Starting phenix.real_space_refine on Sat Jun 28 14:30:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5a1a_2984/06_2025/5a1a_2984.cif Found real_map, /net/cci-nas-00/data/ceres_data/5a1a_2984/06_2025/5a1a_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5a1a_2984/06_2025/5a1a_2984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5a1a_2984/06_2025/5a1a_2984.map" model { file = "/net/cci-nas-00/data/ceres_data/5a1a_2984/06_2025/5a1a_2984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5a1a_2984/06_2025/5a1a_2984.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, D Time building chain proxies: 23.18, per 1000 atoms: 0.69 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: 8.01 Conformation dependent library (CDL) restraints added in 4.0 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: 4.82 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: 17.96 Time building geometry restraints manager: 9.09 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: 18360 17.63 - 35.27: 1176 35.27 - 52.90: 264 52.90 - 70.53: 60 70.53 - 88.17: 48 Dihedral angle restraints: 19908 sinusoidal: 8092 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 19905 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: 0.22 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.690 Check model and map are aligned: 0.270 Set scattering table: 0.320 Process input model: 83.390 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.090 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:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 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 : 13.177 88.168 12300 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (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 TRP 0.017 0.001 TRP B 90 HIS 0.002 0.001 HIS B 713 PHE 0.006 0.001 PHE B 512 TYR 0.008 0.001 TYR C 856 ARG 0.002 0.001 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.25290 ( 1040) hydrogen bonds : angle 9.22259 ( 2796) covalent geometry : bond 0.00881 (33876) covalent geometry : angle 1.21286 (46216) *********************** 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 : 3.544 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: 0.5381 (m-30) REVERT: A 277 GLU cc_start: 0.5751 (pm20) cc_final: 0.5476 (tt0) REVERT: A 537 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7964 (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: 0.5383 (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: 0.7964 (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: 0.5384 (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: 0.7966 (mt-10) REVERT: C 677 LYS cc_start: 0.7209 (ptmt) cc_final: 0.6918 (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: 0.6777 (m) cc_final: 0.6545 (m) REVERT: D 233 ASP cc_start: 0.5658 (m-30) cc_final: 0.5383 (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: 0.7966 (mt-10) REVERT: D 677 LYS cc_start: 0.7207 (ptmt) cc_final: 0.6917 (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: 1.6069 time to fit residues: 1538.8203 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 : 3.559 ------------------------------------------------------------------------------- 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 344 optimal weight: 6.9990 chunk 309 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 105 optimal weight: 0.6980 chunk 208 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 319 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 238 optimal weight: 9.9990 chunk 370 optimal weight: 5.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 30 HIS A 38 ASN A 89 ASN 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 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 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 HIS B 25 ASN B 30 HIS B 38 ASN B 89 ASN 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 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 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1015 HIS C 25 ASN C 30 HIS C 38 ASN C 89 ASN 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 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 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1015 HIS D 25 ASN D 30 HIS D 38 ASN D 89 ASN 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 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 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1015 HIS Total number of N/Q/H flips: 92 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.174738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.153581 restraints weight = 33714.928| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.23 r_work: 0.3707 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2159 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= 0.162 Angle : 0.673 10.213 46216 Z= 0.351 Chirality : 0.046 0.173 4840 Planarity : 0.005 0.051 6092 Dihedral : 5.938 83.166 4604 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.35 % Favored : 97.55 % Rotamer: Outliers : 3.20 % Allowed : 13.04 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.12), residues: 4080 helix: -1.04 (0.20), residues: 572 sheet: 0.08 (0.14), residues: 1404 loop : -0.83 (0.12), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 553 HIS 0.007 0.001 HIS D 395 PHE 0.012 0.002 PHE D 63 TYR 0.015 0.002 TYR C 408 ARG 0.006 0.001 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.05064 ( 1040) hydrogen bonds : angle 6.27636 ( 2796) covalent geometry : bond 0.00350 (33876) covalent geometry : angle 0.67292 (46216) *********************** 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 692 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 580 time to evaluate : 3.651 Fit side-chains REVERT: A 46 ARG cc_start: 0.6636 (mmm160) cc_final: 0.5979 (mtm-85) REVERT: A 84 VAL cc_start: 0.7261 (m) cc_final: 0.6987 (m) REVERT: A 144 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7226 (t70) REVERT: A 233 ASP cc_start: 0.5807 (m-30) cc_final: 0.5562 (m-30) REVERT: A 269 SER cc_start: 0.7664 (OUTLIER) cc_final: 0.7390 (m) REVERT: A 277 GLU cc_start: 0.5516 (pm20) cc_final: 0.5190 (tt0) REVERT: A 292 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6753 (ptp90) REVERT: A 438 GLU cc_start: 0.7079 (pp20) cc_final: 0.6833 (pp20) REVERT: A 677 LYS cc_start: 0.7357 (ptmt) cc_final: 0.6819 (ptpp) REVERT: A 745 MET cc_start: 0.4161 (tpt) cc_final: 0.3733 (tpp) REVERT: A 817 GLN cc_start: 0.6507 (mt0) cc_final: 0.6223 (mp10) REVERT: B 46 ARG cc_start: 0.6640 (mmm160) cc_final: 0.5986 (mtm-85) REVERT: B 84 VAL cc_start: 0.7269 (m) cc_final: 0.6995 (m) REVERT: B 144 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7237 (t70) REVERT: B 233 ASP cc_start: 0.5802 (m-30) cc_final: 0.5560 (m-30) REVERT: B 269 SER cc_start: 0.7656 (OUTLIER) cc_final: 0.7383 (m) REVERT: B 277 GLU cc_start: 0.5519 (pm20) cc_final: 0.5201 (tt0) REVERT: B 292 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6749 (ptp90) REVERT: B 438 GLU cc_start: 0.7083 (pp20) cc_final: 0.6832 (pp20) REVERT: B 677 LYS cc_start: 0.7356 (ptmt) cc_final: 0.6813 (ptpp) REVERT: B 745 MET cc_start: 0.4157 (tpt) cc_final: 0.3731 (tpp) REVERT: B 817 GLN cc_start: 0.6509 (mt0) cc_final: 0.6224 (mp10) REVERT: C 46 ARG cc_start: 0.6646 (mmm160) cc_final: 0.5982 (mtm-85) REVERT: C 84 VAL cc_start: 0.7267 (m) cc_final: 0.6995 (m) REVERT: C 144 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7231 (t70) REVERT: C 233 ASP cc_start: 0.5798 (m-30) cc_final: 0.5553 (m-30) REVERT: C 269 SER cc_start: 0.7659 (OUTLIER) cc_final: 0.7387 (m) REVERT: C 277 GLU cc_start: 0.5514 (pm20) cc_final: 0.5187 (tt0) REVERT: C 292 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6761 (ptp90) REVERT: C 438 GLU cc_start: 0.7078 (pp20) cc_final: 0.6830 (pp20) REVERT: C 677 LYS cc_start: 0.7349 (ptmt) cc_final: 0.6806 (ptpp) REVERT: C 745 MET cc_start: 0.4162 (tpt) cc_final: 0.3734 (tpp) REVERT: C 817 GLN cc_start: 0.6501 (mt0) cc_final: 0.6213 (mp10) REVERT: D 46 ARG cc_start: 0.6640 (mmm160) cc_final: 0.5988 (mtm-85) REVERT: D 84 VAL cc_start: 0.7264 (m) cc_final: 0.6991 (m) REVERT: D 144 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7233 (t70) REVERT: D 233 ASP cc_start: 0.5797 (m-30) cc_final: 0.5552 (m-30) REVERT: D 269 SER cc_start: 0.7667 (OUTLIER) cc_final: 0.7395 (m) REVERT: D 277 GLU cc_start: 0.5526 (pm20) cc_final: 0.5199 (tt0) REVERT: D 292 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6740 (ptp90) REVERT: D 438 GLU cc_start: 0.7079 (pp20) cc_final: 0.6832 (pp20) REVERT: D 677 LYS cc_start: 0.7352 (ptmt) cc_final: 0.6815 (ptpp) REVERT: D 745 MET cc_start: 0.4161 (tpt) cc_final: 0.3733 (tpp) REVERT: D 817 GLN cc_start: 0.6507 (mt0) cc_final: 0.6219 (mp10) outliers start: 112 outliers final: 40 residues processed: 664 average time/residue: 1.5242 time to fit residues: 1206.4823 Evaluate side-chains 548 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 496 time to evaluate : 3.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 269 SER Chi-restraints excluded: chain A residue 292 ARG 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 751 LEU Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 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 269 SER Chi-restraints excluded: chain B residue 292 ARG 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 751 LEU Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1004 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 269 SER Chi-restraints excluded: chain C residue 292 ARG 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 751 LEU Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1004 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 269 SER Chi-restraints excluded: chain D residue 292 ARG 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 751 LEU Chi-restraints excluded: chain D residue 871 GLU 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 340 optimal weight: 10.0000 chunk 362 optimal weight: 6.9990 chunk 256 optimal weight: 0.1980 chunk 85 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 257 optimal weight: 20.0000 chunk 128 optimal weight: 6.9990 chunk 238 optimal weight: 9.9990 chunk 277 optimal weight: 20.0000 chunk 74 optimal weight: 0.0870 chunk 260 optimal weight: 5.9990 overall best weight: 4.0564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 30 HIS A 262 GLN A 395 HIS A 485 GLN A 573 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 ASN B 30 HIS B 262 GLN B 395 HIS B 485 GLN B 573 GLN ** B 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 30 HIS C 262 GLN C 395 HIS C 485 GLN C 573 GLN ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 30 HIS D 262 GLN D 395 HIS D 485 GLN D 573 GLN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.173218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.151964 restraints weight = 33739.404| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.23 r_work: 0.3688 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2576 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= 0.153 Angle : 0.652 9.921 46216 Z= 0.336 Chirality : 0.045 0.158 4840 Planarity : 0.005 0.042 6092 Dihedral : 5.113 65.360 4580 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.04 % Favored : 96.86 % Rotamer: Outliers : 3.55 % Allowed : 15.22 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 4080 helix: -0.32 (0.22), residues: 552 sheet: 0.14 (0.13), residues: 1420 loop : -0.69 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 553 HIS 0.006 0.001 HIS A 395 PHE 0.011 0.002 PHE C 63 TYR 0.015 0.002 TYR C 100 ARG 0.006 0.001 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.04522 ( 1040) hydrogen bonds : angle 5.84186 ( 2796) covalent geometry : bond 0.00328 (33876) covalent geometry : angle 0.65215 (46216) *********************** 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 648 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 524 time to evaluate : 3.565 Fit side-chains REVERT: A 41 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6782 (mt-10) REVERT: A 46 ARG cc_start: 0.6682 (mmm160) cc_final: 0.6025 (mtm-85) REVERT: A 77 ASP cc_start: 0.6151 (p0) cc_final: 0.5947 (p0) REVERT: A 84 VAL cc_start: 0.7321 (m) cc_final: 0.7059 (m) REVERT: A 144 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7282 (t70) REVERT: A 233 ASP cc_start: 0.5801 (m-30) cc_final: 0.5574 (m-30) REVERT: A 255 ARG cc_start: 0.7688 (mmt-90) cc_final: 0.7335 (mmt-90) REVERT: A 269 SER cc_start: 0.7717 (OUTLIER) cc_final: 0.7388 (m) REVERT: A 277 GLU cc_start: 0.5604 (pm20) cc_final: 0.5229 (tt0) REVERT: A 292 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6673 (mtt90) REVERT: A 314 GLU cc_start: 0.7765 (pt0) cc_final: 0.7468 (pt0) REVERT: A 322 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.5749 (pp) REVERT: A 438 GLU cc_start: 0.7154 (pp20) cc_final: 0.6919 (pp20) REVERT: A 677 LYS cc_start: 0.7420 (ptmt) cc_final: 0.6849 (ptpp) REVERT: A 724 GLU cc_start: 0.6505 (tt0) cc_final: 0.6247 (tt0) REVERT: A 745 MET cc_start: 0.4177 (tpt) cc_final: 0.3731 (tpp) REVERT: A 817 GLN cc_start: 0.6544 (mt0) cc_final: 0.6252 (mp10) REVERT: A 965 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7231 (tm-30) REVERT: B 41 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6774 (mt-10) REVERT: B 46 ARG cc_start: 0.6683 (mmm160) cc_final: 0.6024 (mtm-85) REVERT: B 84 VAL cc_start: 0.7323 (m) cc_final: 0.7060 (m) REVERT: B 144 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7286 (t70) REVERT: B 233 ASP cc_start: 0.5801 (m-30) cc_final: 0.5574 (m-30) REVERT: B 255 ARG cc_start: 0.7688 (mmt-90) cc_final: 0.7334 (mmt-90) REVERT: B 269 SER cc_start: 0.7723 (OUTLIER) cc_final: 0.7397 (m) REVERT: B 277 GLU cc_start: 0.5595 (pm20) cc_final: 0.5223 (tt0) REVERT: B 292 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6675 (mtt90) REVERT: B 314 GLU cc_start: 0.7763 (pt0) cc_final: 0.7470 (pt0) REVERT: B 322 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.5753 (pp) REVERT: B 438 GLU cc_start: 0.7163 (pp20) cc_final: 0.6925 (pp20) REVERT: B 677 LYS cc_start: 0.7423 (ptmt) cc_final: 0.6851 (ptpp) REVERT: B 724 GLU cc_start: 0.6504 (tt0) cc_final: 0.6244 (tt0) REVERT: B 745 MET cc_start: 0.4166 (tpt) cc_final: 0.3724 (tpp) REVERT: B 817 GLN cc_start: 0.6543 (mt0) cc_final: 0.6253 (mp10) REVERT: B 965 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: C 41 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6783 (mt-10) REVERT: C 46 ARG cc_start: 0.6687 (mmm160) cc_final: 0.6026 (mtm-85) REVERT: C 77 ASP cc_start: 0.6155 (p0) cc_final: 0.5953 (p0) REVERT: C 84 VAL cc_start: 0.7321 (m) cc_final: 0.7061 (m) REVERT: C 144 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7285 (t70) REVERT: C 233 ASP cc_start: 0.5810 (m-30) cc_final: 0.5584 (m-30) REVERT: C 255 ARG cc_start: 0.7693 (mmt-90) cc_final: 0.7340 (mmt-90) REVERT: C 269 SER cc_start: 0.7718 (OUTLIER) cc_final: 0.7391 (m) REVERT: C 277 GLU cc_start: 0.5597 (pm20) cc_final: 0.5219 (tt0) REVERT: C 292 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6669 (mtt90) REVERT: C 314 GLU cc_start: 0.7759 (pt0) cc_final: 0.7465 (pt0) REVERT: C 322 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.5751 (pp) REVERT: C 438 GLU cc_start: 0.7166 (pp20) cc_final: 0.6927 (pp20) REVERT: C 677 LYS cc_start: 0.7420 (ptmt) cc_final: 0.6849 (ptpp) REVERT: C 724 GLU cc_start: 0.6506 (tt0) cc_final: 0.6249 (tt0) REVERT: C 745 MET cc_start: 0.4168 (tpt) cc_final: 0.3725 (tpp) REVERT: C 817 GLN cc_start: 0.6544 (mt0) cc_final: 0.6248 (mp10) REVERT: C 965 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7226 (tm-30) REVERT: D 41 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6782 (mt-10) REVERT: D 46 ARG cc_start: 0.6685 (mmm160) cc_final: 0.6026 (mtm-85) REVERT: D 77 ASP cc_start: 0.6163 (p0) cc_final: 0.5959 (p0) REVERT: D 84 VAL cc_start: 0.7324 (m) cc_final: 0.7063 (m) REVERT: D 144 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7297 (t70) REVERT: D 233 ASP cc_start: 0.5799 (m-30) cc_final: 0.5575 (m-30) REVERT: D 255 ARG cc_start: 0.7687 (mmt-90) cc_final: 0.7334 (mmt-90) REVERT: D 269 SER cc_start: 0.7724 (OUTLIER) cc_final: 0.7400 (m) REVERT: D 277 GLU cc_start: 0.5597 (pm20) cc_final: 0.5223 (tt0) REVERT: D 292 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6673 (mtt90) REVERT: D 314 GLU cc_start: 0.7762 (pt0) cc_final: 0.7465 (pt0) REVERT: D 322 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.5748 (pp) REVERT: D 438 GLU cc_start: 0.7165 (pp20) cc_final: 0.6929 (pp20) REVERT: D 677 LYS cc_start: 0.7422 (ptmt) cc_final: 0.6851 (ptpp) REVERT: D 724 GLU cc_start: 0.6516 (tt0) cc_final: 0.6259 (tt0) REVERT: D 745 MET cc_start: 0.4156 (tpt) cc_final: 0.3719 (tpp) REVERT: D 817 GLN cc_start: 0.6544 (mt0) cc_final: 0.6248 (mp10) REVERT: D 965 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7226 (tm-30) outliers start: 124 outliers final: 56 residues processed: 600 average time/residue: 1.6263 time to fit residues: 1148.3811 Evaluate side-chains 551 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 471 time to evaluate : 3.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 292 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 367 MET 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 751 LEU Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 923 SER 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 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 292 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 367 MET 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 751 LEU Chi-restraints excluded: chain B residue 766 SER Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 923 SER 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 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 292 ARG Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 367 MET 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 751 LEU Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 923 SER 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 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 292 ARG Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 367 MET 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 751 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 923 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 304 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 231 optimal weight: 0.0170 chunk 296 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 chunk 197 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 396 optimal weight: 0.4980 chunk 378 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 193 optimal weight: 20.0000 overall best weight: 4.1024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 262 GLN A 395 HIS A 485 GLN A 510 GLN A 554 GLN A 573 GLN A 704 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 262 GLN B 395 HIS B 485 GLN B 510 GLN B 554 GLN B 573 GLN ** B 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 262 GLN C 395 HIS C 485 GLN C 510 GLN C 554 GLN C 573 GLN C 704 ASN ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS D 262 GLN D 395 HIS D 485 GLN D 510 GLN D 554 GLN D 573 GLN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.172511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.151309 restraints weight = 33815.048| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.23 r_work: 0.3682 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33876 Z= 0.152 Angle : 0.641 9.848 46216 Z= 0.329 Chirality : 0.045 0.156 4840 Planarity : 0.005 0.037 6092 Dihedral : 5.125 65.828 4580 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 4.46 % Allowed : 15.56 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.13), residues: 4080 helix: -0.21 (0.22), residues: 552 sheet: 0.18 (0.13), residues: 1424 loop : -0.64 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 553 HIS 0.007 0.001 HIS B 30 PHE 0.011 0.002 PHE A 63 TYR 0.014 0.002 TYR D 100 ARG 0.006 0.001 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 1040) hydrogen bonds : angle 5.70256 ( 2796) covalent geometry : bond 0.00330 (33876) covalent geometry : angle 0.64082 (46216) *********************** 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 663 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 507 time to evaluate : 3.817 Fit side-chains REVERT: A 41 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6826 (mt-10) REVERT: A 46 ARG cc_start: 0.6697 (mmm160) cc_final: 0.6031 (mtm-85) REVERT: A 52 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7114 (ttm-80) REVERT: A 77 ASP cc_start: 0.6110 (p0) cc_final: 0.5878 (p0) REVERT: A 84 VAL cc_start: 0.7363 (m) cc_final: 0.7116 (m) REVERT: A 178 ARG cc_start: 0.5456 (ptt90) cc_final: 0.5144 (mtm180) REVERT: A 233 ASP cc_start: 0.5825 (m-30) cc_final: 0.5579 (m-30) REVERT: A 255 ARG cc_start: 0.7723 (mmt-90) cc_final: 0.7426 (mmt-90) REVERT: A 269 SER cc_start: 0.7681 (OUTLIER) cc_final: 0.7354 (m) REVERT: A 277 GLU cc_start: 0.5667 (pm20) cc_final: 0.5246 (tt0) REVERT: A 314 GLU cc_start: 0.7762 (pt0) cc_final: 0.7447 (pt0) REVERT: A 438 GLU cc_start: 0.7090 (pp20) cc_final: 0.6835 (pp20) REVERT: A 611 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.4388 (ptp-170) REVERT: A 677 LYS cc_start: 0.7441 (ptmt) cc_final: 0.6868 (ptpp) REVERT: A 745 MET cc_start: 0.4180 (tpt) cc_final: 0.3707 (tpp) REVERT: A 753 ASN cc_start: 0.5694 (p0) cc_final: 0.5342 (t0) REVERT: A 782 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7400 (m-30) REVERT: A 817 GLN cc_start: 0.6542 (mt0) cc_final: 0.6245 (mp10) REVERT: A 965 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7264 (tm-30) REVERT: B 41 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6828 (mt-10) REVERT: B 46 ARG cc_start: 0.6695 (mmm160) cc_final: 0.6033 (mtm-85) REVERT: B 52 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7114 (ttm-80) REVERT: B 84 VAL cc_start: 0.7362 (m) cc_final: 0.7115 (m) REVERT: B 178 ARG cc_start: 0.5450 (ptt90) cc_final: 0.5136 (mtm180) REVERT: B 233 ASP cc_start: 0.5821 (m-30) cc_final: 0.5572 (m-30) REVERT: B 255 ARG cc_start: 0.7724 (mmt-90) cc_final: 0.7426 (mmt-90) REVERT: B 269 SER cc_start: 0.7688 (OUTLIER) cc_final: 0.7362 (m) REVERT: B 277 GLU cc_start: 0.5670 (pm20) cc_final: 0.5251 (tt0) REVERT: B 314 GLU cc_start: 0.7771 (pt0) cc_final: 0.7462 (pt0) REVERT: B 438 GLU cc_start: 0.7091 (pp20) cc_final: 0.6832 (pp20) REVERT: B 611 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.4389 (ptp-170) REVERT: B 677 LYS cc_start: 0.7441 (ptmt) cc_final: 0.6867 (ptpp) REVERT: B 745 MET cc_start: 0.4185 (tpt) cc_final: 0.3711 (tpp) REVERT: B 753 ASN cc_start: 0.5699 (p0) cc_final: 0.5343 (t0) REVERT: B 782 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: B 817 GLN cc_start: 0.6540 (mt0) cc_final: 0.6242 (mp10) REVERT: B 965 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7242 (tm-30) REVERT: C 41 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6842 (mt-10) REVERT: C 46 ARG cc_start: 0.6697 (mmm160) cc_final: 0.6024 (mtm-85) REVERT: C 52 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7114 (ttm-80) REVERT: C 77 ASP cc_start: 0.6116 (p0) cc_final: 0.5895 (p0) REVERT: C 84 VAL cc_start: 0.7365 (m) cc_final: 0.7118 (m) REVERT: C 178 ARG cc_start: 0.5449 (ptt90) cc_final: 0.5139 (mtm180) REVERT: C 233 ASP cc_start: 0.5831 (m-30) cc_final: 0.5587 (m-30) REVERT: C 255 ARG cc_start: 0.7725 (mmt-90) cc_final: 0.7428 (mmt-90) REVERT: C 269 SER cc_start: 0.7689 (OUTLIER) cc_final: 0.7362 (m) REVERT: C 277 GLU cc_start: 0.5676 (pm20) cc_final: 0.5249 (tt0) REVERT: C 314 GLU cc_start: 0.7760 (pt0) cc_final: 0.7450 (pt0) REVERT: C 438 GLU cc_start: 0.7095 (pp20) cc_final: 0.6839 (pp20) REVERT: C 611 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.4384 (ptp-170) REVERT: C 677 LYS cc_start: 0.7444 (ptmt) cc_final: 0.6867 (ptpp) REVERT: C 745 MET cc_start: 0.4180 (tpt) cc_final: 0.3707 (tpp) REVERT: C 753 ASN cc_start: 0.5692 (p0) cc_final: 0.5345 (t0) REVERT: C 782 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7379 (m-30) REVERT: C 817 GLN cc_start: 0.6545 (mt0) cc_final: 0.6243 (mp10) REVERT: C 965 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: D 41 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6844 (mt-10) REVERT: D 46 ARG cc_start: 0.6700 (mmm160) cc_final: 0.6033 (mtm-85) REVERT: D 52 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7109 (ttm-80) REVERT: D 77 ASP cc_start: 0.6112 (p0) cc_final: 0.5887 (p0) REVERT: D 84 VAL cc_start: 0.7366 (m) cc_final: 0.7119 (m) REVERT: D 178 ARG cc_start: 0.5450 (ptt90) cc_final: 0.5140 (mtm180) REVERT: D 233 ASP cc_start: 0.5833 (m-30) cc_final: 0.5586 (m-30) REVERT: D 255 ARG cc_start: 0.7727 (mmt-90) cc_final: 0.7429 (mmt-90) REVERT: D 269 SER cc_start: 0.7689 (OUTLIER) cc_final: 0.7366 (m) REVERT: D 277 GLU cc_start: 0.5673 (pm20) cc_final: 0.5247 (tt0) REVERT: D 314 GLU cc_start: 0.7762 (pt0) cc_final: 0.7451 (pt0) REVERT: D 438 GLU cc_start: 0.7094 (pp20) cc_final: 0.6837 (pp20) REVERT: D 611 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.4372 (ptp-170) REVERT: D 677 LYS cc_start: 0.7444 (ptmt) cc_final: 0.6865 (ptpp) REVERT: D 745 MET cc_start: 0.4172 (tpt) cc_final: 0.3703 (tpp) REVERT: D 753 ASN cc_start: 0.5693 (p0) cc_final: 0.5342 (t0) REVERT: D 782 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7387 (m-30) REVERT: D 817 GLN cc_start: 0.6538 (mt0) cc_final: 0.6244 (mp10) REVERT: D 965 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7254 (tm-30) outliers start: 156 outliers final: 68 residues processed: 603 average time/residue: 1.6647 time to fit residues: 1182.6051 Evaluate side-chains 549 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 457 time to evaluate : 4.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 206 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 321 THR 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 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 923 SER 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 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 206 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 321 THR 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 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 923 SER 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 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 206 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 321 THR 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 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 923 SER 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 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 206 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 321 THR 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 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 923 SER 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 394 optimal weight: 20.0000 chunk 207 optimal weight: 0.7980 chunk 304 optimal weight: 20.0000 chunk 120 optimal weight: 0.8980 chunk 96 optimal weight: 30.0000 chunk 384 optimal weight: 10.0000 chunk 320 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 chunk 297 optimal weight: 20.0000 chunk 129 optimal weight: 7.9990 overall best weight: 5.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 262 GLN A 485 GLN A 573 GLN A 739 HIS ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 262 GLN B 485 GLN B 573 GLN B 739 HIS ** B1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 262 GLN C 485 GLN C 573 GLN C 739 HIS ** C1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS D 262 GLN D 485 GLN D 573 GLN D 739 HIS ** D1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.171362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.150134 restraints weight = 33668.026| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.22 r_work: 0.3670 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33876 Z= 0.177 Angle : 0.671 9.910 46216 Z= 0.345 Chirality : 0.046 0.154 4840 Planarity : 0.005 0.044 6092 Dihedral : 5.327 69.106 4580 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.67 % Rotamer: Outliers : 4.58 % Allowed : 16.48 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 4080 helix: -0.25 (0.22), residues: 552 sheet: 0.13 (0.13), residues: 1424 loop : -0.69 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 553 HIS 0.006 0.001 HIS A 30 PHE 0.010 0.002 PHE B 63 TYR 0.015 0.002 TYR C 100 ARG 0.004 0.001 ARG B 857 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 1040) hydrogen bonds : angle 5.71658 ( 2796) covalent geometry : bond 0.00393 (33876) covalent geometry : angle 0.67085 (46216) *********************** 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 660 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 500 time to evaluate : 3.962 Fit side-chains REVERT: A 41 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6817 (mt-10) REVERT: A 46 ARG cc_start: 0.6686 (mmm160) cc_final: 0.6039 (mtm-85) REVERT: A 52 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7074 (ttm-80) REVERT: A 77 ASP cc_start: 0.6120 (p0) cc_final: 0.5903 (p0) REVERT: A 84 VAL cc_start: 0.7461 (m) cc_final: 0.7223 (m) REVERT: A 178 ARG cc_start: 0.5429 (ptt90) cc_final: 0.5135 (mtm180) REVERT: A 233 ASP cc_start: 0.5815 (m-30) cc_final: 0.5603 (m-30) REVERT: A 255 ARG cc_start: 0.7641 (mmt-90) cc_final: 0.7214 (mmt-90) REVERT: A 269 SER cc_start: 0.7723 (OUTLIER) cc_final: 0.7384 (m) REVERT: A 277 GLU cc_start: 0.5761 (pm20) cc_final: 0.5298 (tt0) REVERT: A 292 ARG cc_start: 0.7155 (mtt90) cc_final: 0.6725 (mtt180) REVERT: A 314 GLU cc_start: 0.7793 (pt0) cc_final: 0.7512 (pt0) REVERT: A 338 GLU cc_start: 0.7465 (tt0) cc_final: 0.7206 (tm-30) REVERT: A 438 GLU cc_start: 0.7215 (pp20) cc_final: 0.6931 (pp20) REVERT: A 611 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.4972 (ptp-170) REVERT: A 677 LYS cc_start: 0.7480 (ptmt) cc_final: 0.6895 (ptpp) REVERT: A 745 MET cc_start: 0.4226 (tpt) cc_final: 0.3709 (tpp) REVERT: A 753 ASN cc_start: 0.5724 (p0) cc_final: 0.5334 (t0) REVERT: A 782 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: A 817 GLN cc_start: 0.6538 (mt0) cc_final: 0.6222 (mp10) REVERT: A 934 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.6912 (tp30) REVERT: A 965 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7292 (tm-30) REVERT: B 41 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6825 (mt-10) REVERT: B 46 ARG cc_start: 0.6683 (mmm160) cc_final: 0.6044 (mtm-85) REVERT: B 52 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7074 (ttm-80) REVERT: B 84 VAL cc_start: 0.7469 (m) cc_final: 0.7230 (m) REVERT: B 178 ARG cc_start: 0.5420 (ptt90) cc_final: 0.5128 (mtm180) REVERT: B 233 ASP cc_start: 0.5813 (m-30) cc_final: 0.5601 (m-30) REVERT: B 255 ARG cc_start: 0.7634 (mmt-90) cc_final: 0.7204 (mmt-90) REVERT: B 269 SER cc_start: 0.7729 (OUTLIER) cc_final: 0.7395 (m) REVERT: B 277 GLU cc_start: 0.5769 (pm20) cc_final: 0.5298 (tt0) REVERT: B 292 ARG cc_start: 0.7149 (mtt90) cc_final: 0.6717 (mtt180) REVERT: B 314 GLU cc_start: 0.7791 (pt0) cc_final: 0.7511 (pt0) REVERT: B 338 GLU cc_start: 0.7465 (tt0) cc_final: 0.7204 (tm-30) REVERT: B 438 GLU cc_start: 0.7210 (pp20) cc_final: 0.6924 (pp20) REVERT: B 611 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.4963 (ptp-170) REVERT: B 677 LYS cc_start: 0.7477 (ptmt) cc_final: 0.6892 (ptpp) REVERT: B 745 MET cc_start: 0.4225 (tpt) cc_final: 0.3708 (tpp) REVERT: B 753 ASN cc_start: 0.5725 (p0) cc_final: 0.5334 (t0) REVERT: B 782 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: B 817 GLN cc_start: 0.6537 (mt0) cc_final: 0.6219 (mp10) REVERT: B 934 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.6906 (tp30) REVERT: B 965 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: C 41 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6835 (mt-10) REVERT: C 46 ARG cc_start: 0.6685 (mmm160) cc_final: 0.6037 (mtm-85) REVERT: C 52 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7073 (ttm-80) REVERT: C 77 ASP cc_start: 0.6127 (p0) cc_final: 0.5910 (p0) REVERT: C 84 VAL cc_start: 0.7463 (m) cc_final: 0.7223 (m) REVERT: C 178 ARG cc_start: 0.5421 (ptt90) cc_final: 0.5131 (mtm180) REVERT: C 233 ASP cc_start: 0.5816 (m-30) cc_final: 0.5602 (m-30) REVERT: C 255 ARG cc_start: 0.7643 (mmt-90) cc_final: 0.7214 (mmt-90) REVERT: C 269 SER cc_start: 0.7727 (OUTLIER) cc_final: 0.7388 (m) REVERT: C 277 GLU cc_start: 0.5773 (pm20) cc_final: 0.5305 (tt0) REVERT: C 292 ARG cc_start: 0.7141 (mtt90) cc_final: 0.6708 (mtt180) REVERT: C 314 GLU cc_start: 0.7788 (pt0) cc_final: 0.7507 (pt0) REVERT: C 338 GLU cc_start: 0.7466 (tt0) cc_final: 0.7208 (tm-30) REVERT: C 438 GLU cc_start: 0.7220 (pp20) cc_final: 0.6934 (pp20) REVERT: C 611 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.4971 (ptp-170) REVERT: C 677 LYS cc_start: 0.7477 (ptmt) cc_final: 0.6892 (ptpp) REVERT: C 745 MET cc_start: 0.4225 (tpt) cc_final: 0.3710 (tpp) REVERT: C 753 ASN cc_start: 0.5714 (p0) cc_final: 0.5330 (t0) REVERT: C 782 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7361 (m-30) REVERT: C 817 GLN cc_start: 0.6533 (mt0) cc_final: 0.6220 (mp10) REVERT: C 934 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.6913 (tp30) REVERT: C 965 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: D 41 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6838 (mt-10) REVERT: D 46 ARG cc_start: 0.6687 (mmm160) cc_final: 0.6038 (mtm-85) REVERT: D 52 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7069 (ttm-80) REVERT: D 77 ASP cc_start: 0.6130 (p0) cc_final: 0.5912 (p0) REVERT: D 84 VAL cc_start: 0.7465 (m) cc_final: 0.7226 (m) REVERT: D 178 ARG cc_start: 0.5420 (ptt90) cc_final: 0.5138 (mtm180) REVERT: D 233 ASP cc_start: 0.5813 (m-30) cc_final: 0.5600 (m-30) REVERT: D 255 ARG cc_start: 0.7641 (mmt-90) cc_final: 0.7212 (mmt-90) REVERT: D 269 SER cc_start: 0.7733 (OUTLIER) cc_final: 0.7396 (m) REVERT: D 277 GLU cc_start: 0.5763 (pm20) cc_final: 0.5291 (tt0) REVERT: D 292 ARG cc_start: 0.7149 (mtt90) cc_final: 0.6715 (mtt180) REVERT: D 314 GLU cc_start: 0.7778 (pt0) cc_final: 0.7497 (pt0) REVERT: D 338 GLU cc_start: 0.7477 (tt0) cc_final: 0.7218 (tm-30) REVERT: D 438 GLU cc_start: 0.7221 (pp20) cc_final: 0.6938 (pp20) REVERT: D 611 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.4961 (ptp-170) REVERT: D 677 LYS cc_start: 0.7479 (ptmt) cc_final: 0.6895 (ptpp) REVERT: D 745 MET cc_start: 0.4216 (tpt) cc_final: 0.3701 (tpp) REVERT: D 753 ASN cc_start: 0.5718 (p0) cc_final: 0.5333 (t0) REVERT: D 782 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7359 (m-30) REVERT: D 817 GLN cc_start: 0.6538 (mt0) cc_final: 0.6222 (mp10) REVERT: D 934 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.6915 (tp30) REVERT: D 965 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7275 (tm-30) outliers start: 160 outliers final: 76 residues processed: 608 average time/residue: 1.6947 time to fit residues: 1205.9944 Evaluate side-chains 569 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 465 time to evaluate : 3.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE 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 206 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 SER 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 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 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 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 206 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 269 SER 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 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 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 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 206 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 269 SER 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 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 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 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 206 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 SER 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 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 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 372 optimal weight: 8.9990 chunk 279 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 232 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 307 optimal weight: 0.6980 chunk 314 optimal weight: 30.0000 chunk 22 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 397 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 overall best weight: 5.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 262 GLN A 485 GLN A 573 GLN ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 262 GLN B 485 GLN B 573 GLN ** B1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 262 GLN C 485 GLN C 573 GLN ** C1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS D 151 HIS D 262 GLN D 485 GLN D 573 GLN ** D1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.171249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.149945 restraints weight = 33567.610| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.23 r_work: 0.3665 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33876 Z= 0.171 Angle : 0.664 9.749 46216 Z= 0.341 Chirality : 0.046 0.151 4840 Planarity : 0.005 0.039 6092 Dihedral : 5.368 70.838 4580 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.33 % Favored : 96.57 % Rotamer: Outliers : 4.69 % Allowed : 16.33 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 4080 helix: -0.25 (0.22), residues: 552 sheet: 0.16 (0.14), residues: 1420 loop : -0.77 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 553 HIS 0.009 0.001 HIS A 30 PHE 0.011 0.002 PHE D 33 TYR 0.017 0.002 TYR A1014 ARG 0.006 0.001 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 1040) hydrogen bonds : angle 5.67733 ( 2796) covalent geometry : bond 0.00375 (33876) covalent geometry : angle 0.66378 (46216) *********************** 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 659 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 495 time to evaluate : 3.497 Fit side-chains REVERT: A 41 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6804 (mt-10) REVERT: A 46 ARG cc_start: 0.6661 (mmm160) cc_final: 0.5847 (ttp-170) REVERT: A 52 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7073 (ttm-80) REVERT: A 77 ASP cc_start: 0.6281 (p0) cc_final: 0.6046 (p0) REVERT: A 84 VAL cc_start: 0.7435 (m) cc_final: 0.7214 (m) REVERT: A 178 ARG cc_start: 0.5394 (ptt90) cc_final: 0.4917 (mtm180) REVERT: A 255 ARG cc_start: 0.7651 (mmt-90) cc_final: 0.7319 (mmt-90) REVERT: A 269 SER cc_start: 0.7712 (OUTLIER) cc_final: 0.7372 (m) REVERT: A 277 GLU cc_start: 0.5813 (pm20) cc_final: 0.5339 (tt0) REVERT: A 292 ARG cc_start: 0.7146 (mtt90) cc_final: 0.6862 (mtt180) REVERT: A 314 GLU cc_start: 0.7753 (pt0) cc_final: 0.7474 (pt0) REVERT: A 338 GLU cc_start: 0.7479 (tt0) cc_final: 0.7207 (tm-30) REVERT: A 438 GLU cc_start: 0.7200 (pp20) cc_final: 0.6907 (pp20) REVERT: A 546 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7797 (mp) REVERT: A 611 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.4881 (ptp-170) REVERT: A 677 LYS cc_start: 0.7478 (ptmt) cc_final: 0.6892 (ptpp) REVERT: A 745 MET cc_start: 0.4178 (tpt) cc_final: 0.3661 (tpp) REVERT: A 782 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7391 (m-30) REVERT: A 817 GLN cc_start: 0.6546 (mt0) cc_final: 0.6203 (mp10) REVERT: A 934 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.6954 (tp30) REVERT: A 965 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7304 (tm-30) REVERT: B 41 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6805 (mt-10) REVERT: B 46 ARG cc_start: 0.6661 (mmm160) cc_final: 0.5852 (ttp-170) REVERT: B 52 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7074 (ttm-80) REVERT: B 77 ASP cc_start: 0.6253 (p0) cc_final: 0.6040 (p0) REVERT: B 84 VAL cc_start: 0.7442 (m) cc_final: 0.7219 (m) REVERT: B 178 ARG cc_start: 0.5396 (ptt90) cc_final: 0.4924 (mtm180) REVERT: B 255 ARG cc_start: 0.7642 (mmt-90) cc_final: 0.7308 (mmt-90) REVERT: B 269 SER cc_start: 0.7714 (OUTLIER) cc_final: 0.7373 (m) REVERT: B 277 GLU cc_start: 0.5788 (pm20) cc_final: 0.5315 (tt0) REVERT: B 292 ARG cc_start: 0.7145 (mtt90) cc_final: 0.6861 (mtt180) REVERT: B 314 GLU cc_start: 0.7752 (pt0) cc_final: 0.7471 (pt0) REVERT: B 338 GLU cc_start: 0.7463 (tt0) cc_final: 0.7191 (tm-30) REVERT: B 438 GLU cc_start: 0.7205 (pp20) cc_final: 0.6909 (pp20) REVERT: B 546 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7796 (mp) REVERT: B 611 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.4857 (ptp-170) REVERT: B 677 LYS cc_start: 0.7472 (ptmt) cc_final: 0.6884 (ptpp) REVERT: B 745 MET cc_start: 0.4186 (tpt) cc_final: 0.3666 (tpp) REVERT: B 782 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: B 817 GLN cc_start: 0.6553 (mt0) cc_final: 0.6207 (mp10) REVERT: B 934 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.6945 (tp30) REVERT: B 965 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: C 41 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6823 (mt-10) REVERT: C 46 ARG cc_start: 0.6666 (mmm160) cc_final: 0.5847 (ttp-170) REVERT: C 52 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7073 (ttm-80) REVERT: C 77 ASP cc_start: 0.6285 (p0) cc_final: 0.6062 (p0) REVERT: C 84 VAL cc_start: 0.7440 (m) cc_final: 0.7217 (m) REVERT: C 178 ARG cc_start: 0.5390 (ptt90) cc_final: 0.4913 (mtm180) REVERT: C 255 ARG cc_start: 0.7656 (mmt-90) cc_final: 0.7323 (mmt-90) REVERT: C 269 SER cc_start: 0.7715 (OUTLIER) cc_final: 0.7374 (m) REVERT: C 277 GLU cc_start: 0.5795 (pm20) cc_final: 0.5325 (tt0) REVERT: C 292 ARG cc_start: 0.7164 (mtt90) cc_final: 0.6884 (mtt180) REVERT: C 314 GLU cc_start: 0.7740 (pt0) cc_final: 0.7460 (pt0) REVERT: C 338 GLU cc_start: 0.7473 (tt0) cc_final: 0.7203 (tm-30) REVERT: C 438 GLU cc_start: 0.7199 (pp20) cc_final: 0.6906 (pp20) REVERT: C 546 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7805 (mp) REVERT: C 611 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.4878 (ptp-170) REVERT: C 677 LYS cc_start: 0.7473 (ptmt) cc_final: 0.6891 (ptpp) REVERT: C 745 MET cc_start: 0.4184 (tpt) cc_final: 0.3664 (tpp) REVERT: C 782 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: C 817 GLN cc_start: 0.6547 (mt0) cc_final: 0.6203 (mp10) REVERT: C 934 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.6952 (tp30) REVERT: C 965 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: D 41 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6808 (mt-10) REVERT: D 46 ARG cc_start: 0.6659 (mmm160) cc_final: 0.5846 (ttp-170) REVERT: D 52 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7070 (ttm-80) REVERT: D 77 ASP cc_start: 0.6276 (p0) cc_final: 0.6051 (p0) REVERT: D 84 VAL cc_start: 0.7439 (m) cc_final: 0.7215 (m) REVERT: D 178 ARG cc_start: 0.5395 (ptt90) cc_final: 0.4934 (mtm180) REVERT: D 255 ARG cc_start: 0.7653 (mmt-90) cc_final: 0.7318 (mmt-90) REVERT: D 269 SER cc_start: 0.7715 (OUTLIER) cc_final: 0.7374 (m) REVERT: D 277 GLU cc_start: 0.5805 (pm20) cc_final: 0.5338 (tt0) REVERT: D 292 ARG cc_start: 0.7143 (mtt90) cc_final: 0.6858 (mtt180) REVERT: D 314 GLU cc_start: 0.7750 (pt0) cc_final: 0.7471 (pt0) REVERT: D 338 GLU cc_start: 0.7470 (tt0) cc_final: 0.7197 (tm-30) REVERT: D 438 GLU cc_start: 0.7214 (pp20) cc_final: 0.6918 (pp20) REVERT: D 546 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7800 (mp) REVERT: D 611 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.4862 (ptp-170) REVERT: D 677 LYS cc_start: 0.7476 (ptmt) cc_final: 0.6895 (ptpp) REVERT: D 745 MET cc_start: 0.4180 (tpt) cc_final: 0.3660 (tpp) REVERT: D 782 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7380 (m-30) REVERT: D 817 GLN cc_start: 0.6546 (mt0) cc_final: 0.6209 (mp10) REVERT: D 934 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.6959 (tp30) REVERT: D 965 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7292 (tm-30) outliers start: 164 outliers final: 84 residues processed: 615 average time/residue: 1.6972 time to fit residues: 1228.4414 Evaluate side-chains 587 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 471 time to evaluate : 3.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE 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 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 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 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 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 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 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 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 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 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 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 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 343 optimal weight: 20.0000 chunk 379 optimal weight: 30.0000 chunk 308 optimal weight: 30.0000 chunk 340 optimal weight: 9.9990 chunk 323 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 355 optimal weight: 20.0000 chunk 270 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 30 HIS A 151 HIS A 485 GLN A 573 GLN B 12 GLN B 30 HIS B 151 HIS B 485 GLN B 573 GLN B 704 ASN ** B1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 GLN C 30 HIS C 151 HIS C 485 GLN C 573 GLN D 12 GLN D 30 HIS D 262 GLN D 485 GLN D 573 GLN D 704 ASN ** D1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.169478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148235 restraints weight = 33656.514| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.23 r_work: 0.3644 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 33876 Z= 0.244 Angle : 0.759 9.908 46216 Z= 0.391 Chirality : 0.049 0.153 4840 Planarity : 0.006 0.051 6092 Dihedral : 5.776 73.081 4580 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 4.92 % Allowed : 16.73 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.12), residues: 4080 helix: -0.53 (0.21), residues: 552 sheet: 0.26 (0.14), residues: 1300 loop : -1.01 (0.12), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 553 HIS 0.011 0.002 HIS A 30 PHE 0.016 0.003 PHE C 33 TYR 0.022 0.003 TYR C1014 ARG 0.007 0.001 ARG D 857 Details of bonding type rmsd hydrogen bonds : bond 0.04747 ( 1040) hydrogen bonds : angle 5.86154 ( 2796) covalent geometry : bond 0.00546 (33876) covalent geometry : angle 0.75950 (46216) *********************** 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 668 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 496 time to evaluate : 3.677 Fit side-chains REVERT: A 41 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6777 (mt-10) REVERT: A 46 ARG cc_start: 0.6604 (mmm160) cc_final: 0.5827 (ttp-170) REVERT: A 52 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7112 (ttm-80) REVERT: A 84 VAL cc_start: 0.7470 (m) cc_final: 0.7257 (m) REVERT: A 181 GLU cc_start: 0.5350 (tm-30) cc_final: 0.5125 (pp20) REVERT: A 205 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7380 (mtp) REVERT: A 269 SER cc_start: 0.7784 (OUTLIER) cc_final: 0.7422 (m) REVERT: A 277 GLU cc_start: 0.5840 (pm20) cc_final: 0.5370 (tt0) REVERT: A 292 ARG cc_start: 0.7249 (mtt90) cc_final: 0.7000 (mtt180) REVERT: A 438 GLU cc_start: 0.7271 (pp20) cc_final: 0.6966 (pp20) REVERT: A 546 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7428 (mp) REVERT: A 611 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.4914 (ptp-170) REVERT: A 745 MET cc_start: 0.4144 (tpt) cc_final: 0.3509 (tpp) REVERT: A 782 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: A 817 GLN cc_start: 0.6528 (mt0) cc_final: 0.6165 (mp10) REVERT: A 919 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7404 (t0) REVERT: A 934 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.6978 (tp30) REVERT: A 965 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: B 41 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6781 (mt-10) REVERT: B 46 ARG cc_start: 0.6600 (mmm160) cc_final: 0.5825 (ttp-170) REVERT: B 52 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7117 (ttm-80) REVERT: B 84 VAL cc_start: 0.7466 (m) cc_final: 0.7253 (m) REVERT: B 181 GLU cc_start: 0.5358 (tm-30) cc_final: 0.5139 (pp20) REVERT: B 205 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7400 (mtp) REVERT: B 269 SER cc_start: 0.7785 (OUTLIER) cc_final: 0.7425 (m) REVERT: B 277 GLU cc_start: 0.5839 (pm20) cc_final: 0.5368 (tt0) REVERT: B 292 ARG cc_start: 0.7241 (mtt90) cc_final: 0.6992 (mtt180) REVERT: B 438 GLU cc_start: 0.7272 (pp20) cc_final: 0.6965 (pp20) REVERT: B 546 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7428 (mp) REVERT: B 611 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.4896 (ptp-170) REVERT: B 745 MET cc_start: 0.4152 (tpt) cc_final: 0.3511 (tpp) REVERT: B 782 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: B 817 GLN cc_start: 0.6535 (mt0) cc_final: 0.6172 (mp10) REVERT: B 919 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7403 (t0) REVERT: B 934 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.6980 (tp30) REVERT: B 965 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: C 41 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6802 (mt-10) REVERT: C 46 ARG cc_start: 0.6601 (mmm160) cc_final: 0.5824 (ttp-170) REVERT: C 52 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7117 (ttm-80) REVERT: C 84 VAL cc_start: 0.7472 (m) cc_final: 0.7258 (m) REVERT: C 181 GLU cc_start: 0.5354 (tm-30) cc_final: 0.5133 (pp20) REVERT: C 205 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7397 (mtp) REVERT: C 269 SER cc_start: 0.7787 (OUTLIER) cc_final: 0.7428 (m) REVERT: C 277 GLU cc_start: 0.5846 (pm20) cc_final: 0.5375 (tt0) REVERT: C 292 ARG cc_start: 0.7243 (mtt90) cc_final: 0.6994 (mtt180) REVERT: C 438 GLU cc_start: 0.7270 (pp20) cc_final: 0.6963 (pp20) REVERT: C 546 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7426 (mp) REVERT: C 611 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.4904 (ptp-170) REVERT: C 745 MET cc_start: 0.4151 (tpt) cc_final: 0.3512 (tpp) REVERT: C 782 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7420 (m-30) REVERT: C 817 GLN cc_start: 0.6535 (mt0) cc_final: 0.6167 (mp10) REVERT: C 919 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7399 (t0) REVERT: C 934 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.6978 (tp30) REVERT: C 965 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7322 (tm-30) REVERT: D 41 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6780 (mt-10) REVERT: D 46 ARG cc_start: 0.6602 (mmm160) cc_final: 0.5827 (ttp-170) REVERT: D 52 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7108 (ttm-80) REVERT: D 84 VAL cc_start: 0.7467 (m) cc_final: 0.7255 (m) REVERT: D 181 GLU cc_start: 0.5351 (tm-30) cc_final: 0.5128 (pp20) REVERT: D 205 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7395 (mtp) REVERT: D 269 SER cc_start: 0.7789 (OUTLIER) cc_final: 0.7431 (m) REVERT: D 277 GLU cc_start: 0.5846 (pm20) cc_final: 0.5370 (tt0) REVERT: D 292 ARG cc_start: 0.7251 (mtt90) cc_final: 0.7001 (mtt180) REVERT: D 438 GLU cc_start: 0.7272 (pp20) cc_final: 0.6967 (pp20) REVERT: D 546 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7422 (mp) REVERT: D 611 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.4907 (ptp-170) REVERT: D 745 MET cc_start: 0.4147 (tpt) cc_final: 0.3510 (tpp) REVERT: D 782 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7415 (m-30) REVERT: D 817 GLN cc_start: 0.6530 (mt0) cc_final: 0.6170 (mp10) REVERT: D 919 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7405 (t0) REVERT: D 934 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.6977 (tp30) REVERT: D 965 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7318 (tm-30) outliers start: 172 outliers final: 92 residues processed: 624 average time/residue: 1.7060 time to fit residues: 1246.9284 Evaluate side-chains 604 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 472 time to evaluate : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE 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 197 LEU 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 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 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 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 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 197 LEU 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 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 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 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 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 197 LEU 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 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 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 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 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 197 LEU 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 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 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 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 52 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 405 optimal weight: 20.0000 chunk 184 optimal weight: 8.9990 chunk 260 optimal weight: 4.9990 chunk 320 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 391 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 485 GLN A 573 GLN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 GLN A 824 GLN ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 485 GLN B 573 GLN B 761 GLN B 824 GLN ** B 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 485 GLN C 573 GLN ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 GLN C 824 GLN ** C 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS D 262 GLN D 485 GLN D 573 GLN D 761 GLN D 824 GLN ** D 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.171209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.150251 restraints weight = 33520.324| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.22 r_work: 0.3669 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33876 Z= 0.155 Angle : 0.658 9.757 46216 Z= 0.336 Chirality : 0.045 0.149 4840 Planarity : 0.005 0.038 6092 Dihedral : 5.415 72.577 4580 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.38 % Allowed : 16.85 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.13), residues: 4080 helix: -0.25 (0.22), residues: 552 sheet: 0.19 (0.14), residues: 1420 loop : -0.87 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 553 HIS 0.010 0.001 HIS D 30 PHE 0.015 0.002 PHE C 33 TYR 0.018 0.002 TYR B1014 ARG 0.005 0.001 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 1040) hydrogen bonds : angle 5.68055 ( 2796) covalent geometry : bond 0.00336 (33876) covalent geometry : angle 0.65819 (46216) *********************** 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 635 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 482 time to evaluate : 3.815 Fit side-chains REVERT: A 41 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6796 (mt-10) REVERT: A 46 ARG cc_start: 0.6580 (mmm160) cc_final: 0.5823 (ttp-170) REVERT: A 84 VAL cc_start: 0.7463 (m) cc_final: 0.7242 (m) REVERT: A 178 ARG cc_start: 0.5651 (ptp90) cc_final: 0.5259 (mtm180) REVERT: A 269 SER cc_start: 0.7736 (OUTLIER) cc_final: 0.7385 (m) REVERT: A 277 GLU cc_start: 0.5825 (pm20) cc_final: 0.5348 (tt0) REVERT: A 338 GLU cc_start: 0.7471 (tt0) cc_final: 0.7198 (tm-30) REVERT: A 438 GLU cc_start: 0.7202 (pp20) cc_final: 0.6883 (pp20) REVERT: A 611 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.4795 (ptp-170) REVERT: A 745 MET cc_start: 0.4083 (tpt) cc_final: 0.3558 (tpp) REVERT: A 782 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7364 (m-30) REVERT: A 817 GLN cc_start: 0.6513 (mt0) cc_final: 0.6147 (mp10) REVERT: A 934 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.6935 (tp30) REVERT: A 965 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: B 41 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6802 (mt-10) REVERT: B 46 ARG cc_start: 0.6578 (mmm160) cc_final: 0.5825 (ttp-170) REVERT: B 84 VAL cc_start: 0.7459 (m) cc_final: 0.7236 (m) REVERT: B 178 ARG cc_start: 0.5633 (ptp90) cc_final: 0.5248 (mtm180) REVERT: B 269 SER cc_start: 0.7739 (OUTLIER) cc_final: 0.7390 (m) REVERT: B 277 GLU cc_start: 0.5806 (pm20) cc_final: 0.5316 (tt0) REVERT: B 338 GLU cc_start: 0.7470 (tt0) cc_final: 0.7198 (tm-30) REVERT: B 438 GLU cc_start: 0.7208 (pp20) cc_final: 0.6883 (pp20) REVERT: B 611 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.4785 (ptp-170) REVERT: B 745 MET cc_start: 0.4082 (tpt) cc_final: 0.3560 (tpp) REVERT: B 782 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7371 (m-30) REVERT: B 817 GLN cc_start: 0.6512 (mt0) cc_final: 0.6139 (mp10) REVERT: B 934 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.6940 (tp30) REVERT: B 965 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: C 41 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6822 (mt-10) REVERT: C 46 ARG cc_start: 0.6582 (mmm160) cc_final: 0.5823 (ttp-170) REVERT: C 84 VAL cc_start: 0.7461 (m) cc_final: 0.7239 (m) REVERT: C 178 ARG cc_start: 0.5634 (ptp90) cc_final: 0.5250 (mtm180) REVERT: C 269 SER cc_start: 0.7743 (OUTLIER) cc_final: 0.7392 (m) REVERT: C 277 GLU cc_start: 0.5837 (pm20) cc_final: 0.5355 (tt0) REVERT: C 338 GLU cc_start: 0.7471 (tt0) cc_final: 0.7197 (tm-30) REVERT: C 438 GLU cc_start: 0.7199 (pp20) cc_final: 0.6885 (pp20) REVERT: C 611 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.4801 (ptp-170) REVERT: C 745 MET cc_start: 0.4082 (tpt) cc_final: 0.3558 (tpp) REVERT: C 782 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7348 (m-30) REVERT: C 817 GLN cc_start: 0.6516 (mt0) cc_final: 0.6143 (mp10) REVERT: C 934 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.6935 (tp30) REVERT: C 965 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7294 (tm-30) REVERT: D 41 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6813 (mt-10) REVERT: D 46 ARG cc_start: 0.6585 (mmm160) cc_final: 0.5830 (ttp-170) REVERT: D 84 VAL cc_start: 0.7458 (m) cc_final: 0.7237 (m) REVERT: D 178 ARG cc_start: 0.5623 (ptp90) cc_final: 0.5238 (mtm180) REVERT: D 269 SER cc_start: 0.7746 (OUTLIER) cc_final: 0.7398 (m) REVERT: D 277 GLU cc_start: 0.5837 (pm20) cc_final: 0.5351 (tt0) REVERT: D 338 GLU cc_start: 0.7483 (tt0) cc_final: 0.7208 (tm-30) REVERT: D 438 GLU cc_start: 0.7196 (pp20) cc_final: 0.6882 (pp20) REVERT: D 611 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.4785 (ptp-170) REVERT: D 745 MET cc_start: 0.4086 (tpt) cc_final: 0.3561 (tpp) REVERT: D 782 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7349 (m-30) REVERT: D 817 GLN cc_start: 0.6512 (mt0) cc_final: 0.6144 (mp10) REVERT: D 934 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.6933 (tp30) REVERT: D 965 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7297 (tm-30) outliers start: 153 outliers final: 80 residues processed: 591 average time/residue: 1.7161 time to fit residues: 1186.6742 Evaluate side-chains 560 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 456 time to evaluate : 4.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 41 GLU 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 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 604 ASN Chi-restraints excluded: chain A residue 611 ARG 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 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 41 GLU 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 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 604 ASN Chi-restraints excluded: chain B residue 611 ARG 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 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 41 GLU 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 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 604 ASN Chi-restraints excluded: chain C residue 611 ARG 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 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 41 GLU 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 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 604 ASN Chi-restraints excluded: chain D residue 611 ARG 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 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 228 optimal weight: 20.0000 chunk 352 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 313 optimal weight: 8.9990 chunk 373 optimal weight: 7.9990 chunk 306 optimal weight: 3.9990 chunk 371 optimal weight: 8.9990 chunk 275 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 143 optimal weight: 30.0000 chunk 353 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 262 GLN A 485 GLN A 573 GLN A 761 GLN A 824 GLN ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 262 GLN B 485 GLN B 573 GLN B 761 GLN B 824 GLN ** B 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS D 262 GLN D 485 GLN D 573 GLN D 761 GLN D 824 GLN ** D 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.169938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148766 restraints weight = 33541.197| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.22 r_work: 0.3654 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3199 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= 0.210 Angle : 0.727 9.809 46216 Z= 0.372 Chirality : 0.048 0.149 4840 Planarity : 0.006 0.047 6092 Dihedral : 5.706 74.128 4580 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.92 % Allowed : 17.62 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 4080 helix: -0.38 (0.22), residues: 552 sheet: 0.19 (0.14), residues: 1412 loop : -0.95 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 553 HIS 0.011 0.002 HIS D 30 PHE 0.017 0.002 PHE D 33 TYR 0.023 0.003 TYR A1014 ARG 0.006 0.001 ARG C 857 Details of bonding type rmsd hydrogen bonds : bond 0.04471 ( 1040) hydrogen bonds : angle 5.77250 ( 2796) covalent geometry : bond 0.00464 (33876) covalent geometry : angle 0.72715 (46216) *********************** 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 606 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 469 time to evaluate : 3.669 Fit side-chains REVERT: A 41 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6772 (mt-10) REVERT: A 46 ARG cc_start: 0.6594 (mmm160) cc_final: 0.5838 (ttp-170) REVERT: A 84 VAL cc_start: 0.7459 (m) cc_final: 0.7243 (m) REVERT: A 269 SER cc_start: 0.7797 (OUTLIER) cc_final: 0.7430 (m) REVERT: A 277 GLU cc_start: 0.5821 (pm20) cc_final: 0.5399 (tt0) REVERT: A 438 GLU cc_start: 0.7238 (pp20) cc_final: 0.6920 (pp20) REVERT: A 611 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.4966 (ptp-170) REVERT: A 745 MET cc_start: 0.4011 (tpt) cc_final: 0.3475 (tpp) REVERT: A 782 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7373 (m-30) REVERT: A 817 GLN cc_start: 0.6562 (mt0) cc_final: 0.6186 (mp10) REVERT: A 888 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7521 (mt) REVERT: A 934 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7000 (tp30) REVERT: A 965 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: A 1013 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7080 (mpt-90) REVERT: B 41 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6766 (mt-10) REVERT: B 46 ARG cc_start: 0.6607 (mmm160) cc_final: 0.5841 (ttp-170) REVERT: B 84 VAL cc_start: 0.7459 (m) cc_final: 0.7244 (m) REVERT: B 269 SER cc_start: 0.7795 (OUTLIER) cc_final: 0.7429 (m) REVERT: B 277 GLU cc_start: 0.5837 (pm20) cc_final: 0.5362 (tt0) REVERT: B 438 GLU cc_start: 0.7246 (pp20) cc_final: 0.6925 (pp20) REVERT: B 611 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.4891 (ptp-170) REVERT: B 745 MET cc_start: 0.4011 (tpt) cc_final: 0.3479 (tpp) REVERT: B 782 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7378 (m-30) REVERT: B 817 GLN cc_start: 0.6565 (mt0) cc_final: 0.6190 (mp10) REVERT: B 934 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.6958 (tp30) REVERT: B 965 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: B 1013 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7071 (mpt-90) REVERT: C 41 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6793 (mt-10) REVERT: C 46 ARG cc_start: 0.6594 (mmm160) cc_final: 0.5836 (ttp-170) REVERT: C 84 VAL cc_start: 0.7463 (m) cc_final: 0.7247 (m) REVERT: C 269 SER cc_start: 0.7798 (OUTLIER) cc_final: 0.7433 (m) REVERT: C 277 GLU cc_start: 0.5838 (pm20) cc_final: 0.5363 (tt0) REVERT: C 438 GLU cc_start: 0.7226 (pp20) cc_final: 0.6912 (pp20) REVERT: C 611 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.4968 (ptp-170) REVERT: C 745 MET cc_start: 0.4023 (tpt) cc_final: 0.3486 (tpp) REVERT: C 782 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: C 817 GLN cc_start: 0.6570 (mt0) cc_final: 0.6191 (mp10) REVERT: C 934 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7001 (tp30) REVERT: C 965 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: C 1013 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7078 (mpt-90) REVERT: D 41 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6772 (mt-10) REVERT: D 46 ARG cc_start: 0.6608 (mmm160) cc_final: 0.5848 (ttp-170) REVERT: D 84 VAL cc_start: 0.7455 (m) cc_final: 0.7239 (m) REVERT: D 269 SER cc_start: 0.7797 (OUTLIER) cc_final: 0.7435 (m) REVERT: D 277 GLU cc_start: 0.5836 (pm20) cc_final: 0.5402 (tt0) REVERT: D 438 GLU cc_start: 0.7242 (pp20) cc_final: 0.6921 (pp20) REVERT: D 611 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.4952 (ptp-170) REVERT: D 745 MET cc_start: 0.4010 (tpt) cc_final: 0.3476 (tpp) REVERT: D 782 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7368 (m-30) REVERT: D 817 GLN cc_start: 0.6563 (mt0) cc_final: 0.6192 (mp10) REVERT: D 888 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7518 (mt) REVERT: D 934 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7012 (tp30) REVERT: D 965 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: D 1013 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7082 (mpt-90) outliers start: 137 outliers final: 80 residues processed: 565 average time/residue: 1.7238 time to fit residues: 1142.5258 Evaluate side-chains 562 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 452 time to evaluate : 3.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 41 GLU 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 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 604 ASN Chi-restraints excluded: chain A residue 611 ARG 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 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 A residue 1013 ARG Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 41 GLU 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 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 604 ASN Chi-restraints excluded: chain B residue 611 ARG 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 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 B residue 1013 ARG Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 41 GLU 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 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 604 ASN Chi-restraints excluded: chain C residue 611 ARG 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 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 C residue 1013 ARG Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 41 GLU 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 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 604 ASN Chi-restraints excluded: chain D residue 611 ARG 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 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 Chi-restraints excluded: chain D residue 1013 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 64 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 chunk 299 optimal weight: 0.4980 chunk 201 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 301 optimal weight: 9.9990 chunk 381 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 chunk 255 optimal weight: 2.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 262 GLN A 485 GLN A 573 GLN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 GLN A 824 GLN ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 262 GLN B 485 GLN B 573 GLN B 761 GLN B 824 GLN ** B 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 262 GLN C 485 GLN C 573 GLN ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN ** C 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS D 262 GLN D 485 GLN D 573 GLN D 761 GLN D 824 GLN ** D 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.170787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.149746 restraints weight = 33632.503| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.22 r_work: 0.3664 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33876 Z= 0.174 Angle : 0.685 9.770 46216 Z= 0.349 Chirality : 0.046 0.150 4840 Planarity : 0.005 0.039 6092 Dihedral : 5.556 74.182 4580 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.38 % Allowed : 18.25 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.13), residues: 4080 helix: -0.27 (0.22), residues: 552 sheet: 0.23 (0.14), residues: 1412 loop : -0.93 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 553 HIS 0.011 0.001 HIS D 30 PHE 0.018 0.002 PHE A 33 TYR 0.021 0.002 TYR B1014 ARG 0.007 0.001 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 1040) hydrogen bonds : angle 5.69993 ( 2796) covalent geometry : bond 0.00381 (33876) covalent geometry : angle 0.68453 (46216) ********************** 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 577 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 459 time to evaluate : 4.025 Fit side-chains REVERT: A 41 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6764 (mt-10) REVERT: A 46 ARG cc_start: 0.6596 (mmm160) cc_final: 0.5835 (ttp-170) REVERT: A 84 VAL cc_start: 0.7458 (m) cc_final: 0.7241 (m) REVERT: A 178 ARG cc_start: 0.5882 (ptp90) cc_final: 0.5426 (mtm180) REVERT: A 269 SER cc_start: 0.7749 (OUTLIER) cc_final: 0.7386 (m) REVERT: A 277 GLU cc_start: 0.5821 (pm20) cc_final: 0.5390 (tt0) REVERT: A 438 GLU cc_start: 0.7192 (pp20) cc_final: 0.6881 (pp20) REVERT: A 542 MET cc_start: 0.8140 (ttt) cc_final: 0.7935 (ttt) REVERT: A 611 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.4834 (ptp-170) REVERT: A 737 ILE cc_start: 0.6415 (OUTLIER) cc_final: 0.6169 (tp) REVERT: A 745 MET cc_start: 0.4081 (tpt) cc_final: 0.3551 (tpp) REVERT: A 782 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: A 817 GLN cc_start: 0.6579 (mt0) cc_final: 0.6170 (mp10) REVERT: A 934 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.6950 (tp30) REVERT: A 965 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: B 41 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6777 (mt-10) REVERT: B 46 ARG cc_start: 0.6598 (mmm160) cc_final: 0.5831 (ttp-170) REVERT: B 84 VAL cc_start: 0.7453 (m) cc_final: 0.7234 (m) REVERT: B 178 ARG cc_start: 0.5869 (ptp90) cc_final: 0.5420 (mtm180) REVERT: B 269 SER cc_start: 0.7750 (OUTLIER) cc_final: 0.7389 (m) REVERT: B 277 GLU cc_start: 0.5825 (pm20) cc_final: 0.5394 (tt0) REVERT: B 438 GLU cc_start: 0.7207 (pp20) cc_final: 0.6887 (pp20) REVERT: B 611 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.4822 (ptp-170) REVERT: B 737 ILE cc_start: 0.6417 (OUTLIER) cc_final: 0.6173 (tp) REVERT: B 745 MET cc_start: 0.4088 (tpt) cc_final: 0.3555 (tpp) REVERT: B 782 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: B 817 GLN cc_start: 0.6588 (mt0) cc_final: 0.6173 (mp10) REVERT: B 888 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7471 (mt) REVERT: B 934 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.6945 (tp30) REVERT: B 965 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7285 (tm-30) REVERT: C 41 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6790 (mt-10) REVERT: C 46 ARG cc_start: 0.6597 (mmm160) cc_final: 0.5833 (ttp-170) REVERT: C 84 VAL cc_start: 0.7456 (m) cc_final: 0.7236 (m) REVERT: C 178 ARG cc_start: 0.5888 (ptp90) cc_final: 0.5432 (mtm180) REVERT: C 269 SER cc_start: 0.7754 (OUTLIER) cc_final: 0.7392 (m) REVERT: C 277 GLU cc_start: 0.5823 (pm20) cc_final: 0.5401 (tt0) REVERT: C 438 GLU cc_start: 0.7191 (pp20) cc_final: 0.6884 (pp20) REVERT: C 542 MET cc_start: 0.8145 (ttt) cc_final: 0.7938 (ttt) REVERT: C 611 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.4844 (ptp-170) REVERT: C 737 ILE cc_start: 0.6411 (OUTLIER) cc_final: 0.6166 (tp) REVERT: C 745 MET cc_start: 0.4080 (tpt) cc_final: 0.3553 (tpp) REVERT: C 782 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7363 (m-30) REVERT: C 817 GLN cc_start: 0.6595 (mt0) cc_final: 0.6175 (mp10) REVERT: C 888 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7470 (mt) REVERT: C 934 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.6948 (tp30) REVERT: C 965 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: D 41 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6780 (mt-10) REVERT: D 46 ARG cc_start: 0.6596 (mmm160) cc_final: 0.5836 (ttp-170) REVERT: D 84 VAL cc_start: 0.7452 (m) cc_final: 0.7234 (m) REVERT: D 178 ARG cc_start: 0.5887 (ptp90) cc_final: 0.5432 (mtm180) REVERT: D 269 SER cc_start: 0.7761 (OUTLIER) cc_final: 0.7403 (m) REVERT: D 277 GLU cc_start: 0.5818 (pm20) cc_final: 0.5382 (tt0) REVERT: D 438 GLU cc_start: 0.7197 (pp20) cc_final: 0.6884 (pp20) REVERT: D 542 MET cc_start: 0.8136 (ttt) cc_final: 0.7931 (ttt) REVERT: D 611 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.4821 (ptp-170) REVERT: D 737 ILE cc_start: 0.6436 (OUTLIER) cc_final: 0.6191 (tp) REVERT: D 745 MET cc_start: 0.4082 (tpt) cc_final: 0.3553 (tpp) REVERT: D 782 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7371 (m-30) REVERT: D 817 GLN cc_start: 0.6584 (mt0) cc_final: 0.6172 (mp10) REVERT: D 934 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.6945 (tp30) REVERT: D 965 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7287 (tm-30) outliers start: 118 outliers final: 72 residues processed: 533 average time/residue: 1.8427 time to fit residues: 1143.8240 Evaluate side-chains 541 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 439 time to evaluate : 3.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 SER 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 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 604 ASN Chi-restraints excluded: chain A residue 611 ARG 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 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 41 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 SER 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 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 604 ASN Chi-restraints excluded: chain B residue 611 ARG 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 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 41 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 124 SER 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 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 604 ASN Chi-restraints excluded: chain C residue 611 ARG 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 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 41 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 124 SER 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 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 604 ASN Chi-restraints excluded: chain D residue 611 ARG 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 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 30 optimal weight: 0.0980 chunk 254 optimal weight: 20.0000 chunk 383 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 334 optimal weight: 10.0000 chunk 260 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 396 optimal weight: 2.9990 chunk 379 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 262 GLN A 485 GLN A 573 GLN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 GLN A 791 ASN A 824 GLN ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 262 GLN B 485 GLN B 573 GLN B 761 GLN B 791 ASN B 824 GLN ** B 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 262 GLN C 485 GLN C 573 GLN ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 791 ASN C 824 GLN ** C 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS D 262 GLN D 485 GLN D 573 GLN D 761 GLN D 791 ASN D 824 GLN ** D 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.170769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.149725 restraints weight = 33585.582| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.22 r_work: 0.3661 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3245 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= 0.171 Angle : 0.680 9.733 46216 Z= 0.347 Chirality : 0.046 0.152 4840 Planarity : 0.005 0.042 6092 Dihedral : 5.531 73.936 4580 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.72 % Allowed : 18.05 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 4080 helix: -0.19 (0.22), residues: 552 sheet: 0.25 (0.14), residues: 1412 loop : -0.91 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 553 HIS 0.012 0.001 HIS B 30 PHE 0.021 0.002 PHE B 33 TYR 0.020 0.002 TYR B1014 ARG 0.007 0.001 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 1040) hydrogen bonds : angle 5.67759 ( 2796) covalent geometry : bond 0.00376 (33876) covalent geometry : angle 0.68033 (46216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34117.81 seconds wall clock time: 582 minutes 36.69 seconds (34956.69 seconds total)