Starting phenix.real_space_refine on Sun Dec 29 02:14:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wu4_37850/12_2024/8wu4_37850.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wu4_37850/12_2024/8wu4_37850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wu4_37850/12_2024/8wu4_37850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wu4_37850/12_2024/8wu4_37850.map" model { file = "/net/cci-nas-00/data/ceres_data/8wu4_37850/12_2024/8wu4_37850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wu4_37850/12_2024/8wu4_37850.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 224 5.16 5 C 34146 2.51 5 N 9548 2.21 5 O 10752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 54670 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "B" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "C" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "D" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "E" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "F" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "G" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "I" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "J" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "K" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "L" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "M" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "N" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Time building chain proxies: 23.05, per 1000 atoms: 0.42 Number of scatterers: 54670 At special positions: 0 Unit cell: (155.4, 156.24, 157.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 224 16.00 O 10752 8.00 N 9548 7.00 C 34146 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: 10.12 Conformation dependent library (CDL) restraints added in 5.6 seconds 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13412 Finding SS restraints... Secondary structure from input PDB file: 296 helices and 98 sheets defined 60.0% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.45 Creating SS restraints... Processing helix chain 'A' and resid 9 through 28 removed outlier: 4.360A pdb=" N ARG A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.519A pdb=" N VAL A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 86 removed outlier: 3.994A pdb=" N GLY A 70 " --> pdb=" O PHE A 66 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 84 " --> pdb=" O LYS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 109 removed outlier: 3.853A pdb=" N LYS A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 135 removed outlier: 3.931A pdb=" N ALA A 133 " --> pdb=" O GLU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 155 through 170 removed outlier: 3.987A pdb=" N LYS A 168 " --> pdb=" O GLN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 256 through 269 Processing helix chain 'A' and resid 282 through 297 removed outlier: 4.339A pdb=" N LYS A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 removed outlier: 4.105A pdb=" N GLU A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 374 Processing helix chain 'A' and resid 385 through 410 removed outlier: 3.519A pdb=" N GLU A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 430 removed outlier: 3.645A pdb=" N LEU A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 449 Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.518A pdb=" N ILE A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 518 Processing helix chain 'B' and resid 9 through 28 removed outlier: 4.369A pdb=" N ARG B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 52 through 59 removed outlier: 3.535A pdb=" N VAL B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 86 removed outlier: 4.140A pdb=" N GLY B 70 " --> pdb=" O PHE B 66 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 109 removed outlier: 3.740A pdb=" N LYS B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 135 removed outlier: 3.914A pdb=" N ALA B 133 " --> pdb=" O GLU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.957A pdb=" N LYS B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 256 through 269 Processing helix chain 'B' and resid 282 through 297 removed outlier: 4.334A pdb=" N LYS B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 removed outlier: 4.103A pdb=" N GLU B 354 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 374 Processing helix chain 'B' and resid 385 through 410 removed outlier: 3.514A pdb=" N GLU B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 430 removed outlier: 3.634A pdb=" N LEU B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 449 Processing helix chain 'B' and resid 450 through 461 Processing helix chain 'B' and resid 463 through 474 removed outlier: 3.509A pdb=" N ILE B 467 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 518 Processing helix chain 'C' and resid 9 through 28 removed outlier: 4.350A pdb=" N ARG C 15 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 52 through 60 removed outlier: 3.502A pdb=" N VAL C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 86 removed outlier: 3.951A pdb=" N GLY C 70 " --> pdb=" O PHE C 66 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL C 84 " --> pdb=" O LYS C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 109 removed outlier: 3.772A pdb=" N LYS C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 135 removed outlier: 3.917A pdb=" N ALA C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 155 through 170 removed outlier: 3.980A pdb=" N LYS C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 233 through 244 removed outlier: 3.526A pdb=" N GLN C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 268 Processing helix chain 'C' and resid 282 through 297 removed outlier: 4.352A pdb=" N LYS C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 354 removed outlier: 4.103A pdb=" N GLU C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 374 Processing helix chain 'C' and resid 385 through 410 removed outlier: 3.520A pdb=" N GLU C 408 " --> pdb=" O ARG C 404 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 430 removed outlier: 3.646A pdb=" N LEU C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 449 Processing helix chain 'C' and resid 450 through 461 Processing helix chain 'C' and resid 463 through 474 removed outlier: 3.527A pdb=" N ILE C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 518 Processing helix chain 'D' and resid 9 through 28 removed outlier: 4.343A pdb=" N ARG D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 52 through 60 removed outlier: 3.512A pdb=" N VAL D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 removed outlier: 4.179A pdb=" N GLY D 70 " --> pdb=" O PHE D 66 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 109 removed outlier: 3.754A pdb=" N LYS D 105 " --> pdb=" O ARG D 101 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 135 removed outlier: 3.933A pdb=" N ALA D 133 " --> pdb=" O GLU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 155 through 170 removed outlier: 3.969A pdb=" N LYS D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 205 Processing helix chain 'D' and resid 229 through 232 Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 256 through 269 Processing helix chain 'D' and resid 282 through 297 removed outlier: 4.353A pdb=" N LYS D 286 " --> pdb=" O GLY D 282 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 287 " --> pdb=" O ASP D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 354 removed outlier: 4.099A pdb=" N GLU D 354 " --> pdb=" O ARG D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 374 Processing helix chain 'D' and resid 385 through 410 removed outlier: 3.532A pdb=" N GLU D 408 " --> pdb=" O ARG D 404 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 430 removed outlier: 3.635A pdb=" N LEU D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 449 Processing helix chain 'D' and resid 450 through 461 Processing helix chain 'D' and resid 463 through 474 removed outlier: 3.521A pdb=" N ILE D 467 " --> pdb=" O GLU D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 518 Processing helix chain 'E' and resid 9 through 28 removed outlier: 4.355A pdb=" N ARG E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 26 " --> pdb=" O LEU E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 52 through 60 removed outlier: 3.517A pdb=" N VAL E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 86 removed outlier: 4.160A pdb=" N GLY E 70 " --> pdb=" O PHE E 66 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL E 84 " --> pdb=" O LYS E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 109 removed outlier: 3.804A pdb=" N LYS E 105 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 135 removed outlier: 3.917A pdb=" N ALA E 133 " --> pdb=" O GLU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 155 through 170 removed outlier: 3.998A pdb=" N LYS E 168 " --> pdb=" O GLN E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'E' and resid 229 through 232 Processing helix chain 'E' and resid 233 through 244 Processing helix chain 'E' and resid 256 through 269 Processing helix chain 'E' and resid 282 through 297 removed outlier: 4.338A pdb=" N LYS E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA E 287 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 354 removed outlier: 4.100A pdb=" N GLU E 354 " --> pdb=" O ARG E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 374 Processing helix chain 'E' and resid 385 through 410 removed outlier: 3.519A pdb=" N GLU E 408 " --> pdb=" O ARG E 404 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU E 409 " --> pdb=" O ALA E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 430 removed outlier: 3.648A pdb=" N LEU E 420 " --> pdb=" O GLY E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 449 Processing helix chain 'E' and resid 450 through 461 Processing helix chain 'E' and resid 463 through 474 removed outlier: 3.506A pdb=" N ILE E 467 " --> pdb=" O GLU E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 518 Processing helix chain 'F' and resid 9 through 28 removed outlier: 4.367A pdb=" N ARG F 15 " --> pdb=" O SER F 11 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA F 26 " --> pdb=" O LEU F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 52 through 60 removed outlier: 3.501A pdb=" N VAL F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 86 removed outlier: 4.127A pdb=" N GLY F 70 " --> pdb=" O PHE F 66 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL F 84 " --> pdb=" O LYS F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 109 removed outlier: 3.806A pdb=" N LYS F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 135 removed outlier: 3.939A pdb=" N ALA F 133 " --> pdb=" O GLU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 155 through 170 removed outlier: 3.981A pdb=" N LYS F 168 " --> pdb=" O GLN F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 229 through 232 Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 256 through 269 Processing helix chain 'F' and resid 282 through 297 removed outlier: 4.316A pdb=" N LYS F 286 " --> pdb=" O GLY F 282 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA F 287 " --> pdb=" O ASP F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 306 Processing helix chain 'F' and resid 338 through 354 removed outlier: 4.099A pdb=" N GLU F 354 " --> pdb=" O ARG F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 374 Processing helix chain 'F' and resid 385 through 410 removed outlier: 3.513A pdb=" N GLU F 408 " --> pdb=" O ARG F 404 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU F 409 " --> pdb=" O ALA F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 430 removed outlier: 3.675A pdb=" N LEU F 420 " --> pdb=" O GLY F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 449 Processing helix chain 'F' and resid 450 through 461 Processing helix chain 'F' and resid 463 through 474 removed outlier: 3.508A pdb=" N ILE F 467 " --> pdb=" O GLU F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 518 Processing helix chain 'G' and resid 9 through 28 removed outlier: 4.342A pdb=" N ARG G 15 " --> pdb=" O SER G 11 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 52 through 60 removed outlier: 3.519A pdb=" N VAL G 56 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE G 60 " --> pdb=" O VAL G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 86 removed outlier: 3.977A pdb=" N GLY G 70 " --> pdb=" O PHE G 66 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL G 84 " --> pdb=" O LYS G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 109 removed outlier: 3.780A pdb=" N LYS G 105 " --> pdb=" O ARG G 101 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 135 removed outlier: 3.939A pdb=" N ALA G 133 " --> pdb=" O GLU G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 155 through 170 removed outlier: 3.981A pdb=" N LYS G 168 " --> pdb=" O GLN G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 205 Processing helix chain 'G' and resid 229 through 232 Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 256 through 269 Processing helix chain 'G' and resid 282 through 297 removed outlier: 4.341A pdb=" N LYS G 286 " --> pdb=" O GLY G 282 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA G 287 " --> pdb=" O ASP G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 354 removed outlier: 4.104A pdb=" N GLU G 354 " --> pdb=" O ARG G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 374 Processing helix chain 'G' and resid 385 through 410 removed outlier: 3.510A pdb=" N GLU G 408 " --> pdb=" O ARG G 404 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU G 409 " --> pdb=" O ALA G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 430 removed outlier: 3.643A pdb=" N LEU G 420 " --> pdb=" O GLY G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 449 Processing helix chain 'G' and resid 450 through 461 Processing helix chain 'G' and resid 463 through 474 removed outlier: 3.501A pdb=" N ILE G 467 " --> pdb=" O GLU G 463 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 518 Processing helix chain 'H' and resid 9 through 28 removed outlier: 4.375A pdb=" N ARG H 15 " --> pdb=" O SER H 11 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA H 26 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 52 through 59 removed outlier: 3.538A pdb=" N VAL H 56 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 86 removed outlier: 4.146A pdb=" N GLY H 70 " --> pdb=" O PHE H 66 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL H 84 " --> pdb=" O LYS H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 109 removed outlier: 3.735A pdb=" N LYS H 105 " --> pdb=" O ARG H 101 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 135 removed outlier: 3.924A pdb=" N ALA H 133 " --> pdb=" O GLU H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 152 Processing helix chain 'H' and resid 155 through 170 removed outlier: 3.956A pdb=" N LYS H 168 " --> pdb=" O GLN H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 205 Processing helix chain 'H' and resid 229 through 232 Processing helix chain 'H' and resid 233 through 244 Processing helix chain 'H' and resid 256 through 269 Processing helix chain 'H' and resid 282 through 297 removed outlier: 4.311A pdb=" N LYS H 286 " --> pdb=" O GLY H 282 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA H 287 " --> pdb=" O ASP H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 354 removed outlier: 4.103A pdb=" N GLU H 354 " --> pdb=" O ARG H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 374 Processing helix chain 'H' and resid 385 through 410 removed outlier: 3.516A pdb=" N GLU H 408 " --> pdb=" O ARG H 404 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU H 409 " --> pdb=" O ALA H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 430 removed outlier: 3.638A pdb=" N LEU H 420 " --> pdb=" O GLY H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 449 Processing helix chain 'H' and resid 450 through 461 Processing helix chain 'H' and resid 463 through 474 removed outlier: 3.507A pdb=" N ILE H 467 " --> pdb=" O GLU H 463 " (cutoff:3.500A) Processing helix chain 'H' and resid 499 through 518 Processing helix chain 'I' and resid 9 through 28 removed outlier: 4.365A pdb=" N ARG I 15 " --> pdb=" O SER I 11 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA I 26 " --> pdb=" O LEU I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 52 through 60 removed outlier: 3.503A pdb=" N VAL I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 86 removed outlier: 3.945A pdb=" N GLY I 70 " --> pdb=" O PHE I 66 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL I 84 " --> pdb=" O LYS I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 109 removed outlier: 3.795A pdb=" N LYS I 105 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 135 removed outlier: 3.916A pdb=" N ALA I 133 " --> pdb=" O GLU I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 152 Processing helix chain 'I' and resid 155 through 170 removed outlier: 3.980A pdb=" N LYS I 168 " --> pdb=" O GLN I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 205 Processing helix chain 'I' and resid 229 through 232 Processing helix chain 'I' and resid 233 through 244 Processing helix chain 'I' and resid 256 through 269 Processing helix chain 'I' and resid 282 through 297 removed outlier: 4.349A pdb=" N LYS I 286 " --> pdb=" O GLY I 282 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA I 287 " --> pdb=" O ASP I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 354 removed outlier: 4.105A pdb=" N GLU I 354 " --> pdb=" O ARG I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 374 Processing helix chain 'I' and resid 385 through 410 removed outlier: 3.519A pdb=" N GLU I 408 " --> pdb=" O ARG I 404 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU I 409 " --> pdb=" O ALA I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 430 removed outlier: 3.645A pdb=" N LEU I 420 " --> pdb=" O GLY I 416 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 449 Processing helix chain 'I' and resid 450 through 461 Processing helix chain 'I' and resid 463 through 474 removed outlier: 3.520A pdb=" N ILE I 467 " --> pdb=" O GLU I 463 " (cutoff:3.500A) Processing helix chain 'I' and resid 499 through 518 Processing helix chain 'J' and resid 9 through 28 removed outlier: 4.351A pdb=" N ARG J 15 " --> pdb=" O SER J 11 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA J 26 " --> pdb=" O LEU J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'J' and resid 52 through 60 removed outlier: 3.514A pdb=" N VAL J 56 " --> pdb=" O ASP J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 86 removed outlier: 4.114A pdb=" N GLY J 70 " --> pdb=" O PHE J 66 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL J 84 " --> pdb=" O LYS J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 109 removed outlier: 3.755A pdb=" N LYS J 105 " --> pdb=" O ARG J 101 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 135 removed outlier: 3.931A pdb=" N ALA J 133 " --> pdb=" O GLU J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 152 Processing helix chain 'J' and resid 155 through 170 removed outlier: 3.985A pdb=" N LYS J 168 " --> pdb=" O GLN J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 205 Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 233 through 244 Processing helix chain 'J' and resid 256 through 269 Processing helix chain 'J' and resid 282 through 297 removed outlier: 4.360A pdb=" N LYS J 286 " --> pdb=" O GLY J 282 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA J 287 " --> pdb=" O ASP J 283 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 354 removed outlier: 4.102A pdb=" N GLU J 354 " --> pdb=" O ARG J 350 " (cutoff:3.500A) Processing helix chain 'J' and resid 358 through 374 Processing helix chain 'J' and resid 385 through 410 removed outlier: 3.542A pdb=" N GLU J 408 " --> pdb=" O ARG J 404 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU J 409 " --> pdb=" O ALA J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 430 removed outlier: 3.633A pdb=" N LEU J 420 " --> pdb=" O GLY J 416 " (cutoff:3.500A) Processing helix chain 'J' and resid 435 through 449 Processing helix chain 'J' and resid 450 through 461 Processing helix chain 'J' and resid 463 through 474 removed outlier: 3.515A pdb=" N ILE J 467 " --> pdb=" O GLU J 463 " (cutoff:3.500A) Processing helix chain 'J' and resid 499 through 518 Processing helix chain 'K' and resid 9 through 28 removed outlier: 4.389A pdb=" N ARG K 15 " --> pdb=" O SER K 11 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA K 26 " --> pdb=" O LEU K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'K' and resid 52 through 60 removed outlier: 3.513A pdb=" N VAL K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 86 removed outlier: 4.192A pdb=" N GLY K 70 " --> pdb=" O PHE K 66 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL K 84 " --> pdb=" O LYS K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 109 removed outlier: 3.779A pdb=" N LYS K 105 " --> pdb=" O ARG K 101 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR K 106 " --> pdb=" O GLU K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 135 removed outlier: 3.917A pdb=" N ALA K 133 " --> pdb=" O GLU K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 155 through 170 removed outlier: 4.007A pdb=" N LYS K 168 " --> pdb=" O GLN K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 205 Processing helix chain 'K' and resid 229 through 232 Processing helix chain 'K' and resid 233 through 244 Processing helix chain 'K' and resid 256 through 269 Processing helix chain 'K' and resid 282 through 297 removed outlier: 4.372A pdb=" N LYS K 286 " --> pdb=" O GLY K 282 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA K 287 " --> pdb=" O ASP K 283 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 354 removed outlier: 4.093A pdb=" N GLU K 354 " --> pdb=" O ARG K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 374 Processing helix chain 'K' and resid 385 through 410 removed outlier: 3.515A pdb=" N GLU K 408 " --> pdb=" O ARG K 404 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU K 409 " --> pdb=" O ALA K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 430 removed outlier: 3.644A pdb=" N LEU K 420 " --> pdb=" O GLY K 416 " (cutoff:3.500A) Processing helix chain 'K' and resid 435 through 449 Processing helix chain 'K' and resid 450 through 461 Processing helix chain 'K' and resid 463 through 474 removed outlier: 3.504A pdb=" N ILE K 467 " --> pdb=" O GLU K 463 " (cutoff:3.500A) Processing helix chain 'K' and resid 499 through 518 Processing helix chain 'L' and resid 9 through 28 removed outlier: 4.366A pdb=" N ARG L 15 " --> pdb=" O SER L 11 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA L 26 " --> pdb=" O LEU L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 52 through 60 removed outlier: 3.505A pdb=" N VAL L 56 " --> pdb=" O ASP L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 86 removed outlier: 4.162A pdb=" N GLY L 70 " --> pdb=" O PHE L 66 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL L 84 " --> pdb=" O LYS L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 109 removed outlier: 3.815A pdb=" N LYS L 105 " --> pdb=" O ARG L 101 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 135 removed outlier: 3.942A pdb=" N ALA L 133 " --> pdb=" O GLU L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 152 Processing helix chain 'L' and resid 155 through 170 removed outlier: 3.987A pdb=" N LYS L 168 " --> pdb=" O GLN L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 201 through 205 Processing helix chain 'L' and resid 229 through 232 Processing helix chain 'L' and resid 233 through 244 Processing helix chain 'L' and resid 256 through 269 Processing helix chain 'L' and resid 282 through 297 removed outlier: 4.313A pdb=" N LYS L 286 " --> pdb=" O GLY L 282 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA L 287 " --> pdb=" O ASP L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 302 through 306 Processing helix chain 'L' and resid 338 through 354 removed outlier: 4.097A pdb=" N GLU L 354 " --> pdb=" O ARG L 350 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 374 Processing helix chain 'L' and resid 385 through 410 removed outlier: 3.509A pdb=" N GLU L 408 " --> pdb=" O ARG L 404 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU L 409 " --> pdb=" O ALA L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 416 through 430 removed outlier: 3.675A pdb=" N LEU L 420 " --> pdb=" O GLY L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 435 through 449 Processing helix chain 'L' and resid 450 through 461 Processing helix chain 'L' and resid 463 through 474 removed outlier: 3.505A pdb=" N ILE L 467 " --> pdb=" O GLU L 463 " (cutoff:3.500A) Processing helix chain 'L' and resid 499 through 518 Processing helix chain 'M' and resid 9 through 28 removed outlier: 4.332A pdb=" N ARG M 15 " --> pdb=" O SER M 11 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA M 26 " --> pdb=" O LEU M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 31 No H-bonds generated for 'chain 'M' and resid 29 through 31' Processing helix chain 'M' and resid 52 through 60 removed outlier: 3.503A pdb=" N VAL M 56 " --> pdb=" O ASP M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 86 removed outlier: 3.929A pdb=" N GLY M 70 " --> pdb=" O PHE M 66 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL M 84 " --> pdb=" O LYS M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 109 removed outlier: 3.783A pdb=" N LYS M 105 " --> pdb=" O ARG M 101 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR M 106 " --> pdb=" O GLU M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 135 removed outlier: 3.938A pdb=" N ALA M 133 " --> pdb=" O GLU M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 152 Processing helix chain 'M' and resid 155 through 170 removed outlier: 3.970A pdb=" N LYS M 168 " --> pdb=" O GLN M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 205 Processing helix chain 'M' and resid 229 through 232 Processing helix chain 'M' and resid 233 through 244 Processing helix chain 'M' and resid 256 through 269 Processing helix chain 'M' and resid 282 through 297 removed outlier: 4.321A pdb=" N LYS M 286 " --> pdb=" O GLY M 282 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA M 287 " --> pdb=" O ASP M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 354 removed outlier: 4.106A pdb=" N GLU M 354 " --> pdb=" O ARG M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 374 Processing helix chain 'M' and resid 385 through 410 removed outlier: 3.508A pdb=" N GLU M 408 " --> pdb=" O ARG M 404 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU M 409 " --> pdb=" O ALA M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 430 removed outlier: 3.636A pdb=" N LEU M 420 " --> pdb=" O GLY M 416 " (cutoff:3.500A) Processing helix chain 'M' and resid 435 through 449 Processing helix chain 'M' and resid 450 through 461 Processing helix chain 'M' and resid 463 through 474 removed outlier: 3.502A pdb=" N ILE M 467 " --> pdb=" O GLU M 463 " (cutoff:3.500A) Processing helix chain 'M' and resid 499 through 518 Processing helix chain 'N' and resid 9 through 28 removed outlier: 4.398A pdb=" N ARG N 15 " --> pdb=" O SER N 11 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA N 26 " --> pdb=" O LEU N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 52 through 60 removed outlier: 3.519A pdb=" N VAL N 56 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 86 removed outlier: 4.001A pdb=" N GLY N 70 " --> pdb=" O PHE N 66 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL N 84 " --> pdb=" O LYS N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 109 removed outlier: 3.855A pdb=" N LYS N 105 " --> pdb=" O ARG N 101 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR N 106 " --> pdb=" O GLU N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 135 removed outlier: 3.929A pdb=" N ALA N 133 " --> pdb=" O GLU N 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 152 Processing helix chain 'N' and resid 155 through 170 removed outlier: 3.985A pdb=" N LYS N 168 " --> pdb=" O GLN N 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 205 Processing helix chain 'N' and resid 229 through 232 Processing helix chain 'N' and resid 233 through 244 Processing helix chain 'N' and resid 256 through 269 Processing helix chain 'N' and resid 282 through 297 removed outlier: 4.327A pdb=" N LYS N 286 " --> pdb=" O GLY N 282 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA N 287 " --> pdb=" O ASP N 283 " (cutoff:3.500A) Processing helix chain 'N' and resid 338 through 354 removed outlier: 4.100A pdb=" N GLU N 354 " --> pdb=" O ARG N 350 " (cutoff:3.500A) Processing helix chain 'N' and resid 358 through 374 Processing helix chain 'N' and resid 385 through 410 removed outlier: 3.513A pdb=" N GLU N 408 " --> pdb=" O ARG N 404 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU N 409 " --> pdb=" O ALA N 405 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 430 removed outlier: 3.638A pdb=" N LEU N 420 " --> pdb=" O GLY N 416 " (cutoff:3.500A) Processing helix chain 'N' and resid 435 through 449 Processing helix chain 'N' and resid 450 through 461 Processing helix chain 'N' and resid 463 through 474 removed outlier: 3.519A pdb=" N ILE N 467 " --> pdb=" O GLU N 463 " (cutoff:3.500A) Processing helix chain 'N' and resid 499 through 518 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.367A pdb=" N ASN G 37 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS A 521 " --> pdb=" O ASN G 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.893A pdb=" N ASN A 37 " --> pdb=" O CYS B 521 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N ILE B 523 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A 39 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N GLU B 525 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 179 Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 195 removed outlier: 6.569A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 195 removed outlier: 6.569A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE A 250 " --> pdb=" O TYR A 219 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA7, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AA8, first strand: chain 'A' and resid 478 through 480 Processing sheet with id=AA9, first strand: chain 'B' and resid 48 through 50 removed outlier: 6.963A pdb=" N ASN B 37 " --> pdb=" O CYS C 521 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ILE C 523 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 39 " --> pdb=" O ILE C 523 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N GLU C 525 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 174 through 179 Processing sheet with id=AB2, first strand: chain 'B' and resid 192 through 195 removed outlier: 6.572A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 192 through 195 removed outlier: 6.572A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE B 250 " --> pdb=" O TYR B 219 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AB5, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AB6, first strand: chain 'B' and resid 478 through 480 Processing sheet with id=AB7, first strand: chain 'C' and resid 48 through 50 removed outlier: 6.908A pdb=" N ASN C 37 " --> pdb=" O CYS D 521 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ILE D 523 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL C 39 " --> pdb=" O ILE D 523 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLU D 525 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 175 through 179 Processing sheet with id=AB9, first strand: chain 'C' and resid 192 through 195 removed outlier: 6.573A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 192 through 195 removed outlier: 6.573A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE C 250 " --> pdb=" O TYR C 219 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 226 through 227 Processing sheet with id=AC3, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AC4, first strand: chain 'C' and resid 478 through 480 Processing sheet with id=AC5, first strand: chain 'D' and resid 48 through 50 removed outlier: 6.933A pdb=" N ASN D 37 " --> pdb=" O CYS E 521 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N ILE E 523 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL D 39 " --> pdb=" O ILE E 523 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N GLU E 525 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 175 through 179 Processing sheet with id=AC7, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.561A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.561A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE D 250 " --> pdb=" O TYR D 219 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 226 through 227 Processing sheet with id=AD1, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AD2, first strand: chain 'D' and resid 478 through 480 Processing sheet with id=AD3, first strand: chain 'E' and resid 48 through 50 removed outlier: 6.938A pdb=" N ASN E 37 " --> pdb=" O CYS F 521 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N ILE F 523 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL E 39 " --> pdb=" O ILE F 523 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLU F 525 " --> pdb=" O VAL E 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 175 through 179 Processing sheet with id=AD5, first strand: chain 'E' and resid 192 through 195 removed outlier: 6.572A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA E 320 " --> pdb=" O GLY E 335 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 192 through 195 removed outlier: 6.572A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA E 320 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE E 250 " --> pdb=" O TYR E 219 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 226 through 227 Processing sheet with id=AD8, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AD9, first strand: chain 'E' and resid 478 through 480 Processing sheet with id=AE1, first strand: chain 'F' and resid 48 through 50 removed outlier: 6.994A pdb=" N ASN F 37 " --> pdb=" O CYS G 521 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ILE G 523 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL F 39 " --> pdb=" O ILE G 523 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N GLU G 525 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 175 through 179 Processing sheet with id=AE3, first strand: chain 'F' and resid 192 through 195 removed outlier: 6.571A pdb=" N GLY F 335 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA F 320 " --> pdb=" O GLY F 335 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 192 through 195 removed outlier: 6.571A pdb=" N GLY F 335 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA F 320 " --> pdb=" O GLY F 335 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE F 250 " --> pdb=" O TYR F 219 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 226 through 227 Processing sheet with id=AE6, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AE7, first strand: chain 'F' and resid 478 through 480 Processing sheet with id=AE8, first strand: chain 'G' and resid 175 through 179 Processing sheet with id=AE9, first strand: chain 'G' and resid 192 through 195 removed outlier: 6.570A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA G 320 " --> pdb=" O GLY G 335 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 192 through 195 removed outlier: 6.570A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA G 320 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE G 250 " --> pdb=" O TYR G 219 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 226 through 227 Processing sheet with id=AF3, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AF4, first strand: chain 'G' and resid 478 through 480 Processing sheet with id=AF5, first strand: chain 'H' and resid 4 through 8 removed outlier: 6.353A pdb=" N ASN N 37 " --> pdb=" O THR H 519 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS H 521 " --> pdb=" O ASN N 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 48 through 50 removed outlier: 6.899A pdb=" N ASN H 37 " --> pdb=" O CYS I 521 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ILE I 523 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL H 39 " --> pdb=" O ILE I 523 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N GLU I 525 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 174 through 179 Processing sheet with id=AF8, first strand: chain 'H' and resid 192 through 195 removed outlier: 6.572A pdb=" N GLY H 335 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA H 320 " --> pdb=" O GLY H 335 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 192 through 195 removed outlier: 6.572A pdb=" N GLY H 335 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA H 320 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N TYR H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE H 250 " --> pdb=" O TYR H 219 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 226 through 227 Processing sheet with id=AG2, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AG3, first strand: chain 'H' and resid 478 through 480 Processing sheet with id=AG4, first strand: chain 'I' and resid 48 through 50 removed outlier: 6.857A pdb=" N ASN I 37 " --> pdb=" O CYS J 521 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ILE J 523 " --> pdb=" O ASN I 37 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL I 39 " --> pdb=" O ILE J 523 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N GLU J 525 " --> pdb=" O VAL I 39 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 175 through 179 Processing sheet with id=AG6, first strand: chain 'I' and resid 192 through 195 removed outlier: 6.576A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 192 through 195 removed outlier: 6.576A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE I 250 " --> pdb=" O TYR I 219 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 226 through 227 Processing sheet with id=AG9, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AH1, first strand: chain 'I' and resid 478 through 480 Processing sheet with id=AH2, first strand: chain 'J' and resid 48 through 50 removed outlier: 6.871A pdb=" N ASN J 37 " --> pdb=" O CYS K 521 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ILE K 523 " --> pdb=" O ASN J 37 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL J 39 " --> pdb=" O ILE K 523 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N GLU K 525 " --> pdb=" O VAL J 39 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 175 through 179 Processing sheet with id=AH4, first strand: chain 'J' and resid 192 through 195 removed outlier: 6.566A pdb=" N GLY J 335 " --> pdb=" O ALA J 320 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA J 320 " --> pdb=" O GLY J 335 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 192 through 195 removed outlier: 6.566A pdb=" N GLY J 335 " --> pdb=" O ALA J 320 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA J 320 " --> pdb=" O GLY J 335 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TYR J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE J 250 " --> pdb=" O TYR J 219 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 226 through 227 Processing sheet with id=AH7, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AH8, first strand: chain 'J' and resid 478 through 480 Processing sheet with id=AH9, first strand: chain 'K' and resid 48 through 50 removed outlier: 6.936A pdb=" N ASN K 37 " --> pdb=" O CYS L 521 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE L 523 " --> pdb=" O ASN K 37 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL K 39 " --> pdb=" O ILE L 523 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N GLU L 525 " --> pdb=" O VAL K 39 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 175 through 179 Processing sheet with id=AI2, first strand: chain 'K' and resid 192 through 195 removed outlier: 6.573A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 192 through 195 removed outlier: 6.573A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE K 250 " --> pdb=" O TYR K 219 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 226 through 227 Processing sheet with id=AI5, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AI6, first strand: chain 'K' and resid 478 through 480 Processing sheet with id=AI7, first strand: chain 'L' and resid 48 through 50 removed outlier: 6.992A pdb=" N ASN L 37 " --> pdb=" O CYS M 521 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N ILE M 523 " --> pdb=" O ASN L 37 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL L 39 " --> pdb=" O ILE M 523 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N GLU M 525 " --> pdb=" O VAL L 39 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 174 through 179 Processing sheet with id=AI9, first strand: chain 'L' and resid 192 through 195 removed outlier: 6.576A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 192 through 195 removed outlier: 6.576A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE L 250 " --> pdb=" O TYR L 219 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 226 through 227 Processing sheet with id=AJ3, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AJ4, first strand: chain 'L' and resid 478 through 480 Processing sheet with id=AJ5, first strand: chain 'M' and resid 48 through 50 removed outlier: 6.903A pdb=" N ASN M 37 " --> pdb=" O CYS N 521 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ILE N 523 " --> pdb=" O ASN M 37 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL M 39 " --> pdb=" O ILE N 523 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N GLU N 525 " --> pdb=" O VAL M 39 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'M' and resid 175 through 179 Processing sheet with id=AJ7, first strand: chain 'M' and resid 192 through 195 removed outlier: 6.573A pdb=" N GLY M 335 " --> pdb=" O ALA M 320 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA M 320 " --> pdb=" O GLY M 335 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'M' and resid 192 through 195 removed outlier: 6.573A pdb=" N GLY M 335 " --> pdb=" O ALA M 320 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA M 320 " --> pdb=" O GLY M 335 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE M 250 " --> pdb=" O TYR M 219 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'M' and resid 226 through 227 Processing sheet with id=AK1, first strand: chain 'M' and resid 411 through 413 Processing sheet with id=AK2, first strand: chain 'M' and resid 478 through 480 Processing sheet with id=AK3, first strand: chain 'N' and resid 175 through 179 Processing sheet with id=AK4, first strand: chain 'N' and resid 192 through 195 removed outlier: 6.577A pdb=" N GLY N 335 " --> pdb=" O ALA N 320 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA N 320 " --> pdb=" O GLY N 335 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'N' and resid 192 through 195 removed outlier: 6.577A pdb=" N GLY N 335 " --> pdb=" O ALA N 320 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA N 320 " --> pdb=" O GLY N 335 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE N 250 " --> pdb=" O TYR N 219 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'N' and resid 226 through 227 Processing sheet with id=AK7, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AK8, first strand: chain 'N' and resid 478 through 480 3745 hydrogen bonds defined for protein. 10803 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: 27.91 Time building geometry restraints manager: 12.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 18926 1.34 - 1.46: 9071 1.46 - 1.58: 26743 1.58 - 1.69: 0 1.69 - 1.81: 406 Bond restraints: 55146 Sorted by residual: bond pdb=" CB GLN D 211 " pdb=" CG GLN D 211 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 bond pdb=" CA ASN D 217 " pdb=" CB ASN D 217 " ideal model delta sigma weight residual 1.522 1.531 -0.008 7.00e-03 2.04e+04 1.42e+00 bond pdb=" CA ASN M 217 " pdb=" CB ASN M 217 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.31e+00 bond pdb=" CA ASN J 217 " pdb=" CB ASN J 217 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.29e+00 bond pdb=" CA ASN F 217 " pdb=" CB ASN F 217 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.21e+00 ... (remaining 55141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 73830 2.24 - 4.48: 529 4.48 - 6.73: 58 6.73 - 8.97: 20 8.97 - 11.21: 1 Bond angle restraints: 74438 Sorted by residual: angle pdb=" C HIS J 9 " pdb=" CA HIS J 9 " pdb=" CB HIS J 9 " ideal model delta sigma weight residual 116.63 109.52 7.11 1.16e+00 7.43e-01 3.76e+01 angle pdb=" C HIS D 9 " pdb=" CA HIS D 9 " pdb=" CB HIS D 9 " ideal model delta sigma weight residual 116.63 109.56 7.07 1.16e+00 7.43e-01 3.72e+01 angle pdb=" C HIS B 9 " pdb=" CA HIS B 9 " pdb=" CB HIS B 9 " ideal model delta sigma weight residual 116.54 109.61 6.93 1.15e+00 7.56e-01 3.63e+01 angle pdb=" C HIS I 9 " pdb=" CA HIS I 9 " pdb=" CB HIS I 9 " ideal model delta sigma weight residual 116.54 109.67 6.87 1.15e+00 7.56e-01 3.57e+01 angle pdb=" CA GLN D 211 " pdb=" CB GLN D 211 " pdb=" CG GLN D 211 " ideal model delta sigma weight residual 114.10 123.05 -8.95 2.00e+00 2.50e-01 2.00e+01 ... (remaining 74433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 31347 17.98 - 35.96: 2427 35.96 - 53.93: 384 53.93 - 71.91: 173 71.91 - 89.89: 53 Dihedral angle restraints: 34384 sinusoidal: 13524 harmonic: 20860 Sorted by residual: dihedral pdb=" CA GLU A 61 " pdb=" C GLU A 61 " pdb=" N LEU A 62 " pdb=" CA LEU A 62 " ideal model delta harmonic sigma weight residual -180.00 -162.18 -17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA GLU J 61 " pdb=" C GLU J 61 " pdb=" N LEU J 62 " pdb=" CA LEU J 62 " ideal model delta harmonic sigma weight residual 180.00 -162.58 -17.42 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA GLU F 61 " pdb=" C GLU F 61 " pdb=" N LEU F 62 " pdb=" CA LEU F 62 " ideal model delta harmonic sigma weight residual -180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 34381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 5677 0.031 - 0.061: 2163 0.061 - 0.092: 690 0.092 - 0.123: 430 0.123 - 0.153: 28 Chirality restraints: 8988 Sorted by residual: chirality pdb=" CB VAL K 412 " pdb=" CA VAL K 412 " pdb=" CG1 VAL K 412 " pdb=" CG2 VAL K 412 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CB VAL L 412 " pdb=" CA VAL L 412 " pdb=" CG1 VAL L 412 " pdb=" CG2 VAL L 412 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CB VAL B 412 " pdb=" CA VAL B 412 " pdb=" CG1 VAL B 412 " pdb=" CG2 VAL B 412 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 8985 not shown) Planarity restraints: 9730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 412 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO B 413 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 413 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 413 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 412 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO I 413 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO I 413 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 413 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 412 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO F 413 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 413 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 413 " -0.026 5.00e-02 4.00e+02 ... (remaining 9727 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 11656 2.78 - 3.31: 55671 3.31 - 3.84: 92411 3.84 - 4.37: 104808 4.37 - 4.90: 188108 Nonbonded interactions: 452654 Sorted by model distance: nonbonded pdb=" NH2 ARG H 284 " pdb=" OD1 ASP H 361 " model vdw 2.254 3.120 nonbonded pdb=" NH2 ARG A 284 " pdb=" OD1 ASP A 361 " model vdw 2.257 3.120 nonbonded pdb=" OG1 THR J 81 " pdb=" OD1 ASN J 508 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR N 81 " pdb=" OD1 ASN N 508 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR A 81 " pdb=" OD1 ASN A 508 " model vdw 2.264 3.040 ... (remaining 452649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.570 Check model and map are aligned: 0.300 Set scattering table: 0.380 Process input model: 102.150 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 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 : 0.002 0.046 55146 Z= 0.157 Angle : 0.530 11.210 74438 Z= 0.306 Chirality : 0.040 0.153 8988 Planarity : 0.004 0.047 9730 Dihedral : 13.978 89.890 20972 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.09 % Allowed : 8.33 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.10), residues: 7336 helix: 1.50 (0.08), residues: 4074 sheet: 0.79 (0.15), residues: 1176 loop : 1.07 (0.15), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 223 PHE 0.005 0.001 PHE K 66 TYR 0.017 0.001 TYR C 360 ARG 0.004 0.000 ARG N 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 279 time to evaluate : 4.682 Fit side-chains REVERT: A 193 MET cc_start: 0.8697 (ptm) cc_final: 0.8103 (ttp) REVERT: C 219 TYR cc_start: 0.8957 (m-10) cc_final: 0.8638 (m-80) REVERT: D 111 MET cc_start: 0.8760 (mtp) cc_final: 0.8557 (ttm) REVERT: F 193 MET cc_start: 0.8695 (ttp) cc_final: 0.8345 (ttm) REVERT: G 69 MET cc_start: 0.8444 (mtt) cc_final: 0.8168 (mtp) REVERT: H 219 TYR cc_start: 0.8745 (m-10) cc_final: 0.8354 (m-80) REVERT: J 111 MET cc_start: 0.8778 (mtp) cc_final: 0.8566 (ttm) REVERT: J 193 MET cc_start: 0.8664 (ptm) cc_final: 0.8128 (ttp) REVERT: L 193 MET cc_start: 0.8711 (ptm) cc_final: 0.8311 (ttp) REVERT: N 193 MET cc_start: 0.8678 (ptm) cc_final: 0.8057 (ttp) outliers start: 5 outliers final: 2 residues processed: 279 average time/residue: 0.4711 time to fit residues: 233.6070 Evaluate side-chains 279 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 277 time to evaluate : 4.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain M residue 288 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 10.0000 chunk 551 optimal weight: 30.0000 chunk 306 optimal weight: 0.2980 chunk 188 optimal weight: 20.0000 chunk 372 optimal weight: 3.9990 chunk 294 optimal weight: 20.0000 chunk 570 optimal weight: 0.9990 chunk 220 optimal weight: 9.9990 chunk 346 optimal weight: 20.0000 chunk 424 optimal weight: 3.9990 chunk 661 optimal weight: 20.0000 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN B 508 ASN C 508 ASN D 508 ASN E 508 ASN F 508 ASN G 508 ASN H 508 ASN I 508 ASN J 508 ASN K 508 ASN L 508 ASN M 508 ASN N 508 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 55146 Z= 0.285 Angle : 0.508 6.083 74438 Z= 0.269 Chirality : 0.043 0.166 8988 Planarity : 0.004 0.047 9730 Dihedral : 3.882 44.531 7790 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.89 % Allowed : 7.88 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.10), residues: 7336 helix: 1.51 (0.08), residues: 4144 sheet: 0.43 (0.15), residues: 1120 loop : 0.80 (0.15), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 9 PHE 0.006 0.001 PHE A 195 TYR 0.018 0.001 TYR K 360 ARG 0.003 0.000 ARG L 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 292 time to evaluate : 4.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8056 (ttp) REVERT: A 389 MET cc_start: 0.8543 (tpp) cc_final: 0.8311 (tpp) REVERT: B 193 MET cc_start: 0.8659 (ptm) cc_final: 0.8094 (ttp) REVERT: C 193 MET cc_start: 0.8658 (ptm) cc_final: 0.8139 (ttp) REVERT: D 193 MET cc_start: 0.8638 (ttm) cc_final: 0.8365 (ttm) REVERT: E 193 MET cc_start: 0.8566 (ptm) cc_final: 0.8343 (ttp) REVERT: F 193 MET cc_start: 0.8623 (ttp) cc_final: 0.8396 (ttm) REVERT: G 193 MET cc_start: 0.8691 (ttm) cc_final: 0.8393 (ttm) REVERT: H 193 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8143 (ttp) REVERT: I 193 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8222 (ttp) REVERT: J 193 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8102 (ttp) REVERT: K 62 LEU cc_start: 0.9300 (mt) cc_final: 0.9078 (mp) REVERT: K 193 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8128 (ttp) REVERT: L 193 MET cc_start: 0.8468 (ptm) cc_final: 0.8136 (ttp) REVERT: N 193 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8012 (ttp) outliers start: 108 outliers final: 61 residues processed: 367 average time/residue: 0.4888 time to fit residues: 316.8262 Evaluate side-chains 354 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 287 time to evaluate : 4.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 466 VAL Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 519 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain J residue 519 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 466 VAL Chi-restraints excluded: chain K residue 519 THR Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 519 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 466 VAL Chi-restraints excluded: chain M residue 519 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 466 VAL Chi-restraints excluded: chain N residue 519 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 7.9990 chunk 205 optimal weight: 8.9990 chunk 550 optimal weight: 7.9990 chunk 450 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 chunk 662 optimal weight: 9.9990 chunk 715 optimal weight: 2.9990 chunk 589 optimal weight: 7.9990 chunk 656 optimal weight: 10.0000 chunk 225 optimal weight: 8.9990 chunk 531 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN J 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 55146 Z= 0.423 Angle : 0.558 5.504 74438 Z= 0.293 Chirality : 0.045 0.173 8988 Planarity : 0.004 0.045 9730 Dihedral : 3.941 19.033 7784 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.80 % Allowed : 9.13 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.10), residues: 7336 helix: 1.40 (0.08), residues: 4158 sheet: 0.59 (0.15), residues: 1176 loop : 0.64 (0.15), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 401 PHE 0.009 0.001 PHE D 66 TYR 0.009 0.002 TYR J 478 ARG 0.003 0.000 ARG I 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 293 time to evaluate : 4.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.7943 (ttp) REVERT: A 389 MET cc_start: 0.8647 (tpp) cc_final: 0.8373 (tpp) REVERT: B 111 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8952 (mtm) REVERT: C 219 TYR cc_start: 0.8738 (m-80) cc_final: 0.8423 (m-80) REVERT: D 193 MET cc_start: 0.8679 (ttm) cc_final: 0.8372 (ttm) REVERT: E 237 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9135 (pp) REVERT: F 193 MET cc_start: 0.8584 (ttp) cc_final: 0.8215 (ttm) REVERT: G 193 MET cc_start: 0.8754 (ttm) cc_final: 0.8381 (ttm) REVERT: G 219 TYR cc_start: 0.8908 (m-10) cc_final: 0.8440 (m-80) REVERT: G 237 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8967 (pp) REVERT: H 111 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8938 (mtm) REVERT: H 219 TYR cc_start: 0.8921 (m-10) cc_final: 0.8460 (m-80) REVERT: I 193 MET cc_start: 0.8778 (ptm) cc_final: 0.8147 (ttp) REVERT: J 193 MET cc_start: 0.8651 (ptm) cc_final: 0.8019 (ttp) REVERT: L 193 MET cc_start: 0.8589 (ptm) cc_final: 0.8036 (ttp) REVERT: M 219 TYR cc_start: 0.8919 (m-10) cc_final: 0.8447 (m-80) REVERT: M 237 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8960 (pp) REVERT: N 193 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.7871 (ttp) REVERT: N 219 TYR cc_start: 0.8959 (m-10) cc_final: 0.8383 (m-80) outliers start: 103 outliers final: 65 residues processed: 364 average time/residue: 0.4806 time to fit residues: 308.6347 Evaluate side-chains 358 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 286 time to evaluate : 4.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 466 VAL Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 519 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain J residue 519 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 466 VAL Chi-restraints excluded: chain K residue 519 THR Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 519 THR Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 466 VAL Chi-restraints excluded: chain M residue 519 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 466 VAL Chi-restraints excluded: chain N residue 519 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 30.0000 chunk 497 optimal weight: 20.0000 chunk 343 optimal weight: 30.0000 chunk 73 optimal weight: 0.6980 chunk 316 optimal weight: 7.9990 chunk 444 optimal weight: 20.0000 chunk 664 optimal weight: 6.9990 chunk 703 optimal weight: 30.0000 chunk 347 optimal weight: 20.0000 chunk 629 optimal weight: 0.5980 chunk 189 optimal weight: 20.0000 overall best weight: 7.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 55146 Z= 0.481 Angle : 0.598 8.302 74438 Z= 0.311 Chirality : 0.045 0.213 8988 Planarity : 0.004 0.046 9730 Dihedral : 4.096 19.388 7784 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.38 % Allowed : 9.90 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.10), residues: 7336 helix: 1.30 (0.08), residues: 4130 sheet: 0.92 (0.16), residues: 1008 loop : 0.32 (0.14), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 401 PHE 0.011 0.001 PHE I 66 TYR 0.010 0.002 TYR K 219 ARG 0.002 0.000 ARG I 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 294 time to evaluate : 4.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 TYR cc_start: 0.8683 (m-80) cc_final: 0.8065 (m-80) REVERT: A 389 MET cc_start: 0.8616 (tpp) cc_final: 0.8313 (tpp) REVERT: B 111 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.9024 (mtm) REVERT: B 219 TYR cc_start: 0.8769 (m-10) cc_final: 0.8332 (m-80) REVERT: C 219 TYR cc_start: 0.8754 (m-80) cc_final: 0.8446 (m-80) REVERT: D 193 MET cc_start: 0.8705 (ttm) cc_final: 0.8274 (ttm) REVERT: E 219 TYR cc_start: 0.8773 (m-10) cc_final: 0.8073 (m-80) REVERT: G 193 MET cc_start: 0.8830 (ttm) cc_final: 0.8381 (ttm) REVERT: G 219 TYR cc_start: 0.8935 (m-10) cc_final: 0.8470 (m-80) REVERT: G 237 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8975 (pp) REVERT: H 111 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.9009 (mtm) REVERT: H 219 TYR cc_start: 0.8932 (m-10) cc_final: 0.8447 (m-80) REVERT: I 219 TYR cc_start: 0.8815 (m-10) cc_final: 0.8329 (m-80) REVERT: K 219 TYR cc_start: 0.8782 (m-10) cc_final: 0.8123 (m-80) REVERT: K 237 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9141 (pp) REVERT: M 219 TYR cc_start: 0.8929 (m-10) cc_final: 0.8455 (m-80) REVERT: M 237 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8979 (pp) REVERT: N 219 TYR cc_start: 0.8956 (m-10) cc_final: 0.8539 (m-80) outliers start: 136 outliers final: 96 residues processed: 389 average time/residue: 0.4888 time to fit residues: 335.5406 Evaluate side-chains 394 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 293 time to evaluate : 4.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 466 VAL Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 519 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 288 MET Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain J residue 519 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 466 VAL Chi-restraints excluded: chain K residue 519 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 519 THR Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 466 VAL Chi-restraints excluded: chain M residue 519 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain N residue 466 VAL Chi-restraints excluded: chain N residue 519 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 8.9990 chunk 399 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 523 optimal weight: 2.9990 chunk 290 optimal weight: 10.0000 chunk 600 optimal weight: 10.0000 chunk 486 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 359 optimal weight: 3.9990 chunk 631 optimal weight: 1.9990 chunk 177 optimal weight: 30.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 55146 Z= 0.281 Angle : 0.501 7.524 74438 Z= 0.261 Chirality : 0.042 0.174 8988 Planarity : 0.003 0.047 9730 Dihedral : 3.950 18.355 7784 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.87 % Allowed : 11.49 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.10), residues: 7336 helix: 1.50 (0.08), residues: 4144 sheet: 0.86 (0.16), residues: 1008 loop : 0.45 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 9 PHE 0.008 0.001 PHE C 66 TYR 0.009 0.001 TYR E 199 ARG 0.002 0.000 ARG L 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 296 time to evaluate : 4.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 TYR cc_start: 0.8704 (m-80) cc_final: 0.8344 (m-80) REVERT: A 389 MET cc_start: 0.8618 (tpp) cc_final: 0.8334 (tpp) REVERT: B 111 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.9021 (mtm) REVERT: B 219 TYR cc_start: 0.8794 (m-10) cc_final: 0.8350 (m-80) REVERT: C 219 TYR cc_start: 0.8792 (m-80) cc_final: 0.8462 (m-80) REVERT: D 193 MET cc_start: 0.8654 (ttm) cc_final: 0.8202 (ttm) REVERT: E 219 TYR cc_start: 0.8803 (m-10) cc_final: 0.8150 (m-80) REVERT: E 237 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9130 (pp) REVERT: F 211 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8887 (tp-100) REVERT: G 193 MET cc_start: 0.8814 (ttm) cc_final: 0.8361 (ttm) REVERT: G 219 TYR cc_start: 0.8889 (m-10) cc_final: 0.8388 (m-80) REVERT: G 237 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9003 (pp) REVERT: H 111 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8999 (mtm) REVERT: H 219 TYR cc_start: 0.8912 (m-10) cc_final: 0.8482 (m-80) REVERT: K 219 TYR cc_start: 0.8820 (m-10) cc_final: 0.8166 (m-80) REVERT: L 211 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8925 (tp-100) REVERT: M 219 TYR cc_start: 0.8908 (m-10) cc_final: 0.8418 (m-80) REVERT: N 219 TYR cc_start: 0.8971 (m-10) cc_final: 0.8562 (m-80) outliers start: 107 outliers final: 74 residues processed: 369 average time/residue: 0.4750 time to fit residues: 308.9437 Evaluate side-chains 375 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 295 time to evaluate : 4.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 211 GLN Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 466 VAL Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 288 MET Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain J residue 519 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 466 VAL Chi-restraints excluded: chain K residue 519 THR Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 211 GLN Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 519 THR Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 466 VAL Chi-restraints excluded: chain M residue 519 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain N residue 466 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 9.9990 chunk 633 optimal weight: 3.9990 chunk 139 optimal weight: 20.0000 chunk 413 optimal weight: 0.7980 chunk 173 optimal weight: 8.9990 chunk 704 optimal weight: 6.9990 chunk 584 optimal weight: 0.7980 chunk 326 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 232 optimal weight: 10.0000 chunk 369 optimal weight: 7.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 55146 Z= 0.284 Angle : 0.498 8.806 74438 Z= 0.258 Chirality : 0.042 0.152 8988 Planarity : 0.003 0.047 9730 Dihedral : 3.898 18.183 7784 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.32 % Allowed : 11.51 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.10), residues: 7336 helix: 1.59 (0.08), residues: 4144 sheet: 0.75 (0.16), residues: 1008 loop : 0.44 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 9 PHE 0.008 0.001 PHE I 66 TYR 0.008 0.001 TYR K 199 ARG 0.002 0.000 ARG N 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 296 time to evaluate : 4.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 TYR cc_start: 0.8753 (m-80) cc_final: 0.8384 (m-80) REVERT: A 389 MET cc_start: 0.8609 (tpp) cc_final: 0.8254 (tpp) REVERT: B 111 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.9007 (mtm) REVERT: B 219 TYR cc_start: 0.8830 (m-10) cc_final: 0.8393 (m-80) REVERT: C 42 ARG cc_start: 0.8470 (ttp80) cc_final: 0.8086 (mtm-85) REVERT: C 219 TYR cc_start: 0.8798 (m-80) cc_final: 0.8450 (m-80) REVERT: D 193 MET cc_start: 0.8654 (ttm) cc_final: 0.8160 (ttm) REVERT: D 219 TYR cc_start: 0.8406 (m-80) cc_final: 0.7903 (m-80) REVERT: E 193 MET cc_start: 0.8563 (tpt) cc_final: 0.8335 (tpt) REVERT: E 219 TYR cc_start: 0.8835 (m-10) cc_final: 0.8194 (m-80) REVERT: E 237 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9142 (pp) REVERT: F 193 MET cc_start: 0.8566 (ttm) cc_final: 0.8229 (ttm) REVERT: F 211 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8889 (tp-100) REVERT: G 219 TYR cc_start: 0.8893 (m-10) cc_final: 0.8395 (m-80) REVERT: H 111 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8981 (mtm) REVERT: H 219 TYR cc_start: 0.8918 (m-10) cc_final: 0.8464 (m-80) REVERT: J 219 TYR cc_start: 0.8451 (m-80) cc_final: 0.7943 (m-80) REVERT: K 193 MET cc_start: 0.8503 (tpt) cc_final: 0.8303 (tpt) REVERT: L 211 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8926 (tp-100) REVERT: M 219 TYR cc_start: 0.8901 (m-10) cc_final: 0.8404 (m-80) REVERT: N 219 TYR cc_start: 0.8959 (m-10) cc_final: 0.8495 (m-80) outliers start: 133 outliers final: 95 residues processed: 396 average time/residue: 0.4793 time to fit residues: 335.9160 Evaluate side-chains 394 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 294 time to evaluate : 4.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 211 GLN Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 466 VAL Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 519 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 288 MET Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain J residue 519 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 466 VAL Chi-restraints excluded: chain K residue 519 THR Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 211 GLN Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 519 THR Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 466 VAL Chi-restraints excluded: chain M residue 519 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain N residue 466 VAL Chi-restraints excluded: chain N residue 519 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 401 optimal weight: 10.0000 chunk 514 optimal weight: 1.9990 chunk 398 optimal weight: 10.0000 chunk 592 optimal weight: 0.9980 chunk 393 optimal weight: 6.9990 chunk 701 optimal weight: 3.9990 chunk 439 optimal weight: 30.0000 chunk 427 optimal weight: 5.9990 chunk 323 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 55146 Z= 0.222 Angle : 0.477 9.985 74438 Z= 0.246 Chirality : 0.041 0.152 8988 Planarity : 0.003 0.047 9730 Dihedral : 3.820 17.652 7784 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.32 % Allowed : 11.54 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.10), residues: 7336 helix: 1.75 (0.08), residues: 4102 sheet: 0.73 (0.15), residues: 1008 loop : 0.49 (0.14), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 9 PHE 0.006 0.001 PHE C 66 TYR 0.007 0.001 TYR I 199 ARG 0.002 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 300 time to evaluate : 4.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 TYR cc_start: 0.8749 (m-80) cc_final: 0.8356 (m-80) REVERT: A 389 MET cc_start: 0.8602 (tpp) cc_final: 0.8256 (tpp) REVERT: B 219 TYR cc_start: 0.8841 (m-10) cc_final: 0.8346 (m-80) REVERT: C 42 ARG cc_start: 0.8437 (ttp80) cc_final: 0.8113 (mtm-85) REVERT: C 219 TYR cc_start: 0.8822 (m-80) cc_final: 0.8453 (m-80) REVERT: D 193 MET cc_start: 0.8637 (ttm) cc_final: 0.8152 (ttm) REVERT: E 69 MET cc_start: 0.8777 (mmt) cc_final: 0.8178 (mtt) REVERT: E 193 MET cc_start: 0.8564 (tpt) cc_final: 0.8335 (tpt) REVERT: E 219 TYR cc_start: 0.8863 (m-10) cc_final: 0.8157 (m-80) REVERT: E 237 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9128 (pp) REVERT: F 69 MET cc_start: 0.8428 (mmt) cc_final: 0.7840 (mmt) REVERT: F 193 MET cc_start: 0.8560 (ttm) cc_final: 0.8234 (ttm) REVERT: F 211 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8877 (tp-100) REVERT: G 219 TYR cc_start: 0.8897 (m-10) cc_final: 0.8365 (m-80) REVERT: H 219 TYR cc_start: 0.8918 (m-10) cc_final: 0.8489 (m-80) REVERT: I 193 MET cc_start: 0.8746 (ttm) cc_final: 0.8335 (ttm) REVERT: I 219 TYR cc_start: 0.8840 (m-10) cc_final: 0.8403 (m-80) REVERT: I 237 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9145 (pp) REVERT: K 193 MET cc_start: 0.8485 (tpt) cc_final: 0.8282 (tpt) REVERT: L 104 MET cc_start: 0.8754 (mmm) cc_final: 0.8365 (mmt) REVERT: L 211 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8920 (tp-100) REVERT: M 193 MET cc_start: 0.8525 (tpt) cc_final: 0.8208 (tpt) REVERT: M 219 TYR cc_start: 0.8910 (m-10) cc_final: 0.8464 (m-80) REVERT: N 219 TYR cc_start: 0.8887 (m-10) cc_final: 0.8461 (m-80) outliers start: 133 outliers final: 83 residues processed: 405 average time/residue: 0.4758 time to fit residues: 340.5192 Evaluate side-chains 384 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 297 time to evaluate : 4.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 211 GLN Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 466 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 519 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 288 MET Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 466 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 211 GLN Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 466 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain N residue 466 VAL Chi-restraints excluded: chain N residue 519 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 5.9990 chunk 280 optimal weight: 0.0010 chunk 419 optimal weight: 8.9990 chunk 211 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 446 optimal weight: 4.9990 chunk 478 optimal weight: 7.9990 chunk 346 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 551 optimal weight: 10.0000 overall best weight: 3.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 55146 Z= 0.262 Angle : 0.499 11.323 74438 Z= 0.254 Chirality : 0.042 0.161 8988 Planarity : 0.003 0.047 9730 Dihedral : 3.820 18.370 7784 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.25 % Allowed : 11.81 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.10), residues: 7336 helix: 1.73 (0.08), residues: 4144 sheet: 0.69 (0.15), residues: 1008 loop : 0.42 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 9 PHE 0.007 0.001 PHE D 66 TYR 0.007 0.001 TYR C 199 ARG 0.002 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 299 time to evaluate : 4.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 TYR cc_start: 0.8766 (m-80) cc_final: 0.8147 (m-80) REVERT: A 288 MET cc_start: 0.8003 (mmp) cc_final: 0.7797 (mmp) REVERT: A 389 MET cc_start: 0.8597 (tpp) cc_final: 0.8250 (tpp) REVERT: B 219 TYR cc_start: 0.8858 (m-10) cc_final: 0.8360 (m-80) REVERT: C 193 MET cc_start: 0.8658 (tpp) cc_final: 0.8160 (tpt) REVERT: C 219 TYR cc_start: 0.8822 (m-80) cc_final: 0.8438 (m-80) REVERT: D 193 MET cc_start: 0.8652 (ttm) cc_final: 0.8132 (ttm) REVERT: E 69 MET cc_start: 0.8772 (mmt) cc_final: 0.8276 (mtt) REVERT: E 219 TYR cc_start: 0.8867 (m-10) cc_final: 0.8465 (m-10) REVERT: E 237 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9127 (pp) REVERT: F 193 MET cc_start: 0.8607 (ttm) cc_final: 0.8209 (ttm) REVERT: F 211 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8898 (tp-100) REVERT: G 219 TYR cc_start: 0.8896 (m-10) cc_final: 0.8443 (m-80) REVERT: H 219 TYR cc_start: 0.8914 (m-10) cc_final: 0.8428 (m-80) REVERT: I 193 MET cc_start: 0.8796 (ttm) cc_final: 0.8392 (ttm) REVERT: I 219 TYR cc_start: 0.8835 (m-10) cc_final: 0.8382 (m-80) REVERT: J 219 TYR cc_start: 0.8496 (m-80) cc_final: 0.7974 (m-80) REVERT: J 389 MET cc_start: 0.8367 (tpt) cc_final: 0.8146 (tpp) REVERT: L 61 GLU cc_start: 0.8370 (pp20) cc_final: 0.8097 (pt0) REVERT: L 193 MET cc_start: 0.8626 (ttm) cc_final: 0.8222 (ttm) REVERT: L 211 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8935 (tp-100) REVERT: M 193 MET cc_start: 0.8515 (tpt) cc_final: 0.8167 (tpt) REVERT: M 219 TYR cc_start: 0.8936 (m-10) cc_final: 0.8478 (m-80) REVERT: N 219 TYR cc_start: 0.8886 (m-10) cc_final: 0.8460 (m-80) outliers start: 129 outliers final: 110 residues processed: 401 average time/residue: 0.4805 time to fit residues: 339.8050 Evaluate side-chains 411 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 298 time to evaluate : 4.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 211 GLN Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 245 ARG Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 466 VAL Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 519 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 288 MET Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain J residue 519 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 466 VAL Chi-restraints excluded: chain K residue 519 THR Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 211 GLN Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 519 THR Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 466 VAL Chi-restraints excluded: chain M residue 519 THR Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain N residue 466 VAL Chi-restraints excluded: chain N residue 519 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 9.9990 chunk 672 optimal weight: 3.9990 chunk 613 optimal weight: 0.9990 chunk 653 optimal weight: 7.9990 chunk 393 optimal weight: 9.9990 chunk 284 optimal weight: 0.1980 chunk 513 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 590 optimal weight: 6.9990 chunk 618 optimal weight: 3.9990 chunk 651 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 55146 Z= 0.166 Angle : 0.475 11.922 74438 Z= 0.240 Chirality : 0.041 0.164 8988 Planarity : 0.003 0.048 9730 Dihedral : 3.711 17.669 7784 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.54 % Allowed : 12.33 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.10), residues: 7336 helix: 1.91 (0.08), residues: 4102 sheet: 0.68 (0.15), residues: 1008 loop : 0.44 (0.14), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 9 PHE 0.004 0.001 PHE E 66 TYR 0.007 0.001 TYR C 199 ARG 0.003 0.000 ARG L 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 299 time to evaluate : 5.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 TYR cc_start: 0.8776 (m-80) cc_final: 0.8182 (m-80) REVERT: A 288 MET cc_start: 0.7946 (mmp) cc_final: 0.7742 (mmp) REVERT: A 389 MET cc_start: 0.8606 (tpp) cc_final: 0.8276 (tpp) REVERT: B 219 TYR cc_start: 0.8883 (m-10) cc_final: 0.8344 (m-80) REVERT: C 69 MET cc_start: 0.8716 (mmm) cc_final: 0.8485 (mtp) REVERT: C 193 MET cc_start: 0.8534 (tpp) cc_final: 0.8028 (tpt) REVERT: C 219 TYR cc_start: 0.8832 (m-80) cc_final: 0.8450 (m-80) REVERT: D 193 MET cc_start: 0.8703 (ttm) cc_final: 0.8229 (ttm) REVERT: E 193 MET cc_start: 0.8256 (tpt) cc_final: 0.8049 (tpt) REVERT: E 219 TYR cc_start: 0.8892 (m-10) cc_final: 0.8485 (m-10) REVERT: E 237 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9105 (pp) REVERT: F 104 MET cc_start: 0.8800 (mmm) cc_final: 0.8414 (mmt) REVERT: F 193 MET cc_start: 0.8589 (ttm) cc_final: 0.8242 (ttm) REVERT: F 211 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8855 (tp-100) REVERT: F 219 TYR cc_start: 0.8741 (m-10) cc_final: 0.7990 (m-80) REVERT: G 219 TYR cc_start: 0.8924 (m-10) cc_final: 0.8472 (m-80) REVERT: H 219 TYR cc_start: 0.8907 (m-10) cc_final: 0.8488 (m-80) REVERT: I 193 MET cc_start: 0.8712 (ttm) cc_final: 0.8359 (ttm) REVERT: I 219 TYR cc_start: 0.8878 (m-10) cc_final: 0.8378 (m-80) REVERT: J 193 MET cc_start: 0.8547 (ttm) cc_final: 0.8289 (ttm) REVERT: J 237 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8969 (pp) REVERT: J 490 MET cc_start: 0.9151 (mmm) cc_final: 0.8580 (mpp) REVERT: K 193 MET cc_start: 0.8281 (tpt) cc_final: 0.7996 (tpt) REVERT: K 522 MET cc_start: 0.8198 (mtp) cc_final: 0.7512 (ttt) REVERT: L 61 GLU cc_start: 0.8373 (pp20) cc_final: 0.8072 (pt0) REVERT: L 69 MET cc_start: 0.8382 (mmt) cc_final: 0.7817 (mmt) REVERT: L 211 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8904 (tp-100) REVERT: L 219 TYR cc_start: 0.8759 (m-10) cc_final: 0.7941 (m-80) REVERT: M 193 MET cc_start: 0.8503 (tpt) cc_final: 0.8134 (tpt) REVERT: M 219 TYR cc_start: 0.8936 (m-10) cc_final: 0.8405 (m-80) REVERT: N 193 MET cc_start: 0.8285 (tpt) cc_final: 0.8024 (tpt) REVERT: N 219 TYR cc_start: 0.8876 (m-10) cc_final: 0.8452 (m-80) outliers start: 88 outliers final: 72 residues processed: 366 average time/residue: 0.4883 time to fit residues: 312.2688 Evaluate side-chains 372 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 296 time to evaluate : 4.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 211 GLN Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 245 ARG Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 519 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 288 MET Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain J residue 519 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 519 THR Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 211 GLN Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 245 ARG Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 519 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 0.2980 chunk 691 optimal weight: 7.9990 chunk 422 optimal weight: 6.9990 chunk 328 optimal weight: 0.5980 chunk 480 optimal weight: 0.9990 chunk 725 optimal weight: 9.9990 chunk 667 optimal weight: 1.9990 chunk 577 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 446 optimal weight: 0.1980 chunk 354 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 55146 Z= 0.138 Angle : 0.472 12.574 74438 Z= 0.237 Chirality : 0.041 0.158 8988 Planarity : 0.003 0.049 9730 Dihedral : 3.609 17.443 7784 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.45 % Allowed : 12.45 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.10), residues: 7336 helix: 2.06 (0.08), residues: 4088 sheet: 0.72 (0.15), residues: 1008 loop : 0.33 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 9 PHE 0.006 0.001 PHE L 8 TYR 0.007 0.001 TYR I 199 ARG 0.002 0.000 ARG F 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 300 time to evaluate : 4.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 TYR cc_start: 0.8756 (m-80) cc_final: 0.8255 (m-80) REVERT: A 288 MET cc_start: 0.7903 (mmp) cc_final: 0.7674 (mmp) REVERT: A 389 MET cc_start: 0.8587 (tpp) cc_final: 0.8269 (tpp) REVERT: B 219 TYR cc_start: 0.8876 (m-10) cc_final: 0.8305 (m-80) REVERT: B 237 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8991 (pp) REVERT: C 193 MET cc_start: 0.8541 (tpp) cc_final: 0.7994 (tpt) REVERT: C 219 TYR cc_start: 0.8865 (m-80) cc_final: 0.8551 (m-10) REVERT: D 193 MET cc_start: 0.8740 (ttm) cc_final: 0.8241 (ttm) REVERT: D 490 MET cc_start: 0.9132 (mmm) cc_final: 0.8554 (mpp) REVERT: E 193 MET cc_start: 0.8272 (tpt) cc_final: 0.7909 (tpt) REVERT: E 219 TYR cc_start: 0.8900 (m-80) cc_final: 0.8562 (m-10) REVERT: E 237 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9117 (pp) REVERT: F 69 MET cc_start: 0.8391 (mmm) cc_final: 0.8157 (mtt) REVERT: F 193 MET cc_start: 0.8551 (ttm) cc_final: 0.8299 (ttm) REVERT: F 219 TYR cc_start: 0.8788 (m-10) cc_final: 0.8043 (m-80) REVERT: G 219 TYR cc_start: 0.8906 (m-10) cc_final: 0.8359 (m-80) REVERT: H 219 TYR cc_start: 0.8917 (m-10) cc_final: 0.8471 (m-80) REVERT: I 69 MET cc_start: 0.8248 (mtp) cc_final: 0.7842 (mmt) REVERT: I 193 MET cc_start: 0.8697 (ttm) cc_final: 0.8369 (ttm) REVERT: I 219 TYR cc_start: 0.8878 (m-10) cc_final: 0.8375 (m-80) REVERT: J 193 MET cc_start: 0.8620 (ttm) cc_final: 0.8354 (ttm) REVERT: J 237 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8951 (pp) REVERT: J 490 MET cc_start: 0.9153 (mmm) cc_final: 0.8612 (mpp) REVERT: K 193 MET cc_start: 0.8219 (tpt) cc_final: 0.7862 (tpt) REVERT: L 61 GLU cc_start: 0.8421 (pp20) cc_final: 0.8074 (pt0) REVERT: L 69 MET cc_start: 0.8382 (mmt) cc_final: 0.7694 (mmt) REVERT: L 211 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8915 (tp-100) REVERT: L 219 TYR cc_start: 0.8811 (m-10) cc_final: 0.8070 (m-80) REVERT: M 193 MET cc_start: 0.8522 (tpt) cc_final: 0.8092 (tpt) REVERT: M 219 TYR cc_start: 0.8912 (m-10) cc_final: 0.8373 (m-80) REVERT: N 193 MET cc_start: 0.8264 (tpt) cc_final: 0.7907 (tpt) REVERT: N 219 TYR cc_start: 0.8887 (m-10) cc_final: 0.8149 (m-80) outliers start: 83 outliers final: 70 residues processed: 361 average time/residue: 0.4915 time to fit residues: 310.0373 Evaluate side-chains 371 residues out of total 5726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 297 time to evaluate : 4.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 245 ARG Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 44 PHE Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 519 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 288 MET Chi-restraints excluded: chain J residue 519 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 211 GLN Chi-restraints excluded: chain L residue 519 THR Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 245 ARG Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 519 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 8.9990 chunk 615 optimal weight: 6.9990 chunk 176 optimal weight: 0.0770 chunk 532 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 160 optimal weight: 0.8980 chunk 578 optimal weight: 0.2980 chunk 242 optimal weight: 5.9990 chunk 593 optimal weight: 0.0070 chunk 73 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.089507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.060054 restraints weight = 157252.597| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.87 r_work: 0.3019 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 55146 Z= 0.128 Angle : 0.469 14.166 74438 Z= 0.234 Chirality : 0.041 0.162 8988 Planarity : 0.003 0.050 9730 Dihedral : 3.496 19.987 7784 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.38 % Allowed : 12.52 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.10), residues: 7336 helix: 2.18 (0.08), residues: 4032 sheet: 0.74 (0.16), residues: 1008 loop : 0.19 (0.13), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 9 PHE 0.013 0.001 PHE L 195 TYR 0.006 0.001 TYR C 199 ARG 0.005 0.000 ARG L 368 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7620.72 seconds wall clock time: 137 minutes 8.06 seconds (8228.06 seconds total)