Starting phenix.real_space_refine on Mon Dec 30 00:36:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vb4_43112/12_2024/8vb4_43112.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vb4_43112/12_2024/8vb4_43112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vb4_43112/12_2024/8vb4_43112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vb4_43112/12_2024/8vb4_43112.map" model { file = "/net/cci-nas-00/data/ceres_data/8vb4_43112/12_2024/8vb4_43112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vb4_43112/12_2024/8vb4_43112.cif" } resolution = 2.98 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= 0.007 sd= 0.065 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 264 5.16 5 C 38244 2.51 5 N 10476 2.21 5 O 11364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 264 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: 60348 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3561 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 14, 'TRANS': 454} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 12, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 86 Chain: "M" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1468 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 177} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L, O, N, Q, P, S, R, U, T, W, V, X Time building chain proxies: 11.98, per 1000 atoms: 0.20 Number of scatterers: 60348 At special positions: 0 Unit cell: (196, 194.6, 173.6, 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 264 16.00 O 11364 8.00 N 10476 7.00 C 38244 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.01 Conformation dependent library (CDL) restraints added in 6.3 seconds 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14832 Finding SS restraints... Secondary structure from input PDB file: 360 helices and 72 sheets defined 55.2% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.27 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 removed outlier: 3.837A pdb=" N LEU A 11 " --> pdb=" O THR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 32 removed outlier: 3.913A pdb=" N GLU A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR A 27 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 28 " --> pdb=" O THR A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 37 removed outlier: 4.017A pdb=" N ALA A 37 " --> pdb=" O THR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 42 removed outlier: 3.819A pdb=" N LEU A 41 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG A 42 " --> pdb=" O PRO A 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 38 through 42' Processing helix chain 'A' and resid 55 through 73 removed outlier: 3.637A pdb=" N ALA A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 96 removed outlier: 3.787A pdb=" N LEU A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 114 removed outlier: 4.493A pdb=" N ASN A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 119 removed outlier: 3.696A pdb=" N LEU A 119 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 137 removed outlier: 4.143A pdb=" N GLN A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 262 through 283 removed outlier: 3.762A pdb=" N LEU A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 324 through 343 Processing helix chain 'A' and resid 344 through 347 Processing helix chain 'A' and resid 360 through 375 Processing helix chain 'A' and resid 377 through 398 removed outlier: 4.173A pdb=" N ILE A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix removed outlier: 3.555A pdb=" N HIS A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 removed outlier: 3.902A pdb=" N ILE A 402 " --> pdb=" O ASN A 398 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 441 removed outlier: 3.646A pdb=" N ALA A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 439 " --> pdb=" O GLN A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 464 removed outlier: 3.519A pdb=" N ILE A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 473 through 483 Processing helix chain 'B' and resid 8 through 15 Processing helix chain 'B' and resid 17 through 32 removed outlier: 3.913A pdb=" N GLU B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR B 27 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 28 " --> pdb=" O THR B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 37 removed outlier: 4.017A pdb=" N ALA B 37 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 42 removed outlier: 3.819A pdb=" N LEU B 41 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG B 42 " --> pdb=" O PRO B 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 38 through 42' Processing helix chain 'B' and resid 55 through 73 removed outlier: 3.637A pdb=" N ALA B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 71 " --> pdb=" O LYS B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 96 removed outlier: 3.787A pdb=" N LEU B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 114 removed outlier: 4.493A pdb=" N ASN B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 119 removed outlier: 3.696A pdb=" N LEU B 119 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 137 removed outlier: 4.144A pdb=" N GLN B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 262 through 283 removed outlier: 3.762A pdb=" N LEU B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 324 through 343 removed outlier: 3.500A pdb=" N GLN B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 347 Processing helix chain 'B' and resid 360 through 375 Processing helix chain 'B' and resid 377 through 398 removed outlier: 4.173A pdb=" N ILE B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Proline residue: B 388 - end of helix removed outlier: 3.555A pdb=" N HIS B 391 " --> pdb=" O ILE B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 409 removed outlier: 3.902A pdb=" N ILE B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 441 removed outlier: 3.647A pdb=" N ALA B 433 " --> pdb=" O LYS B 429 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 439 " --> pdb=" O GLN B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 464 removed outlier: 3.519A pdb=" N ILE B 455 " --> pdb=" O ASP B 451 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 473 through 483 Processing helix chain 'C' and resid 8 through 15 Processing helix chain 'C' and resid 17 through 32 removed outlier: 3.913A pdb=" N GLU C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR C 27 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 28 " --> pdb=" O THR C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 37 removed outlier: 4.017A pdb=" N ALA C 37 " --> pdb=" O THR C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 42 removed outlier: 3.819A pdb=" N LEU C 41 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG C 42 " --> pdb=" O PRO C 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 38 through 42' Processing helix chain 'C' and resid 55 through 73 removed outlier: 3.637A pdb=" N ALA C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 71 " --> pdb=" O LYS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 96 removed outlier: 3.787A pdb=" N LEU C 91 " --> pdb=" O ASP C 87 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 114 removed outlier: 4.493A pdb=" N ASN C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 119 removed outlier: 3.696A pdb=" N LEU C 119 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 137 removed outlier: 4.143A pdb=" N GLN C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 183 through 188 Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 262 through 283 removed outlier: 3.762A pdb=" N LEU C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU C 272 " --> pdb=" O LYS C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 324 through 343 Processing helix chain 'C' and resid 344 through 347 Processing helix chain 'C' and resid 360 through 375 Processing helix chain 'C' and resid 377 through 398 removed outlier: 4.173A pdb=" N ILE C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Proline residue: C 388 - end of helix removed outlier: 3.555A pdb=" N HIS C 391 " --> pdb=" O ILE C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 removed outlier: 3.902A pdb=" N ILE C 402 " --> pdb=" O ASN C 398 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 441 removed outlier: 3.647A pdb=" N ALA C 433 " --> pdb=" O LYS C 429 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 439 " --> pdb=" O GLN C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 464 removed outlier: 3.519A pdb=" N ILE C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 470 Processing helix chain 'C' and resid 473 through 483 Processing helix chain 'D' and resid 8 through 15 Processing helix chain 'D' and resid 17 through 32 removed outlier: 3.913A pdb=" N GLU D 25 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR D 27 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA D 28 " --> pdb=" O THR D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 37 removed outlier: 4.017A pdb=" N ALA D 37 " --> pdb=" O THR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 42 removed outlier: 3.819A pdb=" N LEU D 41 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG D 42 " --> pdb=" O PRO D 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 38 through 42' Processing helix chain 'D' and resid 55 through 73 removed outlier: 3.637A pdb=" N ALA D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL D 71 " --> pdb=" O LYS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 96 removed outlier: 3.787A pdb=" N LEU D 91 " --> pdb=" O ASP D 87 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 114 removed outlier: 4.493A pdb=" N ASN D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 119 removed outlier: 3.696A pdb=" N LEU D 119 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 137 removed outlier: 4.143A pdb=" N GLN D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 183 through 188 Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 262 through 283 removed outlier: 3.762A pdb=" N LEU D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU D 272 " --> pdb=" O LYS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 304 Processing helix chain 'D' and resid 324 through 343 Processing helix chain 'D' and resid 344 through 347 Processing helix chain 'D' and resid 360 through 375 Processing helix chain 'D' and resid 377 through 398 removed outlier: 4.173A pdb=" N ILE D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Proline residue: D 388 - end of helix removed outlier: 3.555A pdb=" N HIS D 391 " --> pdb=" O ILE D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 409 removed outlier: 3.902A pdb=" N ILE D 402 " --> pdb=" O ASN D 398 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 441 removed outlier: 3.646A pdb=" N ALA D 433 " --> pdb=" O LYS D 429 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 439 " --> pdb=" O GLN D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 464 removed outlier: 3.519A pdb=" N ILE D 455 " --> pdb=" O ASP D 451 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY D 464 " --> pdb=" O LEU D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 470 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'E' and resid 8 through 15 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.913A pdb=" N GLU E 25 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP E 26 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR E 27 " --> pdb=" O LYS E 23 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA E 28 " --> pdb=" O THR E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 37 removed outlier: 4.017A pdb=" N ALA E 37 " --> pdb=" O THR E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 42 removed outlier: 3.819A pdb=" N LEU E 41 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG E 42 " --> pdb=" O PRO E 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 38 through 42' Processing helix chain 'E' and resid 55 through 73 removed outlier: 3.637A pdb=" N ALA E 69 " --> pdb=" O SER E 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL E 71 " --> pdb=" O LYS E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 96 removed outlier: 3.787A pdb=" N LEU E 91 " --> pdb=" O ASP E 87 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 114 removed outlier: 4.493A pdb=" N ASN E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 119 removed outlier: 3.696A pdb=" N LEU E 119 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 137 removed outlier: 4.144A pdb=" N GLN E 125 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 182 No H-bonds generated for 'chain 'E' and resid 180 through 182' Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'E' and resid 237 through 239 No H-bonds generated for 'chain 'E' and resid 237 through 239' Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 262 through 283 removed outlier: 3.762A pdb=" N LEU E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU E 272 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 304 Processing helix chain 'E' and resid 324 through 343 removed outlier: 3.500A pdb=" N GLN E 333 " --> pdb=" O ILE E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 347 Processing helix chain 'E' and resid 360 through 375 Processing helix chain 'E' and resid 377 through 398 removed outlier: 4.173A pdb=" N ILE E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) Proline residue: E 388 - end of helix removed outlier: 3.555A pdb=" N HIS E 391 " --> pdb=" O ILE E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 409 removed outlier: 3.902A pdb=" N ILE E 402 " --> pdb=" O ASN E 398 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN E 408 " --> pdb=" O GLU E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 441 removed outlier: 3.647A pdb=" N ALA E 433 " --> pdb=" O LYS E 429 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 464 removed outlier: 3.519A pdb=" N ILE E 455 " --> pdb=" O ASP E 451 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR E 461 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY E 464 " --> pdb=" O LEU E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 470 Processing helix chain 'E' and resid 473 through 483 Processing helix chain 'F' and resid 8 through 15 Processing helix chain 'F' and resid 17 through 32 removed outlier: 3.913A pdb=" N GLU F 25 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP F 26 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR F 27 " --> pdb=" O LYS F 23 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA F 28 " --> pdb=" O THR F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 37 removed outlier: 4.017A pdb=" N ALA F 37 " --> pdb=" O THR F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 42 removed outlier: 3.819A pdb=" N LEU F 41 " --> pdb=" O ASP F 38 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG F 42 " --> pdb=" O PRO F 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 38 through 42' Processing helix chain 'F' and resid 55 through 73 removed outlier: 3.637A pdb=" N ALA F 69 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL F 71 " --> pdb=" O LYS F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 96 removed outlier: 3.787A pdb=" N LEU F 91 " --> pdb=" O ASP F 87 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 114 removed outlier: 4.493A pdb=" N ASN F 104 " --> pdb=" O ALA F 100 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 119 removed outlier: 3.696A pdb=" N LEU F 119 " --> pdb=" O ARG F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 137 removed outlier: 4.143A pdb=" N GLN F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 183 through 188 Processing helix chain 'F' and resid 237 through 239 No H-bonds generated for 'chain 'F' and resid 237 through 239' Processing helix chain 'F' and resid 258 through 261 Processing helix chain 'F' and resid 262 through 283 removed outlier: 3.762A pdb=" N LEU F 266 " --> pdb=" O TYR F 262 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU F 272 " --> pdb=" O LYS F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 304 Processing helix chain 'F' and resid 324 through 343 Processing helix chain 'F' and resid 344 through 347 Processing helix chain 'F' and resid 360 through 375 Processing helix chain 'F' and resid 377 through 398 removed outlier: 4.173A pdb=" N ILE F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) Proline residue: F 388 - end of helix removed outlier: 3.555A pdb=" N HIS F 391 " --> pdb=" O ILE F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 409 removed outlier: 3.902A pdb=" N ILE F 402 " --> pdb=" O ASN F 398 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN F 408 " --> pdb=" O GLU F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 441 removed outlier: 3.647A pdb=" N ALA F 433 " --> pdb=" O LYS F 429 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL F 439 " --> pdb=" O GLN F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 464 removed outlier: 3.519A pdb=" N ILE F 455 " --> pdb=" O ASP F 451 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR F 461 " --> pdb=" O ASP F 457 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY F 464 " --> pdb=" O LEU F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 470 Processing helix chain 'F' and resid 473 through 483 Processing helix chain 'G' and resid 8 through 15 Processing helix chain 'G' and resid 17 through 32 removed outlier: 3.913A pdb=" N GLU G 25 " --> pdb=" O ILE G 21 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA G 28 " --> pdb=" O THR G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 37 removed outlier: 4.017A pdb=" N ALA G 37 " --> pdb=" O THR G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 42 removed outlier: 3.819A pdb=" N LEU G 41 " --> pdb=" O ASP G 38 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG G 42 " --> pdb=" O PRO G 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 38 through 42' Processing helix chain 'G' and resid 55 through 73 removed outlier: 3.637A pdb=" N ALA G 69 " --> pdb=" O SER G 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN G 70 " --> pdb=" O ALA G 66 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL G 71 " --> pdb=" O LYS G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 96 removed outlier: 3.787A pdb=" N LEU G 91 " --> pdb=" O ASP G 87 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 114 removed outlier: 4.493A pdb=" N ASN G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE G 114 " --> pdb=" O GLU G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 119 removed outlier: 3.696A pdb=" N LEU G 119 " --> pdb=" O ARG G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 137 removed outlier: 4.143A pdb=" N GLN G 125 " --> pdb=" O SER G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 182 No H-bonds generated for 'chain 'G' and resid 180 through 182' Processing helix chain 'G' and resid 183 through 188 Processing helix chain 'G' and resid 237 through 239 No H-bonds generated for 'chain 'G' and resid 237 through 239' Processing helix chain 'G' and resid 258 through 261 Processing helix chain 'G' and resid 262 through 283 removed outlier: 3.762A pdb=" N LEU G 266 " --> pdb=" O TYR G 262 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA G 271 " --> pdb=" O ALA G 267 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU G 272 " --> pdb=" O LYS G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 304 Processing helix chain 'G' and resid 324 through 343 Processing helix chain 'G' and resid 344 through 347 Processing helix chain 'G' and resid 360 through 375 Processing helix chain 'G' and resid 377 through 398 removed outlier: 4.173A pdb=" N ILE G 387 " --> pdb=" O ASP G 383 " (cutoff:3.500A) Proline residue: G 388 - end of helix removed outlier: 3.555A pdb=" N HIS G 391 " --> pdb=" O ILE G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 398 through 409 removed outlier: 3.902A pdb=" N ILE G 402 " --> pdb=" O ASN G 398 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN G 408 " --> pdb=" O GLU G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 441 removed outlier: 3.646A pdb=" N ALA G 433 " --> pdb=" O LYS G 429 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL G 439 " --> pdb=" O GLN G 435 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 464 removed outlier: 3.519A pdb=" N ILE G 455 " --> pdb=" O ASP G 451 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR G 461 " --> pdb=" O ASP G 457 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY G 464 " --> pdb=" O LEU G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 466 through 470 Processing helix chain 'G' and resid 473 through 483 Processing helix chain 'H' and resid 8 through 15 Processing helix chain 'H' and resid 17 through 32 removed outlier: 3.913A pdb=" N GLU H 25 " --> pdb=" O ILE H 21 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP H 26 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR H 27 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA H 28 " --> pdb=" O THR H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 37 removed outlier: 4.017A pdb=" N ALA H 37 " --> pdb=" O THR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 42 removed outlier: 3.819A pdb=" N LEU H 41 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG H 42 " --> pdb=" O PRO H 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 38 through 42' Processing helix chain 'H' and resid 55 through 73 removed outlier: 3.637A pdb=" N ALA H 69 " --> pdb=" O SER H 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL H 71 " --> pdb=" O LYS H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 96 removed outlier: 3.787A pdb=" N LEU H 91 " --> pdb=" O ASP H 87 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 114 removed outlier: 4.493A pdb=" N ASN H 104 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 119 removed outlier: 3.696A pdb=" N LEU H 119 " --> pdb=" O ARG H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 137 removed outlier: 4.144A pdb=" N GLN H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 182 No H-bonds generated for 'chain 'H' and resid 180 through 182' Processing helix chain 'H' and resid 183 through 188 Processing helix chain 'H' and resid 237 through 239 No H-bonds generated for 'chain 'H' and resid 237 through 239' Processing helix chain 'H' and resid 258 through 261 Processing helix chain 'H' and resid 262 through 283 removed outlier: 3.762A pdb=" N LEU H 266 " --> pdb=" O TYR H 262 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA H 271 " --> pdb=" O ALA H 267 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU H 272 " --> pdb=" O LYS H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 304 Processing helix chain 'H' and resid 324 through 343 removed outlier: 3.500A pdb=" N GLN H 333 " --> pdb=" O ILE H 329 " (cutoff:3.500A) Processing helix chain 'H' and resid 344 through 347 Processing helix chain 'H' and resid 360 through 375 Processing helix chain 'H' and resid 377 through 398 removed outlier: 4.173A pdb=" N ILE H 387 " --> pdb=" O ASP H 383 " (cutoff:3.500A) Proline residue: H 388 - end of helix removed outlier: 3.555A pdb=" N HIS H 391 " --> pdb=" O ILE H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 398 through 409 removed outlier: 3.902A pdb=" N ILE H 402 " --> pdb=" O ASN H 398 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN H 408 " --> pdb=" O GLU H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 426 through 441 removed outlier: 3.647A pdb=" N ALA H 433 " --> pdb=" O LYS H 429 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL H 439 " --> pdb=" O GLN H 435 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 464 removed outlier: 3.519A pdb=" N ILE H 455 " --> pdb=" O ASP H 451 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR H 461 " --> pdb=" O ASP H 457 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY H 464 " --> pdb=" O LEU H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 466 through 470 Processing helix chain 'H' and resid 473 through 483 Processing helix chain 'I' and resid 8 through 15 Processing helix chain 'I' and resid 17 through 32 removed outlier: 3.913A pdb=" N GLU I 25 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP I 26 " --> pdb=" O LEU I 22 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR I 27 " --> pdb=" O LYS I 23 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA I 28 " --> pdb=" O THR I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 37 removed outlier: 4.017A pdb=" N ALA I 37 " --> pdb=" O THR I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 42 removed outlier: 3.819A pdb=" N LEU I 41 " --> pdb=" O ASP I 38 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG I 42 " --> pdb=" O PRO I 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 38 through 42' Processing helix chain 'I' and resid 55 through 73 removed outlier: 3.637A pdb=" N ALA I 69 " --> pdb=" O SER I 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN I 70 " --> pdb=" O ALA I 66 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL I 71 " --> pdb=" O LYS I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 96 removed outlier: 3.787A pdb=" N LEU I 91 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 114 removed outlier: 4.493A pdb=" N ASN I 104 " --> pdb=" O ALA I 100 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE I 114 " --> pdb=" O GLU I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 119 removed outlier: 3.696A pdb=" N LEU I 119 " --> pdb=" O ARG I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 137 removed outlier: 4.143A pdb=" N GLN I 125 " --> pdb=" O SER I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 182 No H-bonds generated for 'chain 'I' and resid 180 through 182' Processing helix chain 'I' and resid 183 through 188 Processing helix chain 'I' and resid 237 through 239 No H-bonds generated for 'chain 'I' and resid 237 through 239' Processing helix chain 'I' and resid 258 through 261 Processing helix chain 'I' and resid 262 through 283 removed outlier: 3.762A pdb=" N LEU I 266 " --> pdb=" O TYR I 262 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA I 271 " --> pdb=" O ALA I 267 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU I 272 " --> pdb=" O LYS I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 304 Processing helix chain 'I' and resid 324 through 343 Processing helix chain 'I' and resid 344 through 347 Processing helix chain 'I' and resid 360 through 375 Processing helix chain 'I' and resid 377 through 398 removed outlier: 4.173A pdb=" N ILE I 387 " --> pdb=" O ASP I 383 " (cutoff:3.500A) Proline residue: I 388 - end of helix removed outlier: 3.555A pdb=" N HIS I 391 " --> pdb=" O ILE I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 removed outlier: 3.902A pdb=" N ILE I 402 " --> pdb=" O ASN I 398 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN I 408 " --> pdb=" O GLU I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 426 through 441 removed outlier: 3.647A pdb=" N ALA I 433 " --> pdb=" O LYS I 429 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL I 439 " --> pdb=" O GLN I 435 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 464 removed outlier: 3.519A pdb=" N ILE I 455 " --> pdb=" O ASP I 451 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR I 461 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY I 464 " --> pdb=" O LEU I 460 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 470 Processing helix chain 'I' and resid 473 through 483 Processing helix chain 'J' and resid 8 through 15 Processing helix chain 'J' and resid 17 through 32 removed outlier: 3.913A pdb=" N GLU J 25 " --> pdb=" O ILE J 21 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP J 26 " --> pdb=" O LEU J 22 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR J 27 " --> pdb=" O LYS J 23 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA J 28 " --> pdb=" O THR J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 37 removed outlier: 4.017A pdb=" N ALA J 37 " --> pdb=" O THR J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 42 removed outlier: 3.819A pdb=" N LEU J 41 " --> pdb=" O ASP J 38 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG J 42 " --> pdb=" O PRO J 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 38 through 42' Processing helix chain 'J' and resid 55 through 73 removed outlier: 3.637A pdb=" N ALA J 69 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL J 71 " --> pdb=" O LYS J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 96 removed outlier: 3.787A pdb=" N LEU J 91 " --> pdb=" O ASP J 87 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET J 95 " --> pdb=" O LEU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 114 removed outlier: 4.493A pdb=" N ASN J 104 " --> pdb=" O ALA J 100 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE J 114 " --> pdb=" O GLU J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 119 removed outlier: 3.696A pdb=" N LEU J 119 " --> pdb=" O ARG J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 137 removed outlier: 4.143A pdb=" N GLN J 125 " --> pdb=" O SER J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 182 No H-bonds generated for 'chain 'J' and resid 180 through 182' Processing helix chain 'J' and resid 183 through 188 Processing helix chain 'J' and resid 237 through 239 No H-bonds generated for 'chain 'J' and resid 237 through 239' Processing helix chain 'J' and resid 258 through 261 Processing helix chain 'J' and resid 262 through 283 removed outlier: 3.762A pdb=" N LEU J 266 " --> pdb=" O TYR J 262 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA J 271 " --> pdb=" O ALA J 267 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU J 272 " --> pdb=" O LYS J 268 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 304 Processing helix chain 'J' and resid 324 through 343 Processing helix chain 'J' and resid 344 through 347 Processing helix chain 'J' and resid 360 through 375 Processing helix chain 'J' and resid 377 through 398 removed outlier: 4.173A pdb=" N ILE J 387 " --> pdb=" O ASP J 383 " (cutoff:3.500A) Proline residue: J 388 - end of helix removed outlier: 3.555A pdb=" N HIS J 391 " --> pdb=" O ILE J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 398 through 409 removed outlier: 3.902A pdb=" N ILE J 402 " --> pdb=" O ASN J 398 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN J 408 " --> pdb=" O GLU J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 426 through 441 removed outlier: 3.646A pdb=" N ALA J 433 " --> pdb=" O LYS J 429 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL J 439 " --> pdb=" O GLN J 435 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 464 removed outlier: 3.519A pdb=" N ILE J 455 " --> pdb=" O ASP J 451 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR J 461 " --> pdb=" O ASP J 457 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY J 464 " --> pdb=" O LEU J 460 " (cutoff:3.500A) Processing helix chain 'J' and resid 466 through 470 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'K' and resid 8 through 15 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.913A pdb=" N GLU K 25 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP K 26 " --> pdb=" O LEU K 22 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR K 27 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA K 28 " --> pdb=" O THR K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 37 removed outlier: 4.017A pdb=" N ALA K 37 " --> pdb=" O THR K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 42 removed outlier: 3.819A pdb=" N LEU K 41 " --> pdb=" O ASP K 38 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG K 42 " --> pdb=" O PRO K 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 38 through 42' Processing helix chain 'K' and resid 55 through 73 removed outlier: 3.637A pdb=" N ALA K 69 " --> pdb=" O SER K 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN K 70 " --> pdb=" O ALA K 66 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL K 71 " --> pdb=" O LYS K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 96 removed outlier: 3.787A pdb=" N LEU K 91 " --> pdb=" O ASP K 87 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET K 95 " --> pdb=" O LEU K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 114 removed outlier: 4.493A pdb=" N ASN K 104 " --> pdb=" O ALA K 100 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 119 removed outlier: 3.696A pdb=" N LEU K 119 " --> pdb=" O ARG K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 137 removed outlier: 4.144A pdb=" N GLN K 125 " --> pdb=" O SER K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 182 No H-bonds generated for 'chain 'K' and resid 180 through 182' Processing helix chain 'K' and resid 183 through 188 Processing helix chain 'K' and resid 237 through 239 No H-bonds generated for 'chain 'K' and resid 237 through 239' Processing helix chain 'K' and resid 258 through 261 Processing helix chain 'K' and resid 262 through 283 removed outlier: 3.762A pdb=" N LEU K 266 " --> pdb=" O TYR K 262 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA K 271 " --> pdb=" O ALA K 267 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU K 272 " --> pdb=" O LYS K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 304 Processing helix chain 'K' and resid 324 through 343 removed outlier: 3.500A pdb=" N GLN K 333 " --> pdb=" O ILE K 329 " (cutoff:3.500A) Processing helix chain 'K' and resid 344 through 347 Processing helix chain 'K' and resid 360 through 375 Processing helix chain 'K' and resid 377 through 398 removed outlier: 4.173A pdb=" N ILE K 387 " --> pdb=" O ASP K 383 " (cutoff:3.500A) Proline residue: K 388 - end of helix removed outlier: 3.555A pdb=" N HIS K 391 " --> pdb=" O ILE K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 398 through 409 removed outlier: 3.902A pdb=" N ILE K 402 " --> pdb=" O ASN K 398 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN K 408 " --> pdb=" O GLU K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 426 through 441 removed outlier: 3.647A pdb=" N ALA K 433 " --> pdb=" O LYS K 429 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL K 439 " --> pdb=" O GLN K 435 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 464 removed outlier: 3.519A pdb=" N ILE K 455 " --> pdb=" O ASP K 451 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR K 461 " --> pdb=" O ASP K 457 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY K 464 " --> pdb=" O LEU K 460 " (cutoff:3.500A) Processing helix chain 'K' and resid 466 through 470 Processing helix chain 'K' and resid 473 through 483 Processing helix chain 'L' and resid 8 through 15 Processing helix chain 'L' and resid 17 through 32 removed outlier: 3.913A pdb=" N GLU L 25 " --> pdb=" O ILE L 21 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP L 26 " --> pdb=" O LEU L 22 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR L 27 " --> pdb=" O LYS L 23 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA L 28 " --> pdb=" O THR L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 33 through 37 removed outlier: 4.017A pdb=" N ALA L 37 " --> pdb=" O THR L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 42 removed outlier: 3.819A pdb=" N LEU L 41 " --> pdb=" O ASP L 38 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG L 42 " --> pdb=" O PRO L 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 38 through 42' Processing helix chain 'L' and resid 55 through 73 removed outlier: 3.637A pdb=" N ALA L 69 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN L 70 " --> pdb=" O ALA L 66 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL L 71 " --> pdb=" O LYS L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 96 removed outlier: 3.787A pdb=" N LEU L 91 " --> pdb=" O ASP L 87 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET L 95 " --> pdb=" O LEU L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 114 removed outlier: 4.493A pdb=" N ASN L 104 " --> pdb=" O ALA L 100 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE L 114 " --> pdb=" O GLU L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 119 removed outlier: 3.696A pdb=" N LEU L 119 " --> pdb=" O ARG L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 137 removed outlier: 4.143A pdb=" N GLN L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 182 No H-bonds generated for 'chain 'L' and resid 180 through 182' Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'L' and resid 237 through 239 No H-bonds generated for 'chain 'L' and resid 237 through 239' Processing helix chain 'L' and resid 258 through 261 Processing helix chain 'L' and resid 262 through 283 removed outlier: 3.762A pdb=" N LEU L 266 " --> pdb=" O TYR L 262 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA L 271 " --> pdb=" O ALA L 267 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU L 272 " --> pdb=" O LYS L 268 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 304 Processing helix chain 'L' and resid 324 through 343 Processing helix chain 'L' and resid 344 through 347 Processing helix chain 'L' and resid 360 through 375 Processing helix chain 'L' and resid 377 through 398 removed outlier: 4.173A pdb=" N ILE L 387 " --> pdb=" O ASP L 383 " (cutoff:3.500A) Proline residue: L 388 - end of helix removed outlier: 3.555A pdb=" N HIS L 391 " --> pdb=" O ILE L 387 " (cutoff:3.500A) Processing helix chain 'L' and resid 398 through 409 removed outlier: 3.902A pdb=" N ILE L 402 " --> pdb=" O ASN L 398 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN L 408 " --> pdb=" O GLU L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 441 removed outlier: 3.647A pdb=" N ALA L 433 " --> pdb=" O LYS L 429 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL L 439 " --> pdb=" O GLN L 435 " (cutoff:3.500A) Processing helix chain 'L' and resid 451 through 464 removed outlier: 3.519A pdb=" N ILE L 455 " --> pdb=" O ASP L 451 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR L 461 " --> pdb=" O ASP L 457 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY L 464 " --> pdb=" O LEU L 460 " (cutoff:3.500A) Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 473 through 483 Processing helix chain 'M' and resid 2 through 15 Processing helix chain 'M' and resid 26 through 44 removed outlier: 4.187A pdb=" N ALA M 30 " --> pdb=" O HIS M 26 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU M 31 " --> pdb=" O PRO M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 118 through 139 removed outlier: 3.610A pdb=" N GLY M 136 " --> pdb=" O ALA M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 167 removed outlier: 3.898A pdb=" N LEU M 147 " --> pdb=" O SER M 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU M 149 " --> pdb=" O GLN M 145 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS M 167 " --> pdb=" O MET M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 172 removed outlier: 3.902A pdb=" N ARG M 172 " --> pdb=" O SER M 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 169 through 172' Processing helix chain 'M' and resid 173 through 183 removed outlier: 3.586A pdb=" N GLY M 177 " --> pdb=" O ARG M 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 15 Processing helix chain 'N' and resid 26 through 44 removed outlier: 4.187A pdb=" N ALA N 30 " --> pdb=" O HIS N 26 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU N 31 " --> pdb=" O PRO N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 139 removed outlier: 3.610A pdb=" N GLY N 136 " --> pdb=" O ALA N 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 167 removed outlier: 3.898A pdb=" N LEU N 147 " --> pdb=" O SER N 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU N 149 " --> pdb=" O GLN N 145 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS N 167 " --> pdb=" O MET N 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 169 through 172 removed outlier: 3.901A pdb=" N ARG N 172 " --> pdb=" O SER N 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 169 through 172' Processing helix chain 'N' and resid 173 through 183 removed outlier: 3.586A pdb=" N GLY N 177 " --> pdb=" O ARG N 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 15 Processing helix chain 'O' and resid 26 through 44 removed outlier: 4.187A pdb=" N ALA O 30 " --> pdb=" O HIS O 26 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU O 31 " --> pdb=" O PRO O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 139 removed outlier: 3.610A pdb=" N GLY O 136 " --> pdb=" O ALA O 132 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 167 removed outlier: 3.898A pdb=" N LEU O 147 " --> pdb=" O SER O 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU O 149 " --> pdb=" O GLN O 145 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS O 167 " --> pdb=" O MET O 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 169 through 172 removed outlier: 3.901A pdb=" N ARG O 172 " --> pdb=" O SER O 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 169 through 172' Processing helix chain 'O' and resid 173 through 183 removed outlier: 3.586A pdb=" N GLY O 177 " --> pdb=" O ARG O 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 15 Processing helix chain 'P' and resid 26 through 44 removed outlier: 4.187A pdb=" N ALA P 30 " --> pdb=" O HIS P 26 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU P 31 " --> pdb=" O PRO P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 139 removed outlier: 3.610A pdb=" N GLY P 136 " --> pdb=" O ALA P 132 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 167 removed outlier: 3.898A pdb=" N LEU P 147 " --> pdb=" O SER P 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU P 149 " --> pdb=" O GLN P 145 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS P 167 " --> pdb=" O MET P 163 " (cutoff:3.500A) Processing helix chain 'P' and resid 169 through 172 removed outlier: 3.902A pdb=" N ARG P 172 " --> pdb=" O SER P 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 169 through 172' Processing helix chain 'P' and resid 173 through 183 removed outlier: 3.586A pdb=" N GLY P 177 " --> pdb=" O ARG P 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 15 Processing helix chain 'Q' and resid 26 through 44 removed outlier: 4.187A pdb=" N ALA Q 30 " --> pdb=" O HIS Q 26 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU Q 31 " --> pdb=" O PRO Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 118 through 139 removed outlier: 3.610A pdb=" N GLY Q 136 " --> pdb=" O ALA Q 132 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 167 removed outlier: 3.898A pdb=" N LEU Q 147 " --> pdb=" O SER Q 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU Q 149 " --> pdb=" O GLN Q 145 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS Q 167 " --> pdb=" O MET Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 169 through 172 removed outlier: 3.901A pdb=" N ARG Q 172 " --> pdb=" O SER Q 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 169 through 172' Processing helix chain 'Q' and resid 173 through 183 removed outlier: 3.586A pdb=" N GLY Q 177 " --> pdb=" O ARG Q 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 15 Processing helix chain 'R' and resid 26 through 44 removed outlier: 4.187A pdb=" N ALA R 30 " --> pdb=" O HIS R 26 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU R 31 " --> pdb=" O PRO R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 139 removed outlier: 3.610A pdb=" N GLY R 136 " --> pdb=" O ALA R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 167 removed outlier: 3.898A pdb=" N LEU R 147 " --> pdb=" O SER R 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU R 149 " --> pdb=" O GLN R 145 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS R 167 " --> pdb=" O MET R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 172 removed outlier: 3.901A pdb=" N ARG R 172 " --> pdb=" O SER R 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 169 through 172' Processing helix chain 'R' and resid 173 through 183 removed outlier: 3.586A pdb=" N GLY R 177 " --> pdb=" O ARG R 173 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 15 Processing helix chain 'S' and resid 26 through 44 removed outlier: 4.187A pdb=" N ALA S 30 " --> pdb=" O HIS S 26 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU S 31 " --> pdb=" O PRO S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 118 through 139 removed outlier: 3.610A pdb=" N GLY S 136 " --> pdb=" O ALA S 132 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 167 removed outlier: 3.898A pdb=" N LEU S 147 " --> pdb=" O SER S 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU S 149 " --> pdb=" O GLN S 145 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS S 167 " --> pdb=" O MET S 163 " (cutoff:3.500A) Processing helix chain 'S' and resid 169 through 172 removed outlier: 3.902A pdb=" N ARG S 172 " --> pdb=" O SER S 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 169 through 172' Processing helix chain 'S' and resid 173 through 183 removed outlier: 3.586A pdb=" N GLY S 177 " --> pdb=" O ARG S 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 15 Processing helix chain 'T' and resid 26 through 44 removed outlier: 4.187A pdb=" N ALA T 30 " --> pdb=" O HIS T 26 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU T 31 " --> pdb=" O PRO T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 118 through 139 removed outlier: 3.610A pdb=" N GLY T 136 " --> pdb=" O ALA T 132 " (cutoff:3.500A) Processing helix chain 'T' and resid 143 through 167 removed outlier: 3.898A pdb=" N LEU T 147 " --> pdb=" O SER T 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU T 149 " --> pdb=" O GLN T 145 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS T 167 " --> pdb=" O MET T 163 " (cutoff:3.500A) Processing helix chain 'T' and resid 169 through 172 removed outlier: 3.901A pdb=" N ARG T 172 " --> pdb=" O SER T 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 169 through 172' Processing helix chain 'T' and resid 173 through 183 removed outlier: 3.586A pdb=" N GLY T 177 " --> pdb=" O ARG T 173 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 15 Processing helix chain 'U' and resid 26 through 44 removed outlier: 4.187A pdb=" N ALA U 30 " --> pdb=" O HIS U 26 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU U 31 " --> pdb=" O PRO U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 118 through 139 removed outlier: 3.610A pdb=" N GLY U 136 " --> pdb=" O ALA U 132 " (cutoff:3.500A) Processing helix chain 'U' and resid 143 through 167 removed outlier: 3.898A pdb=" N LEU U 147 " --> pdb=" O SER U 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU U 149 " --> pdb=" O GLN U 145 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS U 167 " --> pdb=" O MET U 163 " (cutoff:3.500A) Processing helix chain 'U' and resid 169 through 172 removed outlier: 3.901A pdb=" N ARG U 172 " --> pdb=" O SER U 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 169 through 172' Processing helix chain 'U' and resid 173 through 183 removed outlier: 3.586A pdb=" N GLY U 177 " --> pdb=" O ARG U 173 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 15 Processing helix chain 'V' and resid 26 through 44 removed outlier: 4.187A pdb=" N ALA V 30 " --> pdb=" O HIS V 26 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU V 31 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing helix chain 'V' and resid 118 through 139 removed outlier: 3.610A pdb=" N GLY V 136 " --> pdb=" O ALA V 132 " (cutoff:3.500A) Processing helix chain 'V' and resid 143 through 167 removed outlier: 3.898A pdb=" N LEU V 147 " --> pdb=" O SER V 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU V 149 " --> pdb=" O GLN V 145 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS V 167 " --> pdb=" O MET V 163 " (cutoff:3.500A) Processing helix chain 'V' and resid 169 through 172 removed outlier: 3.902A pdb=" N ARG V 172 " --> pdb=" O SER V 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 169 through 172' Processing helix chain 'V' and resid 173 through 183 removed outlier: 3.586A pdb=" N GLY V 177 " --> pdb=" O ARG V 173 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 15 Processing helix chain 'W' and resid 26 through 44 removed outlier: 4.187A pdb=" N ALA W 30 " --> pdb=" O HIS W 26 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU W 31 " --> pdb=" O PRO W 27 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 139 removed outlier: 3.610A pdb=" N GLY W 136 " --> pdb=" O ALA W 132 " (cutoff:3.500A) Processing helix chain 'W' and resid 143 through 167 removed outlier: 3.898A pdb=" N LEU W 147 " --> pdb=" O SER W 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU W 149 " --> pdb=" O GLN W 145 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS W 167 " --> pdb=" O MET W 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 169 through 172 removed outlier: 3.901A pdb=" N ARG W 172 " --> pdb=" O SER W 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 169 through 172' Processing helix chain 'W' and resid 173 through 183 removed outlier: 3.586A pdb=" N GLY W 177 " --> pdb=" O ARG W 173 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 15 Processing helix chain 'X' and resid 26 through 44 removed outlier: 4.187A pdb=" N ALA X 30 " --> pdb=" O HIS X 26 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU X 31 " --> pdb=" O PRO X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 118 through 139 removed outlier: 3.610A pdb=" N GLY X 136 " --> pdb=" O ALA X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 167 removed outlier: 3.898A pdb=" N LEU X 147 " --> pdb=" O SER X 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU X 149 " --> pdb=" O GLN X 145 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS X 167 " --> pdb=" O MET X 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 169 through 172 removed outlier: 3.901A pdb=" N ARG X 172 " --> pdb=" O SER X 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 169 through 172' Processing helix chain 'X' and resid 173 through 183 removed outlier: 3.586A pdb=" N GLY X 177 " --> pdb=" O ARG X 173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 82 removed outlier: 4.034A pdb=" N ARG A 81 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 153 removed outlier: 3.723A pdb=" N VAL A 139 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 162 removed outlier: 6.921A pdb=" N SER A 159 " --> pdb=" O MET A 171 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N MET A 171 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU A 161 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU A 169 " --> pdb=" O ARG A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 319 Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 311 removed outlier: 7.144A pdb=" N VAL A 310 " --> pdb=" O ALA L 290 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 81 through 82 removed outlier: 4.034A pdb=" N ARG B 81 " --> pdb=" O LEU B 415 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 150 through 153 removed outlier: 3.724A pdb=" N VAL B 139 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 158 through 162 removed outlier: 6.921A pdb=" N SER B 159 " --> pdb=" O MET B 171 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N MET B 171 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU B 161 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU B 169 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 317 through 319 Processing sheet with id=AB1, first strand: chain 'C' and resid 81 through 82 removed outlier: 4.034A pdb=" N ARG C 81 " --> pdb=" O LEU C 415 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 150 through 153 removed outlier: 3.724A pdb=" N VAL C 139 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 158 through 162 removed outlier: 6.921A pdb=" N SER C 159 " --> pdb=" O MET C 171 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N MET C 171 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU C 161 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU C 169 " --> pdb=" O ARG C 207 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 317 through 319 Processing sheet with id=AB5, first strand: chain 'D' and resid 81 through 82 removed outlier: 4.034A pdb=" N ARG D 81 " --> pdb=" O LEU D 415 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 150 through 153 removed outlier: 3.723A pdb=" N VAL D 139 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 158 through 162 removed outlier: 6.921A pdb=" N SER D 159 " --> pdb=" O MET D 171 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N MET D 171 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU D 161 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU D 169 " --> pdb=" O ARG D 207 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 317 through 319 Processing sheet with id=AB9, first strand: chain 'E' and resid 81 through 82 removed outlier: 4.034A pdb=" N ARG E 81 " --> pdb=" O LEU E 415 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 150 through 153 removed outlier: 3.724A pdb=" N VAL E 139 " --> pdb=" O ALA E 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 158 through 162 removed outlier: 6.921A pdb=" N SER E 159 " --> pdb=" O MET E 171 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N MET E 171 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU E 161 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU E 169 " --> pdb=" O ARG E 207 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 317 through 319 Processing sheet with id=AC4, first strand: chain 'F' and resid 81 through 82 removed outlier: 4.034A pdb=" N ARG F 81 " --> pdb=" O LEU F 415 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 150 through 153 removed outlier: 3.724A pdb=" N VAL F 139 " --> pdb=" O ALA F 244 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 158 through 162 removed outlier: 6.921A pdb=" N SER F 159 " --> pdb=" O MET F 171 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N MET F 171 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU F 161 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU F 169 " --> pdb=" O ARG F 207 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 317 through 319 Processing sheet with id=AC8, first strand: chain 'G' and resid 81 through 82 removed outlier: 4.034A pdb=" N ARG G 81 " --> pdb=" O LEU G 415 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 150 through 153 removed outlier: 3.723A pdb=" N VAL G 139 " --> pdb=" O ALA G 244 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 158 through 162 removed outlier: 6.921A pdb=" N SER G 159 " --> pdb=" O MET G 171 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N MET G 171 " --> pdb=" O SER G 159 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU G 161 " --> pdb=" O LEU G 169 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU G 169 " --> pdb=" O ARG G 207 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 317 through 319 Processing sheet with id=AD3, first strand: chain 'H' and resid 81 through 82 removed outlier: 4.034A pdb=" N ARG H 81 " --> pdb=" O LEU H 415 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 150 through 153 removed outlier: 3.724A pdb=" N VAL H 139 " --> pdb=" O ALA H 244 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 158 through 162 removed outlier: 6.921A pdb=" N SER H 159 " --> pdb=" O MET H 171 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N MET H 171 " --> pdb=" O SER H 159 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU H 161 " --> pdb=" O LEU H 169 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU H 169 " --> pdb=" O ARG H 207 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 317 through 319 Processing sheet with id=AD7, first strand: chain 'I' and resid 81 through 82 removed outlier: 4.034A pdb=" N ARG I 81 " --> pdb=" O LEU I 415 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 150 through 153 removed outlier: 3.724A pdb=" N VAL I 139 " --> pdb=" O ALA I 244 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 158 through 162 removed outlier: 6.921A pdb=" N SER I 159 " --> pdb=" O MET I 171 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N MET I 171 " --> pdb=" O SER I 159 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU I 161 " --> pdb=" O LEU I 169 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU I 169 " --> pdb=" O ARG I 207 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 317 through 319 Processing sheet with id=AE2, first strand: chain 'J' and resid 81 through 82 removed outlier: 4.034A pdb=" N ARG J 81 " --> pdb=" O LEU J 415 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 150 through 153 removed outlier: 3.723A pdb=" N VAL J 139 " --> pdb=" O ALA J 244 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 158 through 162 removed outlier: 6.921A pdb=" N SER J 159 " --> pdb=" O MET J 171 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N MET J 171 " --> pdb=" O SER J 159 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU J 161 " --> pdb=" O LEU J 169 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU J 169 " --> pdb=" O ARG J 207 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 317 through 319 Processing sheet with id=AE6, first strand: chain 'K' and resid 81 through 82 removed outlier: 4.034A pdb=" N ARG K 81 " --> pdb=" O LEU K 415 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 150 through 153 removed outlier: 3.724A pdb=" N VAL K 139 " --> pdb=" O ALA K 244 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 158 through 162 removed outlier: 6.921A pdb=" N SER K 159 " --> pdb=" O MET K 171 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N MET K 171 " --> pdb=" O SER K 159 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU K 161 " --> pdb=" O LEU K 169 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU K 169 " --> pdb=" O ARG K 207 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 317 through 319 Processing sheet with id=AF1, first strand: chain 'L' and resid 81 through 82 removed outlier: 4.034A pdb=" N ARG L 81 " --> pdb=" O LEU L 415 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 150 through 153 removed outlier: 3.724A pdb=" N VAL L 139 " --> pdb=" O ALA L 244 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 158 through 162 removed outlier: 6.921A pdb=" N SER L 159 " --> pdb=" O MET L 171 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N MET L 171 " --> pdb=" O SER L 159 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU L 161 " --> pdb=" O LEU L 169 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU L 169 " --> pdb=" O ARG L 207 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 52 through 57 removed outlier: 3.640A pdb=" N GLN M 53 " --> pdb=" O VAL M 108 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU M 55 " --> pdb=" O ILE M 106 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N CYS M 105 " --> pdb=" O SER M 76 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N SER M 76 " --> pdb=" O CYS M 105 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG M 107 " --> pdb=" O VAL M 74 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL M 74 " --> pdb=" O ARG M 107 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR M 109 " --> pdb=" O ILE M 72 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 83 through 86 Processing sheet with id=AF6, first strand: chain 'N' and resid 52 through 57 removed outlier: 3.640A pdb=" N GLN N 53 " --> pdb=" O VAL N 108 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU N 55 " --> pdb=" O ILE N 106 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N CYS N 105 " --> pdb=" O SER N 76 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N SER N 76 " --> pdb=" O CYS N 105 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG N 107 " --> pdb=" O VAL N 74 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL N 74 " --> pdb=" O ARG N 107 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR N 109 " --> pdb=" O ILE N 72 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 83 through 86 Processing sheet with id=AF8, first strand: chain 'O' and resid 52 through 57 removed outlier: 3.640A pdb=" N GLN O 53 " --> pdb=" O VAL O 108 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU O 55 " --> pdb=" O ILE O 106 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N CYS O 105 " --> pdb=" O SER O 76 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N SER O 76 " --> pdb=" O CYS O 105 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG O 107 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL O 74 " --> pdb=" O ARG O 107 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR O 109 " --> pdb=" O ILE O 72 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 83 through 86 Processing sheet with id=AG1, first strand: chain 'P' and resid 52 through 57 removed outlier: 3.640A pdb=" N GLN P 53 " --> pdb=" O VAL P 108 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU P 55 " --> pdb=" O ILE P 106 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N CYS P 105 " --> pdb=" O SER P 76 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N SER P 76 " --> pdb=" O CYS P 105 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG P 107 " --> pdb=" O VAL P 74 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL P 74 " --> pdb=" O ARG P 107 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR P 109 " --> pdb=" O ILE P 72 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P' and resid 83 through 86 Processing sheet with id=AG3, first strand: chain 'Q' and resid 52 through 57 removed outlier: 3.640A pdb=" N GLN Q 53 " --> pdb=" O VAL Q 108 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU Q 55 " --> pdb=" O ILE Q 106 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N CYS Q 105 " --> pdb=" O SER Q 76 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N SER Q 76 " --> pdb=" O CYS Q 105 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG Q 107 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL Q 74 " --> pdb=" O ARG Q 107 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR Q 109 " --> pdb=" O ILE Q 72 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Q' and resid 83 through 86 Processing sheet with id=AG5, first strand: chain 'R' and resid 52 through 57 removed outlier: 3.640A pdb=" N GLN R 53 " --> pdb=" O VAL R 108 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU R 55 " --> pdb=" O ILE R 106 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N CYS R 105 " --> pdb=" O SER R 76 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N SER R 76 " --> pdb=" O CYS R 105 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG R 107 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL R 74 " --> pdb=" O ARG R 107 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR R 109 " --> pdb=" O ILE R 72 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'R' and resid 83 through 86 Processing sheet with id=AG7, first strand: chain 'S' and resid 52 through 57 removed outlier: 3.640A pdb=" N GLN S 53 " --> pdb=" O VAL S 108 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU S 55 " --> pdb=" O ILE S 106 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N CYS S 105 " --> pdb=" O SER S 76 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N SER S 76 " --> pdb=" O CYS S 105 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG S 107 " --> pdb=" O VAL S 74 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL S 74 " --> pdb=" O ARG S 107 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR S 109 " --> pdb=" O ILE S 72 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'S' and resid 83 through 86 Processing sheet with id=AG9, first strand: chain 'T' and resid 52 through 57 removed outlier: 3.640A pdb=" N GLN T 53 " --> pdb=" O VAL T 108 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU T 55 " --> pdb=" O ILE T 106 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N CYS T 105 " --> pdb=" O SER T 76 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N SER T 76 " --> pdb=" O CYS T 105 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG T 107 " --> pdb=" O VAL T 74 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL T 74 " --> pdb=" O ARG T 107 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR T 109 " --> pdb=" O ILE T 72 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'T' and resid 83 through 86 Processing sheet with id=AH2, first strand: chain 'U' and resid 52 through 57 removed outlier: 3.640A pdb=" N GLN U 53 " --> pdb=" O VAL U 108 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU U 55 " --> pdb=" O ILE U 106 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N CYS U 105 " --> pdb=" O SER U 76 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N SER U 76 " --> pdb=" O CYS U 105 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG U 107 " --> pdb=" O VAL U 74 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL U 74 " --> pdb=" O ARG U 107 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR U 109 " --> pdb=" O ILE U 72 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'U' and resid 83 through 86 Processing sheet with id=AH4, first strand: chain 'V' and resid 52 through 57 removed outlier: 3.640A pdb=" N GLN V 53 " --> pdb=" O VAL V 108 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU V 55 " --> pdb=" O ILE V 106 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N CYS V 105 " --> pdb=" O SER V 76 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N SER V 76 " --> pdb=" O CYS V 105 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG V 107 " --> pdb=" O VAL V 74 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL V 74 " --> pdb=" O ARG V 107 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR V 109 " --> pdb=" O ILE V 72 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'V' and resid 83 through 86 Processing sheet with id=AH6, first strand: chain 'W' and resid 52 through 57 removed outlier: 3.640A pdb=" N GLN W 53 " --> pdb=" O VAL W 108 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU W 55 " --> pdb=" O ILE W 106 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N CYS W 105 " --> pdb=" O SER W 76 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N SER W 76 " --> pdb=" O CYS W 105 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG W 107 " --> pdb=" O VAL W 74 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL W 74 " --> pdb=" O ARG W 107 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR W 109 " --> pdb=" O ILE W 72 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'W' and resid 83 through 86 Processing sheet with id=AH8, first strand: chain 'X' and resid 52 through 57 removed outlier: 3.640A pdb=" N GLN X 53 " --> pdb=" O VAL X 108 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU X 55 " --> pdb=" O ILE X 106 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N CYS X 105 " --> pdb=" O SER X 76 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N SER X 76 " --> pdb=" O CYS X 105 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG X 107 " --> pdb=" O VAL X 74 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL X 74 " --> pdb=" O ARG X 107 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR X 109 " --> pdb=" O ILE X 72 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'X' and resid 83 through 86 3066 hydrogen bonds defined for protein. 8838 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: 27.24 Time building geometry restraints manager: 14.15 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: 20208 1.34 - 1.46: 11305 1.46 - 1.58: 29459 1.58 - 1.69: 0 1.69 - 1.81: 432 Bond restraints: 61404 Sorted by residual: bond pdb=" N MET P 1 " pdb=" CA MET P 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N MET M 1 " pdb=" CA MET M 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N MET S 1 " pdb=" CA MET S 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N MET V 1 " pdb=" CA MET V 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N MET X 1 " pdb=" CA MET X 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 ... (remaining 61399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 80891 1.21 - 2.42: 2211 2.42 - 3.63: 358 3.63 - 4.84: 72 4.84 - 6.05: 24 Bond angle restraints: 83556 Sorted by residual: angle pdb=" C ASP L 229 " pdb=" CA ASP L 229 " pdb=" CB ASP L 229 " ideal model delta sigma weight residual 116.34 111.82 4.52 1.40e+00 5.10e-01 1.04e+01 angle pdb=" C ASP C 229 " pdb=" CA ASP C 229 " pdb=" CB ASP C 229 " ideal model delta sigma weight residual 116.34 111.82 4.52 1.40e+00 5.10e-01 1.04e+01 angle pdb=" C ASP F 229 " pdb=" CA ASP F 229 " pdb=" CB ASP F 229 " ideal model delta sigma weight residual 116.34 111.82 4.52 1.40e+00 5.10e-01 1.04e+01 angle pdb=" C ASP I 229 " pdb=" CA ASP I 229 " pdb=" CB ASP I 229 " ideal model delta sigma weight residual 116.34 111.82 4.52 1.40e+00 5.10e-01 1.04e+01 angle pdb=" C ASP A 229 " pdb=" CA ASP A 229 " pdb=" CB ASP A 229 " ideal model delta sigma weight residual 116.34 111.84 4.50 1.40e+00 5.10e-01 1.03e+01 ... (remaining 83551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 34068 17.18 - 34.36: 2376 34.36 - 51.54: 336 51.54 - 68.72: 72 68.72 - 85.90: 96 Dihedral angle restraints: 36948 sinusoidal: 13944 harmonic: 23004 Sorted by residual: dihedral pdb=" C HIS E 29 " pdb=" N HIS E 29 " pdb=" CA HIS E 29 " pdb=" CB HIS E 29 " ideal model delta harmonic sigma weight residual -122.60 -131.72 9.12 0 2.50e+00 1.60e-01 1.33e+01 dihedral pdb=" C HIS B 29 " pdb=" N HIS B 29 " pdb=" CA HIS B 29 " pdb=" CB HIS B 29 " ideal model delta harmonic sigma weight residual -122.60 -131.72 9.12 0 2.50e+00 1.60e-01 1.33e+01 dihedral pdb=" C HIS H 29 " pdb=" N HIS H 29 " pdb=" CA HIS H 29 " pdb=" CB HIS H 29 " ideal model delta harmonic sigma weight residual -122.60 -131.72 9.12 0 2.50e+00 1.60e-01 1.33e+01 ... (remaining 36945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 9140 0.071 - 0.142: 652 0.142 - 0.213: 0 0.213 - 0.284: 0 0.284 - 0.356: 12 Chirality restraints: 9804 Sorted by residual: chirality pdb=" CA HIS H 29 " pdb=" N HIS H 29 " pdb=" C HIS H 29 " pdb=" CB HIS H 29 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA HIS B 29 " pdb=" N HIS B 29 " pdb=" C HIS B 29 " pdb=" CB HIS B 29 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA HIS E 29 " pdb=" N HIS E 29 " pdb=" C HIS E 29 " pdb=" CB HIS E 29 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 9801 not shown) Planarity restraints: 10764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU T 117 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.50e+00 pdb=" N PRO T 118 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO T 118 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO T 118 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU Q 117 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.50e+00 pdb=" N PRO Q 118 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO Q 118 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO Q 118 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU W 117 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.50e+00 pdb=" N PRO W 118 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO W 118 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO W 118 " 0.017 5.00e-02 4.00e+02 ... (remaining 10761 not shown) Histogram of nonbonded interaction distances: 0.75 - 1.58: 60 1.58 - 2.41: 432 2.41 - 3.24: 57969 3.24 - 4.07: 133604 4.07 - 4.90: 254955 Warning: very small nonbonded interaction distances. Nonbonded interactions: 447020 Sorted by model distance: nonbonded pdb=" CZ ARG F 449 " pdb=" CD2 TYR G 471 " model vdw 0.748 3.570 nonbonded pdb=" CZ ARG I 449 " pdb=" CD2 TYR J 471 " model vdw 0.748 3.570 nonbonded pdb=" CZ ARG C 449 " pdb=" CD2 TYR D 471 " model vdw 0.748 3.570 nonbonded pdb=" CD2 TYR A 471 " pdb=" CZ ARG L 449 " model vdw 0.748 3.570 nonbonded pdb=" CZ ARG G 449 " pdb=" CD2 TYR H 471 " model vdw 0.749 3.570 ... (remaining 447015 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' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 3.010 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: 0.070 Extract box with map and model: 1.700 Check model and map are aligned: 0.340 Set scattering table: 0.420 Process input model: 95.470 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.470 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: 0.040 Load rotamer database and sin/cos tables:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 0.032 61404 Z= 0.143 Angle : 0.503 6.046 83556 Z= 0.299 Chirality : 0.038 0.356 9804 Planarity : 0.003 0.031 10764 Dihedral : 12.553 85.897 22116 Min Nonbonded Distance : 0.748 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.19 (0.10), residues: 7776 helix: 2.15 (0.09), residues: 3732 sheet: -0.32 (0.15), residues: 1032 loop : -0.52 (0.12), residues: 3012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 246 HIS 0.002 0.001 HIS K 386 PHE 0.006 0.001 PHE D 114 TYR 0.011 0.001 TYR I 320 ARG 0.002 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1267 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1267 time to evaluate : 5.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 GLN cc_start: 0.8228 (mt0) cc_final: 0.7853 (mt0) REVERT: B 176 ARG cc_start: 0.8035 (mtm180) cc_final: 0.7360 (ttm110) REVERT: B 336 GLN cc_start: 0.7525 (tt0) cc_final: 0.7209 (mt0) REVERT: C 130 MET cc_start: 0.8650 (mmt) cc_final: 0.8202 (mpp) REVERT: C 171 MET cc_start: 0.8393 (mtm) cc_final: 0.8178 (mtt) REVERT: C 336 GLN cc_start: 0.7928 (tt0) cc_final: 0.7559 (mt0) REVERT: D 16 ARG cc_start: 0.8565 (mtp85) cc_final: 0.8312 (mtp85) REVERT: D 23 LYS cc_start: 0.8600 (mmmm) cc_final: 0.8342 (mmpt) REVERT: E 175 GLU cc_start: 0.7932 (tt0) cc_final: 0.7696 (tt0) REVERT: E 336 GLN cc_start: 0.7835 (tt0) cc_final: 0.7511 (mt0) REVERT: E 347 MET cc_start: 0.7787 (mtp) cc_final: 0.7546 (mtp) REVERT: F 23 LYS cc_start: 0.8425 (mmmm) cc_final: 0.8162 (mmmt) REVERT: F 336 GLN cc_start: 0.7961 (tt0) cc_final: 0.7580 (mt0) REVERT: F 341 ARG cc_start: 0.8248 (ttp-170) cc_final: 0.7984 (ttp-170) REVERT: G 23 LYS cc_start: 0.8314 (mmmm) cc_final: 0.8020 (mmpt) REVERT: G 336 GLN cc_start: 0.7578 (tt0) cc_final: 0.7347 (mt0) REVERT: H 336 GLN cc_start: 0.7711 (tt0) cc_final: 0.7434 (mt0) REVERT: H 408 ASN cc_start: 0.8005 (m-40) cc_final: 0.7766 (m-40) REVERT: I 112 THR cc_start: 0.7713 (t) cc_final: 0.7448 (t) REVERT: I 336 GLN cc_start: 0.7847 (tt0) cc_final: 0.7520 (mt0) REVERT: J 112 THR cc_start: 0.7720 (t) cc_final: 0.7487 (t) REVERT: J 336 GLN cc_start: 0.7703 (tt0) cc_final: 0.7404 (mt0) REVERT: J 399 GLN cc_start: 0.7646 (mt0) cc_final: 0.7404 (mt0) REVERT: J 477 LEU cc_start: 0.8366 (mt) cc_final: 0.8010 (mt) REVERT: K 112 THR cc_start: 0.7894 (t) cc_final: 0.7642 (t) REVERT: K 336 GLN cc_start: 0.7774 (tt0) cc_final: 0.7299 (mt0) REVERT: K 399 GLN cc_start: 0.7872 (mt0) cc_final: 0.7585 (mt0) REVERT: L 95 MET cc_start: 0.6235 (mtm) cc_final: 0.6007 (mtp) REVERT: L 336 GLN cc_start: 0.7961 (tt0) cc_final: 0.7548 (mt0) REVERT: L 341 ARG cc_start: 0.7943 (ttp-170) cc_final: 0.7708 (ttp-170) REVERT: N 98 MET cc_start: 0.8370 (ttp) cc_final: 0.8143 (ttm) REVERT: N 159 GLU cc_start: 0.7487 (tp30) cc_final: 0.7275 (tp30) REVERT: O 98 MET cc_start: 0.8459 (ttp) cc_final: 0.8116 (ttt) REVERT: O 99 TYR cc_start: 0.9150 (m-80) cc_final: 0.8241 (m-80) REVERT: O 141 ASP cc_start: 0.7878 (t0) cc_final: 0.7646 (t0) REVERT: O 158 VAL cc_start: 0.8701 (t) cc_final: 0.8350 (t) REVERT: O 159 GLU cc_start: 0.7828 (tp30) cc_final: 0.7596 (tp30) REVERT: P 159 GLU cc_start: 0.7543 (tp30) cc_final: 0.7311 (tp30) REVERT: Q 159 GLU cc_start: 0.7526 (tp30) cc_final: 0.7302 (tp30) REVERT: R 57 MET cc_start: 0.8101 (mmm) cc_final: 0.7860 (mmt) REVERT: R 99 TYR cc_start: 0.8765 (m-80) cc_final: 0.8324 (m-80) REVERT: R 159 GLU cc_start: 0.7649 (tp30) cc_final: 0.7411 (tp30) REVERT: S 57 MET cc_start: 0.8169 (mmm) cc_final: 0.7845 (mmt) REVERT: T 137 ASP cc_start: 0.7082 (t70) cc_final: 0.6682 (t0) REVERT: U 155 MET cc_start: 0.8639 (tpp) cc_final: 0.8113 (tpt) REVERT: V 73 SER cc_start: 0.9246 (p) cc_final: 0.9007 (p) REVERT: W 39 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7880 (mptp) REVERT: W 93 ASN cc_start: 0.9262 (m-40) cc_final: 0.8941 (m110) REVERT: X 98 MET cc_start: 0.8669 (ttp) cc_final: 0.8454 (ttt) REVERT: X 99 TYR cc_start: 0.9108 (m-80) cc_final: 0.8857 (m-80) REVERT: X 127 TYR cc_start: 0.8249 (m-80) cc_final: 0.7807 (m-80) REVERT: X 141 ASP cc_start: 0.7715 (t0) cc_final: 0.7511 (t0) REVERT: X 155 MET cc_start: 0.8703 (tpp) cc_final: 0.8395 (tpt) outliers start: 0 outliers final: 2 residues processed: 1267 average time/residue: 1.5645 time to fit residues: 2458.1536 Evaluate side-chains 797 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 795 time to evaluate : 5.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain I residue 192 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 648 optimal weight: 5.9990 chunk 582 optimal weight: 0.9980 chunk 322 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 392 optimal weight: 0.5980 chunk 310 optimal weight: 0.0020 chunk 601 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 366 optimal weight: 0.7980 chunk 448 optimal weight: 0.8980 chunk 697 optimal weight: 4.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN B 466 ASN C 149 ASN C 295 GLN C 399 GLN D 399 GLN E 399 GLN F 149 ASN F 478 GLN G 149 ASN G 399 GLN H 478 GLN I 295 GLN J 77 GLN J 466 ASN K 247 ASN K 478 GLN L 295 GLN M 34 GLN N 34 GLN N 181 ASN P 181 ASN T 96 ASN W 34 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 61404 Z= 0.159 Angle : 0.527 6.597 83556 Z= 0.283 Chirality : 0.040 0.266 9804 Planarity : 0.007 0.205 10764 Dihedral : 4.325 154.898 8644 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.30 % Allowed : 9.18 % Favored : 88.52 % 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: 1.33 (0.10), residues: 7776 helix: 2.13 (0.09), residues: 3804 sheet: 0.29 (0.16), residues: 1020 loop : -0.55 (0.12), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 30 HIS 0.004 0.001 HIS L 124 PHE 0.022 0.001 PHE L 401 TYR 0.052 0.001 TYR L 471 ARG 0.029 0.001 ARG G 449 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 927 time to evaluate : 5.253 Fit side-chains REVERT: A 289 MET cc_start: 0.8547 (mmt) cc_final: 0.8138 (mmt) REVERT: A 399 GLN cc_start: 0.7888 (mt0) cc_final: 0.7480 (mt0) REVERT: A 408 ASN cc_start: 0.8465 (m-40) cc_final: 0.8265 (m-40) REVERT: B 176 ARG cc_start: 0.8026 (mtm180) cc_final: 0.7404 (ttm110) REVERT: B 188 ILE cc_start: 0.8186 (pt) cc_final: 0.7912 (pp) REVERT: B 214 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8431 (mm-30) REVERT: B 336 GLN cc_start: 0.7692 (tt0) cc_final: 0.7389 (mt0) REVERT: B 404 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7424 (mm-30) REVERT: C 95 MET cc_start: 0.6597 (mtm) cc_final: 0.6211 (mtp) REVERT: C 171 MET cc_start: 0.7869 (mtm) cc_final: 0.7536 (mtm) REVERT: C 289 MET cc_start: 0.8694 (mmt) cc_final: 0.8260 (mmt) REVERT: C 336 GLN cc_start: 0.7830 (tt0) cc_final: 0.7466 (mt0) REVERT: E 176 ARG cc_start: 0.7784 (mtm180) cc_final: 0.7565 (ttp80) REVERT: E 336 GLN cc_start: 0.7893 (tt0) cc_final: 0.7552 (mt0) REVERT: F 23 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8202 (mmtt) REVERT: F 181 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7806 (mm-30) REVERT: F 325 TYR cc_start: 0.6644 (t80) cc_final: 0.6070 (t80) REVERT: F 336 GLN cc_start: 0.8035 (tt0) cc_final: 0.7620 (mt0) REVERT: F 457 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: G 23 LYS cc_start: 0.8381 (mmmm) cc_final: 0.8179 (mmpt) REVERT: G 336 GLN cc_start: 0.7767 (tt0) cc_final: 0.7554 (mt0) REVERT: G 401 PHE cc_start: 0.8199 (t80) cc_final: 0.7919 (t80) REVERT: H 18 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: H 336 GLN cc_start: 0.7670 (tt0) cc_final: 0.7348 (mt0) REVERT: I 22 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7734 (tm) REVERT: I 130 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7850 (mpp) REVERT: I 171 MET cc_start: 0.7943 (mtp) cc_final: 0.7582 (mtp) REVERT: I 336 GLN cc_start: 0.8010 (tt0) cc_final: 0.7667 (mt0) REVERT: I 404 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7206 (mm-30) REVERT: J 336 GLN cc_start: 0.7772 (tt0) cc_final: 0.7488 (mt0) REVERT: J 399 GLN cc_start: 0.7518 (mt0) cc_final: 0.7140 (mt0) REVERT: J 436 SER cc_start: 0.8537 (m) cc_final: 0.8333 (m) REVERT: K 171 MET cc_start: 0.7989 (mtm) cc_final: 0.7752 (mtm) REVERT: K 236 GLU cc_start: 0.7669 (tt0) cc_final: 0.7460 (tt0) REVERT: K 282 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: K 336 GLN cc_start: 0.7720 (tt0) cc_final: 0.7217 (mt0) REVERT: K 457 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7671 (t0) REVERT: L 171 MET cc_start: 0.8078 (mtm) cc_final: 0.7685 (mtm) REVERT: L 336 GLN cc_start: 0.8059 (tt0) cc_final: 0.7611 (mt0) REVERT: L 341 ARG cc_start: 0.7895 (ttp-170) cc_final: 0.7688 (ttp-170) REVERT: L 441 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8793 (mt) REVERT: L 457 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.7988 (m-30) REVERT: N 98 MET cc_start: 0.8414 (ttp) cc_final: 0.8112 (ttm) REVERT: N 159 GLU cc_start: 0.7679 (tp30) cc_final: 0.7316 (tp30) REVERT: O 99 TYR cc_start: 0.9206 (m-80) cc_final: 0.8319 (m-80) REVERT: O 141 ASP cc_start: 0.7853 (t0) cc_final: 0.7622 (t0) REVERT: O 158 VAL cc_start: 0.8690 (t) cc_final: 0.8302 (t) REVERT: O 159 GLU cc_start: 0.7961 (tp30) cc_final: 0.7753 (tp30) REVERT: P 75 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: Q 159 GLU cc_start: 0.7718 (tp30) cc_final: 0.7334 (tp30) REVERT: R 99 TYR cc_start: 0.8814 (m-80) cc_final: 0.8289 (m-80) REVERT: R 141 ASP cc_start: 0.8270 (t0) cc_final: 0.7853 (t0) REVERT: R 158 VAL cc_start: 0.8438 (t) cc_final: 0.8192 (t) REVERT: S 127 TYR cc_start: 0.8121 (m-80) cc_final: 0.7701 (m-80) REVERT: T 101 THR cc_start: 0.8581 (m) cc_final: 0.8334 (m) REVERT: T 137 ASP cc_start: 0.7027 (t70) cc_final: 0.6640 (t0) REVERT: T 161 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: U 155 MET cc_start: 0.8804 (tpp) cc_final: 0.8251 (tpt) REVERT: V 73 SER cc_start: 0.9304 (p) cc_final: 0.9103 (p) REVERT: W 39 LYS cc_start: 0.8334 (mmtt) cc_final: 0.7957 (mptp) REVERT: X 99 TYR cc_start: 0.9182 (m-80) cc_final: 0.8762 (m-80) REVERT: X 141 ASP cc_start: 0.7681 (t0) cc_final: 0.7479 (t0) REVERT: X 155 MET cc_start: 0.8664 (tpp) cc_final: 0.8222 (tpt) REVERT: X 158 VAL cc_start: 0.8573 (t) cc_final: 0.8278 (t) outliers start: 144 outliers final: 41 residues processed: 987 average time/residue: 1.4218 time to fit residues: 1780.3264 Evaluate side-chains 815 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 761 time to evaluate : 5.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 192 ASN Chi-restraints excluded: chain I residue 404 GLU Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 282 GLU Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain L residue 439 VAL Chi-restraints excluded: chain L residue 441 LEU Chi-restraints excluded: chain L residue 457 ASP Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain P residue 73 SER Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain R residue 39 LYS Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain T residue 141 ASP Chi-restraints excluded: chain T residue 161 GLN Chi-restraints excluded: chain U residue 46 ARG Chi-restraints excluded: chain W residue 141 ASP Chi-restraints excluded: chain X residue 61 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 387 optimal weight: 0.9990 chunk 216 optimal weight: 0.9990 chunk 580 optimal weight: 7.9990 chunk 474 optimal weight: 4.9990 chunk 192 optimal weight: 7.9990 chunk 698 optimal weight: 2.9990 chunk 754 optimal weight: 5.9990 chunk 622 optimal weight: 2.9990 chunk 692 optimal weight: 3.9990 chunk 238 optimal weight: 8.9990 chunk 560 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN C 399 GLN E 446 ASN J 77 GLN P 181 ASN T 88 ASN U 93 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 61404 Z= 0.304 Angle : 0.613 9.698 83556 Z= 0.325 Chirality : 0.042 0.147 9804 Planarity : 0.006 0.172 10764 Dihedral : 4.173 27.261 8642 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.99 % Allowed : 10.95 % Favored : 86.06 % 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: 0.93 (0.10), residues: 7776 helix: 1.85 (0.09), residues: 3732 sheet: 0.45 (0.17), residues: 1020 loop : -0.90 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 49 HIS 0.008 0.002 HIS H 288 PHE 0.030 0.002 PHE A 401 TYR 0.039 0.002 TYR D 471 ARG 0.031 0.001 ARG H 449 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 821 time to evaluate : 5.436 Fit side-chains REVERT: A 130 MET cc_start: 0.8591 (mpp) cc_final: 0.8114 (mmt) REVERT: A 399 GLN cc_start: 0.8102 (mt0) cc_final: 0.7720 (mt0) REVERT: B 108 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: B 176 ARG cc_start: 0.8097 (mtm180) cc_final: 0.7468 (ttm110) REVERT: B 188 ILE cc_start: 0.8326 (pt) cc_final: 0.8054 (pp) REVERT: B 208 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7193 (mt-10) REVERT: B 232 GLU cc_start: 0.7951 (tp30) cc_final: 0.7726 (mm-30) REVERT: B 336 GLN cc_start: 0.7894 (tt0) cc_final: 0.7425 (mt0) REVERT: C 95 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.6453 (mtp) REVERT: C 130 MET cc_start: 0.8660 (tpp) cc_final: 0.8089 (mpp) REVERT: C 171 MET cc_start: 0.8145 (mtm) cc_final: 0.7903 (mtm) REVERT: C 336 GLN cc_start: 0.8062 (tt0) cc_final: 0.7661 (mt0) REVERT: C 458 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7989 (tmm) REVERT: D 336 GLN cc_start: 0.8034 (tt0) cc_final: 0.7661 (mt0) REVERT: E 167 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8207 (ptmt) REVERT: E 168 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8726 (p) REVERT: E 176 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7667 (ttp80) REVERT: E 232 GLU cc_start: 0.7901 (tp30) cc_final: 0.7476 (mm-30) REVERT: E 280 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8347 (mt-10) REVERT: E 289 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8157 (mmm) REVERT: E 336 GLN cc_start: 0.7882 (tt0) cc_final: 0.7465 (mt0) REVERT: F 130 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8424 (mmp) REVERT: F 325 TYR cc_start: 0.7221 (t80) cc_final: 0.6642 (t80) REVERT: F 336 GLN cc_start: 0.8210 (tt0) cc_final: 0.7777 (mt0) REVERT: F 341 ARG cc_start: 0.8325 (ttp-170) cc_final: 0.7909 (ttp-170) REVERT: F 477 LEU cc_start: 0.8343 (mt) cc_final: 0.8132 (mt) REVERT: G 336 GLN cc_start: 0.7879 (tt0) cc_final: 0.7540 (mt0) REVERT: G 401 PHE cc_start: 0.8263 (t80) cc_final: 0.8022 (t80) REVERT: G 477 LEU cc_start: 0.8484 (mt) cc_final: 0.8148 (mt) REVERT: H 151 HIS cc_start: 0.8211 (t-90) cc_final: 0.7949 (t70) REVERT: H 168 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8644 (p) REVERT: H 301 MET cc_start: 0.8541 (mtm) cc_final: 0.8055 (mtm) REVERT: H 336 GLN cc_start: 0.7813 (tt0) cc_final: 0.7411 (mt0) REVERT: H 468 LYS cc_start: 0.8828 (tptt) cc_final: 0.8613 (tppt) REVERT: I 130 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8146 (mpp) REVERT: I 226 LEU cc_start: 0.8052 (tp) cc_final: 0.7829 (tp) REVERT: I 336 GLN cc_start: 0.8118 (tt0) cc_final: 0.7747 (mt0) REVERT: I 341 ARG cc_start: 0.8284 (ttp-170) cc_final: 0.7983 (ttp-170) REVERT: J 130 MET cc_start: 0.8688 (tpp) cc_final: 0.8128 (mmt) REVERT: J 336 GLN cc_start: 0.7934 (tt0) cc_final: 0.7589 (mt0) REVERT: J 399 GLN cc_start: 0.7908 (mt0) cc_final: 0.7675 (mt0) REVERT: K 130 MET cc_start: 0.8719 (tpp) cc_final: 0.8462 (mpp) REVERT: K 188 ILE cc_start: 0.8189 (pt) cc_final: 0.7931 (pp) REVERT: K 289 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8068 (mmm) REVERT: K 336 GLN cc_start: 0.7891 (tt0) cc_final: 0.7379 (mt0) REVERT: K 399 GLN cc_start: 0.8044 (mt0) cc_final: 0.7819 (mt0) REVERT: K 468 LYS cc_start: 0.8856 (tptt) cc_final: 0.8521 (tppt) REVERT: L 22 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8210 (tp) REVERT: L 95 MET cc_start: 0.5851 (OUTLIER) cc_final: 0.5596 (mtp) REVERT: L 130 MET cc_start: 0.8634 (tpp) cc_final: 0.8021 (mpp) REVERT: L 171 MET cc_start: 0.8168 (mtm) cc_final: 0.7896 (mtm) REVERT: L 289 MET cc_start: 0.8658 (mmt) cc_final: 0.8393 (mmt) REVERT: L 336 GLN cc_start: 0.8153 (tt0) cc_final: 0.7685 (mt0) REVERT: M 45 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.6945 (tm-30) REVERT: N 163 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8430 (tpp) REVERT: O 99 TYR cc_start: 0.9216 (m-80) cc_final: 0.8614 (m-80) REVERT: O 141 ASP cc_start: 0.8115 (t0) cc_final: 0.7808 (t0) REVERT: O 159 GLU cc_start: 0.8067 (tp30) cc_final: 0.7748 (tp30) REVERT: P 141 ASP cc_start: 0.8596 (t0) cc_final: 0.8377 (t0) REVERT: Q 53 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8165 (mm-40) REVERT: Q 160 GLU cc_start: 0.7728 (tt0) cc_final: 0.7454 (tt0) REVERT: Q 163 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8468 (tpp) REVERT: Q 178 LYS cc_start: 0.8722 (mmpt) cc_final: 0.8456 (mttm) REVERT: R 99 TYR cc_start: 0.9130 (m-80) cc_final: 0.8679 (m-80) REVERT: R 115 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6059 (mm-30) REVERT: R 141 ASP cc_start: 0.8492 (t0) cc_final: 0.7977 (t0) REVERT: R 163 MET cc_start: 0.8727 (tpp) cc_final: 0.8442 (tpt) REVERT: R 174 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7197 (ptt-90) REVERT: S 1 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7896 (ttp) REVERT: T 159 GLU cc_start: 0.7816 (tp30) cc_final: 0.7445 (tp30) REVERT: T 161 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7779 (mm-40) REVERT: U 45 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: V 73 SER cc_start: 0.9369 (p) cc_final: 0.9152 (p) REVERT: W 39 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8197 (mptp) REVERT: W 151 GLU cc_start: 0.8519 (tt0) cc_final: 0.8299 (tt0) REVERT: W 161 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7741 (mm-40) REVERT: W 163 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8237 (tpp) REVERT: X 45 GLU cc_start: 0.8030 (tt0) cc_final: 0.7816 (tt0) REVERT: X 99 TYR cc_start: 0.9163 (m-80) cc_final: 0.8647 (m-80) REVERT: X 141 ASP cc_start: 0.7905 (t0) cc_final: 0.7662 (t0) REVERT: X 158 VAL cc_start: 0.8780 (t) cc_final: 0.8532 (t) REVERT: X 159 GLU cc_start: 0.7914 (tp30) cc_final: 0.7629 (tp30) outliers start: 187 outliers final: 50 residues processed: 915 average time/residue: 1.4690 time to fit residues: 1699.0566 Evaluate side-chains 807 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 733 time to evaluate : 5.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 167 LYS Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 407 SER Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 130 MET Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 412 LEU Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 289 MET Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 441 LEU Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 163 MET Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain Q residue 53 GLN Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 163 MET Chi-restraints excluded: chain R residue 39 LYS Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 161 GLN Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain W residue 97 THR Chi-restraints excluded: chain W residue 141 ASP Chi-restraints excluded: chain W residue 161 GLN Chi-restraints excluded: chain W residue 163 MET Chi-restraints excluded: chain X residue 61 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 690 optimal weight: 0.6980 chunk 525 optimal weight: 4.9990 chunk 362 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 333 optimal weight: 0.9980 chunk 469 optimal weight: 8.9990 chunk 701 optimal weight: 0.9980 chunk 742 optimal weight: 7.9990 chunk 366 optimal weight: 1.9990 chunk 664 optimal weight: 0.7980 chunk 200 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 446 ASN J 77 GLN T 181 ASN W 181 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 61404 Z= 0.170 Angle : 0.505 8.987 83556 Z= 0.270 Chirality : 0.039 0.151 9804 Planarity : 0.006 0.305 10764 Dihedral : 3.999 46.493 8640 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.31 % Allowed : 13.11 % Favored : 84.58 % 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: 1.18 (0.10), residues: 7776 helix: 2.07 (0.09), residues: 3756 sheet: 0.61 (0.17), residues: 1020 loop : -0.82 (0.12), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 49 HIS 0.003 0.001 HIS J 124 PHE 0.028 0.001 PHE A 401 TYR 0.057 0.001 TYR E 471 ARG 0.029 0.001 ARG D 449 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 767 time to evaluate : 5.233 Fit side-chains REVERT: A 22 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8603 (tm) REVERT: A 399 GLN cc_start: 0.8039 (mt0) cc_final: 0.7615 (mt0) REVERT: B 108 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7426 (tt0) REVERT: B 176 ARG cc_start: 0.8097 (mtm180) cc_final: 0.7465 (ttm110) REVERT: B 188 ILE cc_start: 0.8405 (pt) cc_final: 0.8105 (pp) REVERT: B 232 GLU cc_start: 0.7732 (tp30) cc_final: 0.7291 (mm-30) REVERT: B 336 GLN cc_start: 0.7846 (tt0) cc_final: 0.7448 (mt0) REVERT: B 404 GLU cc_start: 0.7870 (mp0) cc_final: 0.7576 (mm-30) REVERT: C 289 MET cc_start: 0.8670 (mmt) cc_final: 0.8406 (mmt) REVERT: C 336 GLN cc_start: 0.7969 (tt0) cc_final: 0.7570 (mt0) REVERT: C 441 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8493 (mt) REVERT: D 371 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6703 (tt0) REVERT: E 167 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8304 (ptmt) REVERT: E 168 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8667 (p) REVERT: E 176 ARG cc_start: 0.7948 (mtm180) cc_final: 0.7654 (ttp80) REVERT: E 208 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6886 (mt-10) REVERT: E 232 GLU cc_start: 0.7809 (tp30) cc_final: 0.7103 (mm-30) REVERT: E 280 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8228 (mt-10) REVERT: E 336 GLN cc_start: 0.7838 (tt0) cc_final: 0.7417 (mt0) REVERT: E 468 LYS cc_start: 0.8541 (tptt) cc_final: 0.8322 (tppt) REVERT: F 336 GLN cc_start: 0.8163 (tt0) cc_final: 0.7715 (mt0) REVERT: F 477 LEU cc_start: 0.8311 (mt) cc_final: 0.8109 (mt) REVERT: G 336 GLN cc_start: 0.7900 (tt0) cc_final: 0.7550 (mt0) REVERT: G 401 PHE cc_start: 0.8205 (t80) cc_final: 0.7955 (t80) REVERT: G 477 LEU cc_start: 0.8465 (mt) cc_final: 0.8179 (mt) REVERT: H 161 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8625 (tt) REVERT: H 168 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8625 (p) REVERT: H 214 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8366 (mm-30) REVERT: H 336 GLN cc_start: 0.7818 (tt0) cc_final: 0.7424 (mt0) REVERT: H 468 LYS cc_start: 0.8892 (tptt) cc_final: 0.8635 (tppt) REVERT: H 472 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6548 (mtt-85) REVERT: I 22 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8134 (tm) REVERT: I 130 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8052 (mpp) REVERT: I 336 GLN cc_start: 0.8132 (tt0) cc_final: 0.7694 (mt0) REVERT: I 341 ARG cc_start: 0.8015 (ttp-170) cc_final: 0.7666 (ttp-170) REVERT: J 23 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8266 (mmtp) REVERT: J 336 GLN cc_start: 0.7910 (tt0) cc_final: 0.7509 (mt0) REVERT: J 399 GLN cc_start: 0.7861 (mt0) cc_final: 0.7569 (mt0) REVERT: J 457 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7371 (m-30) REVERT: K 16 ARG cc_start: 0.8502 (mtp85) cc_final: 0.8275 (mtp85) REVERT: K 171 MET cc_start: 0.8037 (mtm) cc_final: 0.7690 (mtm) REVERT: K 188 ILE cc_start: 0.8077 (pt) cc_final: 0.7844 (pp) REVERT: K 336 GLN cc_start: 0.7764 (tt0) cc_final: 0.7224 (mt0) REVERT: K 399 GLN cc_start: 0.7917 (mt0) cc_final: 0.7669 (mt0) REVERT: L 22 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8250 (tp) REVERT: L 95 MET cc_start: 0.5677 (OUTLIER) cc_final: 0.5321 (ttp) REVERT: L 171 MET cc_start: 0.8131 (mtm) cc_final: 0.7862 (mtm) REVERT: L 289 MET cc_start: 0.8511 (mmt) cc_final: 0.8294 (mmt) REVERT: L 336 GLN cc_start: 0.8144 (tt0) cc_final: 0.7667 (mt0) REVERT: N 45 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7252 (tt0) REVERT: O 99 TYR cc_start: 0.9209 (m-80) cc_final: 0.8568 (m-80) REVERT: O 141 ASP cc_start: 0.7989 (t0) cc_final: 0.7715 (t0) REVERT: O 159 GLU cc_start: 0.7890 (tp30) cc_final: 0.7689 (tp30) REVERT: P 55 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: Q 45 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7240 (tt0) REVERT: Q 178 LYS cc_start: 0.8661 (mmpt) cc_final: 0.8386 (mttm) REVERT: R 99 TYR cc_start: 0.9110 (m-80) cc_final: 0.8626 (m-80) REVERT: R 115 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6018 (mm-30) REVERT: R 141 ASP cc_start: 0.8320 (t0) cc_final: 0.8055 (t0) REVERT: R 158 VAL cc_start: 0.8730 (t) cc_final: 0.8416 (t) REVERT: R 163 MET cc_start: 0.8627 (tpp) cc_final: 0.8388 (tpt) REVERT: S 1 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7873 (ttp) REVERT: S 88 ASN cc_start: 0.8102 (t0) cc_final: 0.7874 (t0) REVERT: T 45 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7270 (tt0) REVERT: T 159 GLU cc_start: 0.7766 (tp30) cc_final: 0.7396 (tp30) REVERT: U 45 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: W 39 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8122 (mptp) REVERT: W 45 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: W 151 GLU cc_start: 0.8555 (tt0) cc_final: 0.8328 (tt0) REVERT: W 160 GLU cc_start: 0.7743 (tt0) cc_final: 0.7411 (tt0) REVERT: W 161 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7592 (mm-40) REVERT: X 45 GLU cc_start: 0.8020 (tt0) cc_final: 0.7795 (tt0) REVERT: X 99 TYR cc_start: 0.9131 (m-80) cc_final: 0.8586 (m-80) REVERT: X 141 ASP cc_start: 0.7769 (t0) cc_final: 0.7525 (t0) REVERT: X 158 VAL cc_start: 0.8733 (t) cc_final: 0.8406 (t) outliers start: 145 outliers final: 39 residues processed: 849 average time/residue: 1.6117 time to fit residues: 1757.0002 Evaluate side-chains 786 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 723 time to evaluate : 5.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 167 LYS Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 208 GLU Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 412 LEU Chi-restraints excluded: chain H residue 472 ARG Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain P residue 165 ASN Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain R residue 39 LYS Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 143 SER Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain W residue 141 ASP Chi-restraints excluded: chain W residue 161 GLN Chi-restraints excluded: chain X residue 61 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 618 optimal weight: 3.9990 chunk 421 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 552 optimal weight: 5.9990 chunk 306 optimal weight: 0.8980 chunk 633 optimal weight: 5.9990 chunk 513 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 379 optimal weight: 4.9990 chunk 666 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 408 ASN J 77 GLN ** U 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 61404 Z= 0.415 Angle : 0.663 7.177 83556 Z= 0.351 Chirality : 0.044 0.169 9804 Planarity : 0.009 0.381 10764 Dihedral : 4.468 62.574 8640 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.38 % Allowed : 13.17 % Favored : 83.45 % 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: 0.63 (0.10), residues: 7776 helix: 1.62 (0.08), residues: 3720 sheet: 0.47 (0.16), residues: 1020 loop : -1.15 (0.11), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 246 HIS 0.006 0.002 HIS J 124 PHE 0.032 0.002 PHE A 401 TYR 0.077 0.003 TYR C 471 ARG 0.034 0.001 ARG K 449 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 770 time to evaluate : 5.686 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8230 (mmt) REVERT: A 336 GLN cc_start: 0.8028 (tt0) cc_final: 0.7634 (mt0) REVERT: A 399 GLN cc_start: 0.8207 (mt0) cc_final: 0.7917 (mt0) REVERT: B 108 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: B 176 ARG cc_start: 0.8152 (mtm180) cc_final: 0.7516 (ttm110) REVERT: B 188 ILE cc_start: 0.8468 (pt) cc_final: 0.8163 (pp) REVERT: B 232 GLU cc_start: 0.7906 (tp30) cc_final: 0.7352 (mm-30) REVERT: B 336 GLN cc_start: 0.7886 (tt0) cc_final: 0.7335 (mt0) REVERT: C 46 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8223 (mtp180) REVERT: C 130 MET cc_start: 0.8634 (tpp) cc_final: 0.8113 (mpp) REVERT: C 289 MET cc_start: 0.8705 (mmt) cc_final: 0.8376 (mmt) REVERT: C 325 TYR cc_start: 0.7383 (t80) cc_final: 0.6812 (t80) REVERT: C 336 GLN cc_start: 0.8175 (tt0) cc_final: 0.7698 (mt0) REVERT: C 458 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.8033 (tmm) REVERT: D 336 GLN cc_start: 0.8039 (tt0) cc_final: 0.7650 (mt0) REVERT: D 371 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6927 (tt0) REVERT: E 168 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8673 (p) REVERT: E 176 ARG cc_start: 0.8074 (mtm180) cc_final: 0.7519 (ttm110) REVERT: E 208 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7127 (mt-10) REVERT: E 232 GLU cc_start: 0.7907 (tp30) cc_final: 0.7461 (mm-30) REVERT: E 280 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8378 (mt-10) REVERT: E 289 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8146 (mmm) REVERT: E 336 GLN cc_start: 0.7829 (tt0) cc_final: 0.7352 (mt0) REVERT: E 468 LYS cc_start: 0.8739 (tptt) cc_final: 0.8440 (tppt) REVERT: F 167 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8152 (tttt) REVERT: F 301 MET cc_start: 0.8557 (mtm) cc_final: 0.8292 (mtt) REVERT: F 325 TYR cc_start: 0.7451 (t80) cc_final: 0.6920 (t80) REVERT: F 336 GLN cc_start: 0.8173 (tt0) cc_final: 0.7701 (mt0) REVERT: G 336 GLN cc_start: 0.8025 (tt0) cc_final: 0.7617 (mt0) REVERT: G 401 PHE cc_start: 0.8106 (t80) cc_final: 0.7886 (t80) REVERT: H 161 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8874 (tt) REVERT: H 168 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8672 (p) REVERT: H 214 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8361 (mm-30) REVERT: H 280 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8280 (mt-10) REVERT: H 289 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8009 (mmm) REVERT: H 336 GLN cc_start: 0.7788 (tt0) cc_final: 0.7359 (mt0) REVERT: H 399 GLN cc_start: 0.7906 (mt0) cc_final: 0.7666 (mt0) REVERT: H 468 LYS cc_start: 0.8872 (tptt) cc_final: 0.8580 (tppt) REVERT: I 130 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8119 (mpp) REVERT: I 301 MET cc_start: 0.8524 (mtm) cc_final: 0.8288 (mtt) REVERT: I 334 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7113 (mt-10) REVERT: I 336 GLN cc_start: 0.8125 (tt0) cc_final: 0.7710 (mt0) REVERT: I 341 ARG cc_start: 0.8348 (ttp-170) cc_final: 0.7967 (ttp-170) REVERT: I 458 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7956 (tmm) REVERT: J 23 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8407 (mmtp) REVERT: J 130 MET cc_start: 0.8590 (mpp) cc_final: 0.8253 (mmt) REVERT: J 336 GLN cc_start: 0.7994 (tt0) cc_final: 0.7591 (mt0) REVERT: J 399 GLN cc_start: 0.8118 (mt0) cc_final: 0.7837 (mt0) REVERT: J 477 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7837 (mm) REVERT: K 188 ILE cc_start: 0.8182 (pt) cc_final: 0.7873 (pp) REVERT: K 289 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8088 (mmm) REVERT: K 336 GLN cc_start: 0.7927 (tt0) cc_final: 0.7473 (mt0) REVERT: K 399 GLN cc_start: 0.8075 (mt0) cc_final: 0.7836 (mt0) REVERT: L 95 MET cc_start: 0.5734 (OUTLIER) cc_final: 0.5385 (ttp) REVERT: L 130 MET cc_start: 0.8640 (tpp) cc_final: 0.8110 (mpp) REVERT: L 171 MET cc_start: 0.8212 (mtm) cc_final: 0.7979 (mtm) REVERT: L 289 MET cc_start: 0.8594 (mmt) cc_final: 0.8248 (mmt) REVERT: L 336 GLN cc_start: 0.8166 (tt0) cc_final: 0.7690 (mt0) REVERT: L 404 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7681 (mm-30) REVERT: N 163 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8374 (tpp) REVERT: O 99 TYR cc_start: 0.9254 (m-80) cc_final: 0.8757 (m-80) REVERT: O 115 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6281 (mm-30) REVERT: P 55 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: P 141 ASP cc_start: 0.8626 (t0) cc_final: 0.8398 (t0) REVERT: P 151 GLU cc_start: 0.8591 (tt0) cc_final: 0.8382 (tt0) REVERT: Q 53 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8338 (mm-40) REVERT: Q 178 LYS cc_start: 0.8678 (mmpt) cc_final: 0.8413 (mttm) REVERT: R 99 TYR cc_start: 0.9140 (m-80) cc_final: 0.8715 (m-80) REVERT: R 115 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.5993 (mm-30) REVERT: R 141 ASP cc_start: 0.8483 (t0) cc_final: 0.7928 (t0) REVERT: R 163 MET cc_start: 0.8566 (tpp) cc_final: 0.8361 (tpt) REVERT: S 1 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8080 (ttp) REVERT: T 137 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.7101 (t70) REVERT: T 163 MET cc_start: 0.8667 (tpp) cc_final: 0.8352 (tpp) REVERT: U 36 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8286 (mp) REVERT: U 45 GLU cc_start: 0.8019 (tt0) cc_final: 0.7770 (tt0) REVERT: U 159 GLU cc_start: 0.7896 (tp30) cc_final: 0.7655 (tp30) REVERT: U 163 MET cc_start: 0.8679 (tpt) cc_final: 0.8238 (tpt) REVERT: W 39 LYS cc_start: 0.8481 (mmtt) cc_final: 0.8121 (mptp) REVERT: W 137 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6697 (t70) REVERT: W 161 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7908 (mm-40) REVERT: W 163 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8411 (tpp) REVERT: X 99 TYR cc_start: 0.9269 (m-80) cc_final: 0.8732 (m-80) REVERT: X 141 ASP cc_start: 0.7999 (t0) cc_final: 0.7710 (t0) outliers start: 212 outliers final: 77 residues processed: 876 average time/residue: 1.4618 time to fit residues: 1617.8395 Evaluate side-chains 824 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 719 time to evaluate : 5.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 468 LYS Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 407 SER Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 167 LYS Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 171 MET Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 180 SER Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 383 ASP Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 208 GLU Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain I residue 188 ILE Chi-restraints excluded: chain I residue 458 MET Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain J residue 477 LEU Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 289 MET Chi-restraints excluded: chain K residue 400 GLN Chi-restraints excluded: chain K residue 441 LEU Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 441 LEU Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 163 MET Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain P residue 165 ASN Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 53 GLN Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain R residue 39 LYS Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 143 SER Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain T residue 137 ASP Chi-restraints excluded: chain U residue 36 LEU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain W residue 97 THR Chi-restraints excluded: chain W residue 137 ASP Chi-restraints excluded: chain W residue 141 ASP Chi-restraints excluded: chain W residue 161 GLN Chi-restraints excluded: chain W residue 163 MET Chi-restraints excluded: chain X residue 61 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 249 optimal weight: 2.9990 chunk 668 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 435 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 743 optimal weight: 0.0010 chunk 616 optimal weight: 7.9990 chunk 344 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 245 optimal weight: 1.9990 chunk 390 optimal weight: 3.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 446 ASN J 77 GLN K 446 ASN Q 181 ASN U 93 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 61404 Z= 0.139 Angle : 0.490 9.098 83556 Z= 0.261 Chirality : 0.038 0.173 9804 Planarity : 0.007 0.393 10764 Dihedral : 4.029 64.419 8640 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.98 % Allowed : 15.09 % Favored : 82.93 % 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: 1.19 (0.10), residues: 7776 helix: 2.19 (0.09), residues: 3708 sheet: 0.66 (0.17), residues: 1020 loop : -0.97 (0.12), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 246 HIS 0.002 0.001 HIS G 29 PHE 0.029 0.001 PHE J 401 TYR 0.077 0.001 TYR E 471 ARG 0.034 0.001 ARG H 449 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 772 time to evaluate : 5.376 Fit side-chains REVERT: A 399 GLN cc_start: 0.8038 (mt0) cc_final: 0.7663 (mt0) REVERT: A 457 ASP cc_start: 0.8068 (t0) cc_final: 0.7669 (m-30) REVERT: B 16 ARG cc_start: 0.8620 (mtp85) cc_final: 0.8394 (mtp85) REVERT: B 108 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7480 (tt0) REVERT: B 176 ARG cc_start: 0.8098 (mtm180) cc_final: 0.7414 (ttm110) REVERT: B 188 ILE cc_start: 0.8396 (pt) cc_final: 0.8113 (pp) REVERT: B 336 GLN cc_start: 0.7858 (tt0) cc_final: 0.7355 (mt0) REVERT: C 46 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7642 (mtp180) REVERT: C 289 MET cc_start: 0.8534 (mmt) cc_final: 0.8280 (mmt) REVERT: C 336 GLN cc_start: 0.8025 (tt0) cc_final: 0.7613 (mt0) REVERT: C 441 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8567 (mt) REVERT: C 457 ASP cc_start: 0.8454 (t0) cc_final: 0.8075 (m-30) REVERT: E 16 ARG cc_start: 0.8566 (mtp85) cc_final: 0.8270 (mtp85) REVERT: E 208 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6962 (mt-10) REVERT: E 280 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8178 (mt-10) REVERT: E 336 GLN cc_start: 0.7880 (tt0) cc_final: 0.7404 (mt0) REVERT: E 404 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7318 (mm-30) REVERT: E 468 LYS cc_start: 0.8708 (tptt) cc_final: 0.8362 (tppt) REVERT: E 473 THR cc_start: 0.8330 (m) cc_final: 0.7824 (p) REVERT: F 167 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8077 (tttt) REVERT: F 301 MET cc_start: 0.8398 (mtm) cc_final: 0.8075 (mtt) REVERT: F 336 GLN cc_start: 0.8064 (tt0) cc_final: 0.7644 (mt0) REVERT: G 457 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7477 (m-30) REVERT: H 168 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8520 (p) REVERT: H 280 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8126 (mt-10) REVERT: H 336 GLN cc_start: 0.7813 (tt0) cc_final: 0.7353 (mt0) REVERT: H 371 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7113 (tt0) REVERT: H 468 LYS cc_start: 0.8912 (tptt) cc_final: 0.8557 (tppt) REVERT: I 22 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8192 (tp) REVERT: I 130 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8066 (mpp) REVERT: I 336 GLN cc_start: 0.8062 (tt0) cc_final: 0.7661 (mt0) REVERT: I 341 ARG cc_start: 0.7919 (ttp-170) cc_final: 0.7526 (ttp-170) REVERT: I 458 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.8017 (tmm) REVERT: J 399 GLN cc_start: 0.7932 (mt0) cc_final: 0.7654 (mt0) REVERT: J 457 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7481 (m-30) REVERT: K 16 ARG cc_start: 0.8560 (mtp85) cc_final: 0.8352 (mtp85) REVERT: K 48 ASN cc_start: 0.8601 (p0) cc_final: 0.8370 (p0) REVERT: K 188 ILE cc_start: 0.8224 (pt) cc_final: 0.7951 (pp) REVERT: K 282 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: K 336 GLN cc_start: 0.7802 (tt0) cc_final: 0.7343 (mt0) REVERT: K 399 GLN cc_start: 0.7830 (mt0) cc_final: 0.7607 (mt0) REVERT: L 22 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8304 (tp) REVERT: L 171 MET cc_start: 0.8121 (mtm) cc_final: 0.7802 (mtm) REVERT: L 289 MET cc_start: 0.8481 (mmt) cc_final: 0.8201 (mmt) REVERT: L 336 GLN cc_start: 0.8078 (tt0) cc_final: 0.7658 (mt0) REVERT: O 99 TYR cc_start: 0.9202 (m-80) cc_final: 0.8688 (m-80) REVERT: O 141 ASP cc_start: 0.7905 (t0) cc_final: 0.7584 (t0) REVERT: O 163 MET cc_start: 0.8549 (tpt) cc_final: 0.8309 (tpt) REVERT: P 55 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: Q 45 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7275 (tt0) REVERT: Q 178 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8315 (mttp) REVERT: R 99 TYR cc_start: 0.9172 (m-80) cc_final: 0.8657 (m-80) REVERT: R 115 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.5734 (mm-30) REVERT: R 141 ASP cc_start: 0.8246 (t0) cc_final: 0.8001 (t0) REVERT: R 155 MET cc_start: 0.8634 (tpp) cc_final: 0.8392 (tpp) REVERT: R 158 VAL cc_start: 0.8722 (t) cc_final: 0.8411 (t) REVERT: S 88 ASN cc_start: 0.8182 (t0) cc_final: 0.7965 (t0) REVERT: T 45 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7256 (tt0) REVERT: T 160 GLU cc_start: 0.7659 (tt0) cc_final: 0.7433 (tt0) REVERT: T 163 MET cc_start: 0.8279 (tpp) cc_final: 0.7995 (tpp) REVERT: U 45 GLU cc_start: 0.7927 (tt0) cc_final: 0.7670 (tt0) REVERT: W 39 LYS cc_start: 0.8347 (mmtt) cc_final: 0.8103 (mptp) REVERT: W 160 GLU cc_start: 0.7515 (tt0) cc_final: 0.7225 (tt0) REVERT: W 161 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7573 (mm-40) REVERT: X 99 TYR cc_start: 0.9180 (m-80) cc_final: 0.8547 (m-80) REVERT: X 141 ASP cc_start: 0.7736 (t0) cc_final: 0.7476 (t0) REVERT: X 158 VAL cc_start: 0.8690 (t) cc_final: 0.8298 (t) outliers start: 124 outliers final: 20 residues processed: 840 average time/residue: 1.5056 time to fit residues: 1594.5878 Evaluate side-chains 755 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 715 time to evaluate : 5.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 404 GLU Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 167 LYS Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 383 ASP Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 371 GLU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 458 MET Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain K residue 282 GLU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 165 ASN Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 178 LYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain S residue 143 SER Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain W residue 161 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 716 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 423 optimal weight: 20.0000 chunk 542 optimal weight: 2.9990 chunk 420 optimal weight: 3.9990 chunk 625 optimal weight: 1.9990 chunk 414 optimal weight: 7.9990 chunk 740 optimal weight: 3.9990 chunk 463 optimal weight: 0.9990 chunk 451 optimal weight: 0.9990 chunk 341 optimal weight: 0.1980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 295 GLN F 408 ASN G 408 ASN H 399 GLN I 408 ASN J 77 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 61404 Z= 0.142 Angle : 0.479 10.212 83556 Z= 0.254 Chirality : 0.038 0.202 9804 Planarity : 0.008 0.418 10764 Dihedral : 3.932 73.611 8640 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.71 % Allowed : 15.77 % Favored : 82.52 % 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: 1.45 (0.10), residues: 7776 helix: 2.54 (0.09), residues: 3636 sheet: 0.74 (0.17), residues: 1020 loop : -0.93 (0.11), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 49 HIS 0.002 0.001 HIS E 29 PHE 0.031 0.001 PHE G 401 TYR 0.083 0.001 TYR B 471 ARG 0.046 0.001 ARG H 449 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 764 time to evaluate : 5.375 Fit side-chains REVERT: A 289 MET cc_start: 0.8660 (mmt) cc_final: 0.8191 (mmt) REVERT: A 399 GLN cc_start: 0.7970 (mt0) cc_final: 0.7570 (mt0) REVERT: A 457 ASP cc_start: 0.8115 (t0) cc_final: 0.7712 (m-30) REVERT: B 16 ARG cc_start: 0.8598 (mtp85) cc_final: 0.8336 (mtp85) REVERT: B 176 ARG cc_start: 0.8102 (mtm180) cc_final: 0.7417 (ttm110) REVERT: B 188 ILE cc_start: 0.8314 (pt) cc_final: 0.8096 (pp) REVERT: B 336 GLN cc_start: 0.7882 (tt0) cc_final: 0.7400 (mt0) REVERT: C 46 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8182 (mtp180) REVERT: C 336 GLN cc_start: 0.7987 (tt0) cc_final: 0.7595 (mt0) REVERT: D 457 ASP cc_start: 0.8015 (t0) cc_final: 0.7530 (m-30) REVERT: E 16 ARG cc_start: 0.8716 (mtp85) cc_final: 0.8509 (mtp85) REVERT: E 168 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8529 (p) REVERT: E 208 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7037 (mt-10) REVERT: E 280 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8132 (mt-10) REVERT: E 289 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.7957 (mmm) REVERT: E 336 GLN cc_start: 0.7854 (tt0) cc_final: 0.7411 (mt0) REVERT: E 468 LYS cc_start: 0.8695 (tptt) cc_final: 0.8354 (tppt) REVERT: E 473 THR cc_start: 0.8352 (m) cc_final: 0.7963 (p) REVERT: F 130 MET cc_start: 0.8685 (tpp) cc_final: 0.8085 (mpp) REVERT: F 167 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8057 (tttt) REVERT: F 301 MET cc_start: 0.8390 (mtm) cc_final: 0.8070 (mtt) REVERT: F 336 GLN cc_start: 0.8020 (tt0) cc_final: 0.7596 (mt0) REVERT: G 236 GLU cc_start: 0.7514 (tt0) cc_final: 0.7266 (tt0) REVERT: G 457 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: H 161 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8773 (tt) REVERT: H 168 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8501 (p) REVERT: H 280 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8140 (mt-10) REVERT: H 336 GLN cc_start: 0.7839 (tt0) cc_final: 0.7361 (mt0) REVERT: H 371 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7092 (tt0) REVERT: H 468 LYS cc_start: 0.8835 (tptt) cc_final: 0.8421 (tppt) REVERT: I 22 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8193 (tp) REVERT: I 130 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8041 (mpp) REVERT: I 336 GLN cc_start: 0.8074 (tt0) cc_final: 0.7668 (mt0) REVERT: I 341 ARG cc_start: 0.8058 (ttp-170) cc_final: 0.7609 (ttp-170) REVERT: I 451 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8177 (t0) REVERT: I 458 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.8021 (tmm) REVERT: J 22 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8572 (tm) REVERT: J 399 GLN cc_start: 0.8015 (mt0) cc_final: 0.7680 (mt0) REVERT: J 457 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: K 48 ASN cc_start: 0.8560 (p0) cc_final: 0.8316 (p0) REVERT: K 188 ILE cc_start: 0.8200 (pt) cc_final: 0.7923 (pp) REVERT: K 336 GLN cc_start: 0.7828 (tt0) cc_final: 0.7367 (mt0) REVERT: K 399 GLN cc_start: 0.7846 (mt0) cc_final: 0.7622 (mt0) REVERT: L 22 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8307 (tp) REVERT: L 171 MET cc_start: 0.8089 (mtm) cc_final: 0.7810 (mtm) REVERT: L 336 GLN cc_start: 0.8033 (tt0) cc_final: 0.7620 (mt0) REVERT: N 39 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8072 (mptp) REVERT: O 99 TYR cc_start: 0.9166 (m-80) cc_final: 0.8519 (m-80) REVERT: O 141 ASP cc_start: 0.7876 (t0) cc_final: 0.7562 (t0) REVERT: O 163 MET cc_start: 0.8607 (tpt) cc_final: 0.8263 (tpt) REVERT: P 55 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: Q 45 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: Q 178 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8330 (mttm) REVERT: R 99 TYR cc_start: 0.9170 (m-80) cc_final: 0.8636 (m-80) REVERT: R 115 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.5759 (mm-30) REVERT: R 141 ASP cc_start: 0.8215 (t0) cc_final: 0.7984 (t0) REVERT: R 158 VAL cc_start: 0.8674 (t) cc_final: 0.8333 (t) REVERT: T 45 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7159 (tt0) REVERT: T 160 GLU cc_start: 0.7564 (tt0) cc_final: 0.7309 (tt0) REVERT: U 45 GLU cc_start: 0.7900 (tt0) cc_final: 0.7628 (tt0) REVERT: U 149 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7723 (tp) REVERT: V 166 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8254 (tptm) REVERT: W 39 LYS cc_start: 0.8362 (mmtt) cc_final: 0.8105 (mptp) REVERT: W 160 GLU cc_start: 0.7546 (tt0) cc_final: 0.7248 (tt0) REVERT: W 161 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7532 (mm-40) REVERT: X 99 TYR cc_start: 0.9182 (m-80) cc_final: 0.8508 (m-80) REVERT: X 141 ASP cc_start: 0.7700 (t0) cc_final: 0.7432 (t0) REVERT: X 158 VAL cc_start: 0.8750 (t) cc_final: 0.8385 (t) outliers start: 107 outliers final: 33 residues processed: 827 average time/residue: 1.4874 time to fit residues: 1549.4719 Evaluate side-chains 774 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 718 time to evaluate : 5.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 167 LYS Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 383 ASP Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 371 GLU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 451 ASP Chi-restraints excluded: chain I residue 458 MET Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 165 ASN Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain Q residue 178 LYS Chi-restraints excluded: chain R residue 39 LYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain S residue 143 SER Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 166 LYS Chi-restraints excluded: chain W residue 161 GLN Chi-restraints excluded: chain X residue 54 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 457 optimal weight: 0.9980 chunk 295 optimal weight: 0.9980 chunk 442 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 145 optimal weight: 0.0980 chunk 143 optimal weight: 0.9990 chunk 470 optimal weight: 2.9990 chunk 504 optimal weight: 0.8980 chunk 365 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 581 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 ASN F 408 ASN G 408 ASN I 408 ASN J 77 GLN K 446 ASN L 408 ASN Q 88 ASN S 34 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 61404 Z= 0.143 Angle : 0.478 9.568 83556 Z= 0.253 Chirality : 0.038 0.191 9804 Planarity : 0.008 0.358 10764 Dihedral : 3.805 62.581 8640 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.64 % Allowed : 16.08 % Favored : 82.28 % 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: 1.54 (0.10), residues: 7776 helix: 2.59 (0.09), residues: 3636 sheet: 0.80 (0.17), residues: 1020 loop : -0.87 (0.11), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 246 HIS 0.002 0.001 HIS E 29 PHE 0.029 0.001 PHE G 401 TYR 0.054 0.001 TYR B 471 ARG 0.052 0.001 ARG D 449 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 754 time to evaluate : 5.545 Fit side-chains REVERT: A 22 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8609 (tm) REVERT: A 399 GLN cc_start: 0.7947 (mt0) cc_final: 0.7549 (mt0) REVERT: A 457 ASP cc_start: 0.8162 (t0) cc_final: 0.7763 (m-30) REVERT: B 16 ARG cc_start: 0.8640 (mtp85) cc_final: 0.8366 (mtp85) REVERT: B 176 ARG cc_start: 0.8093 (mtm180) cc_final: 0.7414 (ttm110) REVERT: B 188 ILE cc_start: 0.8319 (pt) cc_final: 0.8098 (pp) REVERT: B 336 GLN cc_start: 0.7884 (tt0) cc_final: 0.7406 (mt0) REVERT: C 289 MET cc_start: 0.8468 (mmt) cc_final: 0.8248 (mmt) REVERT: C 336 GLN cc_start: 0.7981 (tt0) cc_final: 0.7594 (mt0) REVERT: D 457 ASP cc_start: 0.8061 (t0) cc_final: 0.7592 (m-30) REVERT: E 108 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: E 168 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8489 (p) REVERT: E 208 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7047 (mt-10) REVERT: E 280 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8109 (mt-10) REVERT: E 336 GLN cc_start: 0.7753 (tt0) cc_final: 0.7323 (mt0) REVERT: E 404 GLU cc_start: 0.7638 (mp0) cc_final: 0.7372 (mm-30) REVERT: E 468 LYS cc_start: 0.8766 (tptt) cc_final: 0.8468 (tppt) REVERT: E 473 THR cc_start: 0.8279 (m) cc_final: 0.7892 (p) REVERT: F 336 GLN cc_start: 0.7944 (tt0) cc_final: 0.7554 (mt0) REVERT: G 236 GLU cc_start: 0.7504 (tt0) cc_final: 0.7262 (tt0) REVERT: G 412 LEU cc_start: 0.8588 (mt) cc_final: 0.8309 (mp) REVERT: G 457 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7493 (m-30) REVERT: G 458 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.6948 (ttp) REVERT: G 473 THR cc_start: 0.8396 (m) cc_final: 0.8061 (p) REVERT: H 48 ASN cc_start: 0.8669 (p0) cc_final: 0.8379 (p0) REVERT: H 161 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8756 (tt) REVERT: H 168 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8494 (p) REVERT: H 280 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8123 (mt-10) REVERT: H 336 GLN cc_start: 0.7844 (tt0) cc_final: 0.7371 (mt0) REVERT: H 371 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7101 (tt0) REVERT: H 404 GLU cc_start: 0.7879 (mp0) cc_final: 0.7618 (mm-30) REVERT: H 457 ASP cc_start: 0.8433 (t0) cc_final: 0.7886 (m-30) REVERT: H 468 LYS cc_start: 0.8822 (tptt) cc_final: 0.8423 (tppt) REVERT: I 22 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8208 (tp) REVERT: I 130 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8017 (mpp) REVERT: I 336 GLN cc_start: 0.7945 (tt0) cc_final: 0.7576 (mt0) REVERT: I 341 ARG cc_start: 0.8050 (ttp-170) cc_final: 0.7595 (ttp-170) REVERT: I 457 ASP cc_start: 0.8206 (m-30) cc_final: 0.7885 (m-30) REVERT: I 458 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7927 (tmm) REVERT: J 22 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8581 (tm) REVERT: J 399 GLN cc_start: 0.8002 (mt0) cc_final: 0.7679 (mt0) REVERT: J 457 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7236 (m-30) REVERT: J 477 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7834 (mm) REVERT: K 188 ILE cc_start: 0.8289 (pt) cc_final: 0.7992 (pp) REVERT: K 282 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7946 (tm-30) REVERT: K 336 GLN cc_start: 0.7835 (tt0) cc_final: 0.7361 (mt0) REVERT: K 399 GLN cc_start: 0.7543 (mt0) cc_final: 0.7336 (mt0) REVERT: L 22 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8315 (tp) REVERT: L 171 MET cc_start: 0.8090 (mtm) cc_final: 0.7818 (mtm) REVERT: L 336 GLN cc_start: 0.7955 (tt0) cc_final: 0.7574 (mt0) REVERT: L 457 ASP cc_start: 0.8060 (m-30) cc_final: 0.7686 (m-30) REVERT: N 39 LYS cc_start: 0.8407 (mmtt) cc_final: 0.8082 (mptp) REVERT: O 99 TYR cc_start: 0.9158 (m-80) cc_final: 0.8538 (m-80) REVERT: O 141 ASP cc_start: 0.7883 (t0) cc_final: 0.7562 (t0) REVERT: O 163 MET cc_start: 0.8597 (tpt) cc_final: 0.8315 (tpt) REVERT: P 1 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8247 (ttp) REVERT: P 55 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7749 (mt-10) REVERT: Q 45 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7225 (tt0) REVERT: Q 178 LYS cc_start: 0.8584 (mmpt) cc_final: 0.8327 (mttm) REVERT: R 99 TYR cc_start: 0.9166 (m-80) cc_final: 0.8589 (m-80) REVERT: R 115 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.5745 (mm-30) REVERT: R 141 ASP cc_start: 0.8179 (t0) cc_final: 0.7949 (t0) REVERT: R 158 VAL cc_start: 0.8694 (t) cc_final: 0.8334 (t) REVERT: S 1 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7978 (ttt) REVERT: S 178 LYS cc_start: 0.8941 (ttmm) cc_final: 0.8579 (mttm) REVERT: T 45 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7139 (tt0) REVERT: T 160 GLU cc_start: 0.7541 (tt0) cc_final: 0.7277 (tt0) REVERT: U 45 GLU cc_start: 0.7900 (tt0) cc_final: 0.7605 (tt0) REVERT: U 107 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7783 (ttt-90) REVERT: U 149 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7667 (tp) REVERT: V 166 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8211 (tptm) REVERT: W 39 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8100 (mptp) REVERT: W 160 GLU cc_start: 0.7530 (tt0) cc_final: 0.7238 (tt0) REVERT: W 161 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7521 (mm-40) REVERT: X 99 TYR cc_start: 0.9175 (m-80) cc_final: 0.8525 (m-80) REVERT: X 141 ASP cc_start: 0.7895 (t0) cc_final: 0.7591 (t0) REVERT: X 158 VAL cc_start: 0.8700 (t) cc_final: 0.8310 (t) outliers start: 103 outliers final: 41 residues processed: 815 average time/residue: 1.5129 time to fit residues: 1553.4925 Evaluate side-chains 785 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 719 time to evaluate : 5.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 437 LEU Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 383 ASP Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 458 MET Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 371 GLU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 188 ILE Chi-restraints excluded: chain I residue 458 MET Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain J residue 477 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 282 GLU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 165 ASN Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 39 LYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 143 SER Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain U residue 54 ASP Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 166 LYS Chi-restraints excluded: chain W residue 161 GLN Chi-restraints excluded: chain X residue 54 ASP Chi-restraints excluded: chain X residue 61 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 673 optimal weight: 5.9990 chunk 709 optimal weight: 4.9990 chunk 647 optimal weight: 7.9990 chunk 689 optimal weight: 0.6980 chunk 708 optimal weight: 0.6980 chunk 415 optimal weight: 0.9990 chunk 300 optimal weight: 8.9990 chunk 541 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 623 optimal weight: 3.9990 chunk 652 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 ASN F 408 ASN G 408 ASN I 408 ASN J 77 GLN K 48 ASN L 408 ASN P 34 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 61404 Z= 0.260 Angle : 0.558 12.035 83556 Z= 0.294 Chirality : 0.040 0.215 9804 Planarity : 0.009 0.331 10764 Dihedral : 4.275 137.168 8640 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.60 % Allowed : 16.57 % Favored : 81.83 % 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: 1.20 (0.10), residues: 7776 helix: 2.17 (0.09), residues: 3720 sheet: 0.74 (0.17), residues: 1020 loop : -0.97 (0.12), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 246 HIS 0.004 0.001 HIS J 124 PHE 0.031 0.001 PHE G 401 TYR 0.039 0.002 TYR B 471 ARG 0.052 0.001 ARG J 449 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 724 time to evaluate : 5.263 Fit side-chains REVERT: A 289 MET cc_start: 0.8651 (mmt) cc_final: 0.8174 (mmt) REVERT: A 399 GLN cc_start: 0.8003 (mt0) cc_final: 0.7609 (mt0) REVERT: B 108 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: B 176 ARG cc_start: 0.8126 (mtm180) cc_final: 0.7432 (ttm110) REVERT: B 188 ILE cc_start: 0.8198 (pt) cc_final: 0.7946 (pp) REVERT: B 336 GLN cc_start: 0.7897 (tt0) cc_final: 0.7403 (mt0) REVERT: B 457 ASP cc_start: 0.8487 (t0) cc_final: 0.8002 (m-30) REVERT: B 468 LYS cc_start: 0.8833 (tptt) cc_final: 0.8427 (tppt) REVERT: C 289 MET cc_start: 0.8548 (mmt) cc_final: 0.8345 (mmt) REVERT: C 336 GLN cc_start: 0.8046 (tt0) cc_final: 0.7628 (mt0) REVERT: D 180 SER cc_start: 0.8718 (m) cc_final: 0.8404 (p) REVERT: E 168 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8600 (p) REVERT: E 208 GLU cc_start: 0.7313 (mt-10) cc_final: 0.7090 (mt-10) REVERT: E 280 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8228 (mt-10) REVERT: E 289 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.7979 (mmm) REVERT: E 336 GLN cc_start: 0.7867 (tt0) cc_final: 0.7382 (mt0) REVERT: E 404 GLU cc_start: 0.7683 (mp0) cc_final: 0.7432 (mm-30) REVERT: E 473 THR cc_start: 0.8372 (m) cc_final: 0.7982 (p) REVERT: F 301 MET cc_start: 0.8483 (mtm) cc_final: 0.8202 (mtt) REVERT: F 336 GLN cc_start: 0.8038 (tt0) cc_final: 0.7622 (mt0) REVERT: G 236 GLU cc_start: 0.7551 (tt0) cc_final: 0.7289 (tt0) REVERT: G 408 ASN cc_start: 0.7745 (m-40) cc_final: 0.7491 (m-40) REVERT: G 457 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7684 (m-30) REVERT: G 473 THR cc_start: 0.8447 (m) cc_final: 0.8121 (p) REVERT: H 48 ASN cc_start: 0.8655 (p0) cc_final: 0.8376 (p0) REVERT: H 161 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8756 (tt) REVERT: H 168 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8594 (p) REVERT: H 280 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8223 (mt-10) REVERT: H 336 GLN cc_start: 0.7863 (tt0) cc_final: 0.7392 (mt0) REVERT: H 371 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7134 (tt0) REVERT: H 468 LYS cc_start: 0.8874 (tptt) cc_final: 0.8453 (tppt) REVERT: I 22 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8237 (tp) REVERT: I 130 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8070 (mpp) REVERT: I 336 GLN cc_start: 0.8088 (tt0) cc_final: 0.7684 (mt0) REVERT: I 341 ARG cc_start: 0.8148 (ttp-170) cc_final: 0.7702 (ttp-170) REVERT: I 404 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7521 (mm-30) REVERT: I 457 ASP cc_start: 0.8136 (m-30) cc_final: 0.7825 (m-30) REVERT: J 22 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8623 (tm) REVERT: J 130 MET cc_start: 0.8544 (mpp) cc_final: 0.8197 (mmt) REVERT: J 399 GLN cc_start: 0.8070 (mt0) cc_final: 0.7754 (mt0) REVERT: J 457 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7323 (m-30) REVERT: J 477 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7790 (mm) REVERT: K 188 ILE cc_start: 0.8324 (pt) cc_final: 0.8019 (pp) REVERT: K 282 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: K 336 GLN cc_start: 0.7851 (tt0) cc_final: 0.7384 (mt0) REVERT: K 399 GLN cc_start: 0.7870 (mt0) cc_final: 0.7648 (mt0) REVERT: L 22 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8291 (tp) REVERT: L 171 MET cc_start: 0.8192 (mtm) cc_final: 0.7919 (mtm) REVERT: L 336 GLN cc_start: 0.8099 (tt0) cc_final: 0.7686 (mt0) REVERT: L 457 ASP cc_start: 0.8207 (m-30) cc_final: 0.7784 (m-30) REVERT: M 55 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: N 39 LYS cc_start: 0.8433 (mmtt) cc_final: 0.7987 (mptp) REVERT: O 99 TYR cc_start: 0.9216 (m-80) cc_final: 0.8660 (m-80) REVERT: O 141 ASP cc_start: 0.8034 (t0) cc_final: 0.7745 (t0) REVERT: O 163 MET cc_start: 0.8693 (tpt) cc_final: 0.8347 (tpt) REVERT: P 55 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: Q 45 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: Q 178 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8370 (mttp) REVERT: R 99 TYR cc_start: 0.9185 (m-80) cc_final: 0.8660 (m-80) REVERT: R 115 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.5841 (mm-30) REVERT: R 141 ASP cc_start: 0.8295 (t0) cc_final: 0.7742 (t0) REVERT: S 1 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8178 (ttt) REVERT: S 141 ASP cc_start: 0.8319 (t70) cc_final: 0.8058 (t70) REVERT: T 45 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: T 137 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6689 (t70) REVERT: U 45 GLU cc_start: 0.7967 (tt0) cc_final: 0.7690 (tt0) REVERT: V 166 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8367 (tptm) REVERT: W 39 LYS cc_start: 0.8426 (mmtt) cc_final: 0.8016 (mptp) REVERT: W 93 ASN cc_start: 0.9154 (OUTLIER) cc_final: 0.8707 (m110) REVERT: W 160 GLU cc_start: 0.7870 (tt0) cc_final: 0.7532 (tt0) REVERT: W 161 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7678 (mm-40) REVERT: X 99 TYR cc_start: 0.9201 (m-80) cc_final: 0.8588 (m-80) REVERT: X 141 ASP cc_start: 0.7961 (t0) cc_final: 0.7647 (t0) outliers start: 100 outliers final: 42 residues processed: 788 average time/residue: 1.5346 time to fit residues: 1517.7556 Evaluate side-chains 766 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 699 time to evaluate : 5.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 171 MET Chi-restraints excluded: chain F residue 437 LEU Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 383 ASP Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 371 GLU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain I residue 188 ILE Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain J residue 477 LEU Chi-restraints excluded: chain K residue 282 GLU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain M residue 55 GLU Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 165 ASN Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain Q residue 178 LYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 143 SER Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 137 ASP Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 166 LYS Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 93 ASN Chi-restraints excluded: chain W residue 149 LEU Chi-restraints excluded: chain W residue 161 GLN Chi-restraints excluded: chain X residue 54 ASP Chi-restraints excluded: chain X residue 61 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 687 optimal weight: 2.9990 chunk 452 optimal weight: 0.3980 chunk 729 optimal weight: 1.9990 chunk 445 optimal weight: 4.9990 chunk 346 optimal weight: 4.9990 chunk 507 optimal weight: 0.9990 chunk 765 optimal weight: 0.9980 chunk 704 optimal weight: 3.9990 chunk 609 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 470 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 ASN F 408 ASN I 408 ASN J 77 GLN L 408 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 61404 Z= 0.204 Angle : 0.532 17.892 83556 Z= 0.280 Chirality : 0.039 0.225 9804 Planarity : 0.009 0.429 10764 Dihedral : 4.771 179.082 8640 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.33 % Allowed : 16.94 % Favored : 81.74 % 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: 1.24 (0.10), residues: 7776 helix: 2.23 (0.09), residues: 3708 sheet: 0.74 (0.17), residues: 1020 loop : -0.98 (0.11), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 246 HIS 0.003 0.001 HIS J 124 PHE 0.030 0.001 PHE J 401 TYR 0.046 0.001 TYR E 471 ARG 0.053 0.001 ARG G 449 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15552 Ramachandran restraints generated. 7776 Oldfield, 0 Emsley, 7776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 717 time to evaluate : 5.418 Fit side-chains REVERT: A 108 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7229 (tm-30) REVERT: A 399 GLN cc_start: 0.7975 (mt0) cc_final: 0.7585 (mt0) REVERT: B 16 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8127 (mtp85) REVERT: B 48 ASN cc_start: 0.8624 (p0) cc_final: 0.8397 (p0) REVERT: B 108 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7438 (tt0) REVERT: B 176 ARG cc_start: 0.8110 (mtm180) cc_final: 0.7423 (ttm110) REVERT: B 188 ILE cc_start: 0.8182 (pt) cc_final: 0.7937 (pp) REVERT: B 282 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7854 (mm-30) REVERT: B 336 GLN cc_start: 0.7883 (tt0) cc_final: 0.7389 (mt0) REVERT: B 457 ASP cc_start: 0.8172 (t0) cc_final: 0.7947 (m-30) REVERT: C 336 GLN cc_start: 0.8037 (tt0) cc_final: 0.7631 (mt0) REVERT: C 341 ARG cc_start: 0.7891 (ttp-170) cc_final: 0.7346 (ttp-170) REVERT: D 46 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8250 (ttm-80) REVERT: D 180 SER cc_start: 0.8729 (m) cc_final: 0.8419 (p) REVERT: D 457 ASP cc_start: 0.8073 (t0) cc_final: 0.7664 (m-30) REVERT: D 473 THR cc_start: 0.8279 (m) cc_final: 0.7949 (p) REVERT: E 168 VAL cc_start: 0.8837 (OUTLIER) cc_final: 0.8562 (p) REVERT: E 208 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7079 (mt-10) REVERT: E 280 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8194 (mt-10) REVERT: E 289 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.7979 (mmm) REVERT: E 336 GLN cc_start: 0.7848 (tt0) cc_final: 0.7370 (mt0) REVERT: E 473 THR cc_start: 0.8375 (m) cc_final: 0.7988 (p) REVERT: F 336 GLN cc_start: 0.8025 (tt0) cc_final: 0.7610 (mt0) REVERT: F 341 ARG cc_start: 0.7861 (ttp-170) cc_final: 0.7555 (ttp-170) REVERT: G 180 SER cc_start: 0.8633 (m) cc_final: 0.8311 (p) REVERT: G 412 LEU cc_start: 0.8625 (mt) cc_final: 0.8353 (mp) REVERT: G 457 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7721 (m-30) REVERT: G 473 THR cc_start: 0.8375 (m) cc_final: 0.8038 (p) REVERT: H 48 ASN cc_start: 0.8623 (p0) cc_final: 0.8387 (p0) REVERT: H 161 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8753 (tt) REVERT: H 168 VAL cc_start: 0.8835 (OUTLIER) cc_final: 0.8570 (p) REVERT: H 280 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8191 (mt-10) REVERT: H 336 GLN cc_start: 0.7849 (tt0) cc_final: 0.7382 (mt0) REVERT: H 468 LYS cc_start: 0.8882 (tptt) cc_final: 0.8438 (tppt) REVERT: I 22 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8253 (tp) REVERT: I 130 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8054 (mpp) REVERT: I 336 GLN cc_start: 0.8078 (tt0) cc_final: 0.7678 (mt0) REVERT: I 341 ARG cc_start: 0.8104 (ttp-170) cc_final: 0.7620 (ttp-170) REVERT: I 404 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7434 (mm-30) REVERT: J 22 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8639 (tm) REVERT: J 130 MET cc_start: 0.8546 (mpp) cc_final: 0.8203 (mmt) REVERT: J 399 GLN cc_start: 0.8077 (mt0) cc_final: 0.7774 (mt0) REVERT: J 457 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7351 (m-30) REVERT: J 477 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7791 (mm) REVERT: K 282 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: K 336 GLN cc_start: 0.7836 (tt0) cc_final: 0.7376 (mt0) REVERT: K 399 GLN cc_start: 0.7879 (mt0) cc_final: 0.7669 (mt0) REVERT: K 404 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7644 (mm-30) REVERT: L 22 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8296 (tp) REVERT: L 171 MET cc_start: 0.8191 (mtm) cc_final: 0.7907 (mtm) REVERT: L 336 GLN cc_start: 0.8089 (tt0) cc_final: 0.7683 (mt0) REVERT: L 341 ARG cc_start: 0.7774 (ttp-170) cc_final: 0.7386 (ttp-170) REVERT: L 457 ASP cc_start: 0.8237 (m-30) cc_final: 0.7809 (m-30) REVERT: M 55 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: N 39 LYS cc_start: 0.8413 (mmtt) cc_final: 0.7980 (mptp) REVERT: O 99 TYR cc_start: 0.9203 (m-80) cc_final: 0.8637 (m-80) REVERT: O 163 MET cc_start: 0.8685 (tpt) cc_final: 0.8411 (tpt) REVERT: P 55 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7772 (mt-10) REVERT: Q 45 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7262 (tt0) REVERT: Q 178 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8356 (mttp) REVERT: R 99 TYR cc_start: 0.9170 (m-80) cc_final: 0.8654 (m-80) REVERT: R 115 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.5843 (mm-30) REVERT: R 141 ASP cc_start: 0.8246 (t0) cc_final: 0.8023 (t0) REVERT: S 1 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8206 (ttt) REVERT: S 141 ASP cc_start: 0.8279 (t70) cc_final: 0.8039 (t70) REVERT: T 45 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7160 (tt0) REVERT: T 160 GLU cc_start: 0.7725 (tt0) cc_final: 0.7491 (tt0) REVERT: U 45 GLU cc_start: 0.7909 (tt0) cc_final: 0.7641 (tt0) REVERT: W 39 LYS cc_start: 0.8398 (mmtt) cc_final: 0.8002 (mptp) REVERT: W 160 GLU cc_start: 0.7804 (tt0) cc_final: 0.7464 (tt0) REVERT: W 161 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7607 (mm-40) REVERT: X 99 TYR cc_start: 0.9214 (m-80) cc_final: 0.8691 (m-80) outliers start: 83 outliers final: 42 residues processed: 767 average time/residue: 1.5327 time to fit residues: 1471.7901 Evaluate side-chains 767 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 701 time to evaluate : 5.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 171 MET Chi-restraints excluded: chain F residue 437 LEU Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 383 ASP Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 188 ILE Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain J residue 477 LEU Chi-restraints excluded: chain K residue 282 GLU Chi-restraints excluded: chain K residue 404 GLU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain M residue 55 GLU Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 165 ASN Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 178 LYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 143 SER Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 149 LEU Chi-restraints excluded: chain W residue 161 GLN Chi-restraints excluded: chain X residue 54 ASP Chi-restraints excluded: chain X residue 61 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 373 optimal weight: 2.9990 chunk 483 optimal weight: 0.0870 chunk 649 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 561 optimal weight: 6.9990 chunk 89 optimal weight: 0.2980 chunk 169 optimal weight: 2.9990 chunk 610 optimal weight: 3.9990 chunk 255 optimal weight: 6.9990 chunk 626 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.6764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 ASN F 408 ASN I 408 ASN J 77 GLN L 408 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.128524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.103406 restraints weight = 81443.656| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.06 r_work: 0.3107 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 61404 Z= 0.225 Angle : 0.545 14.623 83556 Z= 0.288 Chirality : 0.040 0.216 9804 Planarity : 0.009 0.402 10764 Dihedral : 4.850 175.987 8640 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.44 % Allowed : 16.94 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.17 (0.10), residues: 7776 helix: 2.16 (0.09), residues: 3720 sheet: 0.73 (0.17), residues: 1020 loop : -1.00 (0.12), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 246 HIS 0.004 0.001 HIS J 124 PHE 0.030 0.001 PHE D 401 TYR 0.098 0.002 TYR K 471 ARG 0.048 0.001 ARG G 449 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22540.98 seconds wall clock time: 388 minutes 48.70 seconds (23328.70 seconds total)