Starting phenix.real_space_refine on Mon Sep 14 20:34:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5a1a_2984/09_2026/5a1a_2984.cif Found real_map, /net/cci-nas-00/data/ceres_data/5a1a_2984/09_2026/5a1a_2984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5a1a_2984/09_2026/5a1a_2984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5a1a_2984/09_2026/5a1a_2984.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5a1a_2984/09_2026/5a1a_2984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5a1a_2984/09_2026/5a1a_2984.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5a1a_2984/09_2026/5a1a_2984.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5a1a_2984/09_2026/5a1a_2984.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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: 6 Type Number sf(0) Gaussians Mg 8 5.21 5 S 160 5.16 5 Na 8 4.78 5 C 20816 2.51 5 N 5808 2.21 5 O 6896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33696 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8206 Classifications: {'peptide': 1022} Link IDs: {'CIS': 9, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 950} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' MG': 2, ' NA': 2, 'PTQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "B" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "C" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "D" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Restraints were copied for chains: B, C, D Time building chain proxies: 12.10, per 1000 atoms: 0.36 Number of scatterers: 33696 At special positions: 0 Unit cell: (191.737, 147.147, 102.557, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 160 16.00 Mg 8 11.99 Na 8 11.00 O 6896 8.00 N 5808 7.00 C 20816 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: 2.84 Conformation dependent library (CDL) restraints added in 1.3 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7608 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 64 sheets defined 15.5% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 removed outlier: 3.736A pdb=" N ARG A 13 " --> pdb=" O VAL A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 130 through 136 removed outlier: 3.780A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 368 through 381 Processing helix chain 'A' and resid 395 through 406 removed outlier: 3.698A pdb=" N TYR A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 448 removed outlier: 3.500A pdb=" N GLU A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N MET A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.672A pdb=" N ASP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.983A pdb=" N LEU A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.923A pdb=" N TYR A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 removed outlier: 3.742A pdb=" N CYS A 602 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 624 Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 805 through 814 Processing helix chain 'A' and resid 963 through 970 removed outlier: 3.624A pdb=" N MET A 968 " --> pdb=" O GLN A 964 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 969 " --> pdb=" O GLN A 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 13 removed outlier: 3.736A pdb=" N ARG B 13 " --> pdb=" O VAL B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 130 through 136 removed outlier: 3.780A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 368 through 381 Processing helix chain 'B' and resid 395 through 406 removed outlier: 3.698A pdb=" N TYR B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 448 removed outlier: 3.500A pdb=" N GLU B 438 " --> pdb=" O PRO B 434 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG B 442 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N MET B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.672A pdb=" N ASP B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 removed outlier: 3.983A pdb=" N LEU B 524 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER B 525 " --> pdb=" O LYS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.923A pdb=" N TYR B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 603 removed outlier: 3.742A pdb=" N CYS B 602 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 805 through 814 Processing helix chain 'B' and resid 963 through 970 removed outlier: 3.624A pdb=" N MET B 968 " --> pdb=" O GLN B 964 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 969 " --> pdb=" O GLN B 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 13 removed outlier: 3.736A pdb=" N ARG C 13 " --> pdb=" O VAL C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 130 through 136 removed outlier: 3.780A pdb=" N LEU C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 368 through 381 Processing helix chain 'C' and resid 395 through 406 removed outlier: 3.698A pdb=" N TYR C 399 " --> pdb=" O HIS C 395 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 448 removed outlier: 3.500A pdb=" N GLU C 438 " --> pdb=" O PRO C 434 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C 442 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N MET C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.672A pdb=" N ASP C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 removed outlier: 3.983A pdb=" N LEU C 524 " --> pdb=" O ILE C 520 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER C 525 " --> pdb=" O LYS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.923A pdb=" N TYR C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP C 553 " --> pdb=" O PHE C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 603 removed outlier: 3.742A pdb=" N CYS C 602 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 624 Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 805 through 814 Processing helix chain 'C' and resid 963 through 970 removed outlier: 3.624A pdb=" N MET C 968 " --> pdb=" O GLN C 964 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 969 " --> pdb=" O GLN C 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 13 removed outlier: 3.736A pdb=" N ARG D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 130 through 136 removed outlier: 3.780A pdb=" N LEU D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 368 through 381 Processing helix chain 'D' and resid 395 through 406 removed outlier: 3.698A pdb=" N TYR D 399 " --> pdb=" O HIS D 395 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 448 removed outlier: 3.500A pdb=" N GLU D 438 " --> pdb=" O PRO D 434 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N MET D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 479 removed outlier: 3.672A pdb=" N ASP D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 removed outlier: 3.983A pdb=" N LEU D 524 " --> pdb=" O ILE D 520 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER D 525 " --> pdb=" O LYS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.923A pdb=" N TYR D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP D 553 " --> pdb=" O PHE D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 603 removed outlier: 3.742A pdb=" N CYS D 602 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 624 Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 805 through 814 Processing helix chain 'D' and resid 963 through 970 removed outlier: 3.624A pdb=" N MET D 968 " --> pdb=" O GLN D 964 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU D 969 " --> pdb=" O GLN D 965 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'A' and resid 23 through 24 removed outlier: 5.390A pdb=" N TRP A 158 " --> pdb=" O CYS A 154 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS A 154 " --> pdb=" O TRP A 158 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 160 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR A 126 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N GLU A 57 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AC, first strand: chain 'A' and resid 99 through 101 removed outlier: 3.642A pdb=" N ILE A 99 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR A 101 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET A 202 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AE, first strand: chain 'A' and resid 221 through 227 removed outlier: 5.847A pdb=" N ILE A 222 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N CYS A 247 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'A' and resid 230 through 231 Processing sheet with id=AG, first strand: chain 'A' and resid 288 through 296 Processing sheet with id=AH, first strand: chain 'A' and resid 265 through 273 removed outlier: 5.543A pdb=" N GLN A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN A 262 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 268 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 272 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 256 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR A 309 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP A 329 " --> pdb=" O TYR A 309 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA A 311 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA A 327 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 313 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ALA A 325 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU A 315 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AI, first strand: chain 'A' and resid 335 through 338 Processing sheet with id=AJ, first strand: chain 'A' and resid 484 through 485 removed outlier: 7.291A pdb=" N ASP A 411 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP A 456 " --> pdb=" O ASP A 411 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS A 389 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU A 412 " --> pdb=" O CYS A 389 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA A 386 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU A 535 " --> pdb=" O GLN A 563 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY A 565 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLU A 537 " --> pdb=" O GLY A 565 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A 567 " --> pdb=" O GLU A 537 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA A 539 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing sheet with id=AK, first strand: chain 'A' and resid 575 through 578 Processing sheet with id=AL, first strand: chain 'A' and resid 627 through 629 Processing sheet with id=AM, first strand: chain 'A' and resid 661 through 670 removed outlier: 6.349A pdb=" N LEU A 658 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU A 650 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLY A 692 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ALA A 723 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU A 694 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG A 721 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU A 696 " --> pdb=" O GLN A 719 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN A 719 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 698 " --> pdb=" O TRP A 717 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TRP A 717 " --> pdb=" O VAL A 698 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A 700 " --> pdb=" O SER A 715 " (cutoff:3.500A) Processing sheet with id=AN, first strand: chain 'A' and resid 739 through 742 removed outlier: 6.331A pdb=" N ARG A 755 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET A 768 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLN A 757 " --> pdb=" O SER A 766 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 770 " --> pdb=" O LYS A 773 " (cutoff:3.500A) Processing sheet with id=AO, first strand: chain 'A' and resid 776 through 783 removed outlier: 16.896A pdb=" N ARG A 881 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 12.429A pdb=" N ARG A 781 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A 885 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR A 982 " --> pdb=" O CYS A 886 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU A 984 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.409A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASP A 954 " --> pdb=" O GLN A1017 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLN A1017 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 10.567A pdb=" N GLN A 956 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 13.505A pdb=" N HIS A1015 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 867 " --> pdb=" O THR A 855 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N THR A 848 " --> pdb=" O HIS A 844 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N HIS A 844 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 850 " --> pdb=" O TRP A 842 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU A 835 " --> pdb=" O ALA A 827 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA A 827 " --> pdb=" O LEU A 835 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR A 837 " --> pdb=" O CYS A 825 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N CYS A 825 " --> pdb=" O THR A 837 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA A 839 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 843 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 819 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing sheet with id=AP, first strand: chain 'A' and resid 776 through 783 removed outlier: 16.896A pdb=" N ARG A 881 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 12.429A pdb=" N ARG A 781 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A 885 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR A 982 " --> pdb=" O CYS A 886 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU A 984 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.409A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG A 942 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N PHE A 955 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 940 " --> pdb=" O PHE A 955 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR A 941 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU A 900 " --> pdb=" O THR A 941 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 23 through 24 removed outlier: 5.390A pdb=" N TRP B 158 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS B 154 " --> pdb=" O TRP B 158 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY B 160 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR B 126 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N GLU B 57 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing sheet with id=BB, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=BC, first strand: chain 'B' and resid 99 through 101 removed outlier: 3.642A pdb=" N ILE B 99 " --> pdb=" O ARG B 204 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR B 101 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET B 202 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing sheet with id=BD, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=BE, first strand: chain 'B' and resid 221 through 227 removed outlier: 5.847A pdb=" N ILE B 222 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N CYS B 247 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=BF, first strand: chain 'B' and resid 230 through 231 Processing sheet with id=BG, first strand: chain 'B' and resid 288 through 296 Processing sheet with id=BH, first strand: chain 'B' and resid 265 through 273 removed outlier: 5.543A pdb=" N GLN B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN B 262 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 268 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 272 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 256 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR B 309 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 329 " --> pdb=" O TYR B 309 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA B 311 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA B 327 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B 313 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ALA B 325 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 315 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing sheet with id=BI, first strand: chain 'B' and resid 335 through 338 Processing sheet with id=BJ, first strand: chain 'B' and resid 484 through 485 removed outlier: 7.291A pdb=" N ASP B 411 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP B 456 " --> pdb=" O ASP B 411 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS B 389 " --> pdb=" O VAL B 410 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU B 412 " --> pdb=" O CYS B 389 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA B 386 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU B 535 " --> pdb=" O GLN B 563 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY B 565 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLU B 537 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 567 " --> pdb=" O GLU B 537 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA B 539 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing sheet with id=BK, first strand: chain 'B' and resid 575 through 578 Processing sheet with id=BL, first strand: chain 'B' and resid 627 through 629 Processing sheet with id=BM, first strand: chain 'B' and resid 661 through 670 removed outlier: 6.349A pdb=" N LEU B 658 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU B 650 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLY B 692 " --> pdb=" O ALA B 723 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ALA B 723 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU B 694 " --> pdb=" O ARG B 721 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG B 721 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU B 696 " --> pdb=" O GLN B 719 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN B 719 " --> pdb=" O LEU B 696 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B 698 " --> pdb=" O TRP B 717 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TRP B 717 " --> pdb=" O VAL B 698 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 700 " --> pdb=" O SER B 715 " (cutoff:3.500A) Processing sheet with id=BN, first strand: chain 'B' and resid 739 through 742 removed outlier: 6.331A pdb=" N ARG B 755 " --> pdb=" O MET B 768 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET B 768 " --> pdb=" O ARG B 755 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLN B 757 " --> pdb=" O SER B 766 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 770 " --> pdb=" O LYS B 773 " (cutoff:3.500A) Processing sheet with id=BO, first strand: chain 'B' and resid 776 through 783 removed outlier: 16.896A pdb=" N ARG B 881 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 12.429A pdb=" N ARG B 781 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN B 885 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR B 982 " --> pdb=" O CYS B 886 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU B 984 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.409A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASP B 954 " --> pdb=" O GLN B1017 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLN B1017 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 10.567A pdb=" N GLN B 956 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 13.505A pdb=" N HIS B1015 " --> pdb=" O GLN B 956 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR B 867 " --> pdb=" O THR B 855 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N THR B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N HIS B 844 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 850 " --> pdb=" O TRP B 842 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU B 835 " --> pdb=" O ALA B 827 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA B 827 " --> pdb=" O LEU B 835 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR B 837 " --> pdb=" O CYS B 825 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N CYS B 825 " --> pdb=" O THR B 837 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA B 839 " --> pdb=" O LEU B 823 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 843 " --> pdb=" O GLU B 819 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU B 819 " --> pdb=" O GLN B 843 " (cutoff:3.500A) Processing sheet with id=BP, first strand: chain 'B' and resid 776 through 783 removed outlier: 16.896A pdb=" N ARG B 881 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 12.429A pdb=" N ARG B 781 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN B 885 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR B 982 " --> pdb=" O CYS B 886 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU B 984 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.409A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG B 942 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N PHE B 955 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY B 940 " --> pdb=" O PHE B 955 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR B 941 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU B 900 " --> pdb=" O THR B 941 " (cutoff:3.500A) Processing sheet with id=CA, first strand: chain 'C' and resid 23 through 24 removed outlier: 5.390A pdb=" N TRP C 158 " --> pdb=" O CYS C 154 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS C 154 " --> pdb=" O TRP C 158 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY C 160 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR C 126 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N GLU C 57 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=CC, first strand: chain 'C' and resid 99 through 101 removed outlier: 3.642A pdb=" N ILE C 99 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR C 101 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET C 202 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=CD, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=CE, first strand: chain 'C' and resid 221 through 227 removed outlier: 5.847A pdb=" N ILE C 222 " --> pdb=" O CYS C 247 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N CYS C 247 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing sheet with id=CF, first strand: chain 'C' and resid 230 through 231 Processing sheet with id=CG, first strand: chain 'C' and resid 288 through 296 Processing sheet with id=CH, first strand: chain 'C' and resid 265 through 273 removed outlier: 5.543A pdb=" N GLN C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN C 262 " --> pdb=" O GLN C 266 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 268 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA C 272 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 256 " --> pdb=" O ALA C 272 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR C 309 " --> pdb=" O ASP C 329 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP C 329 " --> pdb=" O TYR C 309 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA C 311 " --> pdb=" O ALA C 327 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA C 327 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL C 313 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ALA C 325 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU C 315 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing sheet with id=CI, first strand: chain 'C' and resid 335 through 338 Processing sheet with id=CJ, first strand: chain 'C' and resid 484 through 485 removed outlier: 7.291A pdb=" N ASP C 411 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP C 456 " --> pdb=" O ASP C 411 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS C 389 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU C 412 " --> pdb=" O CYS C 389 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA C 386 " --> pdb=" O ARG C 352 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU C 535 " --> pdb=" O GLN C 563 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY C 565 " --> pdb=" O LEU C 535 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLU C 537 " --> pdb=" O GLY C 565 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C 567 " --> pdb=" O GLU C 537 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA C 539 " --> pdb=" O VAL C 567 " (cutoff:3.500A) Processing sheet with id=CK, first strand: chain 'C' and resid 575 through 578 Processing sheet with id=CL, first strand: chain 'C' and resid 627 through 629 Processing sheet with id=CM, first strand: chain 'C' and resid 661 through 670 removed outlier: 6.349A pdb=" N LEU C 658 " --> pdb=" O PRO C 662 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU C 650 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLY C 692 " --> pdb=" O ALA C 723 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ALA C 723 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU C 694 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG C 721 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU C 696 " --> pdb=" O GLN C 719 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN C 719 " --> pdb=" O LEU C 696 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 698 " --> pdb=" O TRP C 717 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TRP C 717 " --> pdb=" O VAL C 698 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL C 700 " --> pdb=" O SER C 715 " (cutoff:3.500A) Processing sheet with id=CN, first strand: chain 'C' and resid 739 through 742 removed outlier: 6.331A pdb=" N ARG C 755 " --> pdb=" O MET C 768 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET C 768 " --> pdb=" O ARG C 755 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLN C 757 " --> pdb=" O SER C 766 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 770 " --> pdb=" O LYS C 773 " (cutoff:3.500A) Processing sheet with id=CO, first strand: chain 'C' and resid 776 through 783 removed outlier: 16.896A pdb=" N ARG C 881 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 12.429A pdb=" N ARG C 781 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN C 885 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR C 982 " --> pdb=" O CYS C 886 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU C 984 " --> pdb=" O LEU C 888 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.409A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASP C 954 " --> pdb=" O GLN C1017 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLN C1017 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 10.567A pdb=" N GLN C 956 " --> pdb=" O HIS C1015 " (cutoff:3.500A) removed outlier: 13.505A pdb=" N HIS C1015 " --> pdb=" O GLN C 956 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR C 867 " --> pdb=" O THR C 855 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N THR C 848 " --> pdb=" O HIS C 844 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N HIS C 844 " --> pdb=" O THR C 848 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE C 850 " --> pdb=" O TRP C 842 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU C 835 " --> pdb=" O ALA C 827 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA C 827 " --> pdb=" O LEU C 835 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR C 837 " --> pdb=" O CYS C 825 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N CYS C 825 " --> pdb=" O THR C 837 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA C 839 " --> pdb=" O LEU C 823 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 843 " --> pdb=" O GLU C 819 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU C 819 " --> pdb=" O GLN C 843 " (cutoff:3.500A) Processing sheet with id=CP, first strand: chain 'C' and resid 776 through 783 removed outlier: 16.896A pdb=" N ARG C 881 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 12.429A pdb=" N ARG C 781 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN C 885 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR C 982 " --> pdb=" O CYS C 886 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU C 984 " --> pdb=" O LEU C 888 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.409A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG C 942 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N PHE C 955 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 940 " --> pdb=" O PHE C 955 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR C 941 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU C 900 " --> pdb=" O THR C 941 " (cutoff:3.500A) Processing sheet with id=DA, first strand: chain 'D' and resid 23 through 24 removed outlier: 5.390A pdb=" N TRP D 158 " --> pdb=" O CYS D 154 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS D 154 " --> pdb=" O TRP D 158 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY D 160 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR D 126 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N GLU D 57 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing sheet with id=DB, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=DC, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.642A pdb=" N ILE D 99 " --> pdb=" O ARG D 204 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR D 101 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET D 202 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing sheet with id=DD, first strand: chain 'D' and resid 146 through 147 Processing sheet with id=DE, first strand: chain 'D' and resid 221 through 227 removed outlier: 5.847A pdb=" N ILE D 222 " --> pdb=" O CYS D 247 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N CYS D 247 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Processing sheet with id=DF, first strand: chain 'D' and resid 230 through 231 Processing sheet with id=DG, first strand: chain 'D' and resid 288 through 296 Processing sheet with id=DH, first strand: chain 'D' and resid 265 through 273 removed outlier: 5.543A pdb=" N GLN D 266 " --> pdb=" O GLN D 262 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN D 262 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA D 268 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 272 " --> pdb=" O VAL D 256 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 256 " --> pdb=" O ALA D 272 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR D 309 " --> pdb=" O ASP D 329 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP D 329 " --> pdb=" O TYR D 309 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA D 311 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA D 327 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL D 313 " --> pdb=" O ALA D 325 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ALA D 325 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU D 315 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing sheet with id=DI, first strand: chain 'D' and resid 335 through 338 Processing sheet with id=DJ, first strand: chain 'D' and resid 484 through 485 removed outlier: 7.291A pdb=" N ASP D 411 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP D 456 " --> pdb=" O ASP D 411 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS D 389 " --> pdb=" O VAL D 410 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU D 412 " --> pdb=" O CYS D 389 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA D 386 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU D 535 " --> pdb=" O GLN D 563 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY D 565 " --> pdb=" O LEU D 535 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLU D 537 " --> pdb=" O GLY D 565 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL D 567 " --> pdb=" O GLU D 537 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA D 539 " --> pdb=" O VAL D 567 " (cutoff:3.500A) Processing sheet with id=DK, first strand: chain 'D' and resid 575 through 578 Processing sheet with id=DL, first strand: chain 'D' and resid 627 through 629 Processing sheet with id=DM, first strand: chain 'D' and resid 661 through 670 removed outlier: 6.349A pdb=" N LEU D 658 " --> pdb=" O PRO D 662 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU D 650 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLY D 692 " --> pdb=" O ALA D 723 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ALA D 723 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU D 694 " --> pdb=" O ARG D 721 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG D 721 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU D 696 " --> pdb=" O GLN D 719 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN D 719 " --> pdb=" O LEU D 696 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL D 698 " --> pdb=" O TRP D 717 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TRP D 717 " --> pdb=" O VAL D 698 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL D 700 " --> pdb=" O SER D 715 " (cutoff:3.500A) Processing sheet with id=DN, first strand: chain 'D' and resid 739 through 742 removed outlier: 6.331A pdb=" N ARG D 755 " --> pdb=" O MET D 768 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET D 768 " --> pdb=" O ARG D 755 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLN D 757 " --> pdb=" O SER D 766 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE D 770 " --> pdb=" O LYS D 773 " (cutoff:3.500A) Processing sheet with id=DO, first strand: chain 'D' and resid 776 through 783 removed outlier: 16.896A pdb=" N ARG D 881 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 12.429A pdb=" N ARG D 781 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN D 885 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR D 982 " --> pdb=" O CYS D 886 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU D 984 " --> pdb=" O LEU D 888 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.409A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASP D 954 " --> pdb=" O GLN D1017 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLN D1017 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 10.567A pdb=" N GLN D 956 " --> pdb=" O HIS D1015 " (cutoff:3.500A) removed outlier: 13.505A pdb=" N HIS D1015 " --> pdb=" O GLN D 956 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR D 867 " --> pdb=" O THR D 855 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N THR D 848 " --> pdb=" O HIS D 844 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N HIS D 844 " --> pdb=" O THR D 848 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE D 850 " --> pdb=" O TRP D 842 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU D 835 " --> pdb=" O ALA D 827 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA D 827 " --> pdb=" O LEU D 835 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR D 837 " --> pdb=" O CYS D 825 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N CYS D 825 " --> pdb=" O THR D 837 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA D 839 " --> pdb=" O LEU D 823 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN D 843 " --> pdb=" O GLU D 819 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU D 819 " --> pdb=" O GLN D 843 " (cutoff:3.500A) Processing sheet with id=DP, first strand: chain 'D' and resid 776 through 783 removed outlier: 16.896A pdb=" N ARG D 881 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 12.429A pdb=" N ARG D 781 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN D 885 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR D 982 " --> pdb=" O CYS D 886 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU D 984 " --> pdb=" O LEU D 888 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.409A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG D 942 " --> pdb=" O GLY D 953 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N PHE D 955 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY D 940 " --> pdb=" O PHE D 955 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR D 941 " --> pdb=" O LEU D 900 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU D 900 " --> pdb=" O THR D 941 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 2796 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: 9.72 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 12 1.09 - 1.27: 5516 1.27 - 1.45: 10120 1.45 - 1.63: 17972 1.63 - 1.81: 256 Bond restraints: 33876 Sorted by residual: bond pdb=" C GLU C 461 " pdb=" N SER C 462 " ideal model delta sigma weight residual 1.333 0.985 0.348 1.34e-02 5.57e+03 6.75e+02 bond pdb=" C GLU B 461 " pdb=" N SER B 462 " ideal model delta sigma weight residual 1.333 0.985 0.348 1.34e-02 5.57e+03 6.75e+02 bond pdb=" C GLU D 461 " pdb=" N SER D 462 " ideal model delta sigma weight residual 1.333 0.985 0.348 1.34e-02 5.57e+03 6.75e+02 bond pdb=" C GLU A 461 " pdb=" N SER A 462 " ideal model delta sigma weight residual 1.333 0.985 0.348 1.34e-02 5.57e+03 6.75e+02 bond pdb=" C VAL B 146 " pdb=" N ASN B 147 " ideal model delta sigma weight residual 1.331 0.912 0.419 1.66e-02 3.63e+03 6.36e+02 ... (remaining 33871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.16: 46116 6.16 - 12.31: 44 12.31 - 18.47: 36 18.47 - 24.63: 8 24.63 - 30.78: 12 Bond angle restraints: 46216 Sorted by residual: angle pdb=" O GLU C 461 " pdb=" C GLU C 461 " pdb=" N SER C 462 " ideal model delta sigma weight residual 122.59 153.37 -30.78 1.33e+00 5.65e-01 5.36e+02 angle pdb=" O GLU B 461 " pdb=" C GLU B 461 " pdb=" N SER B 462 " ideal model delta sigma weight residual 122.59 153.37 -30.78 1.33e+00 5.65e-01 5.36e+02 angle pdb=" O GLU A 461 " pdb=" C GLU A 461 " pdb=" N SER A 462 " ideal model delta sigma weight residual 122.59 153.37 -30.78 1.33e+00 5.65e-01 5.36e+02 angle pdb=" O GLU D 461 " pdb=" C GLU D 461 " pdb=" N SER D 462 " ideal model delta sigma weight residual 122.59 153.37 -30.78 1.33e+00 5.65e-01 5.36e+02 angle pdb=" O ASN A 147 " pdb=" C ASN A 147 " pdb=" N SER A 148 " ideal model delta sigma weight residual 122.87 99.59 23.28 1.23e+00 6.61e-01 3.58e+02 ... (remaining 46211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 18280 17.63 - 35.27: 1168 35.27 - 52.90: 256 52.90 - 70.53: 60 70.53 - 88.17: 48 Dihedral angle restraints: 19812 sinusoidal: 7996 harmonic: 11816 Sorted by residual: dihedral pdb=" CA ILE D 882 " pdb=" C ILE D 882 " pdb=" N GLY D 883 " pdb=" CA GLY D 883 " ideal model delta harmonic sigma weight residual 180.00 -148.41 -31.59 0 5.00e+00 4.00e-02 3.99e+01 dihedral pdb=" CA ILE B 882 " pdb=" C ILE B 882 " pdb=" N GLY B 883 " pdb=" CA GLY B 883 " ideal model delta harmonic sigma weight residual -180.00 -148.41 -31.59 0 5.00e+00 4.00e-02 3.99e+01 dihedral pdb=" CA ILE C 882 " pdb=" C ILE C 882 " pdb=" N GLY C 883 " pdb=" CA GLY C 883 " ideal model delta harmonic sigma weight residual -180.00 -148.41 -31.59 0 5.00e+00 4.00e-02 3.99e+01 ... (remaining 19809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4224 0.056 - 0.112: 528 0.112 - 0.168: 72 0.168 - 0.225: 12 0.225 - 0.281: 4 Chirality restraints: 4840 Sorted by residual: chirality pdb=" CA ASP A 507 " pdb=" N ASP A 507 " pdb=" C ASP A 507 " pdb=" CB ASP A 507 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA ASP C 507 " pdb=" N ASP C 507 " pdb=" C ASP C 507 " pdb=" CB ASP C 507 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA ASP B 507 " pdb=" N ASP B 507 " pdb=" C ASP B 507 " pdb=" CB ASP B 507 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 4837 not shown) Planarity restraints: 6092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 460 " -0.076 2.00e-02 2.50e+03 1.45e-01 2.09e+02 pdb=" C ASN A 460 " 0.250 2.00e-02 2.50e+03 pdb=" O ASN A 460 " -0.096 2.00e-02 2.50e+03 pdb=" N GLU A 461 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 460 " 0.076 2.00e-02 2.50e+03 1.45e-01 2.09e+02 pdb=" C ASN D 460 " -0.250 2.00e-02 2.50e+03 pdb=" O ASN D 460 " 0.096 2.00e-02 2.50e+03 pdb=" N GLU D 461 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 460 " 0.076 2.00e-02 2.50e+03 1.45e-01 2.09e+02 pdb=" C ASN B 460 " -0.250 2.00e-02 2.50e+03 pdb=" O ASN B 460 " 0.096 2.00e-02 2.50e+03 pdb=" N GLU B 461 " 0.078 2.00e-02 2.50e+03 ... (remaining 6089 not shown) Histogram of nonbonded interaction distances: 0.02 - 1.00: 10 1.00 - 1.97: 0 1.97 - 2.95: 15558 2.95 - 3.92: 99168 3.92 - 4.90: 195186 Warning: very small nonbonded interaction distances. Nonbonded interactions: 309922 Sorted by model distance: nonbonded pdb=" O HOH B5087 " pdb=" O HOH C5084 " model vdw 0.020 3.040 nonbonded pdb=" O HOH A5087 " pdb=" O HOH D5084 " model vdw 0.020 3.040 nonbonded pdb=" O HOH B5084 " pdb=" O HOH C5087 " model vdw 0.020 3.040 nonbonded pdb=" O HOH A5084 " pdb=" O HOH D5087 " model vdw 0.020 3.040 nonbonded pdb=" O HOH B5085 " pdb=" O HOH C5085 " model vdw 0.021 3.040 ... (remaining 309917 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 38.410 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 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 : 0.009 0.419 33876 Z= 0.591 Angle : 1.213 30.785 46216 Z= 0.843 Chirality : 0.039 0.281 4840 Planarity : 0.005 0.145 6092 Dihedral : 13.148 88.168 12204 Min Nonbonded Distance : 0.020 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.92 % Favored : 95.49 % Rotamer: Outliers : 1.03 % Allowed : 7.89 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.86 (0.11), residues: 4080 helix: -2.30 (0.18), residues: 536 sheet: -0.14 (0.15), residues: 1120 loop : -1.56 (0.10), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 183 TYR 0.008 0.001 TYR C 856 PHE 0.006 0.001 PHE B 512 TRP 0.017 0.001 TRP B 90 HIS 0.002 0.001 HIS B 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00881 / 0.59 (33876) covalent geometry : angle 1.21286 / 0.84 (46216) hydrogen bonds : bond 0.25290 / 16.94 ( 1040) hydrogen bonds : angle 9.22259 / 6.46 ( 2796) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 788 time to evaluate : 1.276 Fit side-chains REVERT: A 84 VAL cc_start: 0.6775 (m) cc_final: 0.6542 (m) REVERT: A 233 ASP cc_start: 0.5656 (m-30) cc_final: 0.5382 (m-30) REVERT: A 277 GLU cc_start: 0.5751 (pm20) cc_final: 0.5477 (tt0) REVERT: A 537 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: A 677 LYS cc_start: 0.7208 (ptmt) cc_final: 0.6918 (ptpp) REVERT: A 817 GLN cc_start: 0.6511 (mt0) cc_final: 0.6285 (mp10) REVERT: A 893 GLU cc_start: 0.6149 (mt-10) cc_final: 0.5903 (mm-30) REVERT: B 84 VAL cc_start: 0.6777 (m) cc_final: 0.6544 (m) REVERT: B 233 ASP cc_start: 0.5658 (m-30) cc_final: 0.5384 (m-30) REVERT: B 277 GLU cc_start: 0.5749 (pm20) cc_final: 0.5473 (tt0) REVERT: B 537 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: B 677 LYS cc_start: 0.7207 (ptmt) cc_final: 0.6919 (ptpp) REVERT: B 817 GLN cc_start: 0.6512 (mt0) cc_final: 0.6286 (mp10) REVERT: B 893 GLU cc_start: 0.6149 (mt-10) cc_final: 0.5904 (mm-30) REVERT: C 84 VAL cc_start: 0.6777 (m) cc_final: 0.6544 (m) REVERT: C 233 ASP cc_start: 0.5659 (m-30) cc_final: 0.5385 (m-30) REVERT: C 277 GLU cc_start: 0.5750 (pm20) cc_final: 0.5475 (tt0) REVERT: C 537 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: C 677 LYS cc_start: 0.7209 (ptmt) cc_final: 0.6919 (ptpp) REVERT: C 817 GLN cc_start: 0.6511 (mt0) cc_final: 0.6286 (mp10) REVERT: C 893 GLU cc_start: 0.6147 (mt-10) cc_final: 0.5903 (mm-30) REVERT: D 84 VAL cc_start: 0.6778 (m) cc_final: 0.6545 (m) REVERT: D 233 ASP cc_start: 0.5658 (m-30) cc_final: 0.5384 (m-30) REVERT: D 277 GLU cc_start: 0.5750 (pm20) cc_final: 0.5475 (tt0) REVERT: D 537 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: D 677 LYS cc_start: 0.7207 (ptmt) cc_final: 0.6918 (ptpp) REVERT: D 817 GLN cc_start: 0.6513 (mt0) cc_final: 0.6286 (mp10) REVERT: D 893 GLU cc_start: 0.6150 (mt-10) cc_final: 0.5905 (mm-30) outliers start: 36 outliers final: 4 residues processed: 812 average time/residue: 0.7519 time to fit residues: 722.4384 Evaluate side-chains 508 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 500 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 537 GLU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 537 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 ASN A 30 HIS A 38 ASN A 89 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A 355 ASN A 391 HIS A 395 HIS A 445 GLN A 485 GLN A 573 GLN A 597 ASN A 653 HIS A 739 HIS A 757 GLN A 767 GLN A 775 GLN A 791 ASN A 824 GLN A 863 GLN A 896 ASN A 935 ASN A 945 ASN A 949 HIS A 985 ASN A1015 HIS B 25 ASN B 30 HIS B 38 ASN B 89 ASN ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 355 ASN B 391 HIS B 395 HIS B 445 GLN B 485 GLN B 573 GLN B 597 ASN B 653 HIS B 739 HIS B 757 GLN B 767 GLN B 775 GLN B 791 ASN B 824 GLN B 863 GLN B 896 ASN B 935 ASN B 945 ASN B 949 HIS B 985 ASN B1015 HIS C 25 ASN C 30 HIS C 38 ASN C 89 ASN C 262 GLN C 339 ASN C 355 ASN C 391 HIS C 395 HIS C 445 GLN C 485 GLN C 573 GLN C 597 ASN C 653 HIS C 739 HIS C 757 GLN C 767 GLN C 775 GLN C 791 ASN C 824 GLN C 863 GLN C 896 ASN C 935 ASN C 945 ASN C 949 HIS C 985 ASN C1015 HIS D 25 ASN D 30 HIS D 38 ASN D 89 ASN ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN D 355 ASN D 391 HIS D 395 HIS D 445 GLN D 485 GLN D 573 GLN D 597 ASN D 653 HIS D 739 HIS D 757 GLN D 767 GLN D 775 GLN D 791 ASN D 824 GLN D 863 GLN D 896 ASN D 935 ASN D 945 ASN D 949 HIS D 985 ASN D1015 HIS Total number of N/Q/H flips: 105 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.171868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.150433 restraints weight = 33668.078| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.24 r_work: 0.3669 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 33876 Z= 0.232 Angle : 0.776 9.987 46216 Z= 0.405 Chirality : 0.050 0.180 4840 Planarity : 0.007 0.052 6092 Dihedral : 6.280 85.084 4508 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.55 % Favored : 97.35 % Rotamer: Outliers : 4.23 % Allowed : 12.93 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % 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: -0.99 (0.12), residues: 4080 helix: -1.07 (0.20), residues: 552 sheet: -0.03 (0.14), residues: 1380 loop : -0.91 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 210 TYR 0.020 0.003 TYR D 123 PHE 0.018 0.002 PHE A 63 TRP 0.023 0.002 TRP D 553 HIS 0.008 0.002 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 (33876) covalent geometry : angle 0.77580 / 0.41 (46216) hydrogen bonds : bond 0.05411 / 3.60 ( 1040) hydrogen bonds : angle 6.28435 / 4.45 ( 2796) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 568 time to evaluate : 1.303 Fit side-chains REVERT: A 46 ARG cc_start: 0.6656 (mmm160) cc_final: 0.6010 (mtm-85) REVERT: A 82 ASP cc_start: 0.6447 (m-30) cc_final: 0.6232 (m-30) REVERT: A 84 VAL cc_start: 0.7363 (m) cc_final: 0.7112 (m) REVERT: A 144 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7275 (t70) REVERT: A 178 ARG cc_start: 0.5466 (ptt90) cc_final: 0.5105 (mtm180) REVERT: A 233 ASP cc_start: 0.5842 (m-30) cc_final: 0.5636 (m-30) REVERT: A 269 SER cc_start: 0.7721 (OUTLIER) cc_final: 0.7468 (p) REVERT: A 277 GLU cc_start: 0.5612 (pm20) cc_final: 0.5230 (tt0) REVERT: A 313 VAL cc_start: 0.8177 (t) cc_final: 0.7906 (p) REVERT: A 677 LYS cc_start: 0.7462 (ptmt) cc_final: 0.6933 (ptpp) REVERT: A 745 MET cc_start: 0.4197 (tpt) cc_final: 0.3721 (tpp) REVERT: A 750 GLU cc_start: 0.6838 (pm20) cc_final: 0.6472 (mp0) REVERT: A 817 GLN cc_start: 0.6513 (mt0) cc_final: 0.6201 (mp10) REVERT: A 919 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7448 (t70) REVERT: B 46 ARG cc_start: 0.6657 (mmm160) cc_final: 0.6016 (mtm-85) REVERT: B 82 ASP cc_start: 0.6450 (m-30) cc_final: 0.6235 (m-30) REVERT: B 84 VAL cc_start: 0.7364 (m) cc_final: 0.7112 (m) REVERT: B 144 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7266 (t70) REVERT: B 178 ARG cc_start: 0.5461 (ptt90) cc_final: 0.5107 (mtm180) REVERT: B 233 ASP cc_start: 0.5836 (m-30) cc_final: 0.5634 (m-30) REVERT: B 269 SER cc_start: 0.7720 (OUTLIER) cc_final: 0.7469 (p) REVERT: B 277 GLU cc_start: 0.5605 (pm20) cc_final: 0.5231 (tt0) REVERT: B 313 VAL cc_start: 0.8175 (t) cc_final: 0.7908 (p) REVERT: B 677 LYS cc_start: 0.7458 (ptmt) cc_final: 0.6924 (ptpp) REVERT: B 745 MET cc_start: 0.4196 (tpt) cc_final: 0.3718 (tpp) REVERT: B 750 GLU cc_start: 0.6841 (pm20) cc_final: 0.6472 (mp0) REVERT: B 817 GLN cc_start: 0.6517 (mt0) cc_final: 0.6209 (mp10) REVERT: B 919 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7448 (t70) REVERT: C 46 ARG cc_start: 0.6662 (mmm160) cc_final: 0.6015 (mtm-85) REVERT: C 82 ASP cc_start: 0.6432 (m-30) cc_final: 0.6217 (m-30) REVERT: C 84 VAL cc_start: 0.7362 (m) cc_final: 0.7110 (m) REVERT: C 144 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7272 (t70) REVERT: C 178 ARG cc_start: 0.5468 (ptt90) cc_final: 0.5115 (mtm180) REVERT: C 233 ASP cc_start: 0.5840 (m-30) cc_final: 0.5635 (m-30) REVERT: C 269 SER cc_start: 0.7720 (OUTLIER) cc_final: 0.7469 (p) REVERT: C 277 GLU cc_start: 0.5608 (pm20) cc_final: 0.5222 (tt0) REVERT: C 313 VAL cc_start: 0.8174 (t) cc_final: 0.7906 (p) REVERT: C 677 LYS cc_start: 0.7469 (ptmt) cc_final: 0.6935 (ptpp) REVERT: C 745 MET cc_start: 0.4198 (tpt) cc_final: 0.3721 (tpp) REVERT: C 750 GLU cc_start: 0.6845 (pm20) cc_final: 0.6477 (mp0) REVERT: C 817 GLN cc_start: 0.6520 (mt0) cc_final: 0.6203 (mp10) REVERT: C 919 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7451 (t70) REVERT: D 46 ARG cc_start: 0.6656 (mmm160) cc_final: 0.6009 (mtm-85) REVERT: D 82 ASP cc_start: 0.6446 (m-30) cc_final: 0.6230 (m-30) REVERT: D 84 VAL cc_start: 0.7364 (m) cc_final: 0.7113 (m) REVERT: D 144 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7282 (t70) REVERT: D 178 ARG cc_start: 0.5466 (ptt90) cc_final: 0.5115 (mtm180) REVERT: D 233 ASP cc_start: 0.5835 (m-30) cc_final: 0.5630 (m-30) REVERT: D 269 SER cc_start: 0.7728 (OUTLIER) cc_final: 0.7478 (p) REVERT: D 277 GLU cc_start: 0.5614 (pm20) cc_final: 0.5225 (tt0) REVERT: D 313 VAL cc_start: 0.8175 (t) cc_final: 0.7907 (p) REVERT: D 677 LYS cc_start: 0.7458 (ptmt) cc_final: 0.6931 (ptpp) REVERT: D 745 MET cc_start: 0.4199 (tpt) cc_final: 0.3719 (tpp) REVERT: D 750 GLU cc_start: 0.6842 (pm20) cc_final: 0.6470 (mp0) REVERT: D 817 GLN cc_start: 0.6512 (mt0) cc_final: 0.6205 (mp10) REVERT: D 919 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7454 (t70) outliers start: 148 outliers final: 64 residues processed: 664 average time/residue: 0.7196 time to fit residues: 569.2325 Evaluate side-chains 572 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 496 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 924 ASP Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 924 ASP Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 748 CYS Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 919 ASP Chi-restraints excluded: chain C residue 924 ASP Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 748 CYS Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 924 ASP Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 31 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 221 optimal weight: 0.9990 chunk 228 optimal weight: 10.0000 chunk 307 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 351 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 HIS A 262 GLN A 485 GLN A 510 GLN A 554 GLN A 573 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN A 896 ASN B 30 HIS B 262 GLN B 485 GLN B 510 GLN B 554 GLN B 573 GLN ** B 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN B 896 ASN C 30 HIS C 262 GLN C 485 GLN C 510 GLN C 554 GLN C 573 GLN ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN C 896 ASN D 30 HIS D 262 GLN D 485 GLN D 510 GLN D 554 GLN D 573 GLN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 824 GLN D 896 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.171958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.150723 restraints weight = 33694.144| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.22 r_work: 0.3674 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33876 Z= 0.173 Angle : 0.677 9.914 46216 Z= 0.350 Chirality : 0.046 0.165 4840 Planarity : 0.005 0.042 6092 Dihedral : 5.307 65.876 4484 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.84 % Favored : 97.06 % Rotamer: Outliers : 4.81 % Allowed : 14.87 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % 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 (0.13), residues: 4080 helix: -0.60 (0.22), residues: 552 sheet: 0.07 (0.13), residues: 1412 loop : -0.80 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 190 TYR 0.016 0.002 TYR C 100 PHE 0.012 0.002 PHE C 63 TRP 0.026 0.002 TRP C 553 HIS 0.007 0.001 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (33876) covalent geometry : angle 0.67746 / 0.35 (46216) hydrogen bonds : bond 0.04772 / 3.16 ( 1040) hydrogen bonds : angle 5.93608 / 4.20 ( 2796) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 512 time to evaluate : 1.411 Fit side-chains REVERT: A 41 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6836 (mt-10) REVERT: A 46 ARG cc_start: 0.6695 (mmm160) cc_final: 0.5844 (ttp-170) REVERT: A 84 VAL cc_start: 0.7388 (m) cc_final: 0.7155 (m) REVERT: A 144 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7285 (t70) REVERT: A 178 ARG cc_start: 0.5461 (ptt90) cc_final: 0.5155 (mtm180) REVERT: A 233 ASP cc_start: 0.5834 (m-30) cc_final: 0.5602 (m-30) REVERT: A 255 ARG cc_start: 0.7711 (mmt-90) cc_final: 0.7332 (mmt-90) REVERT: A 269 SER cc_start: 0.7784 (OUTLIER) cc_final: 0.7450 (m) REVERT: A 277 GLU cc_start: 0.5676 (pm20) cc_final: 0.5282 (tt0) REVERT: A 313 VAL cc_start: 0.8234 (t) cc_final: 0.7977 (p) REVERT: A 677 LYS cc_start: 0.7472 (ptmt) cc_final: 0.6916 (ptpp) REVERT: A 745 MET cc_start: 0.4172 (tpt) cc_final: 0.3716 (tpp) REVERT: A 782 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7478 (m-30) REVERT: A 817 GLN cc_start: 0.6541 (mt0) cc_final: 0.6217 (mp10) REVERT: A 919 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7364 (t0) REVERT: A 965 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7243 (tm-30) REVERT: B 41 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6831 (mt-10) REVERT: B 46 ARG cc_start: 0.6696 (mmm160) cc_final: 0.5851 (ttp-170) REVERT: B 84 VAL cc_start: 0.7393 (m) cc_final: 0.7159 (m) REVERT: B 144 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7285 (t70) REVERT: B 178 ARG cc_start: 0.5457 (ptt90) cc_final: 0.5160 (mtm180) REVERT: B 233 ASP cc_start: 0.5835 (m-30) cc_final: 0.5601 (m-30) REVERT: B 255 ARG cc_start: 0.7707 (mmt-90) cc_final: 0.7326 (mmt-90) REVERT: B 269 SER cc_start: 0.7787 (OUTLIER) cc_final: 0.7453 (m) REVERT: B 277 GLU cc_start: 0.5676 (pm20) cc_final: 0.5281 (tt0) REVERT: B 313 VAL cc_start: 0.8241 (t) cc_final: 0.7984 (p) REVERT: B 677 LYS cc_start: 0.7470 (ptmt) cc_final: 0.6914 (ptpp) REVERT: B 745 MET cc_start: 0.4166 (tpt) cc_final: 0.3712 (tpp) REVERT: B 782 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7482 (m-30) REVERT: B 817 GLN cc_start: 0.6532 (mt0) cc_final: 0.6205 (mp10) REVERT: B 919 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7363 (t0) REVERT: B 965 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: C 41 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6860 (mt-10) REVERT: C 46 ARG cc_start: 0.6702 (mmm160) cc_final: 0.5855 (ttp-170) REVERT: C 84 VAL cc_start: 0.7390 (m) cc_final: 0.7158 (m) REVERT: C 144 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7290 (t70) REVERT: C 178 ARG cc_start: 0.5459 (ptt90) cc_final: 0.5165 (mtm180) REVERT: C 233 ASP cc_start: 0.5837 (m-30) cc_final: 0.5600 (m-30) REVERT: C 255 ARG cc_start: 0.7716 (mmt-90) cc_final: 0.7338 (mmt-90) REVERT: C 269 SER cc_start: 0.7785 (OUTLIER) cc_final: 0.7450 (m) REVERT: C 277 GLU cc_start: 0.5690 (pm20) cc_final: 0.5289 (tt0) REVERT: C 313 VAL cc_start: 0.8236 (t) cc_final: 0.7982 (p) REVERT: C 677 LYS cc_start: 0.7476 (ptmt) cc_final: 0.6919 (ptpp) REVERT: C 745 MET cc_start: 0.4176 (tpt) cc_final: 0.3716 (tpp) REVERT: C 782 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: C 817 GLN cc_start: 0.6539 (mt0) cc_final: 0.6211 (mp10) REVERT: C 919 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7373 (t0) REVERT: C 965 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: D 41 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6836 (mt-10) REVERT: D 46 ARG cc_start: 0.6697 (mmm160) cc_final: 0.5851 (ttp-170) REVERT: D 84 VAL cc_start: 0.7387 (m) cc_final: 0.7155 (m) REVERT: D 144 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7297 (t70) REVERT: D 178 ARG cc_start: 0.5459 (ptt90) cc_final: 0.5164 (mtm180) REVERT: D 233 ASP cc_start: 0.5835 (m-30) cc_final: 0.5602 (m-30) REVERT: D 255 ARG cc_start: 0.7714 (mmt-90) cc_final: 0.7334 (mmt-90) REVERT: D 269 SER cc_start: 0.7797 (OUTLIER) cc_final: 0.7462 (m) REVERT: D 277 GLU cc_start: 0.5686 (pm20) cc_final: 0.5284 (tt0) REVERT: D 313 VAL cc_start: 0.8237 (t) cc_final: 0.7981 (p) REVERT: D 677 LYS cc_start: 0.7466 (ptmt) cc_final: 0.6910 (ptpp) REVERT: D 745 MET cc_start: 0.4169 (tpt) cc_final: 0.3714 (tpp) REVERT: D 782 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7464 (m-30) REVERT: D 817 GLN cc_start: 0.6543 (mt0) cc_final: 0.6212 (mp10) REVERT: D 919 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7368 (t0) REVERT: D 965 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7234 (tm-30) outliers start: 168 outliers final: 76 residues processed: 600 average time/residue: 0.7361 time to fit residues: 525.7225 Evaluate side-chains 564 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 464 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 766 SER Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 968 MET Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 748 CYS Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 919 ASP Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 968 MET Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 748 CYS Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 965 GLN Chi-restraints excluded: chain D residue 968 MET Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 123 optimal weight: 7.9990 chunk 206 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 chunk 226 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 170 optimal weight: 0.0030 chunk 103 optimal weight: 9.9990 chunk 73 optimal weight: 0.5980 chunk 312 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 358 optimal weight: 3.9990 overall best weight: 3.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 HIS A 262 GLN A 395 HIS A 485 GLN A 573 GLN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN A 896 ASN B 30 HIS B 262 GLN B 395 HIS B 485 GLN B 573 GLN ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN B 896 ASN C 30 HIS C 262 GLN C 395 HIS C 485 GLN C 573 GLN ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN C 896 ASN D 30 HIS D 262 GLN D 395 HIS D 485 GLN D 573 GLN ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 824 GLN D 896 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.172541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.151444 restraints weight = 33524.884| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.22 r_work: 0.3683 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 33876 Z= 0.146 Angle : 0.639 9.790 46216 Z= 0.328 Chirality : 0.045 0.156 4840 Planarity : 0.005 0.037 6092 Dihedral : 5.128 63.190 4484 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.84 % Favored : 97.06 % Rotamer: Outliers : 4.89 % Allowed : 15.36 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % 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: -0.57 (0.13), residues: 4080 helix: -0.29 (0.22), residues: 552 sheet: 0.13 (0.14), residues: 1424 loop : -0.70 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 43 TYR 0.015 0.002 TYR C 100 PHE 0.011 0.001 PHE C 63 TRP 0.025 0.002 TRP B 553 HIS 0.007 0.001 HIS C 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (33876) covalent geometry : angle 0.63923 / 0.33 (46216) hydrogen bonds : bond 0.04105 / 2.71 ( 1040) hydrogen bonds : angle 5.70598 / 4.04 ( 2796) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 476 time to evaluate : 1.296 Fit side-chains REVERT: A 41 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6519 (tt0) REVERT: A 46 ARG cc_start: 0.6676 (mmm160) cc_final: 0.6037 (mtm-85) REVERT: A 77 ASP cc_start: 0.6146 (p0) cc_final: 0.5920 (p0) REVERT: A 84 VAL cc_start: 0.7377 (m) cc_final: 0.7136 (m) REVERT: A 144 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7313 (t70) REVERT: A 178 ARG cc_start: 0.5452 (ptt90) cc_final: 0.5156 (mtm180) REVERT: A 233 ASP cc_start: 0.5825 (m-30) cc_final: 0.5581 (m-30) REVERT: A 255 ARG cc_start: 0.7723 (mmt-90) cc_final: 0.7435 (mmt-90) REVERT: A 269 SER cc_start: 0.7747 (OUTLIER) cc_final: 0.7410 (m) REVERT: A 277 GLU cc_start: 0.5696 (pm20) cc_final: 0.5278 (tt0) REVERT: A 611 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.4640 (ptp-170) REVERT: A 677 LYS cc_start: 0.7464 (ptmt) cc_final: 0.6889 (ptpp) REVERT: A 745 MET cc_start: 0.4201 (tpt) cc_final: 0.3683 (tpp) REVERT: A 782 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7456 (m-30) REVERT: A 817 GLN cc_start: 0.6567 (mt0) cc_final: 0.6237 (mp10) REVERT: A 919 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7378 (t0) REVERT: A 934 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.6936 (tp30) REVERT: A 965 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7266 (tm-30) REVERT: B 41 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6520 (tt0) REVERT: B 46 ARG cc_start: 0.6676 (mmm160) cc_final: 0.6043 (mtm-85) REVERT: B 77 ASP cc_start: 0.6143 (p0) cc_final: 0.5925 (p0) REVERT: B 84 VAL cc_start: 0.7385 (m) cc_final: 0.7145 (m) REVERT: B 144 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7320 (t70) REVERT: B 178 ARG cc_start: 0.5449 (ptt90) cc_final: 0.5155 (mtm180) REVERT: B 233 ASP cc_start: 0.5824 (m-30) cc_final: 0.5578 (m-30) REVERT: B 255 ARG cc_start: 0.7717 (mmt-90) cc_final: 0.7427 (mmt-90) REVERT: B 269 SER cc_start: 0.7754 (OUTLIER) cc_final: 0.7414 (m) REVERT: B 277 GLU cc_start: 0.5692 (pm20) cc_final: 0.5277 (tt0) REVERT: B 611 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.4639 (ptp-170) REVERT: B 677 LYS cc_start: 0.7460 (ptmt) cc_final: 0.6886 (ptpp) REVERT: B 745 MET cc_start: 0.4208 (tpt) cc_final: 0.3688 (tpp) REVERT: B 782 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: B 817 GLN cc_start: 0.6563 (mt0) cc_final: 0.6230 (mp10) REVERT: B 919 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7379 (t0) REVERT: B 934 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.6926 (tp30) REVERT: B 965 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: C 41 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6538 (tt0) REVERT: C 46 ARG cc_start: 0.6679 (mmm160) cc_final: 0.6042 (mtm-85) REVERT: C 77 ASP cc_start: 0.6151 (p0) cc_final: 0.5933 (p0) REVERT: C 84 VAL cc_start: 0.7378 (m) cc_final: 0.7139 (m) REVERT: C 144 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7328 (t70) REVERT: C 178 ARG cc_start: 0.5444 (ptt90) cc_final: 0.5153 (mtm180) REVERT: C 233 ASP cc_start: 0.5824 (m-30) cc_final: 0.5579 (m-30) REVERT: C 255 ARG cc_start: 0.7724 (mmt-90) cc_final: 0.7436 (mmt-90) REVERT: C 269 SER cc_start: 0.7757 (OUTLIER) cc_final: 0.7418 (m) REVERT: C 277 GLU cc_start: 0.5703 (pm20) cc_final: 0.5289 (tt0) REVERT: C 611 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.4638 (ptp-170) REVERT: C 677 LYS cc_start: 0.7467 (ptmt) cc_final: 0.6890 (ptpp) REVERT: C 745 MET cc_start: 0.4208 (tpt) cc_final: 0.3689 (tpp) REVERT: C 782 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7441 (m-30) REVERT: C 817 GLN cc_start: 0.6565 (mt0) cc_final: 0.6238 (mp10) REVERT: C 919 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7392 (t0) REVERT: C 934 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.6933 (tp30) REVERT: C 965 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: D 41 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6519 (tt0) REVERT: D 46 ARG cc_start: 0.6680 (mmm160) cc_final: 0.6038 (mtm-85) REVERT: D 77 ASP cc_start: 0.6151 (p0) cc_final: 0.5924 (p0) REVERT: D 84 VAL cc_start: 0.7379 (m) cc_final: 0.7139 (m) REVERT: D 144 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7312 (t70) REVERT: D 178 ARG cc_start: 0.5447 (ptt90) cc_final: 0.5160 (mtm180) REVERT: D 233 ASP cc_start: 0.5826 (m-30) cc_final: 0.5585 (m-30) REVERT: D 255 ARG cc_start: 0.7718 (mmt-90) cc_final: 0.7428 (mmt-90) REVERT: D 269 SER cc_start: 0.7762 (OUTLIER) cc_final: 0.7424 (m) REVERT: D 277 GLU cc_start: 0.5698 (pm20) cc_final: 0.5278 (tt0) REVERT: D 611 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.4635 (ptp-170) REVERT: D 677 LYS cc_start: 0.7462 (ptmt) cc_final: 0.6886 (ptpp) REVERT: D 745 MET cc_start: 0.4199 (tpt) cc_final: 0.3683 (tpp) REVERT: D 782 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7444 (m-30) REVERT: D 817 GLN cc_start: 0.6567 (mt0) cc_final: 0.6233 (mp10) REVERT: D 919 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7387 (t0) REVERT: D 934 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.6933 (tp30) REVERT: D 965 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7245 (tm-30) outliers start: 171 outliers final: 76 residues processed: 580 average time/residue: 0.7935 time to fit residues: 544.2192 Evaluate side-chains 572 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 464 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 924 ASP Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 766 SER Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 924 ASP Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 919 ASP Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 924 ASP Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 924 ASP Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 965 GLN Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 84 optimal weight: 10.0000 chunk 384 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 337 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 369 optimal weight: 8.9990 chunk 370 optimal weight: 8.9990 chunk 372 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 HIS A 262 GLN A 485 GLN A 573 GLN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN B 30 HIS B 262 GLN B 485 GLN B 573 GLN ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN C 30 HIS C 262 GLN C 485 GLN C 573 GLN ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN D 30 HIS D 262 GLN D 485 GLN D 573 GLN ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 824 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.171674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.150537 restraints weight = 33747.552| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.22 r_work: 0.3673 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 33876 Z= 0.160 Angle : 0.651 9.775 46216 Z= 0.335 Chirality : 0.045 0.153 4840 Planarity : 0.005 0.038 6092 Dihedral : 5.169 61.265 4484 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.67 % Rotamer: Outliers : 4.89 % Allowed : 15.93 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % 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: -0.55 (0.13), residues: 4080 helix: -0.16 (0.22), residues: 552 sheet: 0.17 (0.14), residues: 1416 loop : -0.73 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 43 TYR 0.015 0.002 TYR D1014 PHE 0.009 0.002 PHE D 63 TRP 0.025 0.002 TRP B 553 HIS 0.007 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (33876) covalent geometry : angle 0.65107 / 0.33 (46216) hydrogen bonds : bond 0.04145 / 2.75 ( 1040) hydrogen bonds : angle 5.65245 / 4.01 ( 2796) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 496 time to evaluate : 1.380 Fit side-chains REVERT: A 41 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6564 (tt0) REVERT: A 46 ARG cc_start: 0.6659 (mmm160) cc_final: 0.5844 (ttp-170) REVERT: A 52 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7109 (ttm-80) REVERT: A 77 ASP cc_start: 0.6065 (p0) cc_final: 0.5825 (p0) REVERT: A 84 VAL cc_start: 0.7405 (m) cc_final: 0.7180 (m) REVERT: A 144 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7320 (t70) REVERT: A 178 ARG cc_start: 0.5412 (ptt90) cc_final: 0.5119 (mtm180) REVERT: A 233 ASP cc_start: 0.5754 (m-30) cc_final: 0.5547 (m-30) REVERT: A 255 ARG cc_start: 0.7657 (mmt-90) cc_final: 0.7231 (mmt-90) REVERT: A 269 SER cc_start: 0.7757 (OUTLIER) cc_final: 0.7411 (m) REVERT: A 277 GLU cc_start: 0.5811 (pm20) cc_final: 0.5352 (tt0) REVERT: A 292 ARG cc_start: 0.7324 (mtt90) cc_final: 0.6940 (mtt180) REVERT: A 338 GLU cc_start: 0.7429 (tt0) cc_final: 0.7163 (tm-30) REVERT: A 546 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7808 (mp) REVERT: A 611 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.4580 (ptp-170) REVERT: A 677 LYS cc_start: 0.7463 (ptmt) cc_final: 0.6893 (ptpp) REVERT: A 745 MET cc_start: 0.4187 (tpt) cc_final: 0.3660 (tpp) REVERT: A 753 ASN cc_start: 0.5652 (p0) cc_final: 0.5293 (t0) REVERT: A 782 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: A 817 GLN cc_start: 0.6531 (mt0) cc_final: 0.6190 (mp10) REVERT: A 919 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7368 (t70) REVERT: A 934 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.6912 (tp30) REVERT: A 965 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: B 41 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6565 (tt0) REVERT: B 46 ARG cc_start: 0.6652 (mmm160) cc_final: 0.5842 (ttp-170) REVERT: B 52 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7104 (ttm-80) REVERT: B 77 ASP cc_start: 0.6067 (p0) cc_final: 0.5837 (p0) REVERT: B 84 VAL cc_start: 0.7413 (m) cc_final: 0.7184 (m) REVERT: B 144 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7323 (t70) REVERT: B 178 ARG cc_start: 0.5407 (ptt90) cc_final: 0.5119 (mtm180) REVERT: B 233 ASP cc_start: 0.5753 (m-30) cc_final: 0.5548 (m-30) REVERT: B 255 ARG cc_start: 0.7651 (mmt-90) cc_final: 0.7225 (mmt-90) REVERT: B 269 SER cc_start: 0.7762 (OUTLIER) cc_final: 0.7420 (m) REVERT: B 277 GLU cc_start: 0.5813 (pm20) cc_final: 0.5358 (tt0) REVERT: B 292 ARG cc_start: 0.7326 (mtt90) cc_final: 0.6942 (mtt180) REVERT: B 338 GLU cc_start: 0.7428 (tt0) cc_final: 0.7162 (tm-30) REVERT: B 546 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7810 (mp) REVERT: B 611 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.4567 (ptp-170) REVERT: B 677 LYS cc_start: 0.7461 (ptmt) cc_final: 0.6892 (ptpp) REVERT: B 745 MET cc_start: 0.4188 (tpt) cc_final: 0.3660 (tpp) REVERT: B 753 ASN cc_start: 0.5657 (p0) cc_final: 0.5296 (t0) REVERT: B 782 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7371 (m-30) REVERT: B 817 GLN cc_start: 0.6530 (mt0) cc_final: 0.6192 (mp10) REVERT: B 919 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7368 (t70) REVERT: B 934 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.6908 (tp30) REVERT: B 965 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: C 41 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6595 (tt0) REVERT: C 46 ARG cc_start: 0.6658 (mmm160) cc_final: 0.5845 (ttp-170) REVERT: C 52 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7101 (ttm-80) REVERT: C 77 ASP cc_start: 0.6068 (p0) cc_final: 0.5836 (p0) REVERT: C 84 VAL cc_start: 0.7408 (m) cc_final: 0.7181 (m) REVERT: C 144 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7326 (t70) REVERT: C 178 ARG cc_start: 0.5408 (ptt90) cc_final: 0.5124 (mtm180) REVERT: C 233 ASP cc_start: 0.5749 (m-30) cc_final: 0.5545 (m-30) REVERT: C 255 ARG cc_start: 0.7660 (mmt-90) cc_final: 0.7236 (mmt-90) REVERT: C 269 SER cc_start: 0.7766 (OUTLIER) cc_final: 0.7423 (m) REVERT: C 277 GLU cc_start: 0.5818 (pm20) cc_final: 0.5364 (tt0) REVERT: C 292 ARG cc_start: 0.7320 (mtt90) cc_final: 0.6934 (mtt180) REVERT: C 338 GLU cc_start: 0.7428 (tt0) cc_final: 0.7162 (tm-30) REVERT: C 546 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7812 (mp) REVERT: C 611 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.4563 (ptp-170) REVERT: C 677 LYS cc_start: 0.7465 (ptmt) cc_final: 0.6896 (ptpp) REVERT: C 745 MET cc_start: 0.4182 (tpt) cc_final: 0.3658 (tpp) REVERT: C 753 ASN cc_start: 0.5653 (p0) cc_final: 0.5299 (t0) REVERT: C 782 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7352 (m-30) REVERT: C 817 GLN cc_start: 0.6539 (mt0) cc_final: 0.6196 (mp10) REVERT: C 919 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7381 (t70) REVERT: C 934 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.6908 (tp30) REVERT: C 965 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7285 (tm-30) REVERT: D 41 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6571 (tt0) REVERT: D 46 ARG cc_start: 0.6659 (mmm160) cc_final: 0.5850 (ttp-170) REVERT: D 52 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7116 (ttm-80) REVERT: D 77 ASP cc_start: 0.6064 (p0) cc_final: 0.5819 (p0) REVERT: D 84 VAL cc_start: 0.7406 (m) cc_final: 0.7181 (m) REVERT: D 144 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7320 (t70) REVERT: D 178 ARG cc_start: 0.5410 (ptt90) cc_final: 0.5130 (mtm180) REVERT: D 233 ASP cc_start: 0.5756 (m-30) cc_final: 0.5550 (m-30) REVERT: D 255 ARG cc_start: 0.7657 (mmt-90) cc_final: 0.7232 (mmt-90) REVERT: D 269 SER cc_start: 0.7763 (OUTLIER) cc_final: 0.7422 (m) REVERT: D 277 GLU cc_start: 0.5809 (pm20) cc_final: 0.5350 (tt0) REVERT: D 292 ARG cc_start: 0.7324 (mtt90) cc_final: 0.6936 (mtt180) REVERT: D 338 GLU cc_start: 0.7437 (tt0) cc_final: 0.7170 (tm-30) REVERT: D 546 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7809 (mp) REVERT: D 611 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.4550 (ptp-170) REVERT: D 677 LYS cc_start: 0.7460 (ptmt) cc_final: 0.6891 (ptpp) REVERT: D 745 MET cc_start: 0.4181 (tpt) cc_final: 0.3655 (tpp) REVERT: D 753 ASN cc_start: 0.5651 (p0) cc_final: 0.5299 (t0) REVERT: D 782 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7356 (m-30) REVERT: D 817 GLN cc_start: 0.6528 (mt0) cc_final: 0.6186 (mp10) REVERT: D 919 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7378 (t70) REVERT: D 934 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.6913 (tp30) REVERT: D 965 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7281 (tm-30) outliers start: 171 outliers final: 92 residues processed: 607 average time/residue: 0.8107 time to fit residues: 580.4242 Evaluate side-chains 588 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 456 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 766 SER Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 919 ASP Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 965 GLN Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 346 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 247 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 395 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 373 optimal weight: 0.6980 chunk 299 optimal weight: 20.0000 chunk 283 optimal weight: 8.9990 chunk 356 optimal weight: 20.0000 chunk 297 optimal weight: 8.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 HIS A 262 GLN A 395 HIS A 485 GLN A 573 GLN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN A 896 ASN B 30 HIS B 151 HIS B 262 GLN B 395 HIS B 485 GLN B 573 GLN ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN B 896 ASN C 30 HIS C 262 GLN C 395 HIS C 485 GLN C 573 GLN ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN C 896 ASN D 30 HIS D 151 HIS D 262 GLN D 395 HIS D 485 GLN D 573 GLN ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 824 GLN D 896 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.171120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.150108 restraints weight = 33525.122| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.21 r_work: 0.3668 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33876 Z= 0.172 Angle : 0.665 9.733 46216 Z= 0.342 Chirality : 0.046 0.151 4840 Planarity : 0.005 0.039 6092 Dihedral : 5.252 61.232 4484 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.37 % Rotamer: Outliers : 4.92 % Allowed : 16.16 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % 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: -0.56 (0.13), residues: 4080 helix: -0.13 (0.22), residues: 552 sheet: 0.22 (0.14), residues: 1412 loop : -0.80 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 43 TYR 0.017 0.002 TYR C1014 PHE 0.010 0.002 PHE A 63 TRP 0.026 0.002 TRP C 553 HIS 0.007 0.001 HIS C 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (33876) covalent geometry : angle 0.66497 / 0.34 (46216) hydrogen bonds : bond 0.04179 / 2.77 ( 1040) hydrogen bonds : angle 5.66639 / 4.02 ( 2796) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 484 time to evaluate : 1.360 Fit side-chains REVERT: A 41 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6567 (tt0) REVERT: A 46 ARG cc_start: 0.6626 (mmm160) cc_final: 0.5852 (ttp-170) REVERT: A 52 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7072 (ttm-80) REVERT: A 77 ASP cc_start: 0.6198 (p0) cc_final: 0.5964 (p0) REVERT: A 84 VAL cc_start: 0.7424 (m) cc_final: 0.7205 (m) REVERT: A 178 ARG cc_start: 0.5454 (ptt90) cc_final: 0.5147 (mtm180) REVERT: A 233 ASP cc_start: 0.5935 (m-30) cc_final: 0.5716 (m-30) REVERT: A 255 ARG cc_start: 0.7637 (mmt-90) cc_final: 0.7327 (mmt-90) REVERT: A 269 SER cc_start: 0.7785 (OUTLIER) cc_final: 0.7427 (m) REVERT: A 277 GLU cc_start: 0.5809 (pm20) cc_final: 0.5341 (tt0) REVERT: A 292 ARG cc_start: 0.7279 (mtt90) cc_final: 0.6891 (mtt180) REVERT: A 338 GLU cc_start: 0.7419 (tt0) cc_final: 0.7139 (tm-30) REVERT: A 546 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7819 (mp) REVERT: A 611 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.4640 (ptp-170) REVERT: A 677 LYS cc_start: 0.7492 (ptmt) cc_final: 0.6931 (ptpp) REVERT: A 745 MET cc_start: 0.4170 (tpt) cc_final: 0.3672 (tpp) REVERT: A 782 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7375 (m-30) REVERT: A 791 ASN cc_start: 0.7785 (m-40) cc_final: 0.7558 (m110) REVERT: A 817 GLN cc_start: 0.6501 (mt0) cc_final: 0.6146 (mp10) REVERT: A 919 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7374 (t0) REVERT: A 934 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.6920 (tp30) REVERT: A 965 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: B 41 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6575 (tt0) REVERT: B 46 ARG cc_start: 0.6627 (mmm160) cc_final: 0.5855 (ttp-170) REVERT: B 52 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7068 (ttm-80) REVERT: B 77 ASP cc_start: 0.6190 (p0) cc_final: 0.5974 (p0) REVERT: B 84 VAL cc_start: 0.7431 (m) cc_final: 0.7210 (m) REVERT: B 178 ARG cc_start: 0.5452 (ptt90) cc_final: 0.5155 (mtm180) REVERT: B 233 ASP cc_start: 0.5926 (m-30) cc_final: 0.5706 (m-30) REVERT: B 255 ARG cc_start: 0.7636 (mmt-90) cc_final: 0.7325 (mmt-90) REVERT: B 269 SER cc_start: 0.7791 (OUTLIER) cc_final: 0.7435 (m) REVERT: B 277 GLU cc_start: 0.5804 (pm20) cc_final: 0.5339 (tt0) REVERT: B 292 ARG cc_start: 0.7281 (mtt90) cc_final: 0.6888 (mtt180) REVERT: B 338 GLU cc_start: 0.7424 (tt0) cc_final: 0.7144 (tm-30) REVERT: B 546 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7819 (mp) REVERT: B 611 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.4627 (ptp-170) REVERT: B 677 LYS cc_start: 0.7481 (ptmt) cc_final: 0.6922 (ptpp) REVERT: B 745 MET cc_start: 0.4181 (tpt) cc_final: 0.3679 (tpp) REVERT: B 782 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7383 (m-30) REVERT: B 791 ASN cc_start: 0.7791 (m-40) cc_final: 0.7564 (m110) REVERT: B 817 GLN cc_start: 0.6506 (mt0) cc_final: 0.6150 (mp10) REVERT: B 919 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7366 (t0) REVERT: B 934 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.6918 (tp30) REVERT: B 965 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7291 (tm-30) REVERT: C 41 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6592 (tt0) REVERT: C 46 ARG cc_start: 0.6630 (mmm160) cc_final: 0.5855 (ttp-170) REVERT: C 52 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7075 (ttm-80) REVERT: C 77 ASP cc_start: 0.6195 (p0) cc_final: 0.5968 (p0) REVERT: C 84 VAL cc_start: 0.7425 (m) cc_final: 0.7204 (m) REVERT: C 178 ARG cc_start: 0.5445 (ptt90) cc_final: 0.5149 (mtm180) REVERT: C 233 ASP cc_start: 0.5940 (m-30) cc_final: 0.5721 (m-30) REVERT: C 255 ARG cc_start: 0.7641 (mmt-90) cc_final: 0.7331 (mmt-90) REVERT: C 269 SER cc_start: 0.7792 (OUTLIER) cc_final: 0.7435 (m) REVERT: C 277 GLU cc_start: 0.5811 (pm20) cc_final: 0.5349 (tt0) REVERT: C 292 ARG cc_start: 0.7279 (mtt90) cc_final: 0.6885 (mtt180) REVERT: C 338 GLU cc_start: 0.7413 (tt0) cc_final: 0.7134 (tm-30) REVERT: C 546 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7823 (mp) REVERT: C 611 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.4627 (ptp-170) REVERT: C 677 LYS cc_start: 0.7485 (ptmt) cc_final: 0.6927 (ptpp) REVERT: C 745 MET cc_start: 0.4172 (tpt) cc_final: 0.3674 (tpp) REVERT: C 782 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7371 (m-30) REVERT: C 791 ASN cc_start: 0.7785 (m-40) cc_final: 0.7563 (m110) REVERT: C 817 GLN cc_start: 0.6511 (mt0) cc_final: 0.6151 (mp10) REVERT: C 919 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7373 (t0) REVERT: C 934 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.6921 (tp30) REVERT: C 965 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7292 (tm-30) REVERT: D 41 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6577 (tt0) REVERT: D 46 ARG cc_start: 0.6635 (mmm160) cc_final: 0.5862 (ttp-170) REVERT: D 52 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7067 (ttm-80) REVERT: D 77 ASP cc_start: 0.6193 (p0) cc_final: 0.5959 (p0) REVERT: D 84 VAL cc_start: 0.7425 (m) cc_final: 0.7205 (m) REVERT: D 178 ARG cc_start: 0.5449 (ptt90) cc_final: 0.5155 (mtm180) REVERT: D 233 ASP cc_start: 0.5930 (m-30) cc_final: 0.5713 (m-30) REVERT: D 255 ARG cc_start: 0.7641 (mmt-90) cc_final: 0.7330 (mmt-90) REVERT: D 269 SER cc_start: 0.7794 (OUTLIER) cc_final: 0.7438 (m) REVERT: D 277 GLU cc_start: 0.5802 (pm20) cc_final: 0.5332 (tt0) REVERT: D 292 ARG cc_start: 0.7279 (mtt90) cc_final: 0.6888 (mtt180) REVERT: D 338 GLU cc_start: 0.7414 (tt0) cc_final: 0.7132 (tm-30) REVERT: D 546 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7816 (mp) REVERT: D 611 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.4615 (ptp-170) REVERT: D 677 LYS cc_start: 0.7482 (ptmt) cc_final: 0.6927 (ptpp) REVERT: D 745 MET cc_start: 0.4169 (tpt) cc_final: 0.3670 (tpp) REVERT: D 782 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: D 791 ASN cc_start: 0.7785 (m-40) cc_final: 0.7565 (m110) REVERT: D 817 GLN cc_start: 0.6508 (mt0) cc_final: 0.6148 (mp10) REVERT: D 919 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7375 (t0) REVERT: D 934 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.6929 (tp30) REVERT: D 965 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7287 (tm-30) outliers start: 172 outliers final: 88 residues processed: 608 average time/residue: 0.7694 time to fit residues: 554.8221 Evaluate side-chains 584 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 460 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 766 SER Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 919 ASP Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 965 GLN Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 215 optimal weight: 0.0570 chunk 360 optimal weight: 20.0000 chunk 123 optimal weight: 30.0000 chunk 379 optimal weight: 30.0000 chunk 296 optimal weight: 20.0000 chunk 235 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 349 optimal weight: 5.9990 chunk 364 optimal weight: 7.9990 overall best weight: 6.0108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 HIS A 151 HIS A 262 GLN A 485 GLN A 573 GLN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN B 30 HIS B 262 GLN B 485 GLN B 573 GLN ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN C 30 HIS C 151 HIS C 262 GLN C 485 GLN C 573 GLN ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN D 30 HIS D 262 GLN D 485 GLN D 573 GLN ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 824 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.170541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.149444 restraints weight = 33776.331| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.22 r_work: 0.3658 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 33876 Z= 0.190 Angle : 0.697 9.792 46216 Z= 0.357 Chirality : 0.047 0.150 4840 Planarity : 0.005 0.043 6092 Dihedral : 5.385 62.348 4484 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.92 % Favored : 95.98 % Rotamer: Outliers : 5.29 % Allowed : 16.45 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % 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: -0.66 (0.13), residues: 4080 helix: -0.20 (0.22), residues: 552 sheet: 0.18 (0.14), residues: 1412 loop : -0.88 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 43 TYR 0.020 0.002 TYR C1014 PHE 0.015 0.002 PHE D 33 TRP 0.027 0.002 TRP B 553 HIS 0.008 0.001 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (33876) covalent geometry : angle 0.69718 / 0.36 (46216) hydrogen bonds : bond 0.04332 / 2.88 ( 1040) hydrogen bonds : angle 5.71308 / 4.06 ( 2796) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 468 time to evaluate : 1.414 Fit side-chains REVERT: A 41 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6607 (tt0) REVERT: A 46 ARG cc_start: 0.6594 (mmm160) cc_final: 0.5830 (ttp-170) REVERT: A 52 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7067 (ttm-80) REVERT: A 77 ASP cc_start: 0.6264 (p0) cc_final: 0.6053 (p0) REVERT: A 84 VAL cc_start: 0.7459 (m) cc_final: 0.7244 (m) REVERT: A 178 ARG cc_start: 0.5468 (ptt90) cc_final: 0.5167 (mtm180) REVERT: A 205 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7244 (mtt) REVERT: A 269 SER cc_start: 0.7785 (OUTLIER) cc_final: 0.7424 (m) REVERT: A 277 GLU cc_start: 0.5836 (pm20) cc_final: 0.5360 (tt0) REVERT: A 292 ARG cc_start: 0.7266 (mtt90) cc_final: 0.6970 (mtt180) REVERT: A 338 GLU cc_start: 0.7424 (tt0) cc_final: 0.7118 (tm-30) REVERT: A 611 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.4904 (ptp-170) REVERT: A 745 MET cc_start: 0.4194 (tpt) cc_final: 0.3652 (tpp) REVERT: A 782 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7383 (m-30) REVERT: A 817 GLN cc_start: 0.6518 (mt0) cc_final: 0.6151 (mp10) REVERT: A 888 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7501 (mt) REVERT: A 919 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7403 (t70) REVERT: A 934 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.6903 (tp30) REVERT: A 965 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: B 41 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6602 (tt0) REVERT: B 46 ARG cc_start: 0.6593 (mmm160) cc_final: 0.5831 (ttp-170) REVERT: B 52 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7062 (ttm-80) REVERT: B 84 VAL cc_start: 0.7464 (m) cc_final: 0.7246 (m) REVERT: B 178 ARG cc_start: 0.5464 (ptt90) cc_final: 0.5170 (mtm180) REVERT: B 205 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7253 (mtt) REVERT: B 269 SER cc_start: 0.7786 (OUTLIER) cc_final: 0.7425 (m) REVERT: B 277 GLU cc_start: 0.5829 (pm20) cc_final: 0.5359 (tt0) REVERT: B 292 ARG cc_start: 0.7262 (mtt90) cc_final: 0.6965 (mtt180) REVERT: B 338 GLU cc_start: 0.7434 (tt0) cc_final: 0.7129 (tm-30) REVERT: B 611 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.4896 (ptp-170) REVERT: B 745 MET cc_start: 0.4201 (tpt) cc_final: 0.3657 (tpp) REVERT: B 782 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7392 (m-30) REVERT: B 817 GLN cc_start: 0.6521 (mt0) cc_final: 0.6150 (mp10) REVERT: B 888 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7501 (mt) REVERT: B 919 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7402 (t70) REVERT: B 934 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.6910 (tp30) REVERT: B 965 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: C 41 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6617 (tt0) REVERT: C 46 ARG cc_start: 0.6597 (mmm160) cc_final: 0.5836 (ttp-170) REVERT: C 52 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7068 (ttm-80) REVERT: C 77 ASP cc_start: 0.6259 (p0) cc_final: 0.6052 (p0) REVERT: C 84 VAL cc_start: 0.7459 (m) cc_final: 0.7244 (m) REVERT: C 178 ARG cc_start: 0.5457 (ptt90) cc_final: 0.5167 (mtm180) REVERT: C 205 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7255 (mtt) REVERT: C 269 SER cc_start: 0.7781 (OUTLIER) cc_final: 0.7420 (m) REVERT: C 277 GLU cc_start: 0.5854 (pm20) cc_final: 0.5375 (tt0) REVERT: C 292 ARG cc_start: 0.7265 (mtt90) cc_final: 0.6967 (mtt180) REVERT: C 338 GLU cc_start: 0.7417 (tt0) cc_final: 0.7114 (tm-30) REVERT: C 611 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.4896 (ptp-170) REVERT: C 745 MET cc_start: 0.4197 (tpt) cc_final: 0.3655 (tpp) REVERT: C 782 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7375 (m-30) REVERT: C 817 GLN cc_start: 0.6532 (mt0) cc_final: 0.6173 (mp10) REVERT: C 888 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7496 (mt) REVERT: C 919 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7405 (t70) REVERT: C 934 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.6904 (tp30) REVERT: C 965 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: D 41 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6610 (tt0) REVERT: D 46 ARG cc_start: 0.6597 (mmm160) cc_final: 0.5834 (ttp-170) REVERT: D 52 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7059 (ttm-80) REVERT: D 77 ASP cc_start: 0.6263 (p0) cc_final: 0.6049 (p0) REVERT: D 84 VAL cc_start: 0.7455 (m) cc_final: 0.7239 (m) REVERT: D 178 ARG cc_start: 0.5462 (ptt90) cc_final: 0.5167 (mtm180) REVERT: D 205 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7251 (mtt) REVERT: D 269 SER cc_start: 0.7788 (OUTLIER) cc_final: 0.7428 (m) REVERT: D 277 GLU cc_start: 0.5837 (pm20) cc_final: 0.5362 (tt0) REVERT: D 292 ARG cc_start: 0.7264 (mtt90) cc_final: 0.6968 (mtt180) REVERT: D 338 GLU cc_start: 0.7435 (tt0) cc_final: 0.7130 (tm-30) REVERT: D 611 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.4888 (ptp-170) REVERT: D 745 MET cc_start: 0.4194 (tpt) cc_final: 0.3653 (tpp) REVERT: D 782 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: D 817 GLN cc_start: 0.6525 (mt0) cc_final: 0.6152 (mp10) REVERT: D 888 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7495 (mt) REVERT: D 919 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7401 (t70) REVERT: D 934 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.6904 (tp30) REVERT: D 965 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7304 (tm-30) outliers start: 185 outliers final: 92 residues processed: 601 average time/residue: 0.7900 time to fit residues: 560.6935 Evaluate side-chains 591 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 459 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 766 SER Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 919 ASP Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 965 GLN Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 353 optimal weight: 3.9990 chunk 309 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 265 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 252 optimal weight: 2.9990 chunk 341 optimal weight: 20.0000 chunk 293 optimal weight: 20.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 HIS A 262 GLN A 395 HIS A 485 GLN A 573 GLN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 GLN A 824 GLN A 896 ASN B 30 HIS B 262 GLN B 395 HIS B 485 GLN B 573 GLN ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 783 GLN B 824 GLN B 896 ASN C 30 HIS C 262 GLN C 395 HIS C 485 GLN C 573 GLN ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 783 GLN C 824 GLN C 896 ASN D 30 HIS D 262 GLN D 395 HIS D 485 GLN D 573 GLN ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 783 GLN D 824 GLN D 896 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.171803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.150904 restraints weight = 33608.804| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.22 r_work: 0.3676 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 33876 Z= 0.148 Angle : 0.643 9.721 46216 Z= 0.329 Chirality : 0.045 0.149 4840 Planarity : 0.005 0.037 6092 Dihedral : 5.178 61.301 4484 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.89 % Allowed : 17.11 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % 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: -0.54 (0.13), residues: 4080 helix: 0.01 (0.22), residues: 552 sheet: 0.25 (0.14), residues: 1408 loop : -0.84 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 43 TYR 0.016 0.002 TYR C1014 PHE 0.017 0.002 PHE D 33 TRP 0.027 0.002 TRP B 553 HIS 0.010 0.001 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (33876) covalent geometry : angle 0.64304 / 0.33 (46216) hydrogen bonds : bond 0.03912 / 2.59 ( 1040) hydrogen bonds : angle 5.58016 / 3.96 ( 2796) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 483 time to evaluate : 1.381 Fit side-chains REVERT: A 41 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6565 (tt0) REVERT: A 46 ARG cc_start: 0.6594 (mmm160) cc_final: 0.5838 (ttp-170) REVERT: A 52 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7229 (ttm-80) REVERT: A 77 ASP cc_start: 0.6247 (p0) cc_final: 0.6014 (p0) REVERT: A 84 VAL cc_start: 0.7442 (m) cc_final: 0.7223 (m) REVERT: A 178 ARG cc_start: 0.5480 (ptt90) cc_final: 0.5169 (mtm180) REVERT: A 255 ARG cc_start: 0.7527 (mmt-90) cc_final: 0.7255 (mmt-90) REVERT: A 269 SER cc_start: 0.7749 (OUTLIER) cc_final: 0.7393 (m) REVERT: A 277 GLU cc_start: 0.5820 (pm20) cc_final: 0.5333 (tt0) REVERT: A 292 ARG cc_start: 0.7244 (mtt90) cc_final: 0.6990 (mtt180) REVERT: A 338 GLU cc_start: 0.7419 (tt0) cc_final: 0.7141 (tm-30) REVERT: A 367 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7342 (tpp) REVERT: A 611 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.4961 (ptp-170) REVERT: A 745 MET cc_start: 0.4190 (tpt) cc_final: 0.3669 (tpp) REVERT: A 782 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7347 (m-30) REVERT: A 817 GLN cc_start: 0.6530 (mt0) cc_final: 0.6159 (mp10) REVERT: A 888 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7442 (mt) REVERT: A 919 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7371 (t0) REVERT: A 934 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.6938 (tp30) REVERT: A 965 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7298 (tm-30) REVERT: B 41 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6579 (tt0) REVERT: B 46 ARG cc_start: 0.6591 (mmm160) cc_final: 0.5833 (ttp-170) REVERT: B 52 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7227 (ttm-80) REVERT: B 84 VAL cc_start: 0.7443 (m) cc_final: 0.7219 (m) REVERT: B 178 ARG cc_start: 0.5480 (ptt90) cc_final: 0.5177 (mtm180) REVERT: B 255 ARG cc_start: 0.7521 (mmt-90) cc_final: 0.7250 (mmt-90) REVERT: B 269 SER cc_start: 0.7749 (OUTLIER) cc_final: 0.7392 (m) REVERT: B 277 GLU cc_start: 0.5814 (pm20) cc_final: 0.5333 (tt0) REVERT: B 292 ARG cc_start: 0.7245 (mtt90) cc_final: 0.6989 (mtt180) REVERT: B 338 GLU cc_start: 0.7424 (tt0) cc_final: 0.7146 (tm-30) REVERT: B 367 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7346 (tpp) REVERT: B 611 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.4951 (ptp-170) REVERT: B 745 MET cc_start: 0.4199 (tpt) cc_final: 0.3676 (tpp) REVERT: B 782 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7351 (m-30) REVERT: B 817 GLN cc_start: 0.6534 (mt0) cc_final: 0.6158 (mp10) REVERT: B 888 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7440 (mt) REVERT: B 919 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7374 (t0) REVERT: B 934 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.6939 (tp30) REVERT: B 965 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7287 (tm-30) REVERT: C 41 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6594 (tt0) REVERT: C 46 ARG cc_start: 0.6590 (mmm160) cc_final: 0.5835 (ttp-170) REVERT: C 52 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7230 (ttm-80) REVERT: C 77 ASP cc_start: 0.6243 (p0) cc_final: 0.6018 (p0) REVERT: C 84 VAL cc_start: 0.7440 (m) cc_final: 0.7218 (m) REVERT: C 178 ARG cc_start: 0.5469 (ptt90) cc_final: 0.5167 (mtm180) REVERT: C 255 ARG cc_start: 0.7531 (mmt-90) cc_final: 0.7260 (mmt-90) REVERT: C 269 SER cc_start: 0.7754 (OUTLIER) cc_final: 0.7397 (m) REVERT: C 277 GLU cc_start: 0.5829 (pm20) cc_final: 0.5343 (tt0) REVERT: C 292 ARG cc_start: 0.7244 (mtt90) cc_final: 0.6988 (mtt180) REVERT: C 338 GLU cc_start: 0.7409 (tt0) cc_final: 0.7132 (tm-30) REVERT: C 367 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7334 (tpp) REVERT: C 611 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.4954 (ptp-170) REVERT: C 745 MET cc_start: 0.4186 (tpt) cc_final: 0.3669 (tpp) REVERT: C 782 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7334 (m-30) REVERT: C 817 GLN cc_start: 0.6556 (mt0) cc_final: 0.6174 (mp10) REVERT: C 888 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7435 (mt) REVERT: C 919 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7377 (t0) REVERT: C 934 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.6916 (tp30) REVERT: C 965 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7290 (tm-30) REVERT: D 41 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6584 (tt0) REVERT: D 46 ARG cc_start: 0.6589 (mmm160) cc_final: 0.5834 (ttp-170) REVERT: D 52 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7225 (ttm-80) REVERT: D 77 ASP cc_start: 0.6246 (p0) cc_final: 0.6010 (p0) REVERT: D 84 VAL cc_start: 0.7439 (m) cc_final: 0.7219 (m) REVERT: D 178 ARG cc_start: 0.5474 (ptt90) cc_final: 0.5170 (mtm180) REVERT: D 255 ARG cc_start: 0.7529 (mmt-90) cc_final: 0.7256 (mmt-90) REVERT: D 269 SER cc_start: 0.7758 (OUTLIER) cc_final: 0.7404 (m) REVERT: D 277 GLU cc_start: 0.5813 (pm20) cc_final: 0.5326 (tt0) REVERT: D 292 ARG cc_start: 0.7242 (mtt90) cc_final: 0.6986 (mtt180) REVERT: D 338 GLU cc_start: 0.7423 (tt0) cc_final: 0.7144 (tm-30) REVERT: D 367 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7338 (tpp) REVERT: D 611 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.4937 (ptp-170) REVERT: D 745 MET cc_start: 0.4188 (tpt) cc_final: 0.3668 (tpp) REVERT: D 782 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7343 (m-30) REVERT: D 817 GLN cc_start: 0.6528 (mt0) cc_final: 0.6158 (mp10) REVERT: D 888 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7437 (mt) REVERT: D 919 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7378 (t0) REVERT: D 934 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.6940 (tp30) REVERT: D 965 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7291 (tm-30) outliers start: 171 outliers final: 88 residues processed: 598 average time/residue: 0.8045 time to fit residues: 567.5598 Evaluate side-chains 583 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 455 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 766 SER Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 671 ASP Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 919 ASP Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 671 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 965 GLN Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 372 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 277 optimal weight: 30.0000 chunk 283 optimal weight: 8.9990 chunk 390 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 238 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 199 optimal weight: 0.0030 chunk 146 optimal weight: 9.9990 overall best weight: 5.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 HIS A 262 GLN A 395 HIS A 485 GLN A 573 GLN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 ASN A 783 GLN A 824 GLN A 887 GLN B 30 HIS B 262 GLN B 395 HIS B 485 GLN B 573 GLN ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 ASN B 783 GLN B 824 GLN B 887 GLN C 30 HIS C 262 GLN C 395 HIS C 485 GLN C 573 GLN ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 ASN C 783 GLN C 824 GLN C 887 GLN D 30 HIS D 262 GLN D 395 HIS D 485 GLN D 573 GLN ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 704 ASN D 783 GLN D 824 GLN D 887 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.170841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.149838 restraints weight = 33601.920| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.21 r_work: 0.3665 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 33876 Z= 0.179 Angle : 0.680 9.673 46216 Z= 0.349 Chirality : 0.046 0.148 4840 Planarity : 0.005 0.041 6092 Dihedral : 5.339 62.724 4484 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.00 % Allowed : 17.93 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 4080 helix: -0.08 (0.22), residues: 552 sheet: 0.38 (0.15), residues: 1284 loop : -0.99 (0.12), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 43 TYR 0.018 0.002 TYR C1014 PHE 0.018 0.002 PHE D 33 TRP 0.026 0.002 TRP B 553 HIS 0.011 0.001 HIS C 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (33876) covalent geometry : angle 0.68031 / 0.35 (46216) hydrogen bonds : bond 0.04183 / 2.78 ( 1040) hydrogen bonds : angle 5.64962 / 4.01 ( 2796) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 455 time to evaluate : 1.354 Fit side-chains REVERT: A 41 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6605 (tt0) REVERT: A 46 ARG cc_start: 0.6588 (mmm160) cc_final: 0.5834 (ttp-170) REVERT: A 52 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7062 (ttm-80) REVERT: A 77 ASP cc_start: 0.6264 (p0) cc_final: 0.6056 (p0) REVERT: A 84 VAL cc_start: 0.7457 (m) cc_final: 0.7238 (m) REVERT: A 178 ARG cc_start: 0.5494 (ptt90) cc_final: 0.5211 (mtm180) REVERT: A 255 ARG cc_start: 0.7536 (mmt-90) cc_final: 0.7254 (mmt-90) REVERT: A 269 SER cc_start: 0.7790 (OUTLIER) cc_final: 0.7425 (m) REVERT: A 277 GLU cc_start: 0.5837 (pm20) cc_final: 0.5338 (tt0) REVERT: A 292 ARG cc_start: 0.7258 (mtt90) cc_final: 0.7006 (mtt180) REVERT: A 338 GLU cc_start: 0.7433 (tt0) cc_final: 0.7151 (tm-30) REVERT: A 611 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.5328 (ptp-170) REVERT: A 745 MET cc_start: 0.4181 (tpt) cc_final: 0.3658 (tpp) REVERT: A 782 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7363 (m-30) REVERT: A 817 GLN cc_start: 0.6551 (mt0) cc_final: 0.6165 (mp10) REVERT: A 888 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7505 (mt) REVERT: A 919 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7369 (t70) REVERT: A 934 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.6921 (tp30) REVERT: A 965 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: B 41 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6613 (tt0) REVERT: B 46 ARG cc_start: 0.6590 (mmm160) cc_final: 0.5836 (ttp-170) REVERT: B 52 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7062 (ttm-80) REVERT: B 84 VAL cc_start: 0.7460 (m) cc_final: 0.7240 (m) REVERT: B 178 ARG cc_start: 0.5489 (ptt90) cc_final: 0.5212 (mtm180) REVERT: B 255 ARG cc_start: 0.7532 (mmt-90) cc_final: 0.7248 (mmt-90) REVERT: B 269 SER cc_start: 0.7791 (OUTLIER) cc_final: 0.7428 (m) REVERT: B 277 GLU cc_start: 0.5844 (pm20) cc_final: 0.5341 (tt0) REVERT: B 292 ARG cc_start: 0.7255 (mtt90) cc_final: 0.7003 (mtt180) REVERT: B 338 GLU cc_start: 0.7428 (tt0) cc_final: 0.7145 (tm-30) REVERT: B 611 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.5321 (ptp-170) REVERT: B 745 MET cc_start: 0.4183 (tpt) cc_final: 0.3660 (tpp) REVERT: B 782 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: B 817 GLN cc_start: 0.6549 (mt0) cc_final: 0.6168 (mp10) REVERT: B 888 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7504 (mt) REVERT: B 919 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7382 (t70) REVERT: B 934 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.6926 (tp30) REVERT: B 965 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: C 41 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6619 (tt0) REVERT: C 46 ARG cc_start: 0.6584 (mmm160) cc_final: 0.5831 (ttp-170) REVERT: C 52 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7059 (ttm-80) REVERT: C 77 ASP cc_start: 0.6261 (p0) cc_final: 0.6056 (p0) REVERT: C 84 VAL cc_start: 0.7456 (m) cc_final: 0.7239 (m) REVERT: C 178 ARG cc_start: 0.5482 (ptt90) cc_final: 0.5209 (mtm180) REVERT: C 255 ARG cc_start: 0.7537 (mmt-90) cc_final: 0.7254 (mmt-90) REVERT: C 269 SER cc_start: 0.7786 (OUTLIER) cc_final: 0.7420 (m) REVERT: C 277 GLU cc_start: 0.5857 (pm20) cc_final: 0.5360 (tt0) REVERT: C 292 ARG cc_start: 0.7254 (mtt90) cc_final: 0.7000 (mtt180) REVERT: C 338 GLU cc_start: 0.7418 (tt0) cc_final: 0.7138 (tm-30) REVERT: C 611 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.5330 (ptp-170) REVERT: C 745 MET cc_start: 0.4184 (tpt) cc_final: 0.3660 (tpp) REVERT: C 782 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7351 (m-30) REVERT: C 817 GLN cc_start: 0.6553 (mt0) cc_final: 0.6177 (mp10) REVERT: C 888 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7504 (mt) REVERT: C 919 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7386 (t70) REVERT: C 934 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.6924 (tp30) REVERT: C 965 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: D 41 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6600 (tt0) REVERT: D 46 ARG cc_start: 0.6585 (mmm160) cc_final: 0.5836 (ttp-170) REVERT: D 52 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7056 (ttm-80) REVERT: D 77 ASP cc_start: 0.6259 (p0) cc_final: 0.6045 (p0) REVERT: D 84 VAL cc_start: 0.7455 (m) cc_final: 0.7237 (m) REVERT: D 178 ARG cc_start: 0.5485 (ptt90) cc_final: 0.5209 (mtm180) REVERT: D 255 ARG cc_start: 0.7540 (mmt-90) cc_final: 0.7256 (mmt-90) REVERT: D 269 SER cc_start: 0.7793 (OUTLIER) cc_final: 0.7429 (m) REVERT: D 277 GLU cc_start: 0.5839 (pm20) cc_final: 0.5338 (tt0) REVERT: D 292 ARG cc_start: 0.7250 (mtt90) cc_final: 0.6997 (mtt180) REVERT: D 338 GLU cc_start: 0.7437 (tt0) cc_final: 0.7157 (tm-30) REVERT: D 611 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.5316 (ptp-170) REVERT: D 745 MET cc_start: 0.4176 (tpt) cc_final: 0.3654 (tpp) REVERT: D 782 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7353 (m-30) REVERT: D 817 GLN cc_start: 0.6556 (mt0) cc_final: 0.6170 (mp10) REVERT: D 888 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7499 (mt) REVERT: D 919 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7379 (t70) REVERT: D 934 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.6918 (tp30) REVERT: D 965 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7313 (tm-30) outliers start: 140 outliers final: 92 residues processed: 547 average time/residue: 0.8359 time to fit residues: 536.3902 Evaluate side-chains 576 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 448 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 766 SER Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 919 ASP Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 965 GLN Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 67 optimal weight: 7.9990 chunk 403 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 341 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 274 optimal weight: 9.9990 chunk 377 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 HIS A 262 GLN A 485 GLN A 573 GLN A 824 GLN B 30 HIS B 262 GLN B 485 GLN B 573 GLN ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN C 30 HIS C 262 GLN C 485 GLN C 573 GLN ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN D 30 HIS D 262 GLN D 485 GLN D 573 GLN ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 824 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.169942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148893 restraints weight = 33706.854| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.22 r_work: 0.3652 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 33876 Z= 0.222 Angle : 0.744 9.850 46216 Z= 0.383 Chirality : 0.048 0.156 4840 Planarity : 0.006 0.047 6092 Dihedral : 5.631 65.586 4484 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.18 % Allowed : 17.79 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % 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 (0.13), residues: 4080 helix: -0.32 (0.21), residues: 552 sheet: 0.19 (0.14), residues: 1412 loop : -0.98 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 43 TYR 0.024 0.003 TYR C1014 PHE 0.019 0.002 PHE B 33 TRP 0.026 0.002 TRP A 553 HIS 0.012 0.002 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 (33876) covalent geometry : angle 0.74423 / 0.38 (46216) hydrogen bonds : bond 0.04634 / 3.08 ( 1040) hydrogen bonds : angle 5.79141 / 4.11 ( 2796) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 463 time to evaluate : 1.271 Fit side-chains REVERT: A 46 ARG cc_start: 0.6586 (mmm160) cc_final: 0.5824 (ttp-170) REVERT: A 52 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7090 (ttm-80) REVERT: A 84 VAL cc_start: 0.7454 (m) cc_final: 0.7243 (m) REVERT: A 181 GLU cc_start: 0.5566 (OUTLIER) cc_final: 0.5301 (pp20) REVERT: A 205 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7237 (mtp) REVERT: A 269 SER cc_start: 0.7818 (OUTLIER) cc_final: 0.7437 (m) REVERT: A 277 GLU cc_start: 0.5838 (pm20) cc_final: 0.5393 (tt0) REVERT: A 292 ARG cc_start: 0.7279 (mtt90) cc_final: 0.7012 (mtt180) REVERT: A 546 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7312 (mp) REVERT: A 611 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.5368 (ptp-170) REVERT: A 782 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7408 (m-30) REVERT: A 817 GLN cc_start: 0.6576 (mt0) cc_final: 0.6186 (mp10) REVERT: A 888 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7529 (mt) REVERT: A 919 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7385 (t70) REVERT: A 934 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.6922 (tp30) REVERT: A 965 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7371 (tm-30) REVERT: B 46 ARG cc_start: 0.6584 (mmm160) cc_final: 0.5821 (ttp-170) REVERT: B 52 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7086 (ttm-80) REVERT: B 84 VAL cc_start: 0.7456 (m) cc_final: 0.7246 (m) REVERT: B 181 GLU cc_start: 0.5559 (OUTLIER) cc_final: 0.5301 (pp20) REVERT: B 205 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7236 (mtp) REVERT: B 269 SER cc_start: 0.7817 (OUTLIER) cc_final: 0.7436 (m) REVERT: B 277 GLU cc_start: 0.5828 (pm20) cc_final: 0.5380 (tt0) REVERT: B 292 ARG cc_start: 0.7277 (mtt90) cc_final: 0.7011 (mtt180) REVERT: B 546 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7310 (mp) REVERT: B 611 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.5367 (ptp-170) REVERT: B 782 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7409 (m-30) REVERT: B 817 GLN cc_start: 0.6575 (mt0) cc_final: 0.6184 (mp10) REVERT: B 888 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7529 (mt) REVERT: B 919 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7400 (t70) REVERT: B 934 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.6921 (tp30) REVERT: B 965 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: C 46 ARG cc_start: 0.6582 (mmm160) cc_final: 0.5821 (ttp-170) REVERT: C 52 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7091 (ttm-80) REVERT: C 84 VAL cc_start: 0.7452 (m) cc_final: 0.7242 (m) REVERT: C 181 GLU cc_start: 0.5561 (OUTLIER) cc_final: 0.5297 (pp20) REVERT: C 205 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7241 (mtp) REVERT: C 269 SER cc_start: 0.7821 (OUTLIER) cc_final: 0.7442 (m) REVERT: C 277 GLU cc_start: 0.5862 (pm20) cc_final: 0.5402 (tt0) REVERT: C 292 ARG cc_start: 0.7278 (mtt90) cc_final: 0.7011 (mtt180) REVERT: C 546 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7289 (mp) REVERT: C 611 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.4854 (ptp-170) REVERT: C 782 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7406 (m-30) REVERT: C 817 GLN cc_start: 0.6580 (mt0) cc_final: 0.6190 (mp10) REVERT: C 888 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7525 (mt) REVERT: C 919 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7393 (t70) REVERT: C 934 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.6925 (tp30) REVERT: C 965 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: D 46 ARG cc_start: 0.6583 (mmm160) cc_final: 0.5824 (ttp-170) REVERT: D 52 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7082 (ttm-80) REVERT: D 84 VAL cc_start: 0.7447 (m) cc_final: 0.7237 (m) REVERT: D 181 GLU cc_start: 0.5551 (OUTLIER) cc_final: 0.5291 (pp20) REVERT: D 205 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7233 (mtp) REVERT: D 269 SER cc_start: 0.7824 (OUTLIER) cc_final: 0.7447 (m) REVERT: D 277 GLU cc_start: 0.5851 (pm20) cc_final: 0.5393 (tt0) REVERT: D 292 ARG cc_start: 0.7279 (mtt90) cc_final: 0.7012 (mtt180) REVERT: D 546 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7308 (mp) REVERT: D 611 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.5360 (ptp-170) REVERT: D 782 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: D 817 GLN cc_start: 0.6581 (mt0) cc_final: 0.6191 (mp10) REVERT: D 888 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7523 (mt) REVERT: D 919 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7394 (t70) REVERT: D 934 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.6925 (tp30) REVERT: D 965 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7363 (tm-30) outliers start: 146 outliers final: 88 residues processed: 557 average time/residue: 0.8186 time to fit residues: 536.1727 Evaluate side-chains 584 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 452 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 766 SER Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 919 ASP Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 965 GLN Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 171 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 262 optimal weight: 7.9990 chunk 369 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 334 optimal weight: 9.9990 chunk 228 optimal weight: 7.9990 chunk 335 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 HIS A 262 GLN A 485 GLN A 573 GLN A 761 GLN A 824 GLN A 896 ASN B 30 HIS B 262 GLN B 485 GLN B 573 GLN ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN B 896 ASN C 30 HIS C 262 GLN C 485 GLN C 573 GLN ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 GLN C 824 GLN C 896 ASN D 30 HIS D 262 GLN D 485 GLN D 573 GLN ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 761 GLN D 824 GLN D 896 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.170000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.149044 restraints weight = 33634.519| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.21 r_work: 0.3654 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 33876 Z= 0.218 Angle : 0.739 9.872 46216 Z= 0.380 Chirality : 0.048 0.158 4840 Planarity : 0.005 0.045 6092 Dihedral : 5.670 67.588 4484 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.52 % Allowed : 17.42 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % 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: -0.79 (0.13), residues: 4080 helix: -0.42 (0.21), residues: 552 sheet: 0.17 (0.14), residues: 1412 loop : -1.01 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 43 TYR 0.024 0.003 TYR C1014 PHE 0.017 0.002 PHE D 235 TRP 0.028 0.002 TRP A 553 HIS 0.009 0.002 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 (33876) covalent geometry : angle 0.73910 / 0.38 (46216) hydrogen bonds : bond 0.04575 / 3.04 ( 1040) hydrogen bonds : angle 5.79343 / 4.11 ( 2796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16179.74 seconds wall clock time: 275 minutes 25.64 seconds (16525.64 seconds total)