Starting phenix.real_space_refine on Sun Feb 8 11:42:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v30_64745/02_2026/9v30_64745.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v30_64745/02_2026/9v30_64745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v30_64745/02_2026/9v30_64745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v30_64745/02_2026/9v30_64745.map" model { file = "/net/cci-nas-00/data/ceres_data/9v30_64745/02_2026/9v30_64745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v30_64745/02_2026/9v30_64745.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.072 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 252 5.16 5 C 28270 2.51 5 N 7628 2.21 5 O 8947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45097 Number of models: 1 Model: "" Number of chains: 12 Chain: "K" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3777 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 23, 'TRANS': 467} Chain breaks: 3 Chain: "H" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3777 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 23, 'TRANS': 467} Chain breaks: 3 Chain: "I" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3777 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 23, 'TRANS': 467} Chain breaks: 3 Chain: "A" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3712 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 22, 'TRANS': 460} Chain breaks: 4 Chain: "J" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3777 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 23, 'TRANS': 467} Chain breaks: 3 Chain: "B" Number of atoms: 3723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3723 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 22, 'TRANS': 461} Chain breaks: 4 Chain: "C" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3777 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 23, 'TRANS': 467} Chain breaks: 3 Chain: "D" Number of atoms: 3723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3723 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 22, 'TRANS': 461} Chain breaks: 4 Chain: "L" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3777 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 23, 'TRANS': 467} Chain breaks: 3 Chain: "F" Number of atoms: 3723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3723 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 22, 'TRANS': 461} Chain breaks: 4 Chain: "G" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3777 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 23, 'TRANS': 467} Chain breaks: 3 Chain: "E" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3777 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 23, 'TRANS': 467} Chain breaks: 3 Time building chain proxies: 10.76, per 1000 atoms: 0.24 Number of scatterers: 45097 At special positions: 0 Unit cell: (201.3, 201.3, 163.9, 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 252 16.00 O 8947 8.00 N 7628 7.00 C 28270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 2.1 seconds 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10918 Finding SS restraints... Secondary structure from input PDB file: 238 helices and 46 sheets defined 49.2% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'K' and resid 11 through 20 removed outlier: 3.876A pdb=" N VAL K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR K 16 " --> pdb=" O ALA K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 34 removed outlier: 3.539A pdb=" N ASN K 32 " --> pdb=" O THR K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 77 removed outlier: 4.420A pdb=" N ARG K 63 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS K 64 " --> pdb=" O VAL K 60 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 94 removed outlier: 3.632A pdb=" N ALA K 92 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 123 removed outlier: 3.755A pdb=" N GLY K 108 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU K 113 " --> pdb=" O LEU K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 139 removed outlier: 3.707A pdb=" N LEU K 129 " --> pdb=" O PHE K 125 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE K 130 " --> pdb=" O ARG K 126 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS K 134 " --> pdb=" O PHE K 130 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE K 137 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL K 138 " --> pdb=" O LYS K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 163 No H-bonds generated for 'chain 'K' and resid 161 through 163' Processing helix chain 'K' and resid 187 through 189 No H-bonds generated for 'chain 'K' and resid 187 through 189' Processing helix chain 'K' and resid 190 through 195 Processing helix chain 'K' and resid 263 through 266 removed outlier: 3.774A pdb=" N GLU K 266 " --> pdb=" O TYR K 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 263 through 266' Processing helix chain 'K' and resid 267 through 288 removed outlier: 3.718A pdb=" N LEU K 271 " --> pdb=" O TYR K 267 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR K 276 " --> pdb=" O ASN K 272 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE K 277 " --> pdb=" O SER K 273 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU K 279 " --> pdb=" O GLU K 275 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA K 280 " --> pdb=" O THR K 276 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA K 288 " --> pdb=" O MET K 284 " (cutoff:3.500A) Processing helix chain 'K' and resid 302 through 308 removed outlier: 3.962A pdb=" N LEU K 306 " --> pdb=" O GLN K 302 " (cutoff:3.500A) Processing helix chain 'K' and resid 333 through 348 Processing helix chain 'K' and resid 372 through 376 removed outlier: 3.876A pdb=" N LEU K 376 " --> pdb=" O ALA K 373 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 389 removed outlier: 3.558A pdb=" N SER K 388 " --> pdb=" O SER K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 392 through 407 removed outlier: 3.921A pdb=" N VAL K 398 " --> pdb=" O PRO K 394 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU K 399 " --> pdb=" O ILE K 395 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASN K 401 " --> pdb=" O ARG K 397 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN K 404 " --> pdb=" O MET K 400 " (cutoff:3.500A) Processing helix chain 'K' and resid 428 through 446 removed outlier: 4.122A pdb=" N ASP K 433 " --> pdb=" O GLY K 429 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY K 446 " --> pdb=" O ASN K 442 " (cutoff:3.500A) Processing helix chain 'K' and resid 447 through 453 removed outlier: 3.625A pdb=" N LEU K 450 " --> pdb=" O LEU K 447 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN K 452 " --> pdb=" O PRO K 449 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP K 453 " --> pdb=" O LEU K 450 " (cutoff:3.500A) Processing helix chain 'K' and resid 457 through 468 Processing helix chain 'K' and resid 483 through 520 removed outlier: 3.889A pdb=" N VAL K 497 " --> pdb=" O GLN K 493 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA K 502 " --> pdb=" O GLN K 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 19 removed outlier: 4.032A pdb=" N VAL H 15 " --> pdb=" O GLY H 11 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASP H 17 " --> pdb=" O LYS H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 22 No H-bonds generated for 'chain 'H' and resid 20 through 22' Processing helix chain 'H' and resid 23 through 34 Processing helix chain 'H' and resid 60 through 77 removed outlier: 3.541A pdb=" N CYS H 64 " --> pdb=" O VAL H 60 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.937A pdb=" N MET H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL H 112 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU H 121 " --> pdb=" O MET H 117 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN H 123 " --> pdb=" O TYR H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 139 removed outlier: 3.596A pdb=" N PHE H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU H 131 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE H 137 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL H 138 " --> pdb=" O LYS H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 190 through 196 Processing helix chain 'H' and resid 263 through 266 removed outlier: 3.908A pdb=" N GLU H 266 " --> pdb=" O TYR H 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 263 through 266' Processing helix chain 'H' and resid 267 through 284 removed outlier: 4.022A pdb=" N LEU H 271 " --> pdb=" O TYR H 267 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA H 280 " --> pdb=" O THR H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 349 removed outlier: 3.669A pdb=" N TRP H 349 " --> pdb=" O GLN H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 373 through 378 Processing helix chain 'H' and resid 385 through 389 Processing helix chain 'H' and resid 392 through 407 removed outlier: 3.666A pdb=" N VAL H 396 " --> pdb=" O GLN H 392 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG H 397 " --> pdb=" O LEU H 393 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL H 398 " --> pdb=" O PRO H 394 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN H 404 " --> pdb=" O MET H 400 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER H 405 " --> pdb=" O ASN H 401 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 445 removed outlier: 3.947A pdb=" N LEU H 434 " --> pdb=" O ARG H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 446 through 447 No H-bonds generated for 'chain 'H' and resid 446 through 447' Processing helix chain 'H' and resid 448 through 453 removed outlier: 4.470A pdb=" N GLN H 452 " --> pdb=" O PRO H 449 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP H 453 " --> pdb=" O LEU H 450 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 468 Processing helix chain 'H' and resid 483 through 520 removed outlier: 4.187A pdb=" N MET H 487 " --> pdb=" O LYS H 483 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA H 503 " --> pdb=" O GLY H 499 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY H 504 " --> pdb=" O ALA H 500 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA H 505 " --> pdb=" O SER H 501 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASN H 506 " --> pdb=" O ALA H 502 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 19 removed outlier: 3.869A pdb=" N VAL I 15 " --> pdb=" O GLY I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 22 No H-bonds generated for 'chain 'I' and resid 20 through 22' Processing helix chain 'I' and resid 23 through 34 removed outlier: 3.593A pdb=" N THR I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG I 29 " --> pdb=" O PRO I 25 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA I 30 " --> pdb=" O TYR I 26 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN I 31 " --> pdb=" O GLU I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 64 removed outlier: 4.099A pdb=" N ARG I 63 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS I 64 " --> pdb=" O VAL I 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 59 through 64' Processing helix chain 'I' and resid 67 through 77 removed outlier: 3.638A pdb=" N MET I 73 " --> pdb=" O ALA I 69 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA I 75 " --> pdb=" O LYS I 71 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 94 Processing helix chain 'I' and resid 100 through 108 removed outlier: 3.504A pdb=" N GLY I 108 " --> pdb=" O ARG I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 123 removed outlier: 3.615A pdb=" N GLU I 121 " --> pdb=" O MET I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 139 removed outlier: 3.751A pdb=" N PHE I 130 " --> pdb=" O ARG I 126 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS I 134 " --> pdb=" O PHE I 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE I 137 " --> pdb=" O LEU I 133 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL I 138 " --> pdb=" O LYS I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 163 No H-bonds generated for 'chain 'I' and resid 161 through 163' Processing helix chain 'I' and resid 190 through 195 Processing helix chain 'I' and resid 196 through 197 No H-bonds generated for 'chain 'I' and resid 196 through 197' Processing helix chain 'I' and resid 198 through 202 removed outlier: 3.666A pdb=" N ASP I 201 " --> pdb=" O ASN I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 263 through 266 removed outlier: 3.852A pdb=" N GLU I 266 " --> pdb=" O TYR I 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 263 through 266' Processing helix chain 'I' and resid 267 through 288 removed outlier: 3.597A pdb=" N LEU I 271 " --> pdb=" O TYR I 267 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR I 276 " --> pdb=" O ASN I 272 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE I 277 " --> pdb=" O SER I 273 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU I 279 " --> pdb=" O GLU I 275 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA I 280 " --> pdb=" O THR I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 308 removed outlier: 3.934A pdb=" N LEU I 306 " --> pdb=" O GLN I 302 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS I 308 " --> pdb=" O ARG I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 333 through 349 Processing helix chain 'I' and resid 374 through 378 Processing helix chain 'I' and resid 385 through 389 removed outlier: 3.510A pdb=" N SER I 388 " --> pdb=" O SER I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 391 through 407 removed outlier: 3.886A pdb=" N ILE I 395 " --> pdb=" O LEU I 391 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL I 396 " --> pdb=" O GLN I 392 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN I 401 " --> pdb=" O ARG I 397 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU I 403 " --> pdb=" O LEU I 399 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN I 404 " --> pdb=" O MET I 400 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER I 405 " --> pdb=" O ASN I 401 " (cutoff:3.500A) Processing helix chain 'I' and resid 430 through 446 removed outlier: 3.774A pdb=" N GLY I 446 " --> pdb=" O ASN I 442 " (cutoff:3.500A) Processing helix chain 'I' and resid 447 through 453 removed outlier: 3.699A pdb=" N LEU I 450 " --> pdb=" O LEU I 447 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN I 452 " --> pdb=" O PRO I 449 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP I 453 " --> pdb=" O LEU I 450 " (cutoff:3.500A) Processing helix chain 'I' and resid 457 through 468 removed outlier: 3.514A pdb=" N ALA I 468 " --> pdb=" O ARG I 464 " (cutoff:3.500A) Processing helix chain 'I' and resid 483 through 520 removed outlier: 4.132A pdb=" N SER I 501 " --> pdb=" O VAL I 497 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA I 502 " --> pdb=" O GLN I 498 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA I 503 " --> pdb=" O GLY I 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 19 removed outlier: 4.057A pdb=" N VAL A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASP A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 23 through 34 Processing helix chain 'A' and resid 60 through 77 removed outlier: 3.523A pdb=" N CYS A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 96 Processing helix chain 'A' and resid 104 through 123 removed outlier: 4.509A pdb=" N GLY A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 123 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 139 removed outlier: 4.014A pdb=" N LEU A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 190 through 196 removed outlier: 3.827A pdb=" N GLN A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 266 removed outlier: 3.640A pdb=" N GLU A 266 " --> pdb=" O TYR A 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 263 through 266' Processing helix chain 'A' and resid 267 through 287 removed outlier: 3.971A pdb=" N LEU A 271 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 349 removed outlier: 3.672A pdb=" N ALA A 336 " --> pdb=" O ASP A 332 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP A 349 " --> pdb=" O GLN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.599A pdb=" N LEU A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 407 removed outlier: 3.719A pdb=" N ASN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 404 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 445 removed outlier: 4.645A pdb=" N ASP A 433 " --> pdb=" O GLY A 429 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 451 Proline residue: A 449 - end of helix No H-bonds generated for 'chain 'A' and resid 446 through 451' Processing helix chain 'A' and resid 457 through 468 Processing helix chain 'A' and resid 483 through 520 removed outlier: 3.851A pdb=" N MET A 487 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 20 removed outlier: 3.819A pdb=" N VAL J 15 " --> pdb=" O GLY J 11 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR J 16 " --> pdb=" O ALA J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 34 removed outlier: 3.905A pdb=" N ASN J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N CYS J 33 " --> pdb=" O ARG J 29 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA J 34 " --> pdb=" O ALA J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 77 removed outlier: 4.029A pdb=" N CYS J 64 " --> pdb=" O VAL J 60 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU J 65 " --> pdb=" O GLY J 61 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA J 70 " --> pdb=" O ASN J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 96 removed outlier: 3.609A pdb=" N LEU J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 123 removed outlier: 3.984A pdb=" N ASP J 106 " --> pdb=" O ALA J 102 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU J 107 " --> pdb=" O ALA J 103 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY J 108 " --> pdb=" O ARG J 104 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU J 109 " --> pdb=" O VAL J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 134 removed outlier: 3.534A pdb=" N LYS J 134 " --> pdb=" O PHE J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 163 No H-bonds generated for 'chain 'J' and resid 161 through 163' Processing helix chain 'J' and resid 190 through 195 Processing helix chain 'J' and resid 263 through 266 removed outlier: 3.836A pdb=" N GLU J 266 " --> pdb=" O TYR J 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 263 through 266' Processing helix chain 'J' and resid 267 through 288 removed outlier: 3.832A pdb=" N LEU J 271 " --> pdb=" O TYR J 267 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR J 276 " --> pdb=" O ASN J 272 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA J 280 " --> pdb=" O THR J 276 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 308 removed outlier: 3.945A pdb=" N LEU J 306 " --> pdb=" O GLN J 302 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS J 308 " --> pdb=" O ARG J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 333 through 348 Processing helix chain 'J' and resid 385 through 389 Processing helix chain 'J' and resid 392 through 407 removed outlier: 3.561A pdb=" N VAL J 396 " --> pdb=" O GLN J 392 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET J 400 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN J 401 " --> pdb=" O ARG J 397 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN J 404 " --> pdb=" O MET J 400 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER J 405 " --> pdb=" O ASN J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 445 Processing helix chain 'J' and resid 446 through 447 No H-bonds generated for 'chain 'J' and resid 446 through 447' Processing helix chain 'J' and resid 448 through 453 removed outlier: 4.232A pdb=" N GLN J 452 " --> pdb=" O PRO J 449 " (cutoff:3.500A) Processing helix chain 'J' and resid 457 through 468 Processing helix chain 'J' and resid 484 through 520 removed outlier: 3.610A pdb=" N ALA J 502 " --> pdb=" O GLN J 498 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA J 503 " --> pdb=" O GLY J 499 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP J 518 " --> pdb=" O GLY J 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 19 Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 23 through 34 removed outlier: 3.562A pdb=" N THR B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 77 Processing helix chain 'B' and resid 89 through 94 removed outlier: 3.529A pdb=" N THR B 94 " --> pdb=" O TYR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 Processing helix chain 'B' and resid 110 through 123 Processing helix chain 'B' and resid 125 through 139 removed outlier: 3.949A pdb=" N LEU B 129 " --> pdb=" O PHE B 125 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 190 through 196 removed outlier: 3.814A pdb=" N GLN B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 266 removed outlier: 3.569A pdb=" N GLU B 266 " --> pdb=" O TYR B 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 263 through 266' Processing helix chain 'B' and resid 267 through 288 removed outlier: 4.000A pdb=" N LEU B 271 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 276 " --> pdb=" O ASN B 272 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 288 " --> pdb=" O MET B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 349 removed outlier: 3.603A pdb=" N ALA B 336 " --> pdb=" O ASP B 332 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP B 349 " --> pdb=" O GLN B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 391 Processing helix chain 'B' and resid 392 through 407 removed outlier: 3.512A pdb=" N ARG B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL B 398 " --> pdb=" O PRO B 394 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN B 401 " --> pdb=" O ARG B 397 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN B 404 " --> pdb=" O MET B 400 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 445 removed outlier: 3.856A pdb=" N LEU B 434 " --> pdb=" O ARG B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 453 Proline residue: B 449 - end of helix removed outlier: 4.455A pdb=" N GLN B 452 " --> pdb=" O PRO B 449 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP B 453 " --> pdb=" O LEU B 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 446 through 453' Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 483 through 520 removed outlier: 3.827A pdb=" N MET B 487 " --> pdb=" O LYS B 483 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 20 removed outlier: 3.877A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 34 Processing helix chain 'C' and resid 59 through 77 removed outlier: 4.408A pdb=" N ARG C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS C 64 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU C 65 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 96 removed outlier: 3.551A pdb=" N ALA C 92 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 108 removed outlier: 3.518A pdb=" N GLY C 108 " --> pdb=" O ARG C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 123 removed outlier: 4.046A pdb=" N GLU C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 139 removed outlier: 3.700A pdb=" N LEU C 129 " --> pdb=" O PHE C 125 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 134 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE C 137 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 267 through 286 removed outlier: 3.738A pdb=" N LEU C 271 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR C 276 " --> pdb=" O ASN C 272 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA C 280 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 347 Processing helix chain 'C' and resid 373 through 378 Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.699A pdb=" N SER C 388 " --> pdb=" O SER C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 406 removed outlier: 3.943A pdb=" N VAL C 396 " --> pdb=" O GLN C 392 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL C 398 " --> pdb=" O PRO C 394 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN C 401 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN C 404 " --> pdb=" O MET C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 446 removed outlier: 3.761A pdb=" N GLY C 446 " --> pdb=" O ASN C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 453 removed outlier: 3.549A pdb=" N LEU C 450 " --> pdb=" O LEU C 447 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN C 452 " --> pdb=" O PRO C 449 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP C 453 " --> pdb=" O LEU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 468 Processing helix chain 'C' and resid 483 through 521 removed outlier: 3.876A pdb=" N VAL C 497 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C 502 " --> pdb=" O GLN C 498 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 503 " --> pdb=" O GLY C 499 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN C 521 " --> pdb=" O GLU C 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 19 removed outlier: 3.934A pdb=" N VAL D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASP D 17 " --> pdb=" O LYS D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 23 through 34 removed outlier: 3.667A pdb=" N ASN D 32 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 77 removed outlier: 3.535A pdb=" N CYS D 64 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 96 Processing helix chain 'D' and resid 101 through 123 removed outlier: 3.918A pdb=" N MET D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN D 123 " --> pdb=" O TYR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 139 removed outlier: 3.533A pdb=" N PHE D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU D 131 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 190 through 196 Processing helix chain 'D' and resid 263 through 266 removed outlier: 3.889A pdb=" N GLU D 266 " --> pdb=" O TYR D 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 263 through 266' Processing helix chain 'D' and resid 267 through 288 removed outlier: 4.057A pdb=" N LEU D 271 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA D 288 " --> pdb=" O MET D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 349 removed outlier: 3.653A pdb=" N TRP D 349 " --> pdb=" O GLN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 389 Processing helix chain 'D' and resid 391 through 407 removed outlier: 3.672A pdb=" N ILE D 395 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL D 396 " --> pdb=" O GLN D 392 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG D 397 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 398 " --> pdb=" O PRO D 394 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 399 " --> pdb=" O ILE D 395 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET D 400 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN D 401 " --> pdb=" O ARG D 397 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN D 404 " --> pdb=" O MET D 400 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER D 405 " --> pdb=" O ASN D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 445 removed outlier: 3.985A pdb=" N LEU D 434 " --> pdb=" O ARG D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 453 Proline residue: D 449 - end of helix removed outlier: 4.469A pdb=" N GLN D 452 " --> pdb=" O PRO D 449 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP D 453 " --> pdb=" O LEU D 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 446 through 453' Processing helix chain 'D' and resid 457 through 468 Processing helix chain 'D' and resid 483 through 520 removed outlier: 4.246A pdb=" N MET D 487 " --> pdb=" O LYS D 483 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY D 499 " --> pdb=" O ALA D 495 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY D 504 " --> pdb=" O ALA D 500 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA D 505 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN D 506 " --> pdb=" O ALA D 502 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 20 removed outlier: 3.864A pdb=" N VAL L 15 " --> pdb=" O GLY L 11 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR L 16 " --> pdb=" O ALA L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 34 removed outlier: 3.647A pdb=" N THR L 28 " --> pdb=" O GLN L 24 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG L 29 " --> pdb=" O PRO L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 77 removed outlier: 3.556A pdb=" N CYS L 64 " --> pdb=" O VAL L 60 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA L 70 " --> pdb=" O ASN L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 96 removed outlier: 3.713A pdb=" N ALA L 92 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU L 95 " --> pdb=" O GLU L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 123 removed outlier: 3.687A pdb=" N GLY L 108 " --> pdb=" O ARG L 104 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL L 112 " --> pdb=" O GLY L 108 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU L 113 " --> pdb=" O LEU L 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 139 removed outlier: 3.892A pdb=" N LEU L 129 " --> pdb=" O PHE L 125 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE L 130 " --> pdb=" O ARG L 126 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS L 134 " --> pdb=" O PHE L 130 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE L 137 " --> pdb=" O LEU L 133 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL L 138 " --> pdb=" O LYS L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 163 No H-bonds generated for 'chain 'L' and resid 161 through 163' Processing helix chain 'L' and resid 190 through 195 Processing helix chain 'L' and resid 196 through 197 No H-bonds generated for 'chain 'L' and resid 196 through 197' Processing helix chain 'L' and resid 198 through 202 removed outlier: 3.639A pdb=" N ASP L 201 " --> pdb=" O ASN L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 266 removed outlier: 3.858A pdb=" N GLU L 266 " --> pdb=" O TYR L 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 263 through 266' Processing helix chain 'L' and resid 267 through 288 removed outlier: 3.709A pdb=" N LEU L 271 " --> pdb=" O TYR L 267 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR L 276 " --> pdb=" O ASN L 272 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE L 277 " --> pdb=" O SER L 273 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU L 279 " --> pdb=" O GLU L 275 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA L 280 " --> pdb=" O THR L 276 " (cutoff:3.500A) Processing helix chain 'L' and resid 302 through 308 removed outlier: 3.989A pdb=" N LEU L 306 " --> pdb=" O GLN L 302 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS L 308 " --> pdb=" O ARG L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 318 through 320 No H-bonds generated for 'chain 'L' and resid 318 through 320' Processing helix chain 'L' and resid 333 through 348 Processing helix chain 'L' and resid 373 through 378 Processing helix chain 'L' and resid 385 through 389 removed outlier: 3.519A pdb=" N SER L 388 " --> pdb=" O SER L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 391 through 407 removed outlier: 3.926A pdb=" N ILE L 395 " --> pdb=" O LEU L 391 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL L 396 " --> pdb=" O GLN L 392 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN L 401 " --> pdb=" O ARG L 397 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN L 404 " --> pdb=" O MET L 400 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER L 405 " --> pdb=" O ASN L 401 " (cutoff:3.500A) Processing helix chain 'L' and resid 428 through 446 removed outlier: 4.353A pdb=" N ASP L 433 " --> pdb=" O GLY L 429 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY L 446 " --> pdb=" O ASN L 442 " (cutoff:3.500A) Processing helix chain 'L' and resid 447 through 453 removed outlier: 3.737A pdb=" N LEU L 450 " --> pdb=" O LEU L 447 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN L 452 " --> pdb=" O PRO L 449 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP L 453 " --> pdb=" O LEU L 450 " (cutoff:3.500A) Processing helix chain 'L' and resid 457 through 468 Processing helix chain 'L' and resid 483 through 520 removed outlier: 3.723A pdb=" N ALA L 502 " --> pdb=" O GLN L 498 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA L 503 " --> pdb=" O GLY L 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 19 removed outlier: 4.026A pdb=" N VAL F 15 " --> pdb=" O GLY F 11 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ASP F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 22 No H-bonds generated for 'chain 'F' and resid 20 through 22' Processing helix chain 'F' and resid 23 through 34 Processing helix chain 'F' and resid 60 through 77 removed outlier: 3.524A pdb=" N CYS F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 96 Processing helix chain 'F' and resid 101 through 123 removed outlier: 3.975A pdb=" N MET F 111 " --> pdb=" O GLU F 107 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL F 112 " --> pdb=" O GLY F 108 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET F 120 " --> pdb=" O LEU F 116 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU F 121 " --> pdb=" O MET F 117 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN F 123 " --> pdb=" O TYR F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 139 removed outlier: 4.040A pdb=" N LEU F 129 " --> pdb=" O PHE F 125 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE F 130 " --> pdb=" O ARG F 126 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU F 131 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE F 137 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL F 138 " --> pdb=" O LYS F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 187 through 189 No H-bonds generated for 'chain 'F' and resid 187 through 189' Processing helix chain 'F' and resid 190 through 196 removed outlier: 3.778A pdb=" N GLN F 196 " --> pdb=" O ASP F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 266 removed outlier: 3.642A pdb=" N GLU F 266 " --> pdb=" O TYR F 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 263 through 266' Processing helix chain 'F' and resid 267 through 284 removed outlier: 3.717A pdb=" N LEU F 271 " --> pdb=" O TYR F 267 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA F 280 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE F 281 " --> pdb=" O ILE F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 349 removed outlier: 3.601A pdb=" N TRP F 349 " --> pdb=" O GLN F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 378 Processing helix chain 'F' and resid 386 through 391 removed outlier: 3.532A pdb=" N GLU F 390 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU F 391 " --> pdb=" O GLN F 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 386 through 391' Processing helix chain 'F' and resid 391 through 407 removed outlier: 3.739A pdb=" N ILE F 395 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL F 396 " --> pdb=" O GLN F 392 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN F 404 " --> pdb=" O MET F 400 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER F 405 " --> pdb=" O ASN F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 445 removed outlier: 3.675A pdb=" N GLY F 431 " --> pdb=" O ALA F 427 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP F 433 " --> pdb=" O GLY F 429 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL F 441 " --> pdb=" O LEU F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 451 Proline residue: F 449 - end of helix No H-bonds generated for 'chain 'F' and resid 446 through 451' Processing helix chain 'F' and resid 457 through 468 Processing helix chain 'F' and resid 483 through 520 removed outlier: 3.917A pdb=" N MET F 487 " --> pdb=" O LYS F 483 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY F 499 " --> pdb=" O ALA F 495 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY F 514 " --> pdb=" O ALA F 510 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA F 515 " --> pdb=" O VAL F 511 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY F 516 " --> pdb=" O GLY F 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 20 removed outlier: 3.812A pdb=" N VAL G 15 " --> pdb=" O GLY G 11 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 34 removed outlier: 3.842A pdb=" N ASN G 32 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N CYS G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 77 removed outlier: 4.010A pdb=" N CYS G 64 " --> pdb=" O VAL G 60 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU G 65 " --> pdb=" O GLY G 61 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA G 70 " --> pdb=" O ASN G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 96 removed outlier: 3.609A pdb=" N ALA G 92 " --> pdb=" O SER G 88 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER G 96 " --> pdb=" O ALA G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 123 removed outlier: 3.773A pdb=" N MET G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL G 112 " --> pdb=" O GLY G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 134 removed outlier: 3.518A pdb=" N PHE G 130 " --> pdb=" O ARG G 126 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS G 134 " --> pdb=" O PHE G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 163 No H-bonds generated for 'chain 'G' and resid 161 through 163' Processing helix chain 'G' and resid 190 through 195 Processing helix chain 'G' and resid 263 through 266 removed outlier: 3.898A pdb=" N GLU G 266 " --> pdb=" O TYR G 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 263 through 266' Processing helix chain 'G' and resid 267 through 288 removed outlier: 3.726A pdb=" N LEU G 271 " --> pdb=" O TYR G 267 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU G 279 " --> pdb=" O GLU G 275 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA G 280 " --> pdb=" O THR G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 308 removed outlier: 4.055A pdb=" N LEU G 306 " --> pdb=" O GLN G 302 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN G 307 " --> pdb=" O PRO G 303 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS G 308 " --> pdb=" O ARG G 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 302 through 308' Processing helix chain 'G' and resid 333 through 348 Processing helix chain 'G' and resid 373 through 377 removed outlier: 3.553A pdb=" N GLU G 377 " --> pdb=" O ALA G 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 373 through 377' Processing helix chain 'G' and resid 385 through 389 Processing helix chain 'G' and resid 392 through 407 removed outlier: 3.569A pdb=" N VAL G 396 " --> pdb=" O GLN G 392 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET G 400 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN G 401 " --> pdb=" O ARG G 397 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN G 404 " --> pdb=" O MET G 400 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER G 405 " --> pdb=" O ASN G 401 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 445 Processing helix chain 'G' and resid 446 through 447 No H-bonds generated for 'chain 'G' and resid 446 through 447' Processing helix chain 'G' and resid 448 through 453 removed outlier: 4.239A pdb=" N GLN G 452 " --> pdb=" O PRO G 449 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 468 Processing helix chain 'G' and resid 483 through 520 removed outlier: 3.750A pdb=" N MET G 487 " --> pdb=" O LYS G 483 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL G 497 " --> pdb=" O GLN G 493 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA G 502 " --> pdb=" O GLN G 498 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP G 518 " --> pdb=" O GLY G 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 19 Processing helix chain 'E' and resid 20 through 22 No H-bonds generated for 'chain 'E' and resid 20 through 22' Processing helix chain 'E' and resid 23 through 34 removed outlier: 3.560A pdb=" N THR E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 77 removed outlier: 4.507A pdb=" N ARG E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 94 Processing helix chain 'E' and resid 101 through 123 removed outlier: 3.607A pdb=" N ALA E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N MET E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET E 120 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU E 121 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN E 123 " --> pdb=" O TYR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 139 removed outlier: 3.918A pdb=" N LEU E 129 " --> pdb=" O PHE E 125 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE E 130 " --> pdb=" O ARG E 126 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE E 137 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL E 138 " --> pdb=" O LYS E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 190 through 196 removed outlier: 3.801A pdb=" N GLN E 196 " --> pdb=" O ASP E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 266 removed outlier: 3.546A pdb=" N GLU E 266 " --> pdb=" O TYR E 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 263 through 266' Processing helix chain 'E' and resid 267 through 284 removed outlier: 3.943A pdb=" N LEU E 271 " --> pdb=" O TYR E 267 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA E 280 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 349 removed outlier: 3.616A pdb=" N TRP E 349 " --> pdb=" O GLN E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 378 Processing helix chain 'E' and resid 385 through 389 Processing helix chain 'E' and resid 391 through 407 removed outlier: 3.703A pdb=" N ILE E 395 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL E 396 " --> pdb=" O GLN E 392 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET E 400 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN E 401 " --> pdb=" O ARG E 397 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN E 404 " --> pdb=" O MET E 400 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER E 405 " --> pdb=" O ASN E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 445 Processing helix chain 'E' and resid 457 through 468 Processing helix chain 'E' and resid 484 through 520 removed outlier: 3.745A pdb=" N GLY E 499 " --> pdb=" O ALA E 495 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA E 505 " --> pdb=" O SER E 501 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN E 506 " --> pdb=" O ALA E 502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 158 through 160 removed outlier: 3.766A pdb=" N CYS K 142 " --> pdb=" O VAL K 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 165 through 169 removed outlier: 6.780A pdb=" N VAL K 166 " --> pdb=" O ILE K 178 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE K 178 " --> pdb=" O VAL K 166 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLN K 168 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU K 176 " --> pdb=" O ARG K 216 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG K 216 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR K 212 " --> pdb=" O THR K 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 165 through 169 removed outlier: 6.780A pdb=" N VAL K 166 " --> pdb=" O ILE K 178 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE K 178 " --> pdb=" O VAL K 166 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLN K 168 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU K 176 " --> pdb=" O ARG K 216 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG K 216 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR K 212 " --> pdb=" O THR K 180 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY K 237 " --> pdb=" O ARG K 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 322 through 324 removed outlier: 5.972A pdb=" N GLY K 293 " --> pdb=" O VAL E 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 158 through 160 removed outlier: 3.546A pdb=" N ARG H 158 " --> pdb=" O TYR H 145 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR H 145 " --> pdb=" O ARG H 158 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS H 142 " --> pdb=" O VAL H 249 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 165 through 169 removed outlier: 6.935A pdb=" N VAL H 166 " --> pdb=" O ILE H 178 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE H 178 " --> pdb=" O VAL H 166 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLN H 168 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LEU H 176 " --> pdb=" O ARG H 216 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG H 216 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR H 212 " --> pdb=" O THR H 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 165 through 169 removed outlier: 6.935A pdb=" N VAL H 166 " --> pdb=" O ILE H 178 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE H 178 " --> pdb=" O VAL H 166 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLN H 168 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LEU H 176 " --> pdb=" O ARG H 216 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG H 216 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR H 212 " --> pdb=" O THR H 180 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG H 223 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY H 237 " --> pdb=" O ARG H 223 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 293 through 295 Processing sheet with id=AA9, first strand: chain 'H' and resid 314 through 316 Processing sheet with id=AB1, first strand: chain 'I' and resid 158 through 160 removed outlier: 3.545A pdb=" N TYR I 160 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS I 142 " --> pdb=" O VAL I 249 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 165 through 169 removed outlier: 6.917A pdb=" N VAL I 166 " --> pdb=" O ILE I 178 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE I 178 " --> pdb=" O VAL I 166 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLN I 168 " --> pdb=" O LEU I 176 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU I 176 " --> pdb=" O ARG I 216 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG I 216 " --> pdb=" O LEU I 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 165 through 169 removed outlier: 6.917A pdb=" N VAL I 166 " --> pdb=" O ILE I 178 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE I 178 " --> pdb=" O VAL I 166 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLN I 168 " --> pdb=" O LEU I 176 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU I 176 " --> pdb=" O ARG I 216 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG I 216 " --> pdb=" O LEU I 176 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG I 223 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY I 237 " --> pdb=" O ARG I 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 313 through 316 Processing sheet with id=AB5, first strand: chain 'A' and resid 158 through 160 removed outlier: 3.574A pdb=" N ARG A 158 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR A 145 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS A 142 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 165 through 169 removed outlier: 6.897A pdb=" N VAL A 166 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A 178 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLN A 168 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU A 176 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 216 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR A 212 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 165 through 169 removed outlier: 6.897A pdb=" N VAL A 166 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A 178 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLN A 168 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU A 176 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 216 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR A 212 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 237 " --> pdb=" O ARG A 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 314 through 316 Processing sheet with id=AB9, first strand: chain 'J' and resid 158 through 160 removed outlier: 3.850A pdb=" N CYS J 142 " --> pdb=" O VAL J 249 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 165 through 169 removed outlier: 6.905A pdb=" N VAL J 166 " --> pdb=" O ILE J 178 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE J 178 " --> pdb=" O VAL J 166 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN J 168 " --> pdb=" O LEU J 176 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU J 176 " --> pdb=" O ARG J 216 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG J 216 " --> pdb=" O LEU J 176 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR J 212 " --> pdb=" O THR J 180 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG J 223 " --> pdb=" O GLY J 237 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY J 237 " --> pdb=" O ARG J 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 314 through 316 removed outlier: 6.711A pdb=" N VAL J 315 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 158 through 160 removed outlier: 3.513A pdb=" N ARG B 158 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 145 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS B 142 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 165 through 169 removed outlier: 6.810A pdb=" N VAL B 166 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE B 178 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN B 168 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU B 176 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 216 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR B 212 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 165 through 169 removed outlier: 6.810A pdb=" N VAL B 166 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE B 178 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN B 168 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU B 176 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 216 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR B 212 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 223 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 237 " --> pdb=" O ARG B 223 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 313 through 316 removed outlier: 6.431A pdb=" N GLU B 313 " --> pdb=" O GLY C 293 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL C 295 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 315 " --> pdb=" O VAL C 295 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 158 through 160 removed outlier: 3.506A pdb=" N TYR C 160 " --> pdb=" O LEU C 143 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS C 142 " --> pdb=" O VAL C 249 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 165 through 169 removed outlier: 6.765A pdb=" N VAL C 166 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE C 178 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN C 168 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N LEU C 176 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 216 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 212 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 165 through 169 removed outlier: 6.765A pdb=" N VAL C 166 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE C 178 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN C 168 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N LEU C 176 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 216 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 212 " --> pdb=" O THR C 180 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 237 " --> pdb=" O ARG C 223 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 312 through 316 removed outlier: 6.717A pdb=" N GLU C 313 " --> pdb=" O GLY D 293 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL D 295 " --> pdb=" O GLU C 313 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL C 315 " --> pdb=" O VAL D 295 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 158 through 160 removed outlier: 3.581A pdb=" N ARG D 158 " --> pdb=" O TYR D 145 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR D 145 " --> pdb=" O ARG D 158 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N CYS D 142 " --> pdb=" O VAL D 249 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 165 through 169 removed outlier: 6.934A pdb=" N VAL D 166 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE D 178 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN D 168 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LEU D 176 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG D 216 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR D 212 " --> pdb=" O THR D 180 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 165 through 169 removed outlier: 6.934A pdb=" N VAL D 166 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE D 178 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN D 168 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LEU D 176 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG D 216 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR D 212 " --> pdb=" O THR D 180 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG D 223 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY D 237 " --> pdb=" O ARG D 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 314 through 316 Processing sheet with id=AD6, first strand: chain 'L' and resid 158 through 160 removed outlier: 3.598A pdb=" N TYR L 160 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS L 142 " --> pdb=" O VAL L 249 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 165 through 169 removed outlier: 6.802A pdb=" N VAL L 166 " --> pdb=" O ILE L 178 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE L 178 " --> pdb=" O VAL L 166 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLN L 168 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU L 176 " --> pdb=" O ARG L 216 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG L 216 " --> pdb=" O LEU L 176 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 165 through 169 removed outlier: 6.802A pdb=" N VAL L 166 " --> pdb=" O ILE L 178 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE L 178 " --> pdb=" O VAL L 166 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLN L 168 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU L 176 " --> pdb=" O ARG L 216 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG L 216 " --> pdb=" O LEU L 176 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 314 through 316 Processing sheet with id=AE1, first strand: chain 'F' and resid 158 through 160 removed outlier: 3.556A pdb=" N ARG F 158 " --> pdb=" O TYR F 145 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR F 145 " --> pdb=" O ARG F 158 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS F 142 " --> pdb=" O VAL F 249 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 165 through 169 removed outlier: 6.899A pdb=" N VAL F 166 " --> pdb=" O ILE F 178 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE F 178 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLN F 168 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU F 176 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG F 216 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR F 212 " --> pdb=" O THR F 180 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 165 through 169 removed outlier: 6.899A pdb=" N VAL F 166 " --> pdb=" O ILE F 178 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE F 178 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLN F 168 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU F 176 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG F 216 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR F 212 " --> pdb=" O THR F 180 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG F 223 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY F 237 " --> pdb=" O ARG F 223 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 314 through 316 Processing sheet with id=AE5, first strand: chain 'G' and resid 158 through 160 removed outlier: 3.867A pdb=" N CYS G 142 " --> pdb=" O VAL G 249 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 165 through 169 removed outlier: 6.908A pdb=" N VAL G 166 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE G 178 " --> pdb=" O VAL G 166 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN G 168 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU G 176 " --> pdb=" O ARG G 216 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG G 216 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR G 212 " --> pdb=" O THR G 180 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG G 223 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY G 237 " --> pdb=" O ARG G 223 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 314 through 316 removed outlier: 6.590A pdb=" N VAL G 315 " --> pdb=" O VAL E 295 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 158 through 160 removed outlier: 3.524A pdb=" N ARG E 158 " --> pdb=" O TYR E 145 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR E 145 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS E 142 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 165 through 169 removed outlier: 6.825A pdb=" N VAL E 166 " --> pdb=" O ILE E 178 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE E 178 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLN E 168 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N LEU E 176 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG E 216 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR E 212 " --> pdb=" O THR E 180 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 165 through 169 removed outlier: 6.825A pdb=" N VAL E 166 " --> pdb=" O ILE E 178 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE E 178 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLN E 168 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N LEU E 176 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG E 216 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR E 212 " --> pdb=" O THR E 180 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG E 223 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY E 237 " --> pdb=" O ARG E 223 " (cutoff:3.500A) 2029 hydrogen bonds defined for protein. 5883 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: 10.03 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 8075 1.32 - 1.44: 10752 1.44 - 1.56: 26490 1.56 - 1.69: 0 1.69 - 1.81: 444 Bond restraints: 45761 Sorted by residual: bond pdb=" C ILE C 335 " pdb=" O ILE C 335 " ideal model delta sigma weight residual 1.237 1.290 -0.053 1.13e-02 7.83e+03 2.19e+01 bond pdb=" N ILE E 300 " pdb=" CA ILE E 300 " ideal model delta sigma weight residual 1.457 1.495 -0.038 9.30e-03 1.16e+04 1.65e+01 bond pdb=" C SER C 338 " pdb=" O SER C 338 " ideal model delta sigma weight residual 1.236 1.283 -0.047 1.15e-02 7.56e+03 1.64e+01 bond pdb=" CA SER K 388 " pdb=" CB SER K 388 " ideal model delta sigma weight residual 1.529 1.476 0.053 1.40e-02 5.10e+03 1.42e+01 bond pdb=" N ILE G 300 " pdb=" CA ILE G 300 " ideal model delta sigma weight residual 1.459 1.492 -0.033 9.10e-03 1.21e+04 1.35e+01 ... (remaining 45756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 58390 1.45 - 2.91: 2902 2.91 - 4.36: 584 4.36 - 5.81: 118 5.81 - 7.27: 20 Bond angle restraints: 62014 Sorted by residual: angle pdb=" N GLN A 389 " pdb=" CA GLN A 389 " pdb=" C GLN A 389 " ideal model delta sigma weight residual 114.31 107.90 6.41 1.29e+00 6.01e-01 2.47e+01 angle pdb=" N PHE C 333 " pdb=" CA PHE C 333 " pdb=" C PHE C 333 " ideal model delta sigma weight residual 114.04 108.09 5.95 1.24e+00 6.50e-01 2.30e+01 angle pdb=" N GLN C 389 " pdb=" CA GLN C 389 " pdb=" C GLN C 389 " ideal model delta sigma weight residual 114.64 107.37 7.27 1.52e+00 4.33e-01 2.29e+01 angle pdb=" N GLN I 389 " pdb=" CA GLN I 389 " pdb=" C GLN I 389 " ideal model delta sigma weight residual 114.39 107.58 6.81 1.45e+00 4.76e-01 2.21e+01 angle pdb=" N ILE C 277 " pdb=" CA ILE C 277 " pdb=" C ILE C 277 " ideal model delta sigma weight residual 113.42 107.96 5.46 1.17e+00 7.31e-01 2.18e+01 ... (remaining 62009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 25194 17.95 - 35.90: 2248 35.90 - 53.85: 433 53.85 - 71.80: 214 71.80 - 89.75: 31 Dihedral angle restraints: 28120 sinusoidal: 11163 harmonic: 16957 Sorted by residual: dihedral pdb=" CA GLY J 424 " pdb=" C GLY J 424 " pdb=" N LEU J 425 " pdb=" CA LEU J 425 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLY G 424 " pdb=" C GLY G 424 " pdb=" N LEU G 425 " pdb=" CA LEU G 425 " ideal model delta harmonic sigma weight residual 180.00 159.95 20.05 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA LEU J 85 " pdb=" C LEU J 85 " pdb=" N THR J 86 " pdb=" CA THR J 86 " ideal model delta harmonic sigma weight residual -180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 28117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 5755 0.058 - 0.117: 1049 0.117 - 0.175: 245 0.175 - 0.234: 40 0.234 - 0.292: 6 Chirality restraints: 7095 Sorted by residual: chirality pdb=" CB THR H 153 " pdb=" CA THR H 153 " pdb=" OG1 THR H 153 " pdb=" CG2 THR H 153 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA LEU A 391 " pdb=" N LEU A 391 " pdb=" C LEU A 391 " pdb=" CB LEU A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA LEU B 391 " pdb=" N LEU B 391 " pdb=" C LEU B 391 " pdb=" CB LEU B 391 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 7092 not shown) Planarity restraints: 8194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 412 " 0.053 5.00e-02 4.00e+02 7.86e-02 9.89e+00 pdb=" N PRO H 413 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO H 413 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 413 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 412 " 0.051 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO A 413 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 413 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 413 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 148 " -0.049 5.00e-02 4.00e+02 7.39e-02 8.75e+00 pdb=" N PRO A 149 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " -0.040 5.00e-02 4.00e+02 ... (remaining 8191 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1386 2.71 - 3.26: 40359 3.26 - 3.81: 60142 3.81 - 4.35: 74177 4.35 - 4.90: 133117 Nonbonded interactions: 309181 Sorted by model distance: nonbonded pdb=" O CYS C 264 " pdb=" SG CYS C 264 " model vdw 2.163 3.400 nonbonded pdb=" OD2 ASP A 205 " pdb=" NE2 GLN J 168 " model vdw 2.248 3.120 nonbonded pdb=" OD2 ASP F 205 " pdb=" NE2 GLN G 168 " model vdw 2.254 3.120 nonbonded pdb=" NE2 GLN K 168 " pdb=" OD2 ASP E 205 " model vdw 2.282 3.120 nonbonded pdb=" O GLN A 448 " pdb=" OG SER A 451 " model vdw 2.294 3.040 ... (remaining 309176 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 3 through 297 or resid 306 through 522)) selection = (chain 'C' and (resid 3 through 297 or resid 306 through 522)) selection = (chain 'D' and (resid 3 through 297 or resid 306 through 522)) selection = (chain 'E' and (resid 3 through 297 or resid 306 through 522)) selection = (chain 'F' and (resid 3 through 297 or resid 306 through 522)) selection = (chain 'G' and (resid 3 through 297 or resid 306 through 522)) selection = (chain 'H' and (resid 3 through 297 or resid 306 through 522)) selection = (chain 'I' and (resid 3 through 297 or resid 306 through 522)) selection = (chain 'J' and (resid 3 through 297 or resid 306 through 522)) selection = (chain 'K' and (resid 3 through 297 or resid 306 through 522)) selection = (chain 'L' and (resid 3 through 297 or resid 306 through 522)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 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: 0.080 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.130 Process input model: 42.300 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.100 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.005 0.058 45761 Z= 0.316 Angle : 0.740 7.268 62014 Z= 0.464 Chirality : 0.051 0.292 7095 Planarity : 0.006 0.099 8194 Dihedral : 15.164 89.748 17202 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.75 % Favored : 92.95 % Rotamer: Outliers : 1.00 % Allowed : 1.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.11), residues: 5759 helix: 0.49 (0.10), residues: 2682 sheet: 0.13 (0.20), residues: 602 loop : -2.48 (0.11), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 84 TYR 0.013 0.001 TYR E 119 PHE 0.021 0.002 PHE F 172 TRP 0.013 0.001 TRP H 82 HIS 0.007 0.003 HIS I 213 Details of bonding type rmsd covalent geometry : bond 0.00538 (45761) covalent geometry : angle 0.74033 (62014) hydrogen bonds : bond 0.22992 ( 1887) hydrogen bonds : angle 5.72617 ( 5883) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 795 time to evaluate : 1.903 Fit side-chains REVERT: K 198 ASN cc_start: 0.8184 (p0) cc_final: 0.7344 (p0) REVERT: H 13 LYS cc_start: 0.8528 (ttpp) cc_final: 0.8254 (tttp) REVERT: H 79 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7828 (mm-40) REVERT: H 149 PRO cc_start: 0.8031 (Cg_endo) cc_final: 0.7349 (Cg_endo) REVERT: I 97 GLN cc_start: 0.8229 (mm-40) cc_final: 0.8026 (mm110) REVERT: I 387 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7687 (mp10) REVERT: I 390 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6893 (tt0) REVERT: I 507 MET cc_start: 0.7686 (ttm) cc_final: 0.7374 (ttt) REVERT: A 98 ASP cc_start: 0.7548 (t0) cc_final: 0.7232 (t0) REVERT: A 100 GLU cc_start: 0.7281 (pm20) cc_final: 0.6719 (pm20) REVERT: A 313 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: J 251 MET cc_start: 0.7775 (ttt) cc_final: 0.7528 (ttt) REVERT: B 341 ASP cc_start: 0.7484 (m-30) cc_final: 0.7246 (m-30) REVERT: C 5 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7449 (mm-30) REVERT: C 387 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7349 (mt0) REVERT: D 13 LYS cc_start: 0.8526 (ttpp) cc_final: 0.8254 (tttp) REVERT: D 79 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7810 (mm-40) REVERT: D 98 ASP cc_start: 0.7649 (t0) cc_final: 0.7382 (t0) REVERT: L 198 ASN cc_start: 0.7818 (p0) cc_final: 0.7300 (p0) REVERT: F 159 MET cc_start: 0.8290 (tmm) cc_final: 0.7834 (ttt) REVERT: G 275 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7411 (tm-30) REVERT: G 493 GLN cc_start: 0.8489 (tt0) cc_final: 0.8200 (tt0) REVERT: E 120 MET cc_start: 0.9156 (mtm) cc_final: 0.8933 (mtm) REVERT: E 341 ASP cc_start: 0.7501 (m-30) cc_final: 0.7207 (m-30) outliers start: 48 outliers final: 11 residues processed: 837 average time/residue: 0.2403 time to fit residues: 341.0343 Evaluate side-chains 646 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 631 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 393 LEU Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain H residue 372 VAL Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain I residue 387 GLN Chi-restraints excluded: chain I residue 390 GLU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain J residue 393 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain L residue 372 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 394 optimal weight: 0.0270 chunk 430 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 8.9990 chunk 523 optimal weight: 4.9990 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 7.9990 chunk 310 optimal weight: 9.9990 chunk 488 optimal weight: 0.9990 chunk 366 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 overall best weight: 0.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 79 GLN K 123 ASN I 21 ASN A 97 GLN C 123 ASN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.145318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.118804 restraints weight = 60190.558| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.35 r_work: 0.3262 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 45761 Z= 0.106 Angle : 0.503 7.112 62014 Z= 0.265 Chirality : 0.040 0.247 7095 Planarity : 0.004 0.054 8194 Dihedral : 4.621 63.737 6363 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.49 % Favored : 94.37 % Rotamer: Outliers : 0.67 % Allowed : 6.51 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.11), residues: 5759 helix: 0.99 (0.11), residues: 2693 sheet: 0.18 (0.20), residues: 654 loop : -2.33 (0.11), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 84 TYR 0.009 0.001 TYR J 224 PHE 0.010 0.001 PHE C 333 TRP 0.013 0.001 TRP I 82 HIS 0.002 0.001 HIS G 213 Details of bonding type rmsd covalent geometry : bond 0.00208 (45761) covalent geometry : angle 0.50256 (62014) hydrogen bonds : bond 0.04984 ( 1887) hydrogen bonds : angle 3.73794 ( 5883) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 682 time to evaluate : 1.603 Fit side-chains REVERT: K 198 ASN cc_start: 0.8095 (p0) cc_final: 0.7296 (p0) REVERT: H 79 GLN cc_start: 0.8427 (mm-40) cc_final: 0.7958 (mm-40) REVERT: H 117 MET cc_start: 0.9025 (tpt) cc_final: 0.8822 (mmt) REVERT: A 98 ASP cc_start: 0.7706 (t0) cc_final: 0.7138 (t0) REVERT: A 100 GLU cc_start: 0.7870 (pm20) cc_final: 0.7260 (pm20) REVERT: J 198 ASN cc_start: 0.8001 (p0) cc_final: 0.7460 (p0) REVERT: B 205 ASP cc_start: 0.8024 (t0) cc_final: 0.7731 (t0) REVERT: B 506 ASN cc_start: 0.7073 (m-40) cc_final: 0.6855 (m-40) REVERT: C 5 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7960 (mm-30) REVERT: D 13 LYS cc_start: 0.8516 (ttpp) cc_final: 0.8293 (tttp) REVERT: D 79 GLN cc_start: 0.8399 (mm-40) cc_final: 0.7938 (mm-40) REVERT: L 198 ASN cc_start: 0.8041 (p0) cc_final: 0.7662 (p0) REVERT: F 79 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7831 (mp10) REVERT: F 98 ASP cc_start: 0.7582 (t0) cc_final: 0.7364 (t0) REVERT: F 148 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7730 (tm-30) REVERT: F 149 PRO cc_start: 0.8245 (Cg_exo) cc_final: 0.8034 (Cg_endo) REVERT: F 519 MET cc_start: 0.7591 (tmm) cc_final: 0.7026 (tmm) REVERT: G 198 ASN cc_start: 0.7946 (p0) cc_final: 0.7451 (p0) REVERT: E 98 ASP cc_start: 0.7434 (t0) cc_final: 0.7194 (t0) REVERT: E 177 GLN cc_start: 0.8770 (mt0) cc_final: 0.8419 (mt0) REVERT: E 205 ASP cc_start: 0.8030 (t0) cc_final: 0.7756 (t0) REVERT: E 341 ASP cc_start: 0.8311 (m-30) cc_final: 0.8053 (m-30) outliers start: 32 outliers final: 19 residues processed: 697 average time/residue: 0.2248 time to fit residues: 269.1635 Evaluate side-chains 644 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 624 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain H residue 320 GLU Chi-restraints excluded: chain H residue 372 VAL Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 86 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 388 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 351 optimal weight: 0.7980 chunk 537 optimal weight: 0.9990 chunk 240 optimal weight: 0.4980 chunk 461 optimal weight: 10.0000 chunk 322 optimal weight: 0.0000 chunk 160 optimal weight: 2.9990 chunk 470 optimal weight: 4.9990 chunk 543 optimal weight: 0.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN L 21 ASN E 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.148169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.121599 restraints weight = 60164.893| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.33 r_work: 0.3299 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 45761 Z= 0.088 Angle : 0.448 6.643 62014 Z= 0.233 Chirality : 0.038 0.213 7095 Planarity : 0.004 0.049 8194 Dihedral : 3.637 51.338 6340 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.46 % Favored : 95.42 % Rotamer: Outliers : 0.71 % Allowed : 8.40 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.11), residues: 5759 helix: 1.34 (0.11), residues: 2696 sheet: 0.69 (0.20), residues: 638 loop : -2.23 (0.11), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 84 TYR 0.008 0.001 TYR I 239 PHE 0.008 0.001 PHE C 7 TRP 0.010 0.001 TRP I 82 HIS 0.001 0.000 HIS L 213 Details of bonding type rmsd covalent geometry : bond 0.00173 (45761) covalent geometry : angle 0.44822 (62014) hydrogen bonds : bond 0.03876 ( 1887) hydrogen bonds : angle 3.26946 ( 5883) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 683 time to evaluate : 1.908 Fit side-chains REVERT: K 198 ASN cc_start: 0.8022 (p0) cc_final: 0.7269 (p0) REVERT: K 345 GLN cc_start: 0.8317 (tt0) cc_final: 0.8012 (tp40) REVERT: H 79 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7890 (mm-40) REVERT: I 198 ASN cc_start: 0.7744 (p0) cc_final: 0.7334 (p0) REVERT: I 201 ASP cc_start: 0.8497 (m-30) cc_final: 0.8242 (m-30) REVERT: I 255 ASP cc_start: 0.8606 (m-30) cc_final: 0.8400 (m-30) REVERT: I 387 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8159 (mp10) REVERT: A 98 ASP cc_start: 0.7792 (t0) cc_final: 0.7228 (t0) REVERT: A 100 GLU cc_start: 0.7887 (pm20) cc_final: 0.7262 (pm20) REVERT: A 106 ASP cc_start: 0.8487 (t0) cc_final: 0.8108 (t0) REVERT: A 284 MET cc_start: 0.8302 (ttm) cc_final: 0.8096 (mtm) REVERT: J 198 ASN cc_start: 0.7781 (p0) cc_final: 0.7024 (p0) REVERT: J 200 ASP cc_start: 0.7559 (p0) cc_final: 0.7355 (p0) REVERT: J 201 ASP cc_start: 0.8012 (m-30) cc_final: 0.7633 (m-30) REVERT: J 345 GLN cc_start: 0.8418 (tt0) cc_final: 0.8169 (tp40) REVERT: B 106 ASP cc_start: 0.8832 (t0) cc_final: 0.8630 (t0) REVERT: B 205 ASP cc_start: 0.7939 (t0) cc_final: 0.7620 (t0) REVERT: B 456 ILE cc_start: 0.9022 (mt) cc_final: 0.8759 (mt) REVERT: C 5 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7979 (mm-30) REVERT: C 198 ASN cc_start: 0.8077 (p0) cc_final: 0.7158 (p0) REVERT: C 201 ASP cc_start: 0.8210 (m-30) cc_final: 0.7880 (m-30) REVERT: D 27 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8428 (mt-10) REVERT: D 79 GLN cc_start: 0.8323 (mm-40) cc_final: 0.7868 (mm-40) REVERT: L 205 ASP cc_start: 0.8394 (t0) cc_final: 0.8176 (t0) REVERT: L 284 MET cc_start: 0.8479 (mtt) cc_final: 0.8200 (mtt) REVERT: F 79 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: F 98 ASP cc_start: 0.7417 (t0) cc_final: 0.7131 (t0) REVERT: F 148 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7708 (tm-30) REVERT: F 149 PRO cc_start: 0.8154 (Cg_exo) cc_final: 0.7780 (Cg_endo) REVERT: F 159 MET cc_start: 0.8808 (tmm) cc_final: 0.8303 (ttt) REVERT: G 201 ASP cc_start: 0.8027 (m-30) cc_final: 0.7790 (m-30) REVERT: G 494 GLN cc_start: 0.8123 (mm110) cc_final: 0.7545 (pp30) REVERT: G 519 MET cc_start: 0.6152 (tpt) cc_final: 0.5747 (tpp) REVERT: E 86 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.8125 (p) REVERT: E 98 ASP cc_start: 0.7408 (t0) cc_final: 0.7122 (t0) REVERT: E 121 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7693 (mm-30) REVERT: E 177 GLN cc_start: 0.8714 (mt0) cc_final: 0.8433 (mt0) REVERT: E 205 ASP cc_start: 0.8018 (t0) cc_final: 0.7686 (t0) REVERT: E 341 ASP cc_start: 0.8388 (m-30) cc_final: 0.8136 (m-30) REVERT: E 456 ILE cc_start: 0.8994 (mt) cc_final: 0.8750 (mt) outliers start: 34 outliers final: 19 residues processed: 699 average time/residue: 0.2231 time to fit residues: 270.1177 Evaluate side-chains 667 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 645 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain H residue 320 GLU Chi-restraints excluded: chain H residue 372 VAL Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 349 TRP Chi-restraints excluded: chain I residue 387 GLN Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain E residue 86 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 403 optimal weight: 3.9990 chunk 410 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 478 optimal weight: 10.0000 chunk 399 optimal weight: 0.9990 chunk 446 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 524 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 404 GLN A 404 GLN D 404 GLN L 21 ASN E 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115545 restraints weight = 60299.012| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.27 r_work: 0.3225 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 45761 Z= 0.134 Angle : 0.514 8.205 62014 Z= 0.270 Chirality : 0.040 0.168 7095 Planarity : 0.004 0.047 8194 Dihedral : 3.971 48.067 6339 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.15 % Favored : 93.75 % Rotamer: Outliers : 1.02 % Allowed : 9.73 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.11), residues: 5759 helix: 1.41 (0.11), residues: 2689 sheet: 0.60 (0.21), residues: 638 loop : -2.35 (0.11), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 4 TYR 0.010 0.001 TYR L 215 PHE 0.014 0.001 PHE G 7 TRP 0.011 0.001 TRP D 82 HIS 0.004 0.002 HIS I 213 Details of bonding type rmsd covalent geometry : bond 0.00306 (45761) covalent geometry : angle 0.51373 (62014) hydrogen bonds : bond 0.06012 ( 1887) hydrogen bonds : angle 3.42275 ( 5883) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 639 time to evaluate : 1.515 Fit side-chains REVERT: K 198 ASN cc_start: 0.8115 (p0) cc_final: 0.7347 (p0) REVERT: H 79 GLN cc_start: 0.8459 (mm-40) cc_final: 0.7952 (mm-40) REVERT: I 97 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7952 (mm110) REVERT: I 106 ASP cc_start: 0.9294 (t0) cc_final: 0.9020 (t0) REVERT: I 198 ASN cc_start: 0.7896 (p0) cc_final: 0.7511 (p0) REVERT: I 284 MET cc_start: 0.8773 (mtt) cc_final: 0.8534 (mtt) REVERT: I 387 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8227 (mp10) REVERT: A 98 ASP cc_start: 0.7758 (t0) cc_final: 0.7485 (t0) REVERT: A 100 GLU cc_start: 0.8036 (pm20) cc_final: 0.7601 (pm20) REVERT: A 106 ASP cc_start: 0.8676 (t0) cc_final: 0.8300 (t0) REVERT: A 159 MET cc_start: 0.8825 (tmm) cc_final: 0.8390 (ttt) REVERT: A 415 GLU cc_start: 0.6642 (pm20) cc_final: 0.6028 (pt0) REVERT: J 198 ASN cc_start: 0.7943 (p0) cc_final: 0.7093 (p0) REVERT: J 236 GLU cc_start: 0.7818 (mp0) cc_final: 0.7597 (pm20) REVERT: B 205 ASP cc_start: 0.7992 (t0) cc_final: 0.7657 (t0) REVERT: B 456 ILE cc_start: 0.9044 (mt) cc_final: 0.8774 (mt) REVERT: C 5 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7883 (mm-30) REVERT: C 198 ASN cc_start: 0.8280 (p0) cc_final: 0.7558 (p0) REVERT: D 79 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8017 (mm-40) REVERT: L 181 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8407 (tp) REVERT: F 79 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7829 (mp10) REVERT: F 98 ASP cc_start: 0.7482 (t0) cc_final: 0.7146 (t0) REVERT: F 121 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7984 (mm-30) REVERT: F 148 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7766 (tm-30) REVERT: F 149 PRO cc_start: 0.8286 (Cg_exo) cc_final: 0.7811 (Cg_endo) REVERT: F 519 MET cc_start: 0.7457 (tmm) cc_final: 0.6967 (tmm) REVERT: G 198 ASN cc_start: 0.8058 (p0) cc_final: 0.7293 (p0) REVERT: G 201 ASP cc_start: 0.7993 (m-30) cc_final: 0.7557 (m-30) REVERT: E 79 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8180 (tp40) REVERT: E 86 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8301 (p) REVERT: E 98 ASP cc_start: 0.7626 (t0) cc_final: 0.7356 (t0) REVERT: E 205 ASP cc_start: 0.8039 (t0) cc_final: 0.7695 (t0) REVERT: E 341 ASP cc_start: 0.8265 (m-30) cc_final: 0.8024 (m-30) REVERT: E 436 LYS cc_start: 0.8067 (mtmt) cc_final: 0.7837 (mttm) REVERT: E 456 ILE cc_start: 0.9072 (mt) cc_final: 0.8799 (mt) outliers start: 49 outliers final: 36 residues processed: 662 average time/residue: 0.2060 time to fit residues: 235.3897 Evaluate side-chains 664 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 623 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 331 GLN Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain H residue 320 GLU Chi-restraints excluded: chain H residue 372 VAL Chi-restraints excluded: chain H residue 412 LEU Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 387 GLN Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 487 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 111 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 134 optimal weight: 4.9990 chunk 364 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 282 optimal weight: 0.9990 chunk 408 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 532 optimal weight: 6.9990 chunk 394 optimal weight: 4.9990 chunk 343 optimal weight: 3.9990 chunk 367 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 432 GLN C 177 GLN L 21 ASN E 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.138789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.113095 restraints weight = 60407.549| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.26 r_work: 0.3189 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 45761 Z= 0.161 Angle : 0.548 8.065 62014 Z= 0.290 Chirality : 0.042 0.165 7095 Planarity : 0.004 0.043 8194 Dihedral : 4.217 44.563 6339 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.25 % Favored : 93.66 % Rotamer: Outliers : 1.31 % Allowed : 10.95 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.11), residues: 5759 helix: 1.31 (0.11), residues: 2679 sheet: 0.49 (0.23), residues: 522 loop : -2.19 (0.11), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 4 TYR 0.011 0.001 TYR I 154 PHE 0.017 0.002 PHE D 7 TRP 0.010 0.001 TRP D 82 HIS 0.005 0.003 HIS I 213 Details of bonding type rmsd covalent geometry : bond 0.00377 (45761) covalent geometry : angle 0.54757 (62014) hydrogen bonds : bond 0.06797 ( 1887) hydrogen bonds : angle 3.51462 ( 5883) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 641 time to evaluate : 1.354 Fit side-chains REVERT: K 198 ASN cc_start: 0.8317 (p0) cc_final: 0.7659 (p0) REVERT: H 98 ASP cc_start: 0.7739 (t0) cc_final: 0.7496 (t0) REVERT: I 97 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7909 (mm-40) REVERT: I 106 ASP cc_start: 0.9243 (t0) cc_final: 0.8999 (t0) REVERT: I 120 MET cc_start: 0.9168 (mtp) cc_final: 0.8956 (mtp) REVERT: I 198 ASN cc_start: 0.8010 (p0) cc_final: 0.7713 (p0) REVERT: I 205 ASP cc_start: 0.8457 (t0) cc_final: 0.8179 (t0) REVERT: I 253 ARG cc_start: 0.8759 (mtm180) cc_final: 0.8474 (mtm180) REVERT: I 328 THR cc_start: 0.9460 (t) cc_final: 0.9246 (t) REVERT: I 387 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8260 (mp10) REVERT: A 79 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: A 98 ASP cc_start: 0.7757 (t0) cc_final: 0.7207 (t0) REVERT: A 100 GLU cc_start: 0.8094 (pm20) cc_final: 0.7461 (pm20) REVERT: A 415 GLU cc_start: 0.6679 (pm20) cc_final: 0.6140 (pt0) REVERT: J 198 ASN cc_start: 0.8149 (p0) cc_final: 0.7442 (p0) REVERT: B 120 MET cc_start: 0.8875 (mtp) cc_final: 0.8662 (mtm) REVERT: B 205 ASP cc_start: 0.8135 (t0) cc_final: 0.7780 (t0) REVERT: B 456 ILE cc_start: 0.9056 (mt) cc_final: 0.8752 (mt) REVERT: C 5 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7928 (mm-30) REVERT: C 198 ASN cc_start: 0.8357 (p0) cc_final: 0.7569 (p0) REVERT: C 201 ASP cc_start: 0.8112 (m-30) cc_final: 0.7852 (m-30) REVERT: C 320 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: D 79 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8277 (mm110) REVERT: D 200 ASP cc_start: 0.8487 (m-30) cc_final: 0.8275 (t0) REVERT: L 205 ASP cc_start: 0.8474 (t0) cc_final: 0.8212 (t0) REVERT: L 284 MET cc_start: 0.8772 (mtt) cc_final: 0.8483 (mtt) REVERT: F 79 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: F 98 ASP cc_start: 0.7676 (t0) cc_final: 0.7371 (t0) REVERT: F 148 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7898 (tm-30) REVERT: F 149 PRO cc_start: 0.8272 (Cg_exo) cc_final: 0.7908 (Cg_endo) REVERT: F 519 MET cc_start: 0.7418 (tmm) cc_final: 0.6962 (tmm) REVERT: G 198 ASN cc_start: 0.8114 (p0) cc_final: 0.7308 (p0) REVERT: G 201 ASP cc_start: 0.8191 (m-30) cc_final: 0.7729 (m-30) REVERT: G 447 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8423 (mp) REVERT: E 98 ASP cc_start: 0.7691 (t0) cc_final: 0.7400 (t0) REVERT: E 205 ASP cc_start: 0.8186 (t0) cc_final: 0.7825 (t0) REVERT: E 341 ASP cc_start: 0.8342 (m-30) cc_final: 0.8075 (m-30) REVERT: E 436 LYS cc_start: 0.8202 (mtmt) cc_final: 0.7970 (mttm) REVERT: E 456 ILE cc_start: 0.9070 (mt) cc_final: 0.8768 (mt) REVERT: E 519 MET cc_start: 0.7209 (tmm) cc_final: 0.6863 (tmm) outliers start: 63 outliers final: 43 residues processed: 669 average time/residue: 0.1981 time to fit residues: 228.2492 Evaluate side-chains 669 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 621 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 320 GLU Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 236 GLU Chi-restraints excluded: chain I residue 387 GLN Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 409 ILE Chi-restraints excluded: chain J residue 487 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 484 ILE Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 409 ILE Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain E residue 10 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 92 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 390 optimal weight: 1.9990 chunk 435 optimal weight: 5.9990 chunk 385 optimal weight: 4.9990 chunk 356 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 21 ASN J 21 ASN J 432 GLN L 21 ASN G 432 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.134163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.108025 restraints weight = 61720.755| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.27 r_work: 0.3079 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 45761 Z= 0.199 Angle : 0.592 8.118 62014 Z= 0.316 Chirality : 0.043 0.169 7095 Planarity : 0.005 0.044 8194 Dihedral : 4.459 42.419 6338 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.93 % Favored : 92.98 % Rotamer: Outliers : 1.39 % Allowed : 11.93 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.11), residues: 5759 helix: 1.17 (0.11), residues: 2677 sheet: 0.40 (0.23), residues: 516 loop : -2.33 (0.10), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 4 TYR 0.012 0.002 TYR L 154 PHE 0.020 0.002 PHE D 7 TRP 0.011 0.001 TRP D 82 HIS 0.006 0.004 HIS I 213 Details of bonding type rmsd covalent geometry : bond 0.00482 (45761) covalent geometry : angle 0.59246 (62014) hydrogen bonds : bond 0.07851 ( 1887) hydrogen bonds : angle 3.66268 ( 5883) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 630 time to evaluate : 1.791 Fit side-chains REVERT: K 198 ASN cc_start: 0.8341 (p0) cc_final: 0.7683 (p0) REVERT: H 79 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8052 (mm-40) REVERT: H 98 ASP cc_start: 0.7793 (t0) cc_final: 0.7489 (t0) REVERT: I 97 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7919 (mm110) REVERT: I 106 ASP cc_start: 0.9257 (t0) cc_final: 0.9026 (t0) REVERT: I 198 ASN cc_start: 0.8004 (p0) cc_final: 0.7787 (p0) REVERT: I 253 ARG cc_start: 0.8812 (mtm180) cc_final: 0.8601 (mtm180) REVERT: I 387 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8418 (mp10) REVERT: A 79 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: A 98 ASP cc_start: 0.7759 (t0) cc_final: 0.7193 (t0) REVERT: A 100 GLU cc_start: 0.8097 (pm20) cc_final: 0.7420 (pm20) REVERT: A 415 GLU cc_start: 0.6731 (pm20) cc_final: 0.6132 (pt0) REVERT: J 198 ASN cc_start: 0.8182 (p0) cc_final: 0.7602 (p0) REVERT: J 447 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8347 (mp) REVERT: B 120 MET cc_start: 0.8933 (mtp) cc_final: 0.8689 (mtm) REVERT: B 205 ASP cc_start: 0.8291 (t0) cc_final: 0.7996 (t0) REVERT: B 456 ILE cc_start: 0.9020 (mt) cc_final: 0.8708 (mt) REVERT: C 5 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7904 (mm-30) REVERT: C 320 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8004 (mp0) REVERT: D 200 ASP cc_start: 0.8571 (m-30) cc_final: 0.8264 (t0) REVERT: D 205 ASP cc_start: 0.8113 (t0) cc_final: 0.7713 (t0) REVERT: D 453 ASP cc_start: 0.8598 (t0) cc_final: 0.8179 (t0) REVERT: L 83 MET cc_start: 0.7773 (ptp) cc_final: 0.7573 (ptp) REVERT: L 181 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8762 (tp) REVERT: L 284 MET cc_start: 0.8835 (mtt) cc_final: 0.8566 (mtt) REVERT: F 79 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7936 (mp10) REVERT: F 98 ASP cc_start: 0.7817 (t0) cc_final: 0.7382 (t0) REVERT: F 148 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7886 (tm-30) REVERT: G 198 ASN cc_start: 0.8140 (p0) cc_final: 0.7319 (p0) REVERT: G 201 ASP cc_start: 0.8231 (m-30) cc_final: 0.7798 (m-30) REVERT: G 447 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8358 (mp) REVERT: E 98 ASP cc_start: 0.7791 (t0) cc_final: 0.7475 (t0) REVERT: E 205 ASP cc_start: 0.8279 (t0) cc_final: 0.7982 (t0) REVERT: E 436 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7943 (mttm) REVERT: E 456 ILE cc_start: 0.9028 (mt) cc_final: 0.8721 (mt) REVERT: E 519 MET cc_start: 0.7146 (tmm) cc_final: 0.6884 (tmm) outliers start: 67 outliers final: 49 residues processed: 665 average time/residue: 0.2244 time to fit residues: 256.9126 Evaluate side-chains 675 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 619 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 320 GLU Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 236 GLU Chi-restraints excluded: chain I residue 387 GLN Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 409 ILE Chi-restraints excluded: chain J residue 445 THR Chi-restraints excluded: chain J residue 447 LEU Chi-restraints excluded: chain J residue 487 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain L residue 84 ARG Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 484 ILE Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 409 ILE Chi-restraints excluded: chain G residue 445 THR Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 267 optimal weight: 0.5980 chunk 93 optimal weight: 7.9990 chunk 271 optimal weight: 0.9980 chunk 549 optimal weight: 5.9990 chunk 254 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 378 optimal weight: 2.9990 chunk 319 optimal weight: 0.9990 chunk 255 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 198 optimal weight: 0.0270 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN L 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.144919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119202 restraints weight = 59904.009| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.26 r_work: 0.3271 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 45761 Z= 0.091 Angle : 0.459 7.018 62014 Z= 0.240 Chirality : 0.038 0.165 7095 Planarity : 0.004 0.044 8194 Dihedral : 3.769 39.319 6338 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.65 % Favored : 95.26 % Rotamer: Outliers : 0.91 % Allowed : 12.66 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.11), residues: 5759 helix: 1.39 (0.11), residues: 2715 sheet: 0.59 (0.22), residues: 558 loop : -2.17 (0.11), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 158 TYR 0.007 0.001 TYR H 224 PHE 0.007 0.001 PHE E 333 TRP 0.009 0.001 TRP K 82 HIS 0.001 0.001 HIS I 213 Details of bonding type rmsd covalent geometry : bond 0.00180 (45761) covalent geometry : angle 0.45900 (62014) hydrogen bonds : bond 0.04003 ( 1887) hydrogen bonds : angle 3.22530 ( 5883) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 662 time to evaluate : 1.038 Fit side-chains REVERT: K 198 ASN cc_start: 0.8167 (p0) cc_final: 0.7245 (p0) REVERT: K 201 ASP cc_start: 0.8083 (m-30) cc_final: 0.7759 (m-30) REVERT: K 345 GLN cc_start: 0.8199 (tt0) cc_final: 0.7983 (tp40) REVERT: H 79 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7766 (mm-40) REVERT: H 98 ASP cc_start: 0.7600 (t0) cc_final: 0.7280 (t0) REVERT: H 325 LEU cc_start: 0.9050 (tp) cc_final: 0.8826 (tp) REVERT: I 97 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7881 (mm110) REVERT: I 253 ARG cc_start: 0.8648 (mtm180) cc_final: 0.8314 (mtm180) REVERT: I 328 THR cc_start: 0.9306 (t) cc_final: 0.9093 (t) REVERT: I 387 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8165 (mp10) REVERT: A 79 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7791 (mp10) REVERT: A 84 ARG cc_start: 0.8916 (mmm160) cc_final: 0.8639 (mmm160) REVERT: A 98 ASP cc_start: 0.7698 (t0) cc_final: 0.7116 (t0) REVERT: A 100 GLU cc_start: 0.8076 (pm20) cc_final: 0.7426 (pm20) REVERT: A 415 GLU cc_start: 0.6353 (pm20) cc_final: 0.6063 (pt0) REVERT: A 487 MET cc_start: 0.7228 (mtm) cc_final: 0.6870 (mtm) REVERT: J 198 ASN cc_start: 0.8113 (p0) cc_final: 0.7597 (p0) REVERT: J 345 GLN cc_start: 0.8348 (tt0) cc_final: 0.8140 (tp40) REVERT: J 447 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8397 (mp) REVERT: J 519 MET cc_start: 0.6227 (tpt) cc_final: 0.5994 (tpp) REVERT: B 205 ASP cc_start: 0.8128 (t0) cc_final: 0.7804 (t0) REVERT: B 456 ILE cc_start: 0.8996 (mt) cc_final: 0.8686 (mt) REVERT: C 5 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7918 (mm-30) REVERT: C 198 ASN cc_start: 0.8276 (p0) cc_final: 0.7458 (p0) REVERT: C 201 ASP cc_start: 0.8101 (m-30) cc_final: 0.7828 (m-30) REVERT: C 387 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.7843 (mp10) REVERT: D 79 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7950 (mm110) REVERT: D 200 ASP cc_start: 0.8459 (m-30) cc_final: 0.8251 (t0) REVERT: L 181 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8438 (tp) REVERT: F 79 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7815 (mp10) REVERT: F 98 ASP cc_start: 0.7633 (t0) cc_final: 0.7380 (t0) REVERT: F 148 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7816 (tm-30) REVERT: F 519 MET cc_start: 0.7265 (tmm) cc_final: 0.6729 (tmm) REVERT: G 198 ASN cc_start: 0.7974 (p0) cc_final: 0.7130 (p0) REVERT: G 201 ASP cc_start: 0.8102 (m-30) cc_final: 0.7627 (m-30) REVERT: E 98 ASP cc_start: 0.7542 (t0) cc_final: 0.7201 (t0) REVERT: E 205 ASP cc_start: 0.8181 (t0) cc_final: 0.7850 (t0) REVERT: E 436 LYS cc_start: 0.8140 (mtmt) cc_final: 0.7904 (mttm) REVERT: E 456 ILE cc_start: 0.9017 (mt) cc_final: 0.8718 (mt) outliers start: 44 outliers final: 30 residues processed: 683 average time/residue: 0.1567 time to fit residues: 185.4962 Evaluate side-chains 671 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 635 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain H residue 372 VAL Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 349 TRP Chi-restraints excluded: chain I residue 387 GLN Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 447 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 484 ILE Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 111 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 283 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 279 optimal weight: 0.8980 chunk 536 optimal weight: 6.9990 chunk 435 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 393 optimal weight: 3.9990 chunk 288 optimal weight: 0.1980 chunk 156 optimal weight: 0.0370 chunk 468 optimal weight: 9.9990 chunk 322 optimal weight: 0.9990 overall best weight: 1.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 ASN E 331 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.143511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.117540 restraints weight = 60205.737| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.27 r_work: 0.3248 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 45761 Z= 0.098 Angle : 0.465 7.323 62014 Z= 0.242 Chirality : 0.038 0.160 7095 Planarity : 0.004 0.042 8194 Dihedral : 3.642 36.008 6337 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.52 % Favored : 94.39 % Rotamer: Outliers : 0.94 % Allowed : 13.14 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.11), residues: 5759 helix: 1.54 (0.11), residues: 2712 sheet: 0.65 (0.22), residues: 552 loop : -2.09 (0.11), residues: 2495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 84 TYR 0.007 0.001 TYR K 224 PHE 0.009 0.001 PHE C 7 TRP 0.007 0.001 TRP K 82 HIS 0.002 0.001 HIS I 213 Details of bonding type rmsd covalent geometry : bond 0.00208 (45761) covalent geometry : angle 0.46451 (62014) hydrogen bonds : bond 0.04517 ( 1887) hydrogen bonds : angle 3.15271 ( 5883) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 640 time to evaluate : 1.017 Fit side-chains REVERT: K 198 ASN cc_start: 0.8156 (p0) cc_final: 0.7230 (p0) REVERT: K 201 ASP cc_start: 0.8108 (m-30) cc_final: 0.7760 (m-30) REVERT: K 425 LEU cc_start: 0.6044 (OUTLIER) cc_final: 0.5569 (tp) REVERT: H 98 ASP cc_start: 0.7560 (t0) cc_final: 0.7246 (t0) REVERT: I 97 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7882 (mm110) REVERT: I 328 THR cc_start: 0.9283 (t) cc_final: 0.9060 (t) REVERT: I 387 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8180 (mp10) REVERT: A 79 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: A 84 ARG cc_start: 0.8932 (mmm160) cc_final: 0.8650 (mmm160) REVERT: A 98 ASP cc_start: 0.7710 (t0) cc_final: 0.7128 (t0) REVERT: A 100 GLU cc_start: 0.8069 (pm20) cc_final: 0.7440 (pm20) REVERT: A 415 GLU cc_start: 0.6358 (pm20) cc_final: 0.5904 (pt0) REVERT: A 487 MET cc_start: 0.7196 (mtm) cc_final: 0.6733 (mtm) REVERT: J 198 ASN cc_start: 0.8070 (p0) cc_final: 0.7584 (p0) REVERT: J 345 GLN cc_start: 0.8446 (tt0) cc_final: 0.8183 (tp40) REVERT: J 447 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8375 (mp) REVERT: B 205 ASP cc_start: 0.8121 (t0) cc_final: 0.7787 (t0) REVERT: B 456 ILE cc_start: 0.9105 (mt) cc_final: 0.8825 (mt) REVERT: C 5 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7943 (mm-30) REVERT: C 198 ASN cc_start: 0.8278 (p0) cc_final: 0.7467 (p0) REVERT: C 201 ASP cc_start: 0.8129 (m-30) cc_final: 0.7858 (m-30) REVERT: C 387 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.7792 (mp10) REVERT: D 200 ASP cc_start: 0.8467 (m-30) cc_final: 0.8265 (t0) REVERT: L 181 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8486 (tp) REVERT: F 79 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7766 (mp10) REVERT: F 98 ASP cc_start: 0.7612 (t0) cc_final: 0.7354 (t0) REVERT: F 148 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7894 (tm-30) REVERT: F 519 MET cc_start: 0.7162 (tmm) cc_final: 0.6635 (tmm) REVERT: G 198 ASN cc_start: 0.7927 (p0) cc_final: 0.7077 (p0) REVERT: G 201 ASP cc_start: 0.8043 (m-30) cc_final: 0.7573 (m-30) REVERT: E 98 ASP cc_start: 0.7530 (t0) cc_final: 0.7182 (t0) REVERT: E 205 ASP cc_start: 0.8141 (t0) cc_final: 0.7795 (t0) REVERT: E 436 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7906 (mttm) REVERT: E 456 ILE cc_start: 0.9073 (mt) cc_final: 0.8794 (mt) outliers start: 45 outliers final: 33 residues processed: 664 average time/residue: 0.1512 time to fit residues: 175.3402 Evaluate side-chains 668 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 628 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 425 LEU Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 236 GLU Chi-restraints excluded: chain I residue 387 GLN Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 447 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 484 ILE Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 471 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 482 optimal weight: 1.9990 chunk 404 optimal weight: 8.9990 chunk 172 optimal weight: 0.9980 chunk 252 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 211 optimal weight: 10.0000 chunk 279 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 390 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.142766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116793 restraints weight = 59938.065| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.26 r_work: 0.3237 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 45761 Z= 0.107 Angle : 0.477 7.409 62014 Z= 0.249 Chirality : 0.039 0.158 7095 Planarity : 0.004 0.042 8194 Dihedral : 3.688 34.286 6337 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.38 % Favored : 94.53 % Rotamer: Outliers : 0.96 % Allowed : 13.28 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.11), residues: 5759 helix: 1.58 (0.11), residues: 2707 sheet: 0.67 (0.22), residues: 552 loop : -2.05 (0.11), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 486 TYR 0.007 0.001 TYR J 90 PHE 0.011 0.001 PHE D 7 TRP 0.008 0.001 TRP A 82 HIS 0.003 0.002 HIS I 213 Details of bonding type rmsd covalent geometry : bond 0.00234 (45761) covalent geometry : angle 0.47692 (62014) hydrogen bonds : bond 0.04829 ( 1887) hydrogen bonds : angle 3.17510 ( 5883) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 632 time to evaluate : 1.048 Fit side-chains REVERT: K 198 ASN cc_start: 0.8175 (p0) cc_final: 0.7250 (p0) REVERT: K 201 ASP cc_start: 0.8101 (m-30) cc_final: 0.7767 (m-30) REVERT: K 425 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5559 (tp) REVERT: H 98 ASP cc_start: 0.7637 (t0) cc_final: 0.7327 (t0) REVERT: I 97 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7885 (mm110) REVERT: I 387 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8233 (mp10) REVERT: A 79 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7807 (mp10) REVERT: A 98 ASP cc_start: 0.7702 (t0) cc_final: 0.7169 (t0) REVERT: A 100 GLU cc_start: 0.8085 (pm20) cc_final: 0.7432 (pm20) REVERT: A 415 GLU cc_start: 0.6480 (pm20) cc_final: 0.5959 (pt0) REVERT: A 487 MET cc_start: 0.7218 (mtm) cc_final: 0.6760 (mtm) REVERT: J 198 ASN cc_start: 0.8059 (p0) cc_final: 0.7602 (p0) REVERT: J 345 GLN cc_start: 0.8442 (tt0) cc_final: 0.8198 (tp40) REVERT: J 447 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8375 (mp) REVERT: B 205 ASP cc_start: 0.8112 (t0) cc_final: 0.7777 (t0) REVERT: B 456 ILE cc_start: 0.9093 (mt) cc_final: 0.8822 (mt) REVERT: C 5 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7940 (mm-30) REVERT: C 198 ASN cc_start: 0.8282 (p0) cc_final: 0.7506 (p0) REVERT: C 201 ASP cc_start: 0.8144 (m-30) cc_final: 0.7875 (m-30) REVERT: C 387 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.7775 (mp10) REVERT: D 79 GLN cc_start: 0.8349 (mm-40) cc_final: 0.8048 (mm110) REVERT: D 200 ASP cc_start: 0.8484 (m-30) cc_final: 0.8265 (t0) REVERT: L 181 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8524 (tp) REVERT: F 79 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7792 (mp10) REVERT: F 98 ASP cc_start: 0.7681 (t0) cc_final: 0.7403 (t0) REVERT: F 148 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7892 (tm-30) REVERT: F 519 MET cc_start: 0.7096 (tmm) cc_final: 0.6564 (tmm) REVERT: G 198 ASN cc_start: 0.7906 (p0) cc_final: 0.7072 (p0) REVERT: G 201 ASP cc_start: 0.8039 (m-30) cc_final: 0.7563 (m-30) REVERT: E 98 ASP cc_start: 0.7544 (t0) cc_final: 0.7192 (t0) REVERT: E 205 ASP cc_start: 0.8146 (t0) cc_final: 0.7790 (t0) REVERT: E 436 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7910 (mttm) REVERT: E 456 ILE cc_start: 0.9078 (mt) cc_final: 0.8802 (mt) outliers start: 46 outliers final: 34 residues processed: 659 average time/residue: 0.1451 time to fit residues: 166.5212 Evaluate side-chains 659 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 618 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 425 LEU Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 236 GLU Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain I residue 387 GLN Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 409 ILE Chi-restraints excluded: chain J residue 447 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 484 ILE Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 471 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 262 optimal weight: 8.9990 chunk 287 optimal weight: 0.2980 chunk 535 optimal weight: 0.0470 chunk 43 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 229 optimal weight: 0.9990 chunk 157 optimal weight: 0.0270 chunk 291 optimal weight: 6.9990 chunk 208 optimal weight: 0.2980 chunk 194 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 21 ASN ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN ** F 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.149516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.123389 restraints weight = 60417.788| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.28 r_work: 0.3330 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 45761 Z= 0.082 Angle : 0.435 7.643 62014 Z= 0.224 Chirality : 0.037 0.165 7095 Planarity : 0.004 0.045 8194 Dihedral : 3.279 26.842 6337 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.27 % Favored : 95.66 % Rotamer: Outliers : 0.60 % Allowed : 13.61 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.11), residues: 5759 helix: 1.70 (0.11), residues: 2707 sheet: 0.90 (0.21), residues: 638 loop : -1.99 (0.11), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 84 TYR 0.006 0.001 TYR E 165 PHE 0.008 0.001 PHE L 77 TRP 0.006 0.000 TRP K 82 HIS 0.001 0.000 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00170 (45761) covalent geometry : angle 0.43483 (62014) hydrogen bonds : bond 0.02803 ( 1887) hydrogen bonds : angle 2.97809 ( 5883) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11518 Ramachandran restraints generated. 5759 Oldfield, 0 Emsley, 5759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 656 time to evaluate : 0.975 Fit side-chains REVERT: K 198 ASN cc_start: 0.8074 (p0) cc_final: 0.7265 (p0) REVERT: K 201 ASP cc_start: 0.8056 (m-30) cc_final: 0.7725 (m-30) REVERT: K 203 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7875 (pp20) REVERT: H 98 ASP cc_start: 0.7444 (t0) cc_final: 0.7107 (t0) REVERT: I 200 ASP cc_start: 0.8392 (m-30) cc_final: 0.8064 (p0) REVERT: A 84 ARG cc_start: 0.8859 (mmm160) cc_final: 0.8623 (mmm160) REVERT: A 98 ASP cc_start: 0.7726 (t0) cc_final: 0.7429 (t0) REVERT: A 100 GLU cc_start: 0.8015 (pm20) cc_final: 0.7590 (pm20) REVERT: A 106 ASP cc_start: 0.8555 (t0) cc_final: 0.8242 (t0) REVERT: A 408 MET cc_start: 0.8960 (mtp) cc_final: 0.8661 (mtt) REVERT: A 415 GLU cc_start: 0.6377 (pm20) cc_final: 0.5833 (pt0) REVERT: A 487 MET cc_start: 0.6956 (mtm) cc_final: 0.6517 (mtm) REVERT: J 198 ASN cc_start: 0.7951 (p0) cc_final: 0.7510 (p0) REVERT: J 345 GLN cc_start: 0.8317 (tt0) cc_final: 0.8074 (tp40) REVERT: J 447 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8352 (mp) REVERT: B 205 ASP cc_start: 0.8006 (t0) cc_final: 0.7596 (t0) REVERT: C 5 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7931 (mm-30) REVERT: C 198 ASN cc_start: 0.8061 (p0) cc_final: 0.7136 (p0) REVERT: C 201 ASP cc_start: 0.8097 (m-30) cc_final: 0.7821 (m-30) REVERT: C 203 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7876 (pp20) REVERT: C 387 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.7717 (mp10) REVERT: D 84 ARG cc_start: 0.8806 (mmm160) cc_final: 0.8512 (mmm-85) REVERT: F 79 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7625 (mp10) REVERT: F 98 ASP cc_start: 0.7469 (t0) cc_final: 0.7133 (t0) REVERT: G 198 ASN cc_start: 0.7873 (p0) cc_final: 0.7204 (p0) REVERT: G 257 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7744 (mt-10) REVERT: G 494 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7813 (pp30) REVERT: E 98 ASP cc_start: 0.7477 (t0) cc_final: 0.7114 (t0) REVERT: E 177 GLN cc_start: 0.8590 (mt0) cc_final: 0.8323 (mt0) REVERT: E 205 ASP cc_start: 0.8041 (t0) cc_final: 0.7666 (t0) outliers start: 29 outliers final: 15 residues processed: 671 average time/residue: 0.1364 time to fit residues: 160.8882 Evaluate side-chains 627 residues out of total 4811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 607 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 236 GLU Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 447 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 568 optimal weight: 6.9990 chunk 323 optimal weight: 2.9990 chunk 102 optimal weight: 0.0970 chunk 333 optimal weight: 6.9990 chunk 305 optimal weight: 0.7980 chunk 419 optimal weight: 0.0010 chunk 143 optimal weight: 3.9990 chunk 523 optimal weight: 0.8980 chunk 347 optimal weight: 2.9990 chunk 332 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 506 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 GLN ** F 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.147027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120762 restraints weight = 60995.564| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.28 r_work: 0.3297 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 45761 Z= 0.086 Angle : 0.448 9.386 62014 Z= 0.229 Chirality : 0.038 0.153 7095 Planarity : 0.004 0.044 8194 Dihedral : 3.225 22.570 6335 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 0.52 % Allowed : 14.13 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.11), residues: 5759 helix: 1.87 (0.11), residues: 2692 sheet: 1.00 (0.21), residues: 638 loop : -1.94 (0.11), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 84 TYR 0.008 0.001 TYR L 26 PHE 0.006 0.001 PHE D 7 TRP 0.008 0.001 TRP H 82 HIS 0.002 0.001 HIS K 213 Details of bonding type rmsd covalent geometry : bond 0.00179 (45761) covalent geometry : angle 0.44767 (62014) hydrogen bonds : bond 0.03466 ( 1887) hydrogen bonds : angle 2.93428 ( 5883) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9773.52 seconds wall clock time: 167 minutes 7.50 seconds (10027.50 seconds total)