Starting phenix.real_space_refine on Tue Aug 26 03:43:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5a1a_2984/08_2025/5a1a_2984.cif Found real_map, /net/cci-nas-00/data/ceres_data/5a1a_2984/08_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_2984/08_2025/5a1a_2984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5a1a_2984/08_2025/5a1a_2984.map" model { file = "/net/cci-nas-00/data/ceres_data/5a1a_2984/08_2025/5a1a_2984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5a1a_2984/08_2025/5a1a_2984.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 8 5.21 5 S 160 5.16 5 Na 8 4.78 5 C 20816 2.51 5 N 5808 2.21 5 O 6896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33696 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8206 Classifications: {'peptide': 1022} Link IDs: {'CIS': 9, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 950} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' MG': 2, ' NA': 2, 'PTQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "B" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "C" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "D" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Restraints were copied for chains: B, C, D Time building chain proxies: 8.84, per 1000 atoms: 0.26 Number of scatterers: 33696 At special positions: 0 Unit cell: (191.737, 147.147, 102.557, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 160 16.00 Mg 8 11.99 Na 8 11.00 O 6896 8.00 N 5808 7.00 C 20816 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7608 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 64 sheets defined 15.5% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 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: 8.55 Time building geometry restraints manager: 2.81 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 32.320 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.050 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.11), residues: 4080 helix: -2.30 (0.18), residues: 536 sheet: -0.14 (0.15), residues: 1120 loop : -1.56 (0.10), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 183 TYR 0.008 0.001 TYR C 856 PHE 0.006 0.001 PHE B 512 TRP 0.017 0.001 TRP B 90 HIS 0.002 0.001 HIS B 713 Details of bonding type rmsd covalent geometry : bond 0.00881 (33876) covalent geometry : angle 1.21286 (46216) hydrogen bonds : bond 0.25290 ( 1040) hydrogen bonds : angle 9.22259 ( 2796) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 788 time to evaluate : 0.859 Fit side-chains REVERT: A 84 VAL cc_start: 0.6775 (m) cc_final: 0.6542 (m) REVERT: A 233 ASP cc_start: 0.5656 (m-30) cc_final: 0.5382 (m-30) REVERT: A 277 GLU cc_start: 0.5751 (pm20) cc_final: 0.5477 (tt0) REVERT: A 537 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: A 677 LYS cc_start: 0.7208 (ptmt) cc_final: 0.6918 (ptpp) REVERT: A 817 GLN cc_start: 0.6511 (mt0) cc_final: 0.6285 (mp10) REVERT: A 893 GLU cc_start: 0.6149 (mt-10) cc_final: 0.5903 (mm-30) REVERT: B 84 VAL cc_start: 0.6777 (m) cc_final: 0.6544 (m) REVERT: B 233 ASP cc_start: 0.5658 (m-30) cc_final: 0.5384 (m-30) REVERT: B 277 GLU cc_start: 0.5749 (pm20) cc_final: 0.5473 (tt0) REVERT: B 537 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: B 677 LYS cc_start: 0.7207 (ptmt) cc_final: 0.6919 (ptpp) REVERT: B 817 GLN cc_start: 0.6512 (mt0) cc_final: 0.6286 (mp10) REVERT: B 893 GLU cc_start: 0.6149 (mt-10) cc_final: 0.5904 (mm-30) REVERT: C 84 VAL cc_start: 0.6777 (m) cc_final: 0.6544 (m) REVERT: C 233 ASP cc_start: 0.5659 (m-30) cc_final: 0.5385 (m-30) REVERT: C 277 GLU cc_start: 0.5750 (pm20) cc_final: 0.5475 (tt0) REVERT: C 537 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: C 677 LYS cc_start: 0.7209 (ptmt) cc_final: 0.6919 (ptpp) REVERT: C 817 GLN cc_start: 0.6511 (mt0) cc_final: 0.6286 (mp10) REVERT: C 893 GLU cc_start: 0.6147 (mt-10) cc_final: 0.5903 (mm-30) REVERT: D 84 VAL cc_start: 0.6777 (m) cc_final: 0.6545 (m) REVERT: D 233 ASP cc_start: 0.5658 (m-30) cc_final: 0.5384 (m-30) REVERT: D 277 GLU cc_start: 0.5750 (pm20) cc_final: 0.5475 (tt0) REVERT: D 537 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: D 677 LYS cc_start: 0.7207 (ptmt) cc_final: 0.6918 (ptpp) REVERT: D 817 GLN cc_start: 0.6513 (mt0) cc_final: 0.6286 (mp10) REVERT: D 893 GLU cc_start: 0.6150 (mt-10) cc_final: 0.5905 (mm-30) outliers start: 36 outliers final: 4 residues processed: 812 average time/residue: 0.6816 time to fit residues: 650.9454 Evaluate side-chains 508 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 500 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 537 GLU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 537 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 30 HIS A 38 ASN A 89 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A 355 ASN A 391 HIS A 395 HIS A 445 GLN A 485 GLN A 573 GLN A 597 ASN A 653 HIS A 739 HIS A 757 GLN A 767 GLN A 775 GLN A 791 ASN A 824 GLN A 863 GLN A 896 ASN A 935 ASN A 945 ASN A 949 HIS A 985 ASN A1015 HIS B 25 ASN B 30 HIS B 38 ASN B 89 ASN ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 355 ASN B 391 HIS B 395 HIS B 445 GLN B 485 GLN B 573 GLN B 597 ASN B 653 HIS B 739 HIS B 757 GLN B 767 GLN B 775 GLN B 791 ASN B 824 GLN B 863 GLN B 896 ASN B 935 ASN B 945 ASN B 949 HIS B 985 ASN B1015 HIS C 25 ASN C 30 HIS C 38 ASN C 89 ASN C 339 ASN C 355 ASN C 391 HIS C 395 HIS C 445 GLN C 485 GLN C 573 GLN C 597 ASN C 653 HIS C 739 HIS C 757 GLN C 767 GLN C 775 GLN C 791 ASN C 824 GLN C 863 GLN C 896 ASN C 935 ASN C 945 ASN C 949 HIS C 985 ASN C1015 HIS D 25 ASN D 30 HIS D 38 ASN D 89 ASN ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN D 355 ASN D 391 HIS D 395 HIS D 445 GLN D 485 GLN D 573 GLN D 597 ASN D 653 HIS D 739 HIS D 757 GLN D 767 GLN D 775 GLN D 791 ASN D 824 GLN D 863 GLN D 896 ASN D 935 ASN D 945 ASN D 949 HIS D 985 ASN D1015 HIS Total number of N/Q/H flips: 104 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.171825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.150362 restraints weight = 33677.189| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.24 r_work: 0.3670 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2378 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= 0.231 Angle : 0.771 9.917 46216 Z= 0.404 Chirality : 0.050 0.180 4840 Planarity : 0.006 0.054 6092 Dihedral : 6.306 84.877 4604 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.55 % Favored : 97.35 % Rotamer: Outliers : 4.23 % Allowed : 13.04 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.12), residues: 4080 helix: -1.03 (0.21), residues: 548 sheet: -0.03 (0.14), residues: 1380 loop : -0.91 (0.12), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 210 TYR 0.020 0.003 TYR D 123 PHE 0.017 0.002 PHE A 63 TRP 0.022 0.002 TRP D 553 HIS 0.008 0.002 HIS B 464 Details of bonding type rmsd covalent geometry : bond 0.00510 (33876) covalent geometry : angle 0.77149 (46216) hydrogen bonds : bond 0.05441 ( 1040) hydrogen bonds : angle 6.29645 ( 2796) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 560 time to evaluate : 1.236 Fit side-chains REVERT: A 46 ARG cc_start: 0.6649 (mmm160) cc_final: 0.6041 (mtm-85) REVERT: A 84 VAL cc_start: 0.7356 (m) cc_final: 0.7102 (m) REVERT: A 144 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7272 (t70) REVERT: A 178 ARG cc_start: 0.5441 (ptt90) cc_final: 0.5082 (mtm180) REVERT: A 233 ASP cc_start: 0.5819 (m-30) cc_final: 0.5614 (m-30) REVERT: A 269 SER cc_start: 0.7715 (OUTLIER) cc_final: 0.7465 (p) REVERT: A 277 GLU cc_start: 0.5606 (pm20) cc_final: 0.5227 (tt0) REVERT: A 313 VAL cc_start: 0.8179 (t) cc_final: 0.7907 (p) REVERT: A 677 LYS cc_start: 0.7462 (ptmt) cc_final: 0.6933 (ptpp) REVERT: A 745 MET cc_start: 0.4199 (tpt) cc_final: 0.3724 (tpp) REVERT: A 817 GLN cc_start: 0.6514 (mt0) cc_final: 0.6204 (mp10) REVERT: A 919 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7450 (t70) REVERT: B 46 ARG cc_start: 0.6648 (mmm160) cc_final: 0.6048 (mtm-85) REVERT: B 84 VAL cc_start: 0.7358 (m) cc_final: 0.7103 (m) REVERT: B 144 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7263 (t70) REVERT: B 178 ARG cc_start: 0.5433 (ptt90) cc_final: 0.5082 (mtm180) REVERT: B 269 SER cc_start: 0.7715 (OUTLIER) cc_final: 0.7467 (p) REVERT: B 277 GLU cc_start: 0.5599 (pm20) cc_final: 0.5225 (tt0) REVERT: B 313 VAL cc_start: 0.8179 (t) cc_final: 0.7912 (p) REVERT: B 677 LYS cc_start: 0.7457 (ptmt) cc_final: 0.6926 (ptpp) REVERT: B 745 MET cc_start: 0.4196 (tpt) cc_final: 0.3721 (tpp) REVERT: B 817 GLN cc_start: 0.6511 (mt0) cc_final: 0.6206 (mp10) REVERT: B 919 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7454 (t70) REVERT: C 46 ARG cc_start: 0.6654 (mmm160) cc_final: 0.6046 (mtm-85) REVERT: C 84 VAL cc_start: 0.7358 (m) cc_final: 0.7103 (m) REVERT: C 144 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7270 (t70) REVERT: C 178 ARG cc_start: 0.5441 (ptt90) cc_final: 0.5090 (mtm180) REVERT: C 233 ASP cc_start: 0.5819 (m-30) cc_final: 0.5615 (m-30) REVERT: C 269 SER cc_start: 0.7715 (OUTLIER) cc_final: 0.7466 (p) REVERT: C 277 GLU cc_start: 0.5607 (pm20) cc_final: 0.5221 (tt0) REVERT: C 313 VAL cc_start: 0.8180 (t) cc_final: 0.7910 (p) REVERT: C 677 LYS cc_start: 0.7465 (ptmt) cc_final: 0.6933 (ptpp) REVERT: C 745 MET cc_start: 0.4201 (tpt) cc_final: 0.3725 (tpp) REVERT: C 817 GLN cc_start: 0.6523 (mt0) cc_final: 0.6207 (mp10) REVERT: C 919 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7457 (t70) REVERT: D 46 ARG cc_start: 0.6649 (mmm160) cc_final: 0.6043 (mtm-85) REVERT: D 84 VAL cc_start: 0.7358 (m) cc_final: 0.7104 (m) REVERT: D 144 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7274 (t70) REVERT: D 178 ARG cc_start: 0.5435 (ptt90) cc_final: 0.5086 (mtm180) REVERT: D 233 ASP cc_start: 0.5812 (m-30) cc_final: 0.5609 (m-30) REVERT: D 269 SER cc_start: 0.7721 (OUTLIER) cc_final: 0.7474 (p) REVERT: D 277 GLU cc_start: 0.5607 (pm20) cc_final: 0.5224 (tt0) REVERT: D 313 VAL cc_start: 0.8178 (t) cc_final: 0.7908 (p) REVERT: D 677 LYS cc_start: 0.7457 (ptmt) cc_final: 0.6932 (ptpp) REVERT: D 745 MET cc_start: 0.4201 (tpt) cc_final: 0.3724 (tpp) REVERT: D 817 GLN cc_start: 0.6505 (mt0) cc_final: 0.6200 (mp10) outliers start: 148 outliers final: 64 residues processed: 656 average time/residue: 0.6690 time to fit residues: 519.5211 Evaluate side-chains 555 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 480 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 924 ASP Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 924 ASP Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 748 CYS Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 919 ASP Chi-restraints excluded: chain C residue 924 ASP Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 748 CYS Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 924 ASP Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 31 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 221 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 307 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 351 optimal weight: 9.9990 chunk 277 optimal weight: 20.0000 chunk 127 optimal weight: 30.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- 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 554 GLN A 573 GLN A 583 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN B 30 HIS B 262 GLN B 485 GLN B 554 GLN B 573 GLN B 583 ASN ** B 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN C 30 HIS C 262 GLN C 485 GLN C 554 GLN C 573 GLN C 583 ASN ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN D 30 HIS D 262 GLN D 485 GLN D 554 GLN D 573 GLN D 583 ASN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 824 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.171617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.150221 restraints weight = 33524.216| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.22 r_work: 0.3668 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33876 Z= 0.187 Angle : 0.696 9.861 46216 Z= 0.360 Chirality : 0.046 0.163 4840 Planarity : 0.005 0.045 6092 Dihedral : 5.450 66.946 4580 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.14 % Favored : 96.76 % Rotamer: Outliers : 5.46 % Allowed : 14.53 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.13), residues: 4080 helix: -0.63 (0.22), residues: 552 sheet: 0.04 (0.13), residues: 1412 loop : -0.82 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 43 TYR 0.017 0.002 TYR B 100 PHE 0.013 0.002 PHE D 63 TRP 0.028 0.002 TRP A 553 HIS 0.007 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00412 (33876) covalent geometry : angle 0.69572 (46216) hydrogen bonds : bond 0.04903 ( 1040) hydrogen bonds : angle 5.96080 ( 2796) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 501 time to evaluate : 1.161 Fit side-chains REVERT: A 41 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6859 (mt-10) REVERT: A 46 ARG cc_start: 0.6710 (mmm160) cc_final: 0.5854 (ttp-170) REVERT: A 52 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7074 (ttm-80) REVERT: A 84 VAL cc_start: 0.7394 (m) cc_final: 0.7161 (m) REVERT: A 144 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7322 (t70) REVERT: A 178 ARG cc_start: 0.5434 (ptt90) cc_final: 0.5124 (mtm180) REVERT: A 255 ARG cc_start: 0.7710 (mmt-90) cc_final: 0.7288 (mmt-90) REVERT: A 269 SER cc_start: 0.7758 (OUTLIER) cc_final: 0.7419 (m) REVERT: A 277 GLU cc_start: 0.5658 (pm20) cc_final: 0.5263 (tt0) REVERT: A 677 LYS cc_start: 0.7497 (ptmt) cc_final: 0.6929 (ptpp) REVERT: A 745 MET cc_start: 0.4179 (tpt) cc_final: 0.3676 (tpp) REVERT: A 782 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7482 (m-30) REVERT: A 817 GLN cc_start: 0.6532 (mt0) cc_final: 0.6208 (mp10) REVERT: A 965 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: B 41 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6848 (mt-10) REVERT: B 46 ARG cc_start: 0.6715 (mmm160) cc_final: 0.5861 (ttp-170) REVERT: B 52 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7070 (ttm-80) REVERT: B 84 VAL cc_start: 0.7397 (m) cc_final: 0.7164 (m) REVERT: B 144 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7318 (t70) REVERT: B 178 ARG cc_start: 0.5433 (ptt90) cc_final: 0.5128 (mtm180) REVERT: B 255 ARG cc_start: 0.7702 (mmt-90) cc_final: 0.7289 (mmt-90) REVERT: B 269 SER cc_start: 0.7759 (OUTLIER) cc_final: 0.7419 (m) REVERT: B 277 GLU cc_start: 0.5652 (pm20) cc_final: 0.5258 (tt0) REVERT: B 677 LYS cc_start: 0.7495 (ptmt) cc_final: 0.6927 (ptpp) REVERT: B 745 MET cc_start: 0.4176 (tpt) cc_final: 0.3670 (tpp) REVERT: B 782 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7486 (m-30) REVERT: B 817 GLN cc_start: 0.6528 (mt0) cc_final: 0.6204 (mp10) REVERT: B 965 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: C 41 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6867 (mt-10) REVERT: C 46 ARG cc_start: 0.6719 (mmm160) cc_final: 0.5863 (ttp-170) REVERT: C 52 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7070 (ttm-80) REVERT: C 84 VAL cc_start: 0.7393 (m) cc_final: 0.7162 (m) REVERT: C 144 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7325 (t70) REVERT: C 178 ARG cc_start: 0.5433 (ptt90) cc_final: 0.5129 (mtm180) REVERT: C 255 ARG cc_start: 0.7709 (mmt-90) cc_final: 0.7288 (mmt-90) REVERT: C 269 SER cc_start: 0.7765 (OUTLIER) cc_final: 0.7422 (m) REVERT: C 277 GLU cc_start: 0.5661 (pm20) cc_final: 0.5268 (tt0) REVERT: C 677 LYS cc_start: 0.7500 (ptmt) cc_final: 0.6932 (ptpp) REVERT: C 745 MET cc_start: 0.4180 (tpt) cc_final: 0.3674 (tpp) REVERT: C 782 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7464 (m-30) REVERT: C 817 GLN cc_start: 0.6541 (mt0) cc_final: 0.6215 (mp10) REVERT: C 965 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: D 41 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6857 (mt-10) REVERT: D 46 ARG cc_start: 0.6714 (mmm160) cc_final: 0.5858 (ttp-170) REVERT: D 52 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7062 (ttm-80) REVERT: D 84 VAL cc_start: 0.7392 (m) cc_final: 0.7160 (m) REVERT: D 144 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7321 (t70) REVERT: D 178 ARG cc_start: 0.5433 (ptt90) cc_final: 0.5131 (mtm180) REVERT: D 255 ARG cc_start: 0.7705 (mmt-90) cc_final: 0.7282 (mmt-90) REVERT: D 269 SER cc_start: 0.7763 (OUTLIER) cc_final: 0.7422 (m) REVERT: D 277 GLU cc_start: 0.5656 (pm20) cc_final: 0.5259 (tt0) REVERT: D 677 LYS cc_start: 0.7501 (ptmt) cc_final: 0.6933 (ptpp) REVERT: D 745 MET cc_start: 0.4175 (tpt) cc_final: 0.3674 (tpp) REVERT: D 782 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: D 817 GLN cc_start: 0.6531 (mt0) cc_final: 0.6203 (mp10) REVERT: D 965 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7246 (tm-30) outliers start: 191 outliers final: 84 residues processed: 612 average time/residue: 0.6943 time to fit residues: 501.3595 Evaluate side-chains 573 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 465 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 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 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 12 GLN Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 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 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 12 GLN Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 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 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 12 GLN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.6075 > 50: distance: 41 - 46: 11.386 distance: 46 - 47: 9.066 distance: 47 - 48: 27.390 distance: 47 - 50: 21.818 distance: 48 - 49: 24.928 distance: 48 - 55: 4.112 distance: 50 - 51: 20.386 distance: 51 - 52: 8.670 distance: 52 - 53: 8.997 distance: 52 - 54: 12.623 distance: 55 - 56: 5.806 distance: 56 - 57: 9.768 distance: 56 - 59: 19.882 distance: 57 - 58: 6.672 distance: 57 - 63: 17.497 distance: 59 - 60: 13.676 distance: 60 - 61: 27.400 distance: 60 - 62: 15.525 distance: 63 - 64: 7.703 distance: 63 - 69: 9.303 distance: 64 - 65: 17.643 distance: 64 - 67: 6.983 distance: 65 - 66: 10.567 distance: 65 - 70: 14.280 distance: 67 - 68: 12.079 distance: 68 - 69: 19.982 distance: 70 - 71: 11.378 distance: 71 - 72: 17.831 distance: 71 - 74: 13.437 distance: 72 - 73: 10.392 distance: 72 - 79: 13.278 distance: 74 - 75: 26.452 distance: 75 - 76: 13.417 distance: 76 - 77: 11.784 distance: 76 - 78: 21.372 distance: 79 - 80: 13.095 distance: 80 - 81: 13.164 distance: 80 - 83: 7.883 distance: 81 - 82: 8.284 distance: 81 - 87: 9.452 distance: 83 - 84: 8.197 distance: 84 - 85: 30.163 distance: 84 - 86: 24.844 distance: 87 - 88: 17.157 distance: 87 - 93: 10.228 distance: 88 - 89: 21.814 distance: 88 - 91: 38.626 distance: 89 - 90: 19.359 distance: 89 - 94: 16.642 distance: 91 - 92: 21.176 distance: 92 - 93: 29.318 distance: 94 - 95: 21.086 distance: 95 - 96: 11.123 distance: 95 - 98: 12.967 distance: 96 - 97: 25.763 distance: 96 - 103: 34.118 distance: 98 - 99: 22.032 distance: 99 - 100: 14.110 distance: 100 - 101: 15.296 distance: 100 - 102: 17.554 distance: 103 - 104: 23.637 distance: 103 - 109: 15.087 distance: 104 - 105: 28.135 distance: 104 - 107: 14.481 distance: 105 - 106: 18.775 distance: 105 - 110: 16.570 distance: 107 - 108: 25.285 distance: 108 - 109: 27.299 distance: 110 - 111: 11.031 distance: 111 - 112: 10.546 distance: 111 - 114: 14.516 distance: 112 - 113: 16.823 distance: 112 - 119: 15.298 distance: 114 - 115: 17.579 distance: 115 - 116: 5.588 distance: 116 - 117: 8.231 distance: 116 - 118: 6.507 distance: 119 - 120: 8.845 distance: 120 - 121: 14.192 distance: 120 - 123: 16.173 distance: 121 - 122: 5.924 distance: 121 - 125: 12.501 distance: 123 - 124: 7.637