Starting phenix.real_space_refine on Sat Jan 18 17:37:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vb4_43112/01_2025/8vb4_43112.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vb4_43112/01_2025/8vb4_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_43112/01_2025/8vb4_43112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vb4_43112/01_2025/8vb4_43112.map" model { file = "/net/cci-nas-00/data/ceres_data/8vb4_43112/01_2025/8vb4_43112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vb4_43112/01_2025/8vb4_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-5571/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: 12.00, 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: 11.32 Conformation dependent library (CDL) restraints added in 6.1 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: 5.16 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: 23.16 Time building geometry restraints manager: 13.38 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: 0.41 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' 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: 2.670 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: 1.650 Check model and map are aligned: 0.350 Set scattering table: 0.420 Process input model: 89.030 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.580 ------------------------------------------------------------------------------- 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 : 5.072 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: 1.6241 time to fit residues: 2546.1217 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 : 5.099 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.137921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113256 restraints weight = 81963.976| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.13 r_work: 0.3242 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 5.434 Fit side-chains REVERT: A 289 MET cc_start: 0.8890 (mmt) cc_final: 0.8517 (mmt) REVERT: A 399 GLN cc_start: 0.7775 (mt0) cc_final: 0.7385 (mt0) REVERT: A 412 LEU cc_start: 0.8494 (mt) cc_final: 0.8267 (mp) REVERT: B 176 ARG cc_start: 0.8620 (mtm180) cc_final: 0.7858 (ttm110) REVERT: B 188 ILE cc_start: 0.7741 (pt) cc_final: 0.7537 (pp) REVERT: B 209 ARG cc_start: 0.8189 (ptm160) cc_final: 0.7889 (ttp-110) REVERT: B 214 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8823 (mm-30) REVERT: B 289 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8940 (mmt) REVERT: B 334 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7165 (mt-10) REVERT: B 336 GLN cc_start: 0.8279 (tt0) cc_final: 0.7871 (mt0) REVERT: B 404 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7580 (mm-30) REVERT: C 171 MET cc_start: 0.8432 (mtm) cc_final: 0.8174 (mtm) REVERT: C 289 MET cc_start: 0.9048 (mmt) cc_final: 0.8645 (mmt) REVERT: C 336 GLN cc_start: 0.8336 (tt0) cc_final: 0.7895 (mt0) REVERT: E 167 LYS cc_start: 0.8398 (ttmt) cc_final: 0.8144 (ttpm) REVERT: E 176 ARG cc_start: 0.8356 (mtm180) cc_final: 0.8041 (ttp80) REVERT: E 336 GLN cc_start: 0.8397 (tt0) cc_final: 0.7970 (mt0) REVERT: F 23 LYS cc_start: 0.8655 (mmmm) cc_final: 0.8372 (mmtt) REVERT: F 181 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7957 (mm-30) REVERT: F 258 LEU cc_start: 0.8677 (tp) cc_final: 0.8432 (tt) REVERT: F 325 TYR cc_start: 0.6739 (t80) cc_final: 0.6145 (t80) REVERT: F 336 GLN cc_start: 0.8505 (tt0) cc_final: 0.8026 (mt0) REVERT: G 336 GLN cc_start: 0.8274 (tt0) cc_final: 0.7959 (mt0) REVERT: G 401 PHE cc_start: 0.8063 (t80) cc_final: 0.7807 (t80) REVERT: H 18 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7780 (m-30) REVERT: H 336 GLN cc_start: 0.8202 (tt0) cc_final: 0.7794 (mt0) REVERT: I 22 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7597 (tm) REVERT: I 112 THR cc_start: 0.7868 (t) cc_final: 0.7663 (t) REVERT: I 130 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8328 (mpp) REVERT: I 171 MET cc_start: 0.8391 (mtp) cc_final: 0.8096 (mtp) REVERT: I 336 GLN cc_start: 0.8499 (tt0) cc_final: 0.8109 (mt0) REVERT: I 404 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7192 (mm-30) REVERT: J 336 GLN cc_start: 0.8317 (tt0) cc_final: 0.7952 (mt0) REVERT: J 399 GLN cc_start: 0.7354 (mt0) cc_final: 0.6970 (mt0) REVERT: K 171 MET cc_start: 0.8463 (mtm) cc_final: 0.8231 (mtm) REVERT: K 236 GLU cc_start: 0.8176 (tt0) cc_final: 0.7939 (tt0) REVERT: K 282 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: K 336 GLN cc_start: 0.8327 (tt0) cc_final: 0.7750 (mt0) REVERT: K 457 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8101 (t0) REVERT: L 171 MET cc_start: 0.8537 (mtm) cc_final: 0.8253 (mtm) REVERT: L 336 GLN cc_start: 0.8536 (tt0) cc_final: 0.8022 (mt0) REVERT: L 404 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7512 (mm-30) REVERT: L 457 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8383 (m-30) REVERT: N 98 MET cc_start: 0.8562 (ttp) cc_final: 0.8254 (ttm) REVERT: N 159 GLU cc_start: 0.8366 (tp30) cc_final: 0.8067 (tp30) REVERT: O 98 MET cc_start: 0.8575 (ttp) cc_final: 0.8275 (ttt) REVERT: O 99 TYR cc_start: 0.9076 (m-80) cc_final: 0.8268 (m-80) REVERT: O 141 ASP cc_start: 0.8261 (t0) cc_final: 0.8044 (t0) REVERT: O 158 VAL cc_start: 0.8824 (t) cc_final: 0.8438 (t) REVERT: P 75 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: Q 159 GLU cc_start: 0.8336 (tp30) cc_final: 0.8019 (tp30) REVERT: R 99 TYR cc_start: 0.8789 (m-80) cc_final: 0.8338 (m-80) REVERT: R 141 ASP cc_start: 0.8724 (t0) cc_final: 0.8155 (t0) REVERT: R 158 VAL cc_start: 0.8553 (t) cc_final: 0.8317 (t) REVERT: S 127 TYR cc_start: 0.8409 (m-80) cc_final: 0.7999 (m-80) REVERT: T 101 THR cc_start: 0.8699 (m) cc_final: 0.8488 (m) REVERT: T 137 ASP cc_start: 0.6995 (t70) cc_final: 0.6538 (t0) REVERT: U 155 MET cc_start: 0.8956 (tpp) cc_final: 0.8573 (tpt) REVERT: W 39 LYS cc_start: 0.8241 (mmtt) cc_final: 0.7893 (mptp) REVERT: X 98 MET cc_start: 0.8936 (ttp) cc_final: 0.8691 (ttt) REVERT: X 99 TYR cc_start: 0.8955 (m-80) cc_final: 0.8603 (m-80) REVERT: X 141 ASP cc_start: 0.8282 (t0) cc_final: 0.8015 (t0) REVERT: X 155 MET cc_start: 0.8829 (tpp) cc_final: 0.8529 (tpt) REVERT: X 158 VAL cc_start: 0.8676 (t) cc_final: 0.8378 (t) outliers start: 144 outliers final: 41 residues processed: 987 average time/residue: 1.4525 time to fit residues: 1814.3759 Evaluate side-chains 813 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 760 time to evaluate : 5.129 ------------------------------------------------------------------------------- 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 289 MET 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 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 404 GLU Chi-restraints excluded: chain L residue 439 VAL 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 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 317 optimal weight: 0.8980 chunk 632 optimal weight: 0.6980 chunk 621 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 691 optimal weight: 0.9980 chunk 617 optimal weight: 4.9990 chunk 229 optimal weight: 0.8980 chunk 313 optimal weight: 0.8980 chunk 680 optimal weight: 3.9990 chunk 475 optimal weight: 5.9990 chunk 246 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN E 446 ASN J 77 GLN P 181 ASN T 88 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.135613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.110458 restraints weight = 81749.803| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.12 r_work: 0.3206 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2327 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= 0.158 Angle : 0.491 7.326 83556 Z= 0.262 Chirality : 0.039 0.140 9804 Planarity : 0.005 0.143 10764 Dihedral : 3.782 23.299 8642 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.30 % Allowed : 11.05 % Favored : 86.65 % 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: 1.53 (0.10), residues: 7776 helix: 2.45 (0.09), residues: 3672 sheet: 0.61 (0.17), residues: 1020 loop : -0.64 (0.12), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 49 HIS 0.003 0.001 HIS H 288 PHE 0.025 0.001 PHE A 401 TYR 0.028 0.001 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 989 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 845 time to evaluate : 5.337 Fit side-chains REVERT: A 399 GLN cc_start: 0.7815 (mt0) cc_final: 0.7438 (mt0) REVERT: B 108 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: B 176 ARG cc_start: 0.8684 (mtm180) cc_final: 0.7928 (ttm110) REVERT: B 188 ILE cc_start: 0.7782 (pt) cc_final: 0.7568 (pp) REVERT: B 214 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8798 (mm-30) REVERT: B 232 GLU cc_start: 0.8386 (tp30) cc_final: 0.7610 (mm-30) REVERT: B 289 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8914 (mmt) REVERT: B 334 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7139 (mt-10) REVERT: B 336 GLN cc_start: 0.8328 (tt0) cc_final: 0.7873 (mt0) REVERT: B 404 GLU cc_start: 0.7875 (mp0) cc_final: 0.7649 (mm-30) REVERT: B 468 LYS cc_start: 0.8885 (tptt) cc_final: 0.8684 (tppt) REVERT: C 336 GLN cc_start: 0.8358 (tt0) cc_final: 0.7905 (mt0) REVERT: D 108 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7509 (tm-30) REVERT: D 408 ASN cc_start: 0.7213 (m-40) cc_final: 0.6999 (m-40) REVERT: D 477 LEU cc_start: 0.8520 (mt) cc_final: 0.8286 (mt) REVERT: E 176 ARG cc_start: 0.8486 (mtm180) cc_final: 0.8136 (ttp80) REVERT: E 232 GLU cc_start: 0.8259 (tp30) cc_final: 0.7566 (mm-30) REVERT: E 336 GLN cc_start: 0.8437 (tt0) cc_final: 0.8003 (mt0) REVERT: F 23 LYS cc_start: 0.8640 (mmmm) cc_final: 0.8401 (mmtt) REVERT: F 215 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8288 (t) REVERT: F 258 LEU cc_start: 0.8837 (tp) cc_final: 0.8601 (tt) REVERT: F 336 GLN cc_start: 0.8549 (tt0) cc_final: 0.8083 (mt0) REVERT: F 341 ARG cc_start: 0.8404 (ttp-170) cc_final: 0.8162 (ttp-170) REVERT: F 477 LEU cc_start: 0.8398 (mt) cc_final: 0.8089 (mt) REVERT: G 336 GLN cc_start: 0.8319 (tt0) cc_final: 0.7980 (mt0) REVERT: H 16 ARG cc_start: 0.8885 (mtp85) cc_final: 0.8679 (mtp85) REVERT: H 167 LYS cc_start: 0.8544 (ttmt) cc_final: 0.8311 (ttpp) REVERT: H 168 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8758 (p) REVERT: H 214 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8824 (mm-30) REVERT: H 280 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8703 (mt-10) REVERT: H 336 GLN cc_start: 0.8311 (tt0) cc_final: 0.7878 (mt0) REVERT: I 22 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7761 (tm) REVERT: I 130 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8458 (mpp) REVERT: I 171 MET cc_start: 0.8326 (mtp) cc_final: 0.8105 (mtp) REVERT: I 185 GLU cc_start: 0.8166 (mp0) cc_final: 0.7665 (tm-30) REVERT: I 336 GLN cc_start: 0.8549 (tt0) cc_final: 0.8133 (mt0) REVERT: I 341 ARG cc_start: 0.8698 (ttp-170) cc_final: 0.8458 (ttp-170) REVERT: I 404 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7270 (mm-30) REVERT: I 457 ASP cc_start: 0.8596 (m-30) cc_final: 0.8242 (m-30) REVERT: J 282 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8236 (tp30) REVERT: J 336 GLN cc_start: 0.8314 (tt0) cc_final: 0.7904 (mt0) REVERT: J 399 GLN cc_start: 0.7530 (mt0) cc_final: 0.7154 (mt0) REVERT: J 457 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7751 (m-30) REVERT: K 336 GLN cc_start: 0.8357 (tt0) cc_final: 0.7767 (mt0) REVERT: L 171 MET cc_start: 0.8574 (mtm) cc_final: 0.8363 (mtm) REVERT: L 289 MET cc_start: 0.8841 (mmt) cc_final: 0.8608 (mmt) REVERT: L 336 GLN cc_start: 0.8513 (tt0) cc_final: 0.8055 (mt0) REVERT: L 404 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7499 (mm-30) REVERT: L 457 ASP cc_start: 0.8820 (t0) cc_final: 0.8509 (m-30) REVERT: N 159 GLU cc_start: 0.8440 (tp30) cc_final: 0.8111 (tp30) REVERT: O 98 MET cc_start: 0.8725 (ttp) cc_final: 0.8297 (ttt) REVERT: O 99 TYR cc_start: 0.9067 (m-80) cc_final: 0.8309 (m-80) REVERT: O 141 ASP cc_start: 0.8277 (t0) cc_final: 0.7809 (t0) REVERT: O 158 VAL cc_start: 0.8849 (t) cc_final: 0.8466 (t) REVERT: P 34 GLN cc_start: 0.8467 (mt0) cc_final: 0.8181 (mt0) REVERT: Q 159 GLU cc_start: 0.8305 (tp30) cc_final: 0.7949 (tp30) REVERT: R 99 TYR cc_start: 0.9025 (m-80) cc_final: 0.8456 (m-80) REVERT: R 115 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6716 (mm-30) REVERT: R 141 ASP cc_start: 0.8721 (t0) cc_final: 0.8114 (t0) REVERT: R 158 VAL cc_start: 0.8665 (t) cc_final: 0.8416 (t) REVERT: R 163 MET cc_start: 0.8947 (tpp) cc_final: 0.8483 (tpt) REVERT: R 174 ARG cc_start: 0.8696 (ptt-90) cc_final: 0.8475 (ptm-80) REVERT: S 1 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7340 (ttp) REVERT: S 166 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8250 (tptm) REVERT: T 45 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: U 155 MET cc_start: 0.8972 (tpp) cc_final: 0.8617 (tpt) REVERT: V 166 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8127 (tptm) REVERT: W 39 LYS cc_start: 0.8308 (mmtt) cc_final: 0.7984 (mptp) REVERT: W 161 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7741 (mm-40) REVERT: X 45 GLU cc_start: 0.8650 (tt0) cc_final: 0.8248 (tt0) REVERT: X 98 MET cc_start: 0.8918 (ttp) cc_final: 0.8633 (ttt) REVERT: X 99 TYR cc_start: 0.8988 (m-80) cc_final: 0.8609 (m-80) REVERT: X 141 ASP cc_start: 0.8283 (t0) cc_final: 0.8025 (t0) REVERT: X 155 MET cc_start: 0.8801 (tpp) cc_final: 0.8451 (tpt) REVERT: X 158 VAL cc_start: 0.8698 (t) cc_final: 0.8345 (t) outliers start: 144 outliers final: 48 residues processed: 913 average time/residue: 1.6266 time to fit residues: 1906.7033 Evaluate side-chains 809 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 743 time to evaluate : 5.043 ------------------------------------------------------------------------------- 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 108 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain E residue 41 LEU 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 192 ASN Chi-restraints excluded: chain E residue 215 VAL 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 171 MET Chi-restraints excluded: chain F residue 215 VAL 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 379 SER 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 280 GLU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 41 LEU 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 215 VAL Chi-restraints excluded: chain I residue 404 GLU Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 282 GLU Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 404 GLU Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain Q residue 1 MET 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 73 SER Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain V residue 73 SER Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 166 LYS Chi-restraints excluded: chain W residue 42 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 613 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 291 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 311 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 251 optimal weight: 0.6980 chunk 349 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN F 408 ASN G 408 ASN H 399 GLN J 77 GLN T 88 ASN T 168 HIS U 93 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.126857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.100869 restraints weight = 81939.975| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.13 r_work: 0.3066 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 61404 Z= 0.328 Angle : 0.624 9.817 83556 Z= 0.330 Chirality : 0.043 0.161 9804 Planarity : 0.008 0.358 10764 Dihedral : 4.294 57.734 8640 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.95 % Allowed : 12.55 % Favored : 84.50 % 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: 0.90 (0.10), residues: 7776 helix: 1.78 (0.08), residues: 3756 sheet: 0.54 (0.17), residues: 1020 loop : -0.92 (0.11), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 246 HIS 0.006 0.002 HIS E 288 PHE 0.029 0.002 PHE A 401 TYR 0.069 0.003 TYR C 471 ARG 0.039 0.001 ARG A 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 986 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 801 time to evaluate : 5.239 Fit side-chains REVERT: A 22 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8543 (tm) REVERT: A 336 GLN cc_start: 0.8605 (tt0) cc_final: 0.8161 (mt0) REVERT: A 399 GLN cc_start: 0.8060 (mt0) cc_final: 0.7684 (mt0) REVERT: B 95 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.5579 (mtp) REVERT: B 108 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: B 176 ARG cc_start: 0.8760 (mtm180) cc_final: 0.8011 (ttm110) REVERT: B 188 ILE cc_start: 0.8021 (pt) cc_final: 0.7777 (pp) REVERT: B 232 GLU cc_start: 0.8542 (tp30) cc_final: 0.7879 (mm-30) REVERT: B 289 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8301 (mmm) REVERT: B 336 GLN cc_start: 0.8537 (tt0) cc_final: 0.7960 (mt0) REVERT: B 404 GLU cc_start: 0.7960 (mp0) cc_final: 0.7759 (mp0) REVERT: C 130 MET cc_start: 0.9083 (tpp) cc_final: 0.8520 (mpp) REVERT: C 289 MET cc_start: 0.9107 (mmt) cc_final: 0.8782 (mmt) REVERT: C 301 MET cc_start: 0.8933 (mtm) cc_final: 0.8646 (mtt) REVERT: C 325 TYR cc_start: 0.7508 (t80) cc_final: 0.7000 (t80) REVERT: C 336 GLN cc_start: 0.8599 (tt0) cc_final: 0.8158 (mt0) REVERT: C 341 ARG cc_start: 0.8495 (ttp-170) cc_final: 0.8126 (ttp-170) REVERT: D 336 GLN cc_start: 0.8593 (tt0) cc_final: 0.8186 (mt0) REVERT: D 408 ASN cc_start: 0.7391 (m-40) cc_final: 0.7139 (m-40) REVERT: E 168 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8849 (p) REVERT: E 176 ARG cc_start: 0.8628 (mtm180) cc_final: 0.8215 (ttp80) REVERT: E 232 GLU cc_start: 0.8433 (tp30) cc_final: 0.7767 (mm-30) REVERT: E 289 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8458 (mmm) REVERT: E 336 GLN cc_start: 0.8431 (tt0) cc_final: 0.7946 (mt0) REVERT: E 406 LEU cc_start: 0.7923 (mt) cc_final: 0.7720 (mt) REVERT: E 468 LYS cc_start: 0.8756 (tptt) cc_final: 0.8544 (tppt) REVERT: F 130 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8869 (mmp) REVERT: F 301 MET cc_start: 0.9010 (mtm) cc_final: 0.8702 (mtt) REVERT: F 325 TYR cc_start: 0.7298 (t80) cc_final: 0.6768 (t80) REVERT: F 336 GLN cc_start: 0.8709 (tt0) cc_final: 0.8225 (mt0) REVERT: F 477 LEU cc_start: 0.8327 (mt) cc_final: 0.8080 (mt) REVERT: G 23 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8369 (mmtm) REVERT: G 289 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8537 (mmm) REVERT: G 336 GLN cc_start: 0.8554 (tt0) cc_final: 0.8146 (mt0) REVERT: G 401 PHE cc_start: 0.8088 (t80) cc_final: 0.7832 (t80) REVERT: G 408 ASN cc_start: 0.8033 (m-40) cc_final: 0.7821 (m-40) REVERT: G 477 LEU cc_start: 0.8464 (mt) cc_final: 0.8121 (mt) REVERT: H 16 ARG cc_start: 0.8953 (mtp85) cc_final: 0.8633 (mtp85) REVERT: H 151 HIS cc_start: 0.8642 (t-90) cc_final: 0.8409 (t70) REVERT: H 168 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8779 (p) REVERT: H 214 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8783 (mm-30) REVERT: H 336 GLN cc_start: 0.8427 (tt0) cc_final: 0.7952 (mt0) REVERT: I 22 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8062 (tm) REVERT: I 130 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8630 (mpp) REVERT: I 301 MET cc_start: 0.8913 (mtm) cc_final: 0.8586 (mtt) REVERT: I 336 GLN cc_start: 0.8681 (tt0) cc_final: 0.8254 (mt0) REVERT: I 341 ARG cc_start: 0.8751 (ttp-170) cc_final: 0.8424 (ttp-170) REVERT: I 404 GLU cc_start: 0.7820 (mp0) cc_final: 0.7570 (mm-30) REVERT: I 457 ASP cc_start: 0.8816 (m-30) cc_final: 0.8487 (m-30) REVERT: J 23 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8225 (mmtp) REVERT: J 130 MET cc_start: 0.9130 (tpp) cc_final: 0.8763 (mmt) REVERT: J 336 GLN cc_start: 0.8594 (tt0) cc_final: 0.8164 (mt0) REVERT: J 399 GLN cc_start: 0.7840 (mt0) cc_final: 0.7570 (mt0) REVERT: J 477 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7721 (mm) REVERT: K 171 MET cc_start: 0.8559 (mtm) cc_final: 0.8103 (mtm) REVERT: K 232 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7719 (mm-30) REVERT: K 289 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8387 (mmm) REVERT: K 336 GLN cc_start: 0.8519 (tt0) cc_final: 0.7961 (mt0) REVERT: K 399 GLN cc_start: 0.7937 (mt0) cc_final: 0.7676 (mt0) REVERT: L 22 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8286 (tp) REVERT: L 130 MET cc_start: 0.9101 (tpp) cc_final: 0.8516 (mpp) REVERT: L 289 MET cc_start: 0.8961 (mmt) cc_final: 0.8722 (mmt) REVERT: L 336 GLN cc_start: 0.8678 (tt0) cc_final: 0.8181 (mt0) REVERT: L 404 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7486 (mm-30) REVERT: L 457 ASP cc_start: 0.8861 (t0) cc_final: 0.8574 (m-30) REVERT: M 45 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: O 98 MET cc_start: 0.8895 (ttp) cc_final: 0.8635 (ttt) REVERT: O 99 TYR cc_start: 0.9094 (m-80) cc_final: 0.8588 (m-80) REVERT: O 141 ASP cc_start: 0.8589 (t0) cc_final: 0.8106 (t0) REVERT: P 1 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.7971 (ttp) REVERT: P 18 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.5891 (mtm180) REVERT: P 55 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8623 (mt-10) REVERT: P 141 ASP cc_start: 0.8963 (t0) cc_final: 0.8445 (t0) REVERT: Q 160 GLU cc_start: 0.8280 (tt0) cc_final: 0.8011 (tt0) REVERT: Q 178 LYS cc_start: 0.8932 (mmpt) cc_final: 0.8510 (mttm) REVERT: R 99 TYR cc_start: 0.8994 (m-80) cc_final: 0.8542 (m-80) REVERT: R 115 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6516 (mm-30) REVERT: R 141 ASP cc_start: 0.8827 (t0) cc_final: 0.8540 (t0) REVERT: R 174 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8057 (ptt-90) REVERT: S 1 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7992 (ttp) REVERT: S 53 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.7318 (mp10) REVERT: T 137 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.6998 (t70) REVERT: T 161 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7909 (mm-40) REVERT: U 45 GLU cc_start: 0.8889 (tt0) cc_final: 0.8636 (tt0) REVERT: W 39 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8164 (mptp) REVERT: W 160 GLU cc_start: 0.8472 (tt0) cc_final: 0.8108 (tt0) REVERT: W 161 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8090 (mm-40) REVERT: W 163 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8714 (tpp) REVERT: X 45 GLU cc_start: 0.8873 (tt0) cc_final: 0.8631 (tt0) REVERT: X 98 MET cc_start: 0.8925 (ttp) cc_final: 0.8660 (ttt) REVERT: X 99 TYR cc_start: 0.9104 (m-80) cc_final: 0.8659 (m-80) REVERT: X 141 ASP cc_start: 0.8537 (t0) cc_final: 0.8268 (t0) outliers start: 185 outliers final: 61 residues processed: 897 average time/residue: 1.4822 time to fit residues: 1678.2619 Evaluate side-chains 828 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 737 time to evaluate : 5.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 22 LEU 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 95 MET Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 427 VAL 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 D residue 411 THR 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 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 23 LYS Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 289 MET Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 102 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 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 383 ASP Chi-restraints excluded: chain I residue 450 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 J residue 477 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 289 MET Chi-restraints excluded: chain K residue 441 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 404 GLU 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 97 THR Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 18 ARG Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain Q residue 1 MET 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 R residue 174 ARG Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 53 GLN Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain T residue 137 ASP Chi-restraints excluded: chain T residue 161 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 186 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 245 optimal weight: 0.7980 chunk 757 optimal weight: 4.9990 chunk 613 optimal weight: 3.9990 chunk 61 optimal weight: 0.0060 chunk 489 optimal weight: 0.6980 chunk 531 optimal weight: 0.9980 chunk 449 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 662 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 T 181 ASN W 181 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.132498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.106962 restraints weight = 81119.067| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.12 r_work: 0.3153 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 61404 Z= 0.138 Angle : 0.476 7.735 83556 Z= 0.255 Chirality : 0.038 0.164 9804 Planarity : 0.006 0.206 10764 Dihedral : 3.856 31.406 8640 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.19 % Allowed : 14.27 % Favored : 83.54 % 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: 1.34 (0.10), residues: 7776 helix: 2.24 (0.09), residues: 3732 sheet: 0.71 (0.17), residues: 1020 loop : -0.81 (0.12), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 49 HIS 0.002 0.001 HIS I 124 PHE 0.025 0.001 PHE A 401 TYR 0.019 0.001 TYR U 67 ARG 0.033 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 915 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 778 time to evaluate : 5.153 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8541 (tm) REVERT: A 371 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7025 (tt0) REVERT: A 399 GLN cc_start: 0.7815 (mt0) cc_final: 0.7461 (mt0) REVERT: A 457 ASP cc_start: 0.8479 (t0) cc_final: 0.7994 (m-30) REVERT: B 16 ARG cc_start: 0.8896 (mtp85) cc_final: 0.8643 (mtp85) REVERT: B 95 MET cc_start: 0.5919 (OUTLIER) cc_final: 0.5468 (mtp) REVERT: B 108 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: B 176 ARG cc_start: 0.8733 (mtm180) cc_final: 0.7975 (ttm110) REVERT: B 188 ILE cc_start: 0.7958 (pt) cc_final: 0.7738 (pp) REVERT: B 336 GLN cc_start: 0.8264 (tt0) cc_final: 0.7774 (mt0) REVERT: C 46 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7772 (mtp180) REVERT: C 289 MET cc_start: 0.8981 (mmt) cc_final: 0.8732 (mmt) REVERT: C 336 GLN cc_start: 0.8475 (tt0) cc_final: 0.8032 (mt0) REVERT: C 441 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8353 (mt) REVERT: D 408 ASN cc_start: 0.7207 (m-40) cc_final: 0.6965 (m-40) REVERT: E 168 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8667 (p) REVERT: E 176 ARG cc_start: 0.8575 (mtm180) cc_final: 0.8182 (ttp80) REVERT: E 336 GLN cc_start: 0.8312 (tt0) cc_final: 0.7815 (mt0) REVERT: E 468 LYS cc_start: 0.8754 (tptt) cc_final: 0.8529 (tppt) REVERT: F 167 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8090 (tttt) REVERT: F 185 GLU cc_start: 0.8184 (mp0) cc_final: 0.7736 (tm-30) REVERT: F 301 MET cc_start: 0.8887 (mtm) cc_final: 0.8473 (mtt) REVERT: F 336 GLN cc_start: 0.8564 (tt0) cc_final: 0.8124 (mt0) REVERT: F 477 LEU cc_start: 0.8308 (mt) cc_final: 0.8074 (mt) REVERT: G 401 PHE cc_start: 0.8123 (t80) cc_final: 0.7877 (t80) REVERT: G 408 ASN cc_start: 0.7659 (m-40) cc_final: 0.7437 (m-40) REVERT: G 477 LEU cc_start: 0.8515 (mt) cc_final: 0.8175 (mt) REVERT: H 168 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8641 (p) REVERT: H 214 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8803 (mm-30) REVERT: H 336 GLN cc_start: 0.8415 (tt0) cc_final: 0.7914 (mt0) REVERT: I 130 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8483 (mpp) REVERT: I 301 MET cc_start: 0.8864 (mtm) cc_final: 0.8491 (mtt) REVERT: I 336 GLN cc_start: 0.8622 (tt0) cc_final: 0.8127 (mt0) REVERT: I 341 ARG cc_start: 0.8290 (ttp-170) cc_final: 0.7936 (ttp-170) REVERT: I 404 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7302 (mm-30) REVERT: J 23 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8135 (mmtp) REVERT: J 399 GLN cc_start: 0.7624 (mt0) cc_final: 0.7330 (mt0) REVERT: J 457 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7683 (m-30) REVERT: K 16 ARG cc_start: 0.8879 (mtp85) cc_final: 0.8656 (mtp85) REVERT: K 108 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: K 227 MET cc_start: 0.7967 (mmt) cc_final: 0.7713 (mmp) REVERT: K 336 GLN cc_start: 0.8319 (tt0) cc_final: 0.7766 (mt0) REVERT: K 399 GLN cc_start: 0.7777 (mt0) cc_final: 0.7490 (mt0) REVERT: K 457 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8339 (t0) REVERT: L 336 GLN cc_start: 0.8532 (tt0) cc_final: 0.8081 (mt0) REVERT: L 404 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7340 (mm-30) REVERT: L 439 VAL cc_start: 0.8174 (t) cc_final: 0.7933 (p) REVERT: L 457 ASP cc_start: 0.8764 (t0) cc_final: 0.8448 (m-30) REVERT: M 45 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: N 39 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7860 (mptp) REVERT: N 45 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8179 (tt0) REVERT: O 98 MET cc_start: 0.8827 (ttp) cc_final: 0.8491 (ttt) REVERT: O 99 TYR cc_start: 0.9014 (m-80) cc_final: 0.8475 (m-80) REVERT: O 141 ASP cc_start: 0.8408 (t0) cc_final: 0.7889 (t0) REVERT: O 158 VAL cc_start: 0.8840 (t) cc_final: 0.8418 (t) REVERT: O 163 MET cc_start: 0.9025 (tpp) cc_final: 0.8818 (tpt) REVERT: P 55 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8576 (mt-10) REVERT: Q 45 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: Q 160 GLU cc_start: 0.8014 (tt0) cc_final: 0.7780 (tt0) REVERT: Q 178 LYS cc_start: 0.8804 (mmpt) cc_final: 0.8369 (mttm) REVERT: R 99 TYR cc_start: 0.8928 (m-80) cc_final: 0.8491 (m-80) REVERT: R 115 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6381 (mm-30) REVERT: R 141 ASP cc_start: 0.8646 (t0) cc_final: 0.8321 (t0) REVERT: R 158 VAL cc_start: 0.8827 (t) cc_final: 0.8490 (t) REVERT: S 1 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7939 (ttp) REVERT: S 88 ASN cc_start: 0.8161 (t0) cc_final: 0.7960 (t0) REVERT: T 45 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: T 160 GLU cc_start: 0.8166 (tt0) cc_final: 0.7833 (tt0) REVERT: T 161 GLN cc_start: 0.7870 (tt0) cc_final: 0.7644 (mm-40) REVERT: U 45 GLU cc_start: 0.8865 (tt0) cc_final: 0.8582 (tt0) REVERT: W 39 LYS cc_start: 0.8270 (mmtt) cc_final: 0.8035 (mptp) REVERT: W 45 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: W 160 GLU cc_start: 0.8162 (tt0) cc_final: 0.7808 (tt0) REVERT: W 161 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7762 (mm-40) REVERT: X 45 GLU cc_start: 0.8843 (tt0) cc_final: 0.8590 (tt0) REVERT: X 98 MET cc_start: 0.8834 (ttp) cc_final: 0.8594 (ttt) REVERT: X 99 TYR cc_start: 0.9008 (m-80) cc_final: 0.8524 (m-80) REVERT: X 141 ASP cc_start: 0.8309 (t0) cc_final: 0.8025 (t0) REVERT: X 158 VAL cc_start: 0.8802 (t) cc_final: 0.8441 (t) outliers start: 137 outliers final: 30 residues processed: 851 average time/residue: 1.4645 time to fit residues: 1575.9609 Evaluate side-chains 782 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 726 time to evaluate : 5.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain B residue 95 MET 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 D residue 342 LEU Chi-restraints excluded: chain D residue 427 VAL 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 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 427 VAL 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 214 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 383 ASP Chi-restraints excluded: chain I residue 404 GLU Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain L residue 404 GLU Chi-restraints excluded: chain M residue 45 GLU 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 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 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 U residue 61 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 643 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 664 optimal weight: 2.9990 chunk 650 optimal weight: 4.9990 chunk 681 optimal weight: 0.5980 chunk 287 optimal weight: 7.9990 chunk 667 optimal weight: 0.8980 chunk 310 optimal weight: 0.0270 chunk 254 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 overall best weight: 1.0840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN F 408 ASN I 408 ASN J 77 GLN K 446 ASN U 93 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.105796 restraints weight = 81152.044| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.12 r_work: 0.3137 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 61404 Z= 0.165 Angle : 0.485 7.613 83556 Z= 0.257 Chirality : 0.038 0.157 9804 Planarity : 0.007 0.419 10764 Dihedral : 3.844 75.571 8640 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.03 % Allowed : 15.21 % Favored : 82.76 % 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: 1.40 (0.10), residues: 7776 helix: 2.33 (0.09), residues: 3720 sheet: 0.74 (0.17), residues: 1020 loop : -0.82 (0.12), residues: 3036 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 0.078 0.001 TYR C 471 ARG 0.041 0.001 ARG B 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 872 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 745 time to evaluate : 5.154 Fit side-chains REVERT: A 22 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8489 (tm) REVERT: A 130 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.7440 (mpp) REVERT: A 185 GLU cc_start: 0.8485 (mp0) cc_final: 0.8268 (mp0) REVERT: A 399 GLN cc_start: 0.7815 (mt0) cc_final: 0.7450 (mt0) REVERT: A 457 ASP cc_start: 0.8533 (t0) cc_final: 0.8034 (m-30) REVERT: B 16 ARG cc_start: 0.8871 (mtp85) cc_final: 0.8561 (mtp85) REVERT: B 95 MET cc_start: 0.5853 (OUTLIER) cc_final: 0.5389 (mtp) REVERT: B 108 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: B 176 ARG cc_start: 0.8752 (mtm180) cc_final: 0.7995 (ttm110) REVERT: B 188 ILE cc_start: 0.7980 (pt) cc_final: 0.7753 (pp) REVERT: B 336 GLN cc_start: 0.8273 (tt0) cc_final: 0.7782 (mt0) REVERT: C 108 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: C 301 MET cc_start: 0.8919 (mtm) cc_final: 0.8659 (mtt) REVERT: C 336 GLN cc_start: 0.8499 (tt0) cc_final: 0.8065 (mt0) REVERT: D 408 ASN cc_start: 0.7215 (m-40) cc_final: 0.6960 (m-40) REVERT: E 16 ARG cc_start: 0.8807 (mtp85) cc_final: 0.8492 (mtp85) REVERT: E 168 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8697 (p) REVERT: E 176 ARG cc_start: 0.8612 (mtm180) cc_final: 0.8200 (ttp80) REVERT: E 209 ARG cc_start: 0.8226 (ptm160) cc_final: 0.7948 (ttp-110) REVERT: E 289 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8294 (mmm) REVERT: E 336 GLN cc_start: 0.8346 (tt0) cc_final: 0.7845 (mt0) REVERT: E 468 LYS cc_start: 0.8763 (tptt) cc_final: 0.8496 (tppt) REVERT: F 167 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8126 (tttt) REVERT: F 185 GLU cc_start: 0.8213 (mp0) cc_final: 0.7909 (mp0) REVERT: F 301 MET cc_start: 0.8898 (mtm) cc_final: 0.8481 (mtt) REVERT: F 336 GLN cc_start: 0.8501 (tt0) cc_final: 0.8072 (mt0) REVERT: F 477 LEU cc_start: 0.8294 (mt) cc_final: 0.8056 (mt) REVERT: G 289 MET cc_start: 0.9099 (mmt) cc_final: 0.8725 (mmt) REVERT: G 401 PHE cc_start: 0.8099 (t80) cc_final: 0.7896 (t80) REVERT: G 408 ASN cc_start: 0.7650 (m-40) cc_final: 0.7415 (m-40) REVERT: G 412 LEU cc_start: 0.8573 (mt) cc_final: 0.8236 (mp) REVERT: G 457 ASP cc_start: 0.8513 (t0) cc_final: 0.8038 (m-30) REVERT: H 168 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8649 (p) REVERT: H 214 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8783 (mm-30) REVERT: H 336 GLN cc_start: 0.8451 (tt0) cc_final: 0.7934 (mt0) REVERT: I 130 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8514 (mpp) REVERT: I 301 MET cc_start: 0.8920 (mtm) cc_final: 0.8565 (mtt) REVERT: I 336 GLN cc_start: 0.8654 (tt0) cc_final: 0.8151 (mt0) REVERT: I 341 ARG cc_start: 0.8367 (ttp-170) cc_final: 0.7992 (ttp-170) REVERT: I 404 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7291 (mm-30) REVERT: J 236 GLU cc_start: 0.8040 (tt0) cc_final: 0.7819 (tt0) REVERT: J 282 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8318 (tp30) REVERT: J 399 GLN cc_start: 0.7646 (mt0) cc_final: 0.7334 (mt0) REVERT: J 457 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7789 (m-30) REVERT: K 16 ARG cc_start: 0.8881 (mtp85) cc_final: 0.8624 (mtp85) REVERT: K 108 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: K 227 MET cc_start: 0.8048 (mmt) cc_final: 0.7794 (mmp) REVERT: K 336 GLN cc_start: 0.8389 (tt0) cc_final: 0.7843 (mt0) REVERT: K 371 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: K 399 GLN cc_start: 0.7782 (mt0) cc_final: 0.7527 (mt0) REVERT: K 457 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8372 (t0) REVERT: L 22 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8248 (tp) REVERT: L 336 GLN cc_start: 0.8477 (tt0) cc_final: 0.8052 (mt0) REVERT: L 404 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7429 (mm-30) REVERT: L 439 VAL cc_start: 0.8189 (t) cc_final: 0.7958 (p) REVERT: N 39 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7968 (mptp) REVERT: N 45 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: O 98 MET cc_start: 0.8848 (ttp) cc_final: 0.8551 (ttt) REVERT: O 99 TYR cc_start: 0.9035 (m-80) cc_final: 0.8522 (m-80) REVERT: O 141 ASP cc_start: 0.8389 (t0) cc_final: 0.7888 (t0) REVERT: O 158 VAL cc_start: 0.8864 (t) cc_final: 0.8463 (t) REVERT: P 1 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7885 (ttp) REVERT: P 34 GLN cc_start: 0.8431 (mt0) cc_final: 0.8212 (mt0) REVERT: P 55 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8551 (mt-10) REVERT: Q 45 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: Q 160 GLU cc_start: 0.8074 (tt0) cc_final: 0.7772 (tt0) REVERT: Q 178 LYS cc_start: 0.8797 (mmpt) cc_final: 0.8363 (mttm) REVERT: R 45 GLU cc_start: 0.8820 (tt0) cc_final: 0.8479 (tt0) REVERT: R 55 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8204 (mt-10) REVERT: R 99 TYR cc_start: 0.9015 (m-80) cc_final: 0.8544 (m-80) REVERT: R 115 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6334 (mm-30) REVERT: R 141 ASP cc_start: 0.8656 (t0) cc_final: 0.8344 (t0) REVERT: S 1 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8008 (ttp) REVERT: S 34 GLN cc_start: 0.8451 (mt0) cc_final: 0.8196 (mt0) REVERT: S 53 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7500 (mp10) REVERT: T 45 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: T 137 ASP cc_start: 0.6877 (OUTLIER) cc_final: 0.6544 (t70) REVERT: T 161 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7757 (mm-40) REVERT: U 45 GLU cc_start: 0.8862 (tt0) cc_final: 0.8575 (tt0) REVERT: W 39 LYS cc_start: 0.8288 (mmtt) cc_final: 0.8043 (mptp) REVERT: W 45 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8168 (tt0) REVERT: W 160 GLU cc_start: 0.8163 (tt0) cc_final: 0.7819 (tt0) REVERT: W 161 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7784 (mm-40) REVERT: X 45 GLU cc_start: 0.8855 (tt0) cc_final: 0.8608 (tt0) REVERT: X 98 MET cc_start: 0.8810 (ttp) cc_final: 0.8585 (ttt) REVERT: X 99 TYR cc_start: 0.9012 (m-80) cc_final: 0.8538 (m-80) REVERT: X 141 ASP cc_start: 0.8294 (t0) cc_final: 0.8009 (t0) REVERT: X 158 VAL cc_start: 0.8874 (t) cc_final: 0.8532 (t) outliers start: 127 outliers final: 38 residues processed: 823 average time/residue: 1.4747 time to fit residues: 1534.8419 Evaluate side-chains 800 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 731 time to evaluate : 5.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 95 MET 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 108 GLU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain D residue 342 LEU 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 439 VAL 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 171 MET Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 383 ASP 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 214 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 383 ASP Chi-restraints excluded: chain I residue 404 GLU Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 282 GLU Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 371 GLU Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 404 GLU Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 61 LEU 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 115 GLU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 53 GLN 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 T residue 161 GLN Chi-restraints excluded: chain U residue 61 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 181 optimal weight: 0.0670 chunk 489 optimal weight: 0.6980 chunk 271 optimal weight: 1.9990 chunk 729 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 619 optimal weight: 0.8980 chunk 743 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 587 optimal weight: 0.2980 chunk 156 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN I 408 ASN J 77 GLN Q 88 ASN Q 181 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.108120 restraints weight = 81090.313| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.08 r_work: 0.3174 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 61404 Z= 0.129 Angle : 0.461 9.444 83556 Z= 0.244 Chirality : 0.037 0.182 9804 Planarity : 0.006 0.246 10764 Dihedral : 3.658 39.761 8640 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.68 % Allowed : 15.76 % Favored : 82.57 % 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: 1.66 (0.10), residues: 7776 helix: 2.65 (0.09), residues: 3648 sheet: 0.80 (0.17), residues: 1020 loop : -0.72 (0.12), residues: 3108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 246 HIS 0.002 0.000 HIS G 124 PHE 0.027 0.001 PHE J 401 TYR 0.023 0.001 TYR I 471 ARG 0.043 0.001 ARG J 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 881 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 776 time to evaluate : 5.204 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8460 (tm) REVERT: A 130 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.7487 (mpp) REVERT: A 371 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7125 (tt0) REVERT: A 399 GLN cc_start: 0.7824 (mt0) cc_final: 0.7468 (mt0) REVERT: A 457 ASP cc_start: 0.8557 (t0) cc_final: 0.8067 (m-30) REVERT: B 16 ARG cc_start: 0.8884 (mtp85) cc_final: 0.8581 (mtp85) REVERT: B 95 MET cc_start: 0.5953 (OUTLIER) cc_final: 0.5472 (mtp) REVERT: B 176 ARG cc_start: 0.8726 (mtm180) cc_final: 0.7976 (ttm110) REVERT: B 188 ILE cc_start: 0.8040 (pt) cc_final: 0.7835 (pp) REVERT: B 336 GLN cc_start: 0.8216 (tt0) cc_final: 0.7717 (mt0) REVERT: B 457 ASP cc_start: 0.8799 (t0) cc_final: 0.8294 (m-30) REVERT: C 46 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8171 (mtp180) REVERT: C 301 MET cc_start: 0.8898 (mtm) cc_final: 0.8627 (mtt) REVERT: C 336 GLN cc_start: 0.8488 (tt0) cc_final: 0.8040 (mt0) REVERT: D 408 ASN cc_start: 0.7244 (m-40) cc_final: 0.6992 (m-40) REVERT: D 457 ASP cc_start: 0.8434 (t0) cc_final: 0.7891 (m-30) REVERT: E 16 ARG cc_start: 0.8795 (mtp85) cc_final: 0.8513 (mtp85) REVERT: E 168 VAL cc_start: 0.8886 (OUTLIER) cc_final: 0.8637 (p) REVERT: E 176 ARG cc_start: 0.8605 (mtm180) cc_final: 0.8224 (ttp80) REVERT: E 209 ARG cc_start: 0.8312 (ptm160) cc_final: 0.8058 (ttp-110) REVERT: E 336 GLN cc_start: 0.8292 (tt0) cc_final: 0.7824 (mt0) REVERT: E 468 LYS cc_start: 0.8819 (tptt) cc_final: 0.8517 (tppt) REVERT: F 130 MET cc_start: 0.9081 (tpp) cc_final: 0.8424 (mpp) REVERT: F 167 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8054 (tttt) REVERT: F 336 GLN cc_start: 0.8476 (tt0) cc_final: 0.8036 (mt0) REVERT: F 441 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8359 (mt) REVERT: F 477 LEU cc_start: 0.8296 (mt) cc_final: 0.8082 (mt) REVERT: G 289 MET cc_start: 0.9114 (mmt) cc_final: 0.8875 (mmt) REVERT: G 408 ASN cc_start: 0.7635 (m-40) cc_final: 0.7369 (m-40) REVERT: G 412 LEU cc_start: 0.8566 (mt) cc_final: 0.8300 (mp) REVERT: G 457 ASP cc_start: 0.8476 (t0) cc_final: 0.8011 (m-30) REVERT: G 477 LEU cc_start: 0.8322 (mt) cc_final: 0.8014 (mp) REVERT: H 168 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8600 (p) REVERT: H 336 GLN cc_start: 0.8441 (tt0) cc_final: 0.7936 (mt0) REVERT: H 371 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: H 399 GLN cc_start: 0.7478 (mt0) cc_final: 0.7229 (mt0) REVERT: H 468 LYS cc_start: 0.8736 (tptt) cc_final: 0.8456 (tppt) REVERT: I 130 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8479 (mpp) REVERT: I 301 MET cc_start: 0.8891 (mtm) cc_final: 0.8522 (mtt) REVERT: I 336 GLN cc_start: 0.8591 (tt0) cc_final: 0.8148 (mt0) REVERT: I 341 ARG cc_start: 0.8236 (ttp-170) cc_final: 0.7767 (ttp-170) REVERT: I 404 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7322 (mm-30) REVERT: I 408 ASN cc_start: 0.8075 (m-40) cc_final: 0.7864 (m110) REVERT: J 236 GLU cc_start: 0.8013 (tt0) cc_final: 0.7787 (tt0) REVERT: J 282 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8235 (tp30) REVERT: J 399 GLN cc_start: 0.7796 (mt0) cc_final: 0.7466 (mt0) REVERT: J 457 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7697 (m-30) REVERT: K 16 ARG cc_start: 0.8808 (mtp85) cc_final: 0.8606 (mtp85) REVERT: K 48 ASN cc_start: 0.8769 (p0) cc_final: 0.8558 (p0) REVERT: K 108 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: K 227 MET cc_start: 0.8040 (mmt) cc_final: 0.7828 (mmp) REVERT: K 301 MET cc_start: 0.8663 (mtm) cc_final: 0.8354 (mtt) REVERT: K 336 GLN cc_start: 0.8372 (tt0) cc_final: 0.7818 (mt0) REVERT: K 371 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7311 (tt0) REVERT: K 399 GLN cc_start: 0.7315 (mt0) cc_final: 0.7069 (mt0) REVERT: K 457 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8316 (t0) REVERT: L 22 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8259 (tp) REVERT: L 336 GLN cc_start: 0.8468 (tt0) cc_final: 0.8039 (mt0) REVERT: L 404 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7366 (mm-30) REVERT: L 439 VAL cc_start: 0.8141 (t) cc_final: 0.7911 (p) REVERT: L 457 ASP cc_start: 0.8421 (m-30) cc_final: 0.8116 (m-30) REVERT: N 39 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7920 (mptp) REVERT: N 45 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: N 75 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8361 (tt0) REVERT: O 98 MET cc_start: 0.8807 (ttp) cc_final: 0.8557 (ttt) REVERT: O 99 TYR cc_start: 0.9076 (m-80) cc_final: 0.8509 (m-80) REVERT: O 158 VAL cc_start: 0.8839 (t) cc_final: 0.8440 (t) REVERT: P 55 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8512 (mt-10) REVERT: Q 45 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: Q 160 GLU cc_start: 0.7991 (tt0) cc_final: 0.7674 (tt0) REVERT: Q 178 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8393 (mttm) REVERT: R 45 GLU cc_start: 0.8702 (tt0) cc_final: 0.8377 (tt0) REVERT: R 99 TYR cc_start: 0.9005 (m-80) cc_final: 0.8481 (m-80) REVERT: R 107 ARG cc_start: 0.7871 (ttp80) cc_final: 0.7586 (ttt-90) REVERT: R 115 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6266 (mm-30) REVERT: R 141 ASP cc_start: 0.8565 (t0) cc_final: 0.8233 (t0) REVERT: R 158 VAL cc_start: 0.8843 (t) cc_final: 0.8504 (t) REVERT: S 34 GLN cc_start: 0.8441 (mt0) cc_final: 0.8227 (mt0) REVERT: S 53 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.7532 (mp10) REVERT: S 55 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8335 (mt-10) REVERT: T 45 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: T 161 GLN cc_start: 0.7889 (tt0) cc_final: 0.7682 (mm-40) REVERT: U 45 GLU cc_start: 0.8840 (tt0) cc_final: 0.8526 (tt0) REVERT: U 149 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7543 (tp) REVERT: W 39 LYS cc_start: 0.8263 (mmtt) cc_final: 0.8022 (mptp) REVERT: W 45 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: W 160 GLU cc_start: 0.8074 (tt0) cc_final: 0.7729 (tt0) REVERT: W 161 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7732 (mm-40) REVERT: X 45 GLU cc_start: 0.8851 (tt0) cc_final: 0.8579 (tt0) REVERT: X 99 TYR cc_start: 0.9011 (m-80) cc_final: 0.8501 (m-80) REVERT: X 141 ASP cc_start: 0.8209 (t0) cc_final: 0.7928 (t0) REVERT: X 158 VAL cc_start: 0.8801 (t) cc_final: 0.8420 (t) outliers start: 105 outliers final: 31 residues processed: 830 average time/residue: 1.4804 time to fit residues: 1552.9472 Evaluate side-chains 788 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 726 time to evaluate : 5.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 95 MET 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 117 ILE 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 167 LYS Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 383 ASP 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 371 GLU Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 404 GLU Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 282 GLU Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 371 GLU Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 404 GLU Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 75 GLU 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 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 61 LEU Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain S residue 53 GLN Chi-restraints excluded: chain S residue 55 GLU 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 45 GLU Chi-restraints excluded: chain U residue 46 ARG Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain W residue 45 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 547 optimal weight: 2.9990 chunk 633 optimal weight: 5.9990 chunk 389 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 506 optimal weight: 3.9990 chunk 638 optimal weight: 4.9990 chunk 257 optimal weight: 4.9990 chunk 662 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 464 optimal weight: 0.5980 chunk 183 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN C 408 ASN J 77 GLN L 408 ASN P 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.131079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.105930 restraints weight = 81353.580| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.08 r_work: 0.3141 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3575 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= 0.181 Angle : 0.498 8.431 83556 Z= 0.262 Chirality : 0.039 0.249 9804 Planarity : 0.008 0.353 10764 Dihedral : 3.777 60.603 8640 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.63 % Allowed : 16.32 % Favored : 82.06 % 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: 1.59 (0.10), residues: 7776 helix: 2.54 (0.09), residues: 3660 sheet: 0.78 (0.17), residues: 1020 loop : -0.72 (0.12), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 246 HIS 0.003 0.001 HIS J 124 PHE 0.036 0.001 PHE G 401 TYR 0.074 0.001 TYR F 471 ARG 0.051 0.001 ARG J 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 842 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 740 time to evaluate : 5.170 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8476 (tm) REVERT: A 130 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.7543 (mpp) REVERT: A 371 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7113 (tt0) REVERT: A 399 GLN cc_start: 0.7829 (mt0) cc_final: 0.7438 (mt0) REVERT: B 95 MET cc_start: 0.5836 (OUTLIER) cc_final: 0.5369 (mtp) REVERT: B 108 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7522 (tt0) REVERT: B 176 ARG cc_start: 0.8732 (mtm180) cc_final: 0.7976 (ttm110) REVERT: B 336 GLN cc_start: 0.8232 (tt0) cc_final: 0.7748 (mt0) REVERT: C 108 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: C 336 GLN cc_start: 0.8516 (tt0) cc_final: 0.8080 (mt0) REVERT: D 371 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6961 (tt0) REVERT: D 408 ASN cc_start: 0.7223 (m-40) cc_final: 0.6961 (m-40) REVERT: D 473 THR cc_start: 0.8077 (m) cc_final: 0.7683 (p) REVERT: E 16 ARG cc_start: 0.8886 (mtp85) cc_final: 0.8534 (mtp85) REVERT: E 168 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8672 (p) REVERT: E 176 ARG cc_start: 0.8640 (mtm180) cc_final: 0.8224 (ttp80) REVERT: E 289 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8291 (mmm) REVERT: E 336 GLN cc_start: 0.8354 (tt0) cc_final: 0.7841 (mt0) REVERT: E 468 LYS cc_start: 0.8845 (tptt) cc_final: 0.8520 (tppt) REVERT: F 167 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8068 (tttt) REVERT: F 336 GLN cc_start: 0.8496 (tt0) cc_final: 0.8069 (mt0) REVERT: G 408 ASN cc_start: 0.7685 (m-40) cc_final: 0.7412 (m-40) REVERT: G 412 LEU cc_start: 0.8543 (mt) cc_final: 0.8304 (mp) REVERT: G 457 ASP cc_start: 0.8562 (t0) cc_final: 0.8103 (m-30) REVERT: G 473 THR cc_start: 0.8280 (m) cc_final: 0.7915 (p) REVERT: H 168 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8674 (p) REVERT: H 336 GLN cc_start: 0.8416 (tt0) cc_final: 0.7881 (mt0) REVERT: H 371 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: H 399 GLN cc_start: 0.7549 (mt0) cc_final: 0.7297 (mt0) REVERT: H 468 LYS cc_start: 0.8770 (tptt) cc_final: 0.8502 (tppt) REVERT: I 130 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8500 (mpp) REVERT: I 301 MET cc_start: 0.8890 (mtm) cc_final: 0.8536 (mtt) REVERT: I 336 GLN cc_start: 0.8571 (tt0) cc_final: 0.8129 (mt0) REVERT: I 341 ARG cc_start: 0.8418 (ttp-170) cc_final: 0.7984 (ttp-170) REVERT: I 408 ASN cc_start: 0.8089 (m-40) cc_final: 0.7879 (m110) REVERT: I 439 VAL cc_start: 0.8284 (t) cc_final: 0.7979 (p) REVERT: I 457 ASP cc_start: 0.8469 (m-30) cc_final: 0.8199 (m-30) REVERT: J 282 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8309 (tp30) REVERT: J 399 GLN cc_start: 0.7809 (mt0) cc_final: 0.7494 (mt0) REVERT: J 457 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: K 16 ARG cc_start: 0.8818 (mtp85) cc_final: 0.8591 (mtp85) REVERT: K 48 ASN cc_start: 0.8756 (p0) cc_final: 0.8410 (m110) REVERT: K 108 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: K 336 GLN cc_start: 0.8386 (tt0) cc_final: 0.7832 (mt0) REVERT: K 371 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: K 399 GLN cc_start: 0.7654 (mt0) cc_final: 0.7378 (mt0) REVERT: L 22 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8255 (tp) REVERT: L 108 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7137 (tm-30) REVERT: L 336 GLN cc_start: 0.8489 (tt0) cc_final: 0.8063 (mt0) REVERT: L 404 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7365 (mm-30) REVERT: L 439 VAL cc_start: 0.8157 (t) cc_final: 0.7917 (p) REVERT: L 457 ASP cc_start: 0.8553 (m-30) cc_final: 0.8216 (m-30) REVERT: M 141 ASP cc_start: 0.8425 (t70) cc_final: 0.8208 (t70) REVERT: N 39 LYS cc_start: 0.8311 (mmtt) cc_final: 0.8056 (mptp) REVERT: N 45 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: O 98 MET cc_start: 0.8750 (ttp) cc_final: 0.8504 (ttt) REVERT: O 99 TYR cc_start: 0.9087 (m-80) cc_final: 0.8508 (m-80) REVERT: O 158 VAL cc_start: 0.8892 (t) cc_final: 0.8524 (t) REVERT: P 1 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7823 (ttp) REVERT: P 55 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8536 (mt-10) REVERT: Q 45 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: Q 160 GLU cc_start: 0.8104 (tt0) cc_final: 0.7778 (tt0) REVERT: Q 178 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8335 (mttp) REVERT: R 45 GLU cc_start: 0.8829 (tt0) cc_final: 0.8549 (tt0) REVERT: R 99 TYR cc_start: 0.8963 (m-80) cc_final: 0.8481 (m-80) REVERT: R 107 ARG cc_start: 0.7903 (ttp80) cc_final: 0.7658 (ttt-90) REVERT: R 115 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6257 (mm-30) REVERT: R 141 ASP cc_start: 0.8621 (t0) cc_final: 0.8325 (t0) REVERT: S 53 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: S 55 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8339 (mt-10) REVERT: T 45 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: T 161 GLN cc_start: 0.7990 (tt0) cc_final: 0.7754 (mm-40) REVERT: U 45 GLU cc_start: 0.8869 (tt0) cc_final: 0.8558 (tt0) REVERT: U 107 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7874 (ttt-90) REVERT: U 149 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7713 (tp) REVERT: W 39 LYS cc_start: 0.8288 (mmtt) cc_final: 0.8040 (mptp) REVERT: W 45 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: W 93 ASN cc_start: 0.9292 (OUTLIER) cc_final: 0.8730 (m110) REVERT: W 160 GLU cc_start: 0.8176 (tt0) cc_final: 0.7911 (tt0) REVERT: W 161 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7790 (mm-40) REVERT: X 45 GLU cc_start: 0.8859 (tt0) cc_final: 0.8597 (tt0) REVERT: X 99 TYR cc_start: 0.9053 (m-80) cc_final: 0.8554 (m-80) REVERT: X 141 ASP cc_start: 0.8251 (t0) cc_final: 0.7723 (t0) outliers start: 102 outliers final: 40 residues processed: 796 average time/residue: 1.4768 time to fit residues: 1483.7159 Evaluate side-chains 807 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 734 time to evaluate : 5.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 95 MET 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 108 GLU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain E residue 41 LEU 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 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 383 ASP 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 371 GLU 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 95 MET Chi-restraints excluded: chain J residue 282 GLU Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 371 GLU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 404 GLU Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 55 GLU 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 178 LYS Chi-restraints excluded: chain R residue 54 ASP Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain S residue 53 GLN Chi-restraints excluded: chain S residue 55 GLU Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 73 SER 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 U residue 54 ASP Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain W residue 93 ASN Chi-restraints excluded: chain W residue 161 GLN Chi-restraints excluded: chain X residue 54 ASP Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 149 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 91 optimal weight: 0.2980 chunk 406 optimal weight: 0.4980 chunk 585 optimal weight: 3.9990 chunk 724 optimal weight: 6.9990 chunk 180 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 621 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 609 optimal weight: 0.9980 chunk 649 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 ASN J 77 GLN K 446 ASN L 408 ASN S 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.132070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.107000 restraints weight = 81110.997| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.08 r_work: 0.3153 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 61404 Z= 0.157 Angle : 0.487 9.797 83556 Z= 0.257 Chirality : 0.038 0.218 9804 Planarity : 0.009 0.410 10764 Dihedral : 4.044 117.010 8640 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.48 % Allowed : 16.67 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.10), residues: 7776 helix: 2.57 (0.09), residues: 3660 sheet: 0.79 (0.17), residues: 1020 loop : -0.71 (0.12), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 246 HIS 0.002 0.001 HIS G 124 PHE 0.032 0.001 PHE G 401 TYR 0.046 0.001 TYR G 471 ARG 0.056 0.001 ARG G 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 831 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 738 time to evaluate : 5.108 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8478 (tm) REVERT: A 130 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.7472 (mpp) REVERT: A 371 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7130 (tt0) REVERT: A 399 GLN cc_start: 0.7818 (mt0) cc_final: 0.7434 (mt0) REVERT: B 16 ARG cc_start: 0.8742 (mtp85) cc_final: 0.8481 (mtp85) REVERT: B 95 MET cc_start: 0.5822 (OUTLIER) cc_final: 0.5349 (mtp) REVERT: B 108 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7534 (tt0) REVERT: B 176 ARG cc_start: 0.8689 (mtm180) cc_final: 0.8423 (ttp80) REVERT: B 336 GLN cc_start: 0.8320 (tt0) cc_final: 0.7836 (mt0) REVERT: B 457 ASP cc_start: 0.8725 (t0) cc_final: 0.8211 (m-30) REVERT: C 46 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8256 (mtp180) REVERT: C 301 MET cc_start: 0.8913 (mtm) cc_final: 0.8650 (mtt) REVERT: C 336 GLN cc_start: 0.8504 (tt0) cc_final: 0.8061 (mt0) REVERT: D 371 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6965 (tt0) REVERT: D 408 ASN cc_start: 0.7238 (m-40) cc_final: 0.6975 (m-40) REVERT: D 473 THR cc_start: 0.8025 (m) cc_final: 0.7619 (p) REVERT: E 16 ARG cc_start: 0.8935 (mtp85) cc_final: 0.8705 (mtp85) REVERT: E 168 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8619 (p) REVERT: E 176 ARG cc_start: 0.8629 (mtm180) cc_final: 0.8227 (ttp80) REVERT: E 289 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8283 (mmm) REVERT: E 336 GLN cc_start: 0.8295 (tt0) cc_final: 0.7780 (mt0) REVERT: E 468 LYS cc_start: 0.8860 (tptt) cc_final: 0.8530 (tppt) REVERT: F 167 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8040 (tttt) REVERT: F 336 GLN cc_start: 0.8480 (tt0) cc_final: 0.8051 (mt0) REVERT: G 408 ASN cc_start: 0.7706 (m-40) cc_final: 0.7434 (m-40) REVERT: G 412 LEU cc_start: 0.8622 (mt) cc_final: 0.8278 (mp) REVERT: G 473 THR cc_start: 0.8160 (m) cc_final: 0.7756 (p) REVERT: H 48 ASN cc_start: 0.8823 (p0) cc_final: 0.8588 (p0) REVERT: H 108 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7333 (tm-30) REVERT: H 168 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8641 (p) REVERT: H 336 GLN cc_start: 0.8399 (tt0) cc_final: 0.7863 (mt0) REVERT: H 371 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: H 399 GLN cc_start: 0.7747 (mt0) cc_final: 0.7525 (mt0) REVERT: H 468 LYS cc_start: 0.8773 (tptt) cc_final: 0.8384 (tppt) REVERT: I 130 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8481 (mpp) REVERT: I 336 GLN cc_start: 0.8485 (tt0) cc_final: 0.8063 (mt0) REVERT: I 341 ARG cc_start: 0.8363 (ttp-170) cc_final: 0.7937 (ttp-170) REVERT: I 408 ASN cc_start: 0.8089 (m-40) cc_final: 0.7876 (m110) REVERT: I 439 VAL cc_start: 0.8305 (t) cc_final: 0.8002 (p) REVERT: I 457 ASP cc_start: 0.8461 (m-30) cc_final: 0.8167 (m-30) REVERT: J 22 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8424 (tm) REVERT: J 399 GLN cc_start: 0.7801 (mt0) cc_final: 0.7488 (mt0) REVERT: J 412 LEU cc_start: 0.8241 (mt) cc_final: 0.8019 (OUTLIER) REVERT: J 457 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: K 16 ARG cc_start: 0.8819 (mtp85) cc_final: 0.8592 (mtp85) REVERT: K 48 ASN cc_start: 0.8715 (p0) cc_final: 0.8436 (m-40) REVERT: K 108 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7277 (tm-30) REVERT: K 336 GLN cc_start: 0.8371 (tt0) cc_final: 0.7816 (mt0) REVERT: K 371 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: K 399 GLN cc_start: 0.7682 (mt0) cc_final: 0.7424 (mt0) REVERT: K 457 ASP cc_start: 0.8897 (t0) cc_final: 0.8393 (m-30) REVERT: L 22 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8264 (tp) REVERT: L 336 GLN cc_start: 0.8480 (tt0) cc_final: 0.8050 (mt0) REVERT: L 404 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7373 (mm-30) REVERT: L 439 VAL cc_start: 0.8141 (t) cc_final: 0.7890 (p) REVERT: L 457 ASP cc_start: 0.8618 (m-30) cc_final: 0.8290 (m-30) REVERT: M 141 ASP cc_start: 0.8414 (t70) cc_final: 0.8182 (t70) REVERT: N 39 LYS cc_start: 0.8281 (mmtt) cc_final: 0.8044 (mptp) REVERT: N 45 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: O 98 MET cc_start: 0.8706 (ttp) cc_final: 0.8484 (ttt) REVERT: O 99 TYR cc_start: 0.9093 (m-80) cc_final: 0.8507 (m-80) REVERT: O 158 VAL cc_start: 0.8873 (t) cc_final: 0.8495 (t) REVERT: P 1 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7883 (ttp) REVERT: P 55 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8478 (mt-10) REVERT: Q 45 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: Q 160 GLU cc_start: 0.8071 (tt0) cc_final: 0.7743 (tt0) REVERT: Q 178 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8354 (mttm) REVERT: R 45 GLU cc_start: 0.8788 (tt0) cc_final: 0.8491 (tt0) REVERT: R 99 TYR cc_start: 0.8960 (m-80) cc_final: 0.8405 (m-80) REVERT: R 107 ARG cc_start: 0.7881 (ttp80) cc_final: 0.7649 (ttt-90) REVERT: R 115 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6251 (mm-30) REVERT: R 141 ASP cc_start: 0.8605 (t0) cc_final: 0.8292 (t0) REVERT: S 1 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.7880 (ttt) REVERT: S 53 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.7640 (mp10) REVERT: S 55 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8312 (mt-10) REVERT: T 45 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: T 161 GLN cc_start: 0.7963 (tt0) cc_final: 0.7728 (mm-40) REVERT: U 45 GLU cc_start: 0.8851 (tt0) cc_final: 0.8553 (tt0) REVERT: U 107 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7853 (ttt-90) REVERT: U 149 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7652 (tp) REVERT: W 39 LYS cc_start: 0.8266 (mmtt) cc_final: 0.8040 (mptp) REVERT: W 45 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: W 160 GLU cc_start: 0.8146 (tt0) cc_final: 0.7806 (tt0) REVERT: W 161 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7766 (mm-40) REVERT: X 45 GLU cc_start: 0.8850 (tt0) cc_final: 0.8587 (tt0) REVERT: X 99 TYR cc_start: 0.9061 (m-80) cc_final: 0.8515 (m-80) REVERT: X 158 VAL cc_start: 0.8851 (t) cc_final: 0.8501 (t) outliers start: 93 outliers final: 34 residues processed: 790 average time/residue: 1.5021 time to fit residues: 1497.4559 Evaluate side-chains 786 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 721 time to evaluate : 5.026 ------------------------------------------------------------------------------- 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 130 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 95 MET 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 117 ILE Chi-restraints excluded: chain D residue 371 GLU 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 14 LYS Chi-restraints excluded: chain G residue 383 ASP 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 371 GLU 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 22 LEU Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 371 GLU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 404 GLU Chi-restraints excluded: chain N residue 45 GLU 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 1 MET Chi-restraints excluded: chain P residue 55 GLU 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 54 ASP 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 53 GLN Chi-restraints excluded: chain S residue 55 GLU 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 45 GLU Chi-restraints excluded: chain U residue 54 ASP Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain W residue 45 GLU 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 160 optimal weight: 1.9990 chunk 522 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 133 optimal weight: 0.0670 chunk 82 optimal weight: 1.9990 chunk 349 optimal weight: 1.9990 chunk 759 optimal weight: 5.9990 chunk 475 optimal weight: 0.9990 chunk 619 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 ASN J 77 GLN L 408 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.130509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.105228 restraints weight = 81487.375| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.10 r_work: 0.3125 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 61404 Z= 0.196 Angle : 0.517 11.149 83556 Z= 0.272 Chirality : 0.039 0.233 9804 Planarity : 0.009 0.425 10764 Dihedral : 4.035 83.313 8640 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.31 % Allowed : 16.81 % Favored : 81.88 % 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: 1.52 (0.10), residues: 7776 helix: 2.48 (0.09), residues: 3660 sheet: 0.76 (0.17), residues: 1020 loop : -0.75 (0.12), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 246 HIS 0.004 0.001 HIS K 288 PHE 0.030 0.001 PHE G 401 TYR 0.058 0.001 TYR G 471 ARG 0.048 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 816 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 734 time to evaluate : 5.224 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8520 (tm) REVERT: A 130 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.7554 (mpp) REVERT: A 371 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7148 (tt0) REVERT: A 399 GLN cc_start: 0.7877 (mt0) cc_final: 0.7494 (mt0) REVERT: A 457 ASP cc_start: 0.8620 (m-30) cc_final: 0.8417 (t0) REVERT: B 95 MET cc_start: 0.5741 (OUTLIER) cc_final: 0.5184 (mtp) REVERT: B 108 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7567 (tt0) REVERT: B 176 ARG cc_start: 0.8691 (mtm180) cc_final: 0.7917 (ttm110) REVERT: B 336 GLN cc_start: 0.8423 (tt0) cc_final: 0.7918 (mt0) REVERT: C 46 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8131 (mtp180) REVERT: C 301 MET cc_start: 0.8924 (mtm) cc_final: 0.8657 (mtt) REVERT: C 336 GLN cc_start: 0.8523 (tt0) cc_final: 0.8100 (mt0) REVERT: D 371 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7000 (tt0) REVERT: D 408 ASN cc_start: 0.7355 (m-40) cc_final: 0.7110 (m-40) REVERT: D 473 THR cc_start: 0.8049 (m) cc_final: 0.7647 (p) REVERT: E 16 ARG cc_start: 0.8901 (mtp85) cc_final: 0.8548 (mtp85) REVERT: E 168 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8650 (p) REVERT: E 176 ARG cc_start: 0.8634 (mtm180) cc_final: 0.8209 (ttp80) REVERT: E 289 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8314 (mmm) REVERT: E 336 GLN cc_start: 0.8455 (tt0) cc_final: 0.7942 (mt0) REVERT: E 468 LYS cc_start: 0.8886 (tptt) cc_final: 0.8537 (tppt) REVERT: F 336 GLN cc_start: 0.8517 (tt0) cc_final: 0.8090 (mt0) REVERT: G 408 ASN cc_start: 0.7778 (m-40) cc_final: 0.7489 (m-40) REVERT: G 412 LEU cc_start: 0.8657 (mt) cc_final: 0.8304 (mp) REVERT: G 473 THR cc_start: 0.8169 (m) cc_final: 0.7758 (p) REVERT: H 48 ASN cc_start: 0.8792 (p0) cc_final: 0.8557 (p0) REVERT: H 108 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7290 (tm-30) REVERT: H 168 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8721 (p) REVERT: H 336 GLN cc_start: 0.8456 (tt0) cc_final: 0.7920 (mt0) REVERT: H 371 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: H 399 GLN cc_start: 0.7767 (mt0) cc_final: 0.7518 (mt0) REVERT: H 457 ASP cc_start: 0.8885 (t0) cc_final: 0.8392 (m-30) REVERT: H 468 LYS cc_start: 0.8839 (tptt) cc_final: 0.8526 (tppt) REVERT: I 130 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8526 (mpp) REVERT: I 336 GLN cc_start: 0.8532 (tt0) cc_final: 0.8115 (mt0) REVERT: I 341 ARG cc_start: 0.8454 (ttp-170) cc_final: 0.7979 (ttp-170) REVERT: I 408 ASN cc_start: 0.8298 (m-40) cc_final: 0.8057 (m110) REVERT: I 439 VAL cc_start: 0.8326 (t) cc_final: 0.8015 (p) REVERT: I 457 ASP cc_start: 0.8571 (m-30) cc_final: 0.8271 (m-30) REVERT: J 22 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8492 (tm) REVERT: J 399 GLN cc_start: 0.7855 (mt0) cc_final: 0.7549 (mt0) REVERT: J 412 LEU cc_start: 0.8285 (mt) cc_final: 0.8062 (OUTLIER) REVERT: J 457 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.7856 (m-30) REVERT: K 16 ARG cc_start: 0.8829 (mtp85) cc_final: 0.8591 (mtp85) REVERT: K 108 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: K 336 GLN cc_start: 0.8426 (tt0) cc_final: 0.7875 (mt0) REVERT: K 371 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: K 399 GLN cc_start: 0.7784 (mt0) cc_final: 0.7521 (mt0) REVERT: K 404 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7804 (mm-30) REVERT: K 457 ASP cc_start: 0.8904 (t0) cc_final: 0.8399 (m-30) REVERT: L 22 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8308 (tp) REVERT: L 336 GLN cc_start: 0.8532 (tt0) cc_final: 0.8108 (mt0) REVERT: L 404 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7413 (mm-30) REVERT: L 439 VAL cc_start: 0.8206 (t) cc_final: 0.7950 (p) REVERT: L 457 ASP cc_start: 0.8716 (m-30) cc_final: 0.8385 (m-30) REVERT: N 39 LYS cc_start: 0.8358 (mmtt) cc_final: 0.8104 (mptp) REVERT: N 45 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: O 99 TYR cc_start: 0.9131 (m-80) cc_final: 0.8624 (m-80) REVERT: O 158 VAL cc_start: 0.8914 (t) cc_final: 0.8548 (t) REVERT: P 55 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8489 (mt-10) REVERT: P 141 ASP cc_start: 0.8676 (t70) cc_final: 0.8354 (t70) REVERT: Q 45 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: Q 160 GLU cc_start: 0.8149 (tt0) cc_final: 0.7827 (tt0) REVERT: Q 178 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8406 (mttm) REVERT: R 45 GLU cc_start: 0.8849 (tt0) cc_final: 0.8552 (tt0) REVERT: R 99 TYR cc_start: 0.9002 (m-80) cc_final: 0.8530 (m-80) REVERT: R 107 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7703 (ttt-90) REVERT: R 115 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6349 (mm-30) REVERT: R 141 ASP cc_start: 0.8657 (t0) cc_final: 0.8369 (t0) REVERT: S 1 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8099 (ttt) REVERT: S 53 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.7748 (mp10) REVERT: S 55 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8296 (mt-10) REVERT: S 141 ASP cc_start: 0.8752 (t0) cc_final: 0.8402 (t70) REVERT: T 45 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: T 161 GLN cc_start: 0.8083 (tt0) cc_final: 0.7842 (mm-40) REVERT: U 45 GLU cc_start: 0.8849 (tt0) cc_final: 0.8559 (tt0) REVERT: U 107 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7815 (ttt-90) REVERT: W 39 LYS cc_start: 0.8349 (mmtt) cc_final: 0.8107 (mptp) REVERT: W 45 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: W 93 ASN cc_start: 0.9311 (OUTLIER) cc_final: 0.8739 (m110) REVERT: W 160 GLU cc_start: 0.8239 (tt0) cc_final: 0.7909 (tt0) REVERT: W 161 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7871 (mm-40) REVERT: X 45 GLU cc_start: 0.8854 (tt0) cc_final: 0.8631 (tt0) REVERT: X 99 TYR cc_start: 0.9097 (m-80) cc_final: 0.8619 (m-80) outliers start: 82 outliers final: 40 residues processed: 779 average time/residue: 1.4867 time to fit residues: 1464.6585 Evaluate side-chains 788 residues out of total 6588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 718 time to evaluate : 5.052 ------------------------------------------------------------------------------- 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 130 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 95 MET 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 117 ILE Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 371 GLU 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 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 14 LYS Chi-restraints excluded: chain G residue 383 ASP 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 371 GLU 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 22 LEU Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 371 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 L residue 404 GLU Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain O residue 34 GLN 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 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 178 LYS Chi-restraints excluded: chain R residue 54 ASP 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 53 GLN Chi-restraints excluded: chain S residue 55 GLU 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 45 GLU Chi-restraints excluded: chain U residue 54 ASP Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain W residue 93 ASN 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 726 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 320 optimal weight: 0.7980 chunk 515 optimal weight: 20.0000 chunk 744 optimal weight: 0.7980 chunk 591 optimal weight: 0.6980 chunk 601 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 692 optimal weight: 5.9990 chunk 516 optimal weight: 0.2980 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 J 77 GLN K 446 ASN L 408 ASN W 181 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.107806 restraints weight = 81162.777| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.08 r_work: 0.3165 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 61404 Z= 0.142 Angle : 0.484 13.587 83556 Z= 0.255 Chirality : 0.038 0.202 9804 Planarity : 0.008 0.382 10764 Dihedral : 3.796 63.490 8640 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.12 % Allowed : 17.21 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.10), residues: 7776 helix: 2.60 (0.09), residues: 3660 sheet: 0.81 (0.17), residues: 1020 loop : -0.73 (0.12), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 246 HIS 0.004 0.001 HIS K 288 PHE 0.026 0.001 PHE G 401 TYR 0.047 0.001 TYR G 471 ARG 0.054 0.001 ARG B 449 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37791.55 seconds wall clock time: 646 minutes 18.54 seconds (38778.54 seconds total)