cc_final: 0.9267 (p0) REVERT: F 379 MET cc_start: 0.7341 (tmm) cc_final: 0.7073 (tmm) REVERT: F 593 GLU cc_start: 0.9241 (mp0) cc_final: 0.9013 (mp0) REVERT: F 701 MET cc_start: 0.9639 (mmm) cc_final: 0.9329 (mmm) outliers start: 75 outliers final: 47 residues processed: 368 average time/residue: 0.1547 time to fit residues: 91.2385 Evaluate side-chains 352 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 298 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 424 ARG Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 633 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 248 PHE Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 417 HIS Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 SER Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 726 PHE Chi-restraints excluded: chain E residue 737 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 633 VAL Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 688 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 16 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 310 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 GLN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 HIS C 727 ASN E 507 ASN E 657 GLN F 344 HIS F 426 GLN ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.091615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.062089 restraints weight = 141551.831| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 6.11 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25171 Z= 0.136 Angle : 0.591 13.128 34009 Z= 0.300 Chirality : 0.041 0.172 3930 Planarity : 0.004 0.090 4368 Dihedral : 9.050 106.050 3697 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.74 % Favored : 95.16 % Rotamer: Outliers : 2.08 % Allowed : 21.02 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.16), residues: 3126 helix: 1.81 (0.14), residues: 1489 sheet: 0.78 (0.24), residues: 419 loop : -1.10 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 259 TYR 0.014 0.001 TYR E 531 PHE 0.014 0.001 PHE E 513 TRP 0.003 0.000 TRP B 632 HIS 0.014 0.001 HIS E 742 Details of bonding type rmsd covalent geometry : bond 0.00315 (25171) covalent geometry : angle 0.59129 (34009) hydrogen bonds : bond 0.03388 ( 1038) hydrogen bonds : angle 3.76816 ( 3027) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 310 time to evaluate : 1.043 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 267 GLU cc_start: 0.9502 (tm-30) cc_final: 0.9044 (pp20) REVERT: A 310 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8597 (tm-30) REVERT: A 321 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7986 (tm-30) REVERT: A 353 SER cc_start: 0.9505 (m) cc_final: 0.9286 (p) REVERT: A 398 ASP cc_start: 0.8936 (p0) cc_final: 0.8722 (p0) REVERT: A 415 GLU cc_start: 0.8873 (tt0) cc_final: 0.8649 (tm-30) REVERT: A 590 SER cc_start: 0.9313 (OUTLIER) cc_final: 0.8559 (t) REVERT: A 593 GLU cc_start: 0.9078 (mp0) cc_final: 0.8612 (pm20) REVERT: B 356 LYS cc_start: 0.9381 (mttm) cc_final: 0.9049 (mttm) REVERT: B 424 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8808 (mtm-85) REVERT: B 519 ASP cc_start: 0.9361 (m-30) cc_final: 0.9086 (m-30) REVERT: B 627 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8442 (pm20) REVERT: B 752 GLU cc_start: 0.9497 (OUTLIER) cc_final: 0.9084 (pt0) REVERT: B 754 MET cc_start: 0.9477 (mmm) cc_final: 0.9201 (mmm) REVERT: C 321 GLU cc_start: 0.9492 (OUTLIER) cc_final: 0.8995 (tp30) REVERT: C 331 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8576 (mt-10) REVERT: C 597 MET cc_start: 0.8592 (mtp) cc_final: 0.8252 (mtp) REVERT: C 614 TYR cc_start: 0.9064 (m-80) cc_final: 0.7669 (m-80) REVERT: C 627 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8660 (pt0) REVERT: C 640 SER cc_start: 0.9659 (m) cc_final: 0.9267 (t) REVERT: D 321 GLU cc_start: 0.9093 (tp30) cc_final: 0.8734 (tp30) REVERT: D 521 LYS cc_start: 0.9677 (ttmm) cc_final: 0.9394 (mtmm) REVERT: D 608 ASN cc_start: 0.9598 (m-40) cc_final: 0.9323 (m-40) REVERT: E 320 GLU cc_start: 0.9238 (mt-10) cc_final: 0.9022 (mp0) REVERT: E 593 GLU cc_start: 0.9262 (mp0) cc_final: 0.8961 (mp0) REVERT: E 605 TYR cc_start: 0.9588 (t80) cc_final: 0.9374 (t80) REVERT: E 646 MET cc_start: 0.9090 (tmm) cc_final: 0.8461 (tmm) REVERT: E 691 MET cc_start: 0.7615 (ptp) cc_final: 0.7354 (ptp) REVERT: E 701 MET cc_start: 0.9499 (tpp) cc_final: 0.9187 (tpp) REVERT: E 726 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7944 (t80) REVERT: F 267 GLU cc_start: 0.9568 (tm-30) cc_final: 0.9128 (pt0) REVERT: F 349 ASP cc_start: 0.9517 (t0) cc_final: 0.9252 (p0) REVERT: F 608 ASN cc_start: 0.9641 (m-40) cc_final: 0.9273 (m-40) REVERT: F 701 MET cc_start: 0.9614 (mmm) cc_final: 0.9163 (tpp) outliers start: 57 outliers final: 42 residues processed: 353 average time/residue: 0.1551 time to fit residues: 87.8262 Evaluate side-chains 358 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 308 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 424 ARG Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 726 PHE Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 633 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 248 PHE Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 417 HIS Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 SER Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 726 PHE Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 688 VAL Chi-restraints excluded: chain F residue 726 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 151 optimal weight: 3.9990 chunk 263 optimal weight: 0.1980 chunk 162 optimal weight: 8.9990 chunk 304 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 chunk 299 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 742 HIS C 727 ASN F 344 HIS ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.087755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.059465 restraints weight = 102650.057| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 5.28 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25171 Z= 0.154 Angle : 0.607 12.508 34009 Z= 0.305 Chirality : 0.041 0.165 3930 Planarity : 0.004 0.082 4368 Dihedral : 8.963 105.239 3697 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.94 % Rotamer: Outliers : 2.38 % Allowed : 20.94 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.16), residues: 3126 helix: 1.85 (0.14), residues: 1496 sheet: 0.79 (0.24), residues: 419 loop : -1.09 (0.19), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 611 TYR 0.015 0.001 TYR E 531 PHE 0.016 0.001 PHE E 513 TRP 0.003 0.000 TRP B 632 HIS 0.013 0.001 HIS E 742 Details of bonding type rmsd covalent geometry : bond 0.00360 (25171) covalent geometry : angle 0.60704 (34009) hydrogen bonds : bond 0.03422 ( 1038) hydrogen bonds : angle 3.76623 ( 3027) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 310 time to evaluate : 1.052 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 267 GLU cc_start: 0.9475 (tm-30) cc_final: 0.8981 (pp20) REVERT: A 310 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8577 (tm-30) REVERT: A 321 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8013 (tm-30) REVERT: A 353 SER cc_start: 0.9490 (m) cc_final: 0.9279 (p) REVERT: A 398 ASP cc_start: 0.8932 (p0) cc_final: 0.8729 (p0) REVERT: A 415 GLU cc_start: 0.8895 (tt0) cc_final: 0.8636 (tm-30) REVERT: A 590 SER cc_start: 0.9258 (OUTLIER) cc_final: 0.8468 (t) REVERT: A 593 GLU cc_start: 0.9099 (mp0) cc_final: 0.8632 (pm20) REVERT: B 356 LYS cc_start: 0.9368 (mttm) cc_final: 0.9013 (mttm) REVERT: B 424 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8790 (mtm-85) REVERT: B 517 GLU cc_start: 0.9168 (tp30) cc_final: 0.8300 (tp30) REVERT: B 519 ASP cc_start: 0.9377 (m-30) cc_final: 0.9103 (m-30) REVERT: B 627 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8482 (pm20) REVERT: B 752 GLU cc_start: 0.9509 (OUTLIER) cc_final: 0.9134 (pt0) REVERT: B 754 MET cc_start: 0.9484 (mmm) cc_final: 0.9210 (mmm) REVERT: C 314 LYS cc_start: 0.9519 (ttmt) cc_final: 0.9250 (ttpp) REVERT: C 321 GLU cc_start: 0.9502 (OUTLIER) cc_final: 0.8980 (tp30) REVERT: C 331 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8535 (mt-10) REVERT: C 597 MET cc_start: 0.8549 (mtp) cc_final: 0.8198 (mtp) REVERT: C 614 TYR cc_start: 0.9122 (m-80) cc_final: 0.7826 (m-80) REVERT: C 627 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8657 (pt0) REVERT: C 640 SER cc_start: 0.9657 (m) cc_final: 0.9252 (t) REVERT: D 321 GLU cc_start: 0.9119 (tp30) cc_final: 0.8736 (tp30) REVERT: D 328 LYS cc_start: 0.9204 (mtmm) cc_final: 0.8855 (mtmm) REVERT: D 521 LYS cc_start: 0.9665 (ttmm) cc_final: 0.9397 (mtmm) REVERT: D 608 ASN cc_start: 0.9598 (m-40) cc_final: 0.9326 (m-40) REVERT: E 320 GLU cc_start: 0.9243 (mt-10) cc_final: 0.9026 (mp0) REVERT: E 331 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8726 (mt-10) REVERT: E 413 GLN cc_start: 0.9645 (mt0) cc_final: 0.8932 (mp10) REVERT: E 593 GLU cc_start: 0.9248 (mp0) cc_final: 0.8933 (mp0) REVERT: E 605 TYR cc_start: 0.9583 (t80) cc_final: 0.9369 (t80) REVERT: E 646 MET cc_start: 0.9103 (tmm) cc_final: 0.8500 (tmm) REVERT: E 691 MET cc_start: 0.7699 (ptp) cc_final: 0.7414 (ptp) REVERT: E 701 MET cc_start: 0.9502 (tpp) cc_final: 0.9166 (tpp) REVERT: E 726 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7902 (t80) REVERT: F 267 GLU cc_start: 0.9568 (tm-30) cc_final: 0.9124 (pt0) REVERT: F 349 ASP cc_start: 0.9501 (t0) cc_final: 0.9244 (p0) REVERT: F 379 MET cc_start: 0.7403 (tmm) cc_final: 0.7189 (tmm) REVERT: F 593 GLU cc_start: 0.9247 (mp0) cc_final: 0.8985 (pm20) REVERT: F 608 ASN cc_start: 0.9640 (m-40) cc_final: 0.9276 (m-40) REVERT: F 701 MET cc_start: 0.9629 (mmm) cc_final: 0.9162 (tpp) outliers start: 65 outliers final: 46 residues processed: 360 average time/residue: 0.1531 time to fit residues: 88.5106 Evaluate side-chains 355 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 301 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 424 ARG Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 726 PHE Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 633 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 417 HIS Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 SER Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 726 PHE Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 633 VAL Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 688 VAL Chi-restraints excluded: chain F residue 726 PHE Chi-restraints excluded: chain K residue 172 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 198 optimal weight: 0.0980 chunk 203 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 242 optimal weight: 0.9980 chunk 245 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 218 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 243 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 727 ASN F 344 HIS ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.088131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.060116 restraints weight = 91327.232| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 5.07 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25171 Z= 0.107 Angle : 0.599 13.511 34009 Z= 0.301 Chirality : 0.040 0.202 3930 Planarity : 0.004 0.078 4368 Dihedral : 8.723 100.585 3697 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 1.39 % Allowed : 22.04 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.16), residues: 3126 helix: 1.91 (0.14), residues: 1493 sheet: 0.88 (0.24), residues: 420 loop : -1.00 (0.19), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 611 TYR 0.016 0.001 TYR E 531 PHE 0.017 0.001 PHE E 513 TRP 0.004 0.000 TRP B 632 HIS 0.014 0.001 HIS E 742 Details of bonding type rmsd covalent geometry : bond 0.00239 (25171) covalent geometry : angle 0.59851 (34009) hydrogen bonds : bond 0.02781 ( 1038) hydrogen bonds : angle 3.55954 ( 3027) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 327 time to evaluate : 0.985 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 267 GLU cc_start: 0.9471 (tm-30) cc_final: 0.8983 (pp20) REVERT: A 321 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7928 (tm-30) REVERT: A 353 SER cc_start: 0.9468 (m) cc_final: 0.9256 (p) REVERT: A 590 SER cc_start: 0.9260 (OUTLIER) cc_final: 0.8706 (t) REVERT: A 593 GLU cc_start: 0.9140 (mp0) cc_final: 0.8738 (pm20) REVERT: A 676 MET cc_start: 0.9233 (mtm) cc_final: 0.8752 (mtm) REVERT: B 353 SER cc_start: 0.9605 (t) cc_final: 0.9400 (p) REVERT: B 356 LYS cc_start: 0.9368 (mttm) cc_final: 0.9042 (mttm) REVERT: B 383 ASP cc_start: 0.9310 (m-30) cc_final: 0.8900 (m-30) REVERT: B 519 ASP cc_start: 0.9350 (m-30) cc_final: 0.9114 (m-30) REVERT: B 627 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8203 (pm20) REVERT: B 752 GLU cc_start: 0.9502 (OUTLIER) cc_final: 0.9162 (pt0) REVERT: B 754 MET cc_start: 0.9456 (mmm) cc_final: 0.9199 (mmm) REVERT: C 314 LYS cc_start: 0.9500 (ttmt) cc_final: 0.9254 (ttpp) REVERT: C 331 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8480 (mt-10) REVERT: C 597 MET cc_start: 0.8342 (mtp) cc_final: 0.8022 (mtp) REVERT: C 614 TYR cc_start: 0.9115 (m-80) cc_final: 0.7861 (m-80) REVERT: C 627 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8749 (pt0) REVERT: C 640 SER cc_start: 0.9609 (m) cc_final: 0.9183 (t) REVERT: D 321 GLU cc_start: 0.9126 (tp30) cc_final: 0.8720 (tp30) REVERT: D 328 LYS cc_start: 0.9197 (mtmm) cc_final: 0.8857 (mtmm) REVERT: D 521 LYS cc_start: 0.9657 (ttmm) cc_final: 0.9399 (mtmm) REVERT: D 608 ASN cc_start: 0.9572 (m-40) cc_final: 0.9307 (m-40) REVERT: E 320 GLU cc_start: 0.9237 (mt-10) cc_final: 0.9036 (mp0) REVERT: E 331 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8733 (mt-10) REVERT: E 413 GLN cc_start: 0.9643 (mt0) cc_final: 0.8879 (mp-120) REVERT: E 593 GLU cc_start: 0.9252 (mp0) cc_final: 0.8913 (mp0) REVERT: E 605 TYR cc_start: 0.9545 (t80) cc_final: 0.9326 (t80) REVERT: E 646 MET cc_start: 0.9037 (tmm) cc_final: 0.8521 (tmm) REVERT: E 691 MET cc_start: 0.7658 (ptp) cc_final: 0.7329 (ptp) REVERT: E 701 MET cc_start: 0.9523 (tpp) cc_final: 0.9175 (tpp) REVERT: F 267 GLU cc_start: 0.9568 (tm-30) cc_final: 0.9145 (pt0) REVERT: F 349 ASP cc_start: 0.9523 (t0) cc_final: 0.9217 (p0) REVERT: F 379 MET cc_start: 0.7518 (tmm) cc_final: 0.7302 (tmm) REVERT: F 440 MET cc_start: 0.8580 (pmm) cc_final: 0.8280 (pmm) REVERT: F 593 GLU cc_start: 0.9262 (mp0) cc_final: 0.8954 (pm20) REVERT: F 608 ASN cc_start: 0.9626 (m-40) cc_final: 0.9237 (m-40) REVERT: F 701 MET cc_start: 0.9603 (mmm) cc_final: 0.9160 (tpp) outliers start: 38 outliers final: 32 residues processed: 356 average time/residue: 0.1520 time to fit residues: 86.8414 Evaluate side-chains 352 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 316 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 726 PHE Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 633 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 417 HIS Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 SER Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 633 VAL Chi-restraints excluded: chain F residue 688 VAL Chi-restraints excluded: chain F residue 726 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 156 optimal weight: 2.9990 chunk 222 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 294 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 727 ASN F 344 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.091634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.064160 restraints weight = 112961.742| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 6.33 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25171 Z= 0.140 Angle : 0.621 12.518 34009 Z= 0.313 Chirality : 0.041 0.202 3930 Planarity : 0.004 0.069 4368 Dihedral : 8.608 101.333 3693 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.58 % Favored : 95.33 % Rotamer: Outliers : 1.50 % Allowed : 22.11 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.16), residues: 3126 helix: 1.92 (0.14), residues: 1495 sheet: 0.92 (0.24), residues: 419 loop : -0.95 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 335 TYR 0.016 0.001 TYR E 531 PHE 0.018 0.001 PHE E 513 TRP 0.002 0.000 TRP B 632 HIS 0.013 0.001 HIS E 742 Details of bonding type rmsd covalent geometry : bond 0.00324 (25171) covalent geometry : angle 0.62064 (34009) hydrogen bonds : bond 0.03107 ( 1038) hydrogen bonds : angle 3.68941 ( 3027) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 311 time to evaluate : 1.072 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 267 GLU cc_start: 0.9452 (tm-30) cc_final: 0.8965 (pp20) REVERT: A 321 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8023 (tm-30) REVERT: A 590 SER cc_start: 0.9247 (OUTLIER) cc_final: 0.8682 (t) REVERT: A 593 GLU cc_start: 0.9149 (mp0) cc_final: 0.8738 (pm20) REVERT: A 676 MET cc_start: 0.9240 (mtm) cc_final: 0.8761 (mtm) REVERT: B 353 SER cc_start: 0.9599 (t) cc_final: 0.9396 (p) REVERT: B 356 LYS cc_start: 0.9294 (mttm) cc_final: 0.8980 (mttm) REVERT: B 383 ASP cc_start: 0.9342 (m-30) cc_final: 0.8953 (m-30) REVERT: B 519 ASP cc_start: 0.9370 (m-30) cc_final: 0.9137 (m-30) REVERT: B 529 MET cc_start: 0.9199 (mtm) cc_final: 0.8693 (mpp) REVERT: B 627 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8231 (pm20) REVERT: B 752 GLU cc_start: 0.9512 (OUTLIER) cc_final: 0.9177 (pt0) REVERT: B 754 MET cc_start: 0.9483 (mmm) cc_final: 0.9214 (mmm) REVERT: C 314 LYS cc_start: 0.9501 (ttmt) cc_final: 0.9261 (ttpp) REVERT: C 331 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8506 (mt-10) REVERT: C 441 MET cc_start: 0.9103 (ttt) cc_final: 0.8609 (ttm) REVERT: C 597 MET cc_start: 0.8031 (mtp) cc_final: 0.7667 (mtp) REVERT: C 627 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8619 (pm20) REVERT: C 640 SER cc_start: 0.9630 (m) cc_final: 0.9192 (t) REVERT: D 302 GLU cc_start: 0.9258 (tp30) cc_final: 0.9011 (tp30) REVERT: D 321 GLU cc_start: 0.9154 (tp30) cc_final: 0.8753 (tp30) REVERT: D 328 LYS cc_start: 0.9213 (mtmm) cc_final: 0.8882 (mtmm) REVERT: D 521 LYS cc_start: 0.9656 (ttmm) cc_final: 0.9401 (mtmm) REVERT: D 608 ASN cc_start: 0.9580 (m-40) cc_final: 0.9338 (m-40) REVERT: E 320 GLU cc_start: 0.9268 (mt-10) cc_final: 0.9042 (mp0) REVERT: E 413 GLN cc_start: 0.9638 (mt0) cc_final: 0.8869 (mp-120) REVERT: E 593 GLU cc_start: 0.9301 (mp0) cc_final: 0.8913 (mp0) REVERT: E 605 TYR cc_start: 0.9489 (t80) cc_final: 0.9254 (t80) REVERT: E 624 ASP cc_start: 0.9280 (t0) cc_final: 0.8436 (p0) REVERT: E 646 MET cc_start: 0.9079 (tmm) cc_final: 0.8504 (tmm) REVERT: E 691 MET cc_start: 0.7683 (ptp) cc_final: 0.7390 (ptp) REVERT: E 701 MET cc_start: 0.9526 (tpp) cc_final: 0.9186 (tpp) REVERT: F 267 GLU cc_start: 0.9534 (tm-30) cc_final: 0.9151 (pt0) REVERT: F 379 MET cc_start: 0.7931 (tmm) cc_final: 0.7663 (tmm) REVERT: F 593 GLU cc_start: 0.9270 (mp0) cc_final: 0.8934 (pm20) REVERT: F 608 ASN cc_start: 0.9633 (m-40) cc_final: 0.9282 (m-40) REVERT: F 701 MET cc_start: 0.9620 (mmm) cc_final: 0.9148 (tpp) outliers start: 41 outliers final: 37 residues processed: 344 average time/residue: 0.1687 time to fit residues: 92.5945 Evaluate side-chains 349 residues out of total 2734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 308 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 726 PHE Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 633 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 417 HIS Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 SER Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 688 VAL Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 633 VAL Chi-restraints excluded: chain F residue 688 VAL Chi-restraints excluded: chain F residue 726 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 110 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 313 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 chunk 177 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 727 ASN F 344 HIS K 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.090497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.061224 restraints weight = 131577.375| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 6.01 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25171 Z= 0.117 Angle : 0.610 12.968 34009 Z= 0.306 Chirality : 0.040 0.200 3930 Planarity : 0.004 0.075 4368 Dihedral : 8.545 100.138 3693 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.32 % Favored : 95.58 % Rotamer: Outliers : 1.64 % Allowed : 22.22 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.16), residues: 3126 helix: 1.92 (0.14), residues: 1495 sheet: 0.94 (0.24), residues: 420 loop : -0.93 (0.19), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 611 TYR 0.018 0.001 TYR C 614 PHE 0.019 0.001 PHE E 513 TRP 0.002 0.000 TRP F 632 HIS 0.014 0.001 HIS E 742 Details of bonding type rmsd covalent geometry : bond 0.00269 (25171) covalent geometry : angle 0.60963 (34009) hydrogen bonds : bond 0.02982 ( 1038) hydrogen bonds : angle 3.62211 ( 3027) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5608.39 seconds wall clock time: 96 minutes 59.96 seconds (5819.96 seconds total)