Starting phenix.real_space_refine on Mon Nov 18 12:25:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iol_9696/11_2024/6iol_9696.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iol_9696/11_2024/6iol_9696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iol_9696/11_2024/6iol_9696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iol_9696/11_2024/6iol_9696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iol_9696/11_2024/6iol_9696.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iol_9696/11_2024/6iol_9696.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.023 sd= 2.561 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 141 5.16 5 C 31111 2.51 5 N 8478 2.21 5 O 9347 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 49077 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2538 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 14, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2538 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 14, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2529 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 14, 'TRANS': 317} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2554 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 14, 'TRANS': 321} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2529 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 14, 'TRANS': 317} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2544 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 14, 'TRANS': 320} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "A" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3486 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 17, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3486 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 17, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3486 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 17, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 7764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7764 Classifications: {'peptide': 1024} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 972} Chain breaks: 1 Chain: "G" Number of atoms: 7811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 7811 Classifications: {'peptide': 1030} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 978} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 7812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 7812 Classifications: {'peptide': 1030} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 978} Time building chain proxies: 28.47, per 1000 atoms: 0.58 Number of scatterers: 49077 At special positions: 0 Unit cell: (142.625, 130.375, 345.625, 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 141 16.00 O 9347 8.00 N 8478 7.00 C 31111 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: 12.79 Conformation dependent library (CDL) restraints added in 6.5 seconds 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11876 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 69 sheets defined 46.4% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.64 Creating SS restraints... Processing helix chain 'I' and resid 73 through 101 removed outlier: 3.840A pdb=" N ALA I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP I 79 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR I 80 " --> pdb=" O TYR I 76 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASN I 86 " --> pdb=" O SER I 82 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU I 99 " --> pdb=" O GLN I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 104 No H-bonds generated for 'chain 'I' and resid 102 through 104' Processing helix chain 'I' and resid 107 through 136 removed outlier: 3.619A pdb=" N ASN I 131 " --> pdb=" O GLN I 127 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS I 136 " --> pdb=" O LEU I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 193 removed outlier: 3.632A pdb=" N ALA I 192 " --> pdb=" O ARG I 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 102 removed outlier: 3.705A pdb=" N ALA J 85 " --> pdb=" O GLN J 81 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN J 86 " --> pdb=" O SER J 82 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU J 92 " --> pdb=" O ALA J 88 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA J 102 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 134 removed outlier: 3.911A pdb=" N ALA J 114 " --> pdb=" O GLN J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 193 Processing helix chain 'K' and resid 79 through 102 removed outlier: 3.901A pdb=" N GLU K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU K 99 " --> pdb=" O GLN K 95 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA K 102 " --> pdb=" O LYS K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 135 removed outlier: 4.070A pdb=" N ALA K 114 " --> pdb=" O GLN K 110 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA K 128 " --> pdb=" O ALA K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 193 removed outlier: 3.672A pdb=" N LEU K 185 " --> pdb=" O SER K 181 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU K 190 " --> pdb=" O ARG K 186 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER K 193 " --> pdb=" O ARG K 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 102 removed outlier: 4.026A pdb=" N ASN L 86 " --> pdb=" O SER L 82 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU L 99 " --> pdb=" O GLN L 95 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA L 102 " --> pdb=" O LYS L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 134 removed outlier: 4.284A pdb=" N ALA L 114 " --> pdb=" O GLN L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 193 removed outlier: 3.809A pdb=" N ALA L 192 " --> pdb=" O ARG L 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 102 removed outlier: 3.652A pdb=" N SER M 89 " --> pdb=" O ALA M 85 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU M 92 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA M 102 " --> pdb=" O LYS M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 135 removed outlier: 3.885A pdb=" N ASN M 131 " --> pdb=" O GLN M 127 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU M 132 " --> pdb=" O ALA M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 193 removed outlier: 3.579A pdb=" N LEU M 185 " --> pdb=" O SER M 181 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG M 186 " --> pdb=" O THR M 182 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU M 191 " --> pdb=" O LEU M 187 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA M 192 " --> pdb=" O ARG M 188 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER M 193 " --> pdb=" O ARG M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 275 No H-bonds generated for 'chain 'M' and resid 273 through 275' Processing helix chain 'N' and resid 76 through 102 removed outlier: 4.192A pdb=" N GLU N 92 " --> pdb=" O ALA N 88 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG N 96 " --> pdb=" O GLU N 92 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA N 102 " --> pdb=" O LYS N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 135 removed outlier: 3.897A pdb=" N ALA N 114 " --> pdb=" O GLN N 110 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR N 135 " --> pdb=" O ASN N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 193 Processing helix chain 'A' and resid 39 through 44 removed outlier: 3.897A pdb=" N PHE A 44 " --> pdb=" O TRP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 60 removed outlier: 3.615A pdb=" N GLN A 50 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY A 54 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 83 removed outlier: 4.303A pdb=" N GLU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 198 removed outlier: 3.856A pdb=" N GLN A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 239 removed outlier: 3.984A pdb=" N LEU A 226 " --> pdb=" O GLN A 222 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 removed outlier: 4.059A pdb=" N ARG A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 267 through 272' Processing helix chain 'A' and resid 272 through 294 removed outlier: 3.601A pdb=" N LEU A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY A 290 " --> pdb=" O ASN A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.516A pdb=" N LEU A 316 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 405 removed outlier: 4.211A pdb=" N GLN A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR A 380 " --> pdb=" O ARG A 376 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 385 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 447 removed outlier: 3.970A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 447 " --> pdb=" O TYR A 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 60 removed outlier: 3.896A pdb=" N GLU B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 83 removed outlier: 4.905A pdb=" N GLU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 198 removed outlier: 3.886A pdb=" N ALA B 159 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 239 removed outlier: 3.515A pdb=" N LEU B 206 " --> pdb=" O SER B 202 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA B 228 " --> pdb=" O THR B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 295 removed outlier: 3.787A pdb=" N GLY B 290 " --> pdb=" O ASN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 378 removed outlier: 4.018A pdb=" N GLY B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 407 removed outlier: 4.299A pdb=" N ALA B 385 " --> pdb=" O GLU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 447 removed outlier: 3.920A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN B 434 " --> pdb=" O THR B 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 46 through 57 Processing helix chain 'C' and resid 61 through 83 removed outlier: 4.266A pdb=" N GLU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 199 removed outlier: 3.689A pdb=" N SER C 160 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA C 173 " --> pdb=" O LYS C 169 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP C 180 " --> pdb=" O GLN C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 239 removed outlier: 3.608A pdb=" N LEU C 206 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA C 212 " --> pdb=" O GLN C 208 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C 237 " --> pdb=" O ALA C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 267 through 272 removed outlier: 4.022A pdb=" N ARG C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 294 removed outlier: 3.514A pdb=" N LEU C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 405 removed outlier: 4.096A pdb=" N THR C 380 " --> pdb=" O ARG C 376 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU C 381 " --> pdb=" O GLY C 377 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN C 384 " --> pdb=" O THR C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 447 removed outlier: 3.864A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN C 434 " --> pdb=" O THR C 430 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY C 447 " --> pdb=" O TYR C 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 8 removed outlier: 3.639A pdb=" N ASP F 7 " --> pdb=" O LYS F 3 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG F 8 " --> pdb=" O PHE F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 27 Processing helix chain 'F' and resid 53 through 59 removed outlier: 3.646A pdb=" N VAL F 57 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 69 Processing helix chain 'F' and resid 99 through 113 removed outlier: 3.539A pdb=" N ALA F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'F' and resid 150 through 162 removed outlier: 3.598A pdb=" N LEU F 154 " --> pdb=" O THR F 150 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE F 158 " --> pdb=" O LEU F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 168 Processing helix chain 'F' and resid 189 through 195 Processing helix chain 'F' and resid 199 through 210 removed outlier: 3.532A pdb=" N VAL F 203 " --> pdb=" O THR F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 247 Processing helix chain 'F' and resid 262 through 266 Processing helix chain 'F' and resid 299 through 314 Processing helix chain 'F' and resid 315 through 317 No H-bonds generated for 'chain 'F' and resid 315 through 317' Processing helix chain 'F' and resid 329 through 359 removed outlier: 4.049A pdb=" N VAL F 333 " --> pdb=" O THR F 329 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU F 349 " --> pdb=" O GLY F 345 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU F 357 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE F 358 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU F 359 " --> pdb=" O MET F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 370 removed outlier: 3.971A pdb=" N THR F 369 " --> pdb=" O THR F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 386 removed outlier: 3.963A pdb=" N VAL F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 414 removed outlier: 3.859A pdb=" N MET F 395 " --> pdb=" O ASN F 391 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY F 403 " --> pdb=" O VAL F 399 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU F 404 " --> pdb=" O LEU F 400 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP F 407 " --> pdb=" O GLY F 403 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASP F 408 " --> pdb=" O LEU F 404 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA F 409 " --> pdb=" O LEU F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 423 removed outlier: 3.621A pdb=" N VAL F 419 " --> pdb=" O ASN F 415 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET F 420 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU F 422 " --> pdb=" O ARG F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 439 removed outlier: 3.723A pdb=" N ALA F 430 " --> pdb=" O SER F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 454 removed outlier: 3.674A pdb=" N VAL F 443 " --> pdb=" O GLN F 439 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL F 452 " --> pdb=" O VAL F 448 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE F 453 " --> pdb=" O LEU F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 457 No H-bonds generated for 'chain 'F' and resid 455 through 457' Processing helix chain 'F' and resid 461 through 496 removed outlier: 4.157A pdb=" N THR F 473 " --> pdb=" O GLN F 469 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA F 477 " --> pdb=" O THR F 473 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR F 489 " --> pdb=" O ALA F 485 " (cutoff:3.500A) Proline residue: F 490 - end of helix Processing helix chain 'F' and resid 511 through 537 removed outlier: 3.609A pdb=" N HIS F 537 " --> pdb=" O SER F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 556 removed outlier: 4.102A pdb=" N LEU F 542 " --> pdb=" O ARG F 538 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU F 543 " --> pdb=" O ALA F 539 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE F 553 " --> pdb=" O VAL F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 599 removed outlier: 3.955A pdb=" N THR F 587 " --> pdb=" O SER F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 643 through 651 Processing helix chain 'F' and resid 651 through 656 removed outlier: 3.663A pdb=" N PHE F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 675 removed outlier: 3.962A pdb=" N LEU F 674 " --> pdb=" O VAL F 671 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY F 675 " --> pdb=" O LEU F 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 671 through 675' Processing helix chain 'F' and resid 691 through 707 removed outlier: 4.398A pdb=" N GLN F 697 " --> pdb=" O GLU F 693 " (cutoff:3.500A) Processing helix chain 'F' and resid 731 through 738 Processing helix chain 'F' and resid 743 through 755 removed outlier: 3.794A pdb=" N SER F 755 " --> pdb=" O ILE F 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 781 through 786 removed outlier: 3.676A pdb=" N LEU F 785 " --> pdb=" O PRO F 782 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER F 786 " --> pdb=" O ASP F 783 " (cutoff:3.500A) Processing helix chain 'F' and resid 836 through 848 Processing helix chain 'F' and resid 860 through 869 removed outlier: 3.932A pdb=" N GLU F 864 " --> pdb=" O GLY F 860 " (cutoff:3.500A) Processing helix chain 'F' and resid 871 through 892 removed outlier: 3.707A pdb=" N LEU F 890 " --> pdb=" O CYS F 886 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR F 891 " --> pdb=" O LEU F 887 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU F 892 " --> pdb=" O ALA F 888 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 902 Processing helix chain 'F' and resid 904 through 919 removed outlier: 4.775A pdb=" N GLY F 910 " --> pdb=" O LEU F 906 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG F 918 " --> pdb=" O ALA F 914 " (cutoff:3.500A) Processing helix chain 'F' and resid 923 through 955 removed outlier: 3.568A pdb=" N GLN F 927 " --> pdb=" O ASP F 923 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE F 947 " --> pdb=" O LEU F 943 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA F 948 " --> pdb=" O ILE F 944 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU F 951 " --> pdb=" O PHE F 947 " (cutoff:3.500A) Processing helix chain 'F' and resid 957 through 990 removed outlier: 3.663A pdb=" N ALA F 961 " --> pdb=" O GLY F 957 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ARG F 971 " --> pdb=" O ARG F 967 " (cutoff:3.500A) Proline residue: F 972 - end of helix Proline residue: F 986 - end of helix removed outlier: 3.605A pdb=" N ILE F 989 " --> pdb=" O VAL F 985 " (cutoff:3.500A) Processing helix chain 'F' and resid 994 through 1016 removed outlier: 3.926A pdb=" N GLN F 998 " --> pdb=" O GLY F 994 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR F1011 " --> pdb=" O GLY F1007 " (cutoff:3.500A) Processing helix chain 'F' and resid 1019 through 1025 Processing helix chain 'G' and resid 8 through 28 removed outlier: 4.420A pdb=" N ALA G 12 " --> pdb=" O ARG G 8 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU G 28 " --> pdb=" O GLY G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 67 removed outlier: 5.787A pdb=" N GLN G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL G 64 " --> pdb=" O THR G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 113 removed outlier: 3.774A pdb=" N ALA G 103 " --> pdb=" O ASP G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 124 Processing helix chain 'G' and resid 150 through 162 removed outlier: 3.501A pdb=" N LEU G 154 " --> pdb=" O THR G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 168 removed outlier: 3.580A pdb=" N LEU G 166 " --> pdb=" O ILE G 162 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG G 168 " --> pdb=" O ASP G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 196 removed outlier: 3.524A pdb=" N TYR G 196 " --> pdb=" O LYS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 211 removed outlier: 3.871A pdb=" N GLN G 208 " --> pdb=" O SER G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 314 Processing helix chain 'G' and resid 315 through 317 No H-bonds generated for 'chain 'G' and resid 315 through 317' Processing helix chain 'G' and resid 330 through 359 removed outlier: 3.981A pdb=" N VAL G 340 " --> pdb=" O SER G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 367 removed outlier: 3.837A pdb=" N ILE G 367 " --> pdb=" O ARG G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 385 Proline residue: G 373 - end of helix removed outlier: 4.012A pdb=" N PHE G 380 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY G 381 " --> pdb=" O LEU G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 392 through 406 removed outlier: 4.513A pdb=" N GLY G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU G 404 " --> pdb=" O LEU G 400 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 424 removed outlier: 3.632A pdb=" N GLU G 423 " --> pdb=" O VAL G 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 454 removed outlier: 5.903A pdb=" N GLY G 440 " --> pdb=" O GLY G 436 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ALA G 441 " --> pdb=" O GLN G 437 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL G 443 " --> pdb=" O GLN G 439 " (cutoff:3.500A) Processing helix chain 'G' and resid 455 through 458 Processing helix chain 'G' and resid 461 through 487 removed outlier: 4.357A pdb=" N PHE G 470 " --> pdb=" O ILE G 466 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE G 483 " --> pdb=" O ALA G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 494 Processing helix chain 'G' and resid 510 through 537 removed outlier: 3.679A pdb=" N TRP G 515 " --> pdb=" O GLY G 511 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG G 529 " --> pdb=" O HIS G 525 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N HIS G 537 " --> pdb=" O SER G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 538 through 557 removed outlier: 3.933A pdb=" N LEU G 542 " --> pdb=" O ARG G 538 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU G 543 " --> pdb=" O ALA G 539 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE G 544 " --> pdb=" O PRO G 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 583 through 601 removed outlier: 3.983A pdb=" N THR G 587 " --> pdb=" O SER G 583 " (cutoff:3.500A) Processing helix chain 'G' and resid 643 through 656 removed outlier: 4.777A pdb=" N LYS G 649 " --> pdb=" O PHE G 645 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N HIS G 654 " --> pdb=" O ARG G 650 " (cutoff:3.500A) Processing helix chain 'G' and resid 691 through 707 removed outlier: 3.568A pdb=" N LEU G 695 " --> pdb=" O GLY G 691 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA G 707 " --> pdb=" O LEU G 703 " (cutoff:3.500A) Processing helix chain 'G' and resid 731 through 739 Processing helix chain 'G' and resid 741 through 752 Processing helix chain 'G' and resid 781 through 787 removed outlier: 3.755A pdb=" N LEU G 785 " --> pdb=" O PRO G 782 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER G 786 " --> pdb=" O ASP G 783 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS G 787 " --> pdb=" O ASP G 784 " (cutoff:3.500A) Processing helix chain 'G' and resid 835 through 845 Processing helix chain 'G' and resid 846 through 850 removed outlier: 3.664A pdb=" N GLN G 849 " --> pdb=" O ILE G 846 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU G 850 " --> pdb=" O VAL G 847 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 846 through 850' Processing helix chain 'G' and resid 861 through 868 removed outlier: 3.596A pdb=" N LEU G 867 " --> pdb=" O TYR G 863 " (cutoff:3.500A) Processing helix chain 'G' and resid 871 through 892 removed outlier: 3.855A pdb=" N TYR G 876 " --> pdb=" O ALA G 872 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ALA G 877 " --> pdb=" O PRO G 873 " (cutoff:3.500A) Processing helix chain 'G' and resid 897 through 902 Processing helix chain 'G' and resid 903 through 918 removed outlier: 4.429A pdb=" N GLY G 910 " --> pdb=" O LEU G 906 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA G 911 " --> pdb=" O GLY G 907 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG G 918 " --> pdb=" O ALA G 914 " (cutoff:3.500A) Processing helix chain 'G' and resid 923 through 954 removed outlier: 3.709A pdb=" N LEU G 943 " --> pdb=" O LYS G 939 " (cutoff:3.500A) Processing helix chain 'G' and resid 957 through 969 removed outlier: 3.639A pdb=" N ILE G 963 " --> pdb=" O VAL G 959 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS G 966 " --> pdb=" O ALA G 962 " (cutoff:3.500A) Processing helix chain 'G' and resid 969 through 989 removed outlier: 4.143A pdb=" N ILE G 973 " --> pdb=" O ARG G 969 " (cutoff:3.500A) Proline residue: G 986 - end of helix Processing helix chain 'G' and resid 994 through 1029 removed outlier: 3.773A pdb=" N THR G1003 " --> pdb=" O HIS G 999 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY G1004 " --> pdb=" O ALA G1000 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL G1005 " --> pdb=" O ILE G1001 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR G1011 " --> pdb=" O GLY G1007 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE G1018 " --> pdb=" O VAL G1014 " (cutoff:3.500A) Proline residue: G1021 - end of helix Processing helix chain 'E' and resid 1 through 5 removed outlier: 3.988A pdb=" N PHE E 4 " --> pdb=" O MET E 1 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 27 removed outlier: 4.094A pdb=" N ALA E 12 " --> pdb=" O ARG E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 69 removed outlier: 5.622A pdb=" N GLN E 63 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL E 64 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 108 Processing helix chain 'E' and resid 111 through 115 Processing helix chain 'E' and resid 119 through 124 removed outlier: 3.560A pdb=" N GLN E 123 " --> pdb=" O PRO E 119 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG E 124 " --> pdb=" O GLN E 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 119 through 124' Processing helix chain 'E' and resid 150 through 161 removed outlier: 3.800A pdb=" N LEU E 154 " --> pdb=" O THR E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 195 Processing helix chain 'E' and resid 199 through 208 removed outlier: 3.553A pdb=" N VAL E 203 " --> pdb=" O THR E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 247 Processing helix chain 'E' and resid 298 through 314 removed outlier: 3.765A pdb=" N THR E 302 " --> pdb=" O ASN E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 317 No H-bonds generated for 'chain 'E' and resid 315 through 317' Processing helix chain 'E' and resid 329 through 359 removed outlier: 3.745A pdb=" N VAL E 333 " --> pdb=" O THR E 329 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS E 342 " --> pdb=" O HIS E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 370 removed outlier: 3.691A pdb=" N THR E 365 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE E 367 " --> pdb=" O ARG E 363 " (cutoff:3.500A) Proline residue: E 368 - end of helix Processing helix chain 'E' and resid 371 through 387 removed outlier: 3.848A pdb=" N VAL E 375 " --> pdb=" O ALA E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 401 Processing helix chain 'E' and resid 401 through 423 removed outlier: 3.849A pdb=" N ASP E 407 " --> pdb=" O GLY E 403 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASP E 408 " --> pdb=" O LEU E 404 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA E 409 " --> pdb=" O LEU E 405 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU E 423 " --> pdb=" O VAL E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 452 removed outlier: 4.410A pdb=" N GLY E 436 " --> pdb=" O ARG E 432 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN E 437 " --> pdb=" O LYS E 433 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLY E 440 " --> pdb=" O GLY E 436 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ALA E 441 " --> pdb=" O GLN E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 459 removed outlier: 4.002A pdb=" N PHE E 459 " --> pdb=" O MET E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 486 removed outlier: 4.021A pdb=" N GLN E 469 " --> pdb=" O VAL E 465 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE E 470 " --> pdb=" O ILE E 466 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR E 473 " --> pdb=" O GLN E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 497 removed outlier: 4.467A pdb=" N THR E 495 " --> pdb=" O ALA E 491 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU E 497 " --> pdb=" O CYS E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 537 removed outlier: 3.693A pdb=" N TRP E 515 " --> pdb=" O GLY E 511 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG E 529 " --> pdb=" O HIS E 525 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS E 537 " --> pdb=" O SER E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 556 Processing helix chain 'E' and resid 557 through 559 No H-bonds generated for 'chain 'E' and resid 557 through 559' Processing helix chain 'E' and resid 583 through 599 removed outlier: 3.951A pdb=" N THR E 587 " --> pdb=" O SER E 583 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR E 597 " --> pdb=" O SER E 593 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU E 599 " --> pdb=" O ARG E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 639 through 642 Processing helix chain 'E' and resid 643 through 656 removed outlier: 4.096A pdb=" N HIS E 654 " --> pdb=" O ARG E 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 708 removed outlier: 3.521A pdb=" N MET E 704 " --> pdb=" O ASN E 700 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN E 708 " --> pdb=" O MET E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 731 through 739 Processing helix chain 'E' and resid 741 through 748 removed outlier: 3.635A pdb=" N ILE E 745 " --> pdb=" O SER E 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 775 through 779 Processing helix chain 'E' and resid 781 through 787 removed outlier: 3.688A pdb=" N SER E 786 " --> pdb=" O ASP E 783 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS E 787 " --> pdb=" O ASP E 784 " (cutoff:3.500A) Processing helix chain 'E' and resid 837 through 847 removed outlier: 4.140A pdb=" N VAL E 843 " --> pdb=" O ALA E 839 " (cutoff:3.500A) Processing helix chain 'E' and resid 848 through 850 No H-bonds generated for 'chain 'E' and resid 848 through 850' Processing helix chain 'E' and resid 860 through 891 removed outlier: 3.910A pdb=" N GLU E 864 " --> pdb=" O GLY E 860 " (cutoff:3.500A) Proline residue: E 873 - end of helix removed outlier: 3.610A pdb=" N TYR E 891 " --> pdb=" O LEU E 887 " (cutoff:3.500A) Processing helix chain 'E' and resid 895 through 902 Processing helix chain 'E' and resid 903 through 919 removed outlier: 5.663A pdb=" N ILE E 909 " --> pdb=" O PRO E 905 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLY E 910 " --> pdb=" O LEU E 906 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA E 911 " --> pdb=" O GLY E 907 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG E 918 " --> pdb=" O ALA E 914 " (cutoff:3.500A) Processing helix chain 'E' and resid 925 through 954 removed outlier: 4.414A pdb=" N ILE E 944 " --> pdb=" O ASN E 940 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE E 947 " --> pdb=" O LEU E 943 " (cutoff:3.500A) Processing helix chain 'E' and resid 957 through 969 Processing helix chain 'E' and resid 970 through 989 removed outlier: 4.118A pdb=" N SER E 977 " --> pdb=" O ILE E 973 " (cutoff:3.500A) Proline residue: E 986 - end of helix Processing helix chain 'E' and resid 994 through 1029 removed outlier: 3.748A pdb=" N GLN E 998 " --> pdb=" O GLY E 994 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLY E1004 " --> pdb=" O ALA E1000 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL E1005 " --> pdb=" O ILE E1001 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE E1017 " --> pdb=" O THR E1013 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE E1018 " --> pdb=" O VAL E1014 " (cutoff:3.500A) Proline residue: E1021 - end of helix removed outlier: 3.960A pdb=" N VAL E1025 " --> pdb=" O PRO E1021 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 320 through 324 removed outlier: 5.511A pdb=" N ILE I 322 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL I 18 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL I 338 " --> pdb=" O VAL I 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 61 through 62 removed outlier: 5.889A pdb=" N THR I 166 " --> pdb=" O GLY I 146 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR I 237 " --> pdb=" O SER I 225 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER I 225 " --> pdb=" O THR I 237 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG I 239 " --> pdb=" O GLU I 223 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY I 220 " --> pdb=" O VAL I 206 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS I 205 " --> pdb=" O GLN I 260 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN I 260 " --> pdb=" O LYS I 205 " (cutoff:3.500A) removed outlier: 12.893A pdb=" N THR I 29 " --> pdb=" O GLN I 179 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N GLN I 179 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N LEU I 31 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL I 177 " --> pdb=" O LEU I 31 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLY I 33 " --> pdb=" O VAL I 175 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL I 175 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N THR I 35 " --> pdb=" O ILE I 173 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N ILE I 173 " --> pdb=" O THR I 35 " (cutoff:3.500A) removed outlier: 10.605A pdb=" N ALA I 37 " --> pdb=" O ASP I 171 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N ASP I 171 " --> pdb=" O ALA I 37 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG I 39 " --> pdb=" O GLN I 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 49 through 50 Processing sheet with id=AA4, first strand: chain 'I' and resid 275 through 277 removed outlier: 3.553A pdb=" N THR I 284 " --> pdb=" O THR I 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 301 through 305 removed outlier: 4.201A pdb=" N ARG I 303 " --> pdb=" O LEU I 310 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 275 through 277 removed outlier: 3.904A pdb=" N ALA J 283 " --> pdb=" O ILE J 299 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG J 297 " --> pdb=" O ALA J 285 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 275 through 277 removed outlier: 15.670A pdb=" N THR J 284 " --> pdb=" O GLU J 324 " (cutoff:3.500A) removed outlier: 12.377A pdb=" N GLU J 324 " --> pdb=" O THR J 284 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU J 286 " --> pdb=" O ILE J 322 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LYS J 320 " --> pdb=" O VAL J 288 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE J 321 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY J 16 " --> pdb=" O THR J 323 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 23 through 28 removed outlier: 5.406A pdb=" N GLN J 23 " --> pdb=" O LYS J 266 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS J 266 " --> pdb=" O GLN J 23 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY J 262 " --> pdb=" O LEU J 27 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE J 268 " --> pdb=" O VAL J 311 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG J 303 " --> pdb=" O LEU J 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 33 through 43 removed outlier: 7.752A pdb=" N GLY J 33 " --> pdb=" O VAL J 175 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N VAL J 175 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N THR J 35 " --> pdb=" O ILE J 173 " (cutoff:3.500A) removed outlier: 9.463A pdb=" N ILE J 173 " --> pdb=" O THR J 35 " (cutoff:3.500A) removed outlier: 10.409A pdb=" N ALA J 37 " --> pdb=" O ASP J 171 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ASP J 171 " --> pdb=" O ALA J 37 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG J 39 " --> pdb=" O GLN J 169 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA J 165 " --> pdb=" O VAL J 43 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU J 219 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU J 208 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU J 218 " --> pdb=" O VAL J 206 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL J 206 " --> pdb=" O LEU J 218 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS J 205 " --> pdb=" O GLN J 260 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLN J 260 " --> pdb=" O LYS J 205 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER J 207 " --> pdb=" O GLN J 258 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN J 258 " --> pdb=" O SER J 207 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY J 262 " --> pdb=" O LEU J 27 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS J 266 " --> pdb=" O GLN J 23 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLN J 23 " --> pdb=" O LYS J 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 61 through 62 Processing sheet with id=AB2, first strand: chain 'J' and resid 69 through 71 removed outlier: 6.871A pdb=" N GLN J 70 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 18 through 19 Processing sheet with id=AB4, first strand: chain 'K' and resid 23 through 25 removed outlier: 6.657A pdb=" N VAL K 25 " --> pdb=" O GLN K 265 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLN K 265 " --> pdb=" O VAL K 25 " (cutoff:3.500A) removed outlier: 14.283A pdb=" N LYS K 266 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N GLU K 313 " --> pdb=" O LYS K 266 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE K 268 " --> pdb=" O VAL K 311 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU K 310 " --> pdb=" O ARG K 303 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG K 303 " --> pdb=" O LEU K 310 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N THR K 312 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ALA K 301 " --> pdb=" O THR K 312 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA K 283 " --> pdb=" O ILE K 299 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 207 through 209 removed outlier: 3.779A pdb=" N SER K 207 " --> pdb=" O GLN K 258 " (cutoff:3.500A) removed outlier: 11.630A pdb=" N GLU K 30 " --> pdb=" O PRO K 180 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG K 34 " --> pdb=" O ASP K 176 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE K 38 " --> pdb=" O PRO K 172 " (cutoff:3.500A) removed outlier: 11.059A pdb=" N ILE K 40 " --> pdb=" O LEU K 170 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N LEU K 170 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N GLU K 42 " --> pdb=" O GLN K 168 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N GLN K 168 " --> pdb=" O GLU K 42 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG K 239 " --> pdb=" O PHE K 224 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N PHE K 224 " --> pdb=" O ARG K 239 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL K 241 " --> pdb=" O LEU K 222 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU K 222 " --> pdb=" O VAL K 241 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 49 through 50 Processing sheet with id=AB7, first strand: chain 'K' and resid 61 through 62 removed outlier: 3.532A pdb=" N GLY K 143 " --> pdb=" O VAL K 62 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 67 through 70 removed outlier: 6.568A pdb=" N VAL K 137 " --> pdb=" O LEU K 68 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 321 through 324 removed outlier: 6.732A pdb=" N GLY L 16 " --> pdb=" O THR L 323 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL L 338 " --> pdb=" O VAL L 15 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 23 through 28 removed outlier: 4.981A pdb=" N GLN L 23 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLN L 265 " --> pdb=" O GLN L 23 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL L 25 " --> pdb=" O VAL L 263 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL L 263 " --> pdb=" O VAL L 25 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU L 27 " --> pdb=" O GLU L 261 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER L 207 " --> pdb=" O GLN L 258 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU L 208 " --> pdb=" O TYR L 216 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 23 through 28 removed outlier: 4.981A pdb=" N GLN L 23 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLN L 265 " --> pdb=" O GLN L 23 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL L 25 " --> pdb=" O VAL L 263 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL L 263 " --> pdb=" O VAL L 25 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU L 27 " --> pdb=" O GLU L 261 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG L 34 " --> pdb=" O ASP L 176 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 37 through 40 removed outlier: 10.548A pdb=" N ALA L 37 " --> pdb=" O ASP L 171 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N ASP L 171 " --> pdb=" O ALA L 37 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG L 39 " --> pdb=" O GLN L 169 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 49 through 50 Processing sheet with id=AC5, first strand: chain 'L' and resid 61 through 62 Processing sheet with id=AC6, first strand: chain 'L' and resid 275 through 277 removed outlier: 3.614A pdb=" N ALA L 283 " --> pdb=" O ILE L 299 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA L 285 " --> pdb=" O ARG L 297 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG L 297 " --> pdb=" O ALA L 285 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 301 through 305 removed outlier: 5.118A pdb=" N ARG L 303 " --> pdb=" O LEU L 310 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU L 310 " --> pdb=" O ARG L 303 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 16 through 18 removed outlier: 3.506A pdb=" N GLU M 324 " --> pdb=" O GLY M 16 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL M 18 " --> pdb=" O ILE M 322 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE M 322 " --> pdb=" O VAL M 18 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 23 through 25 removed outlier: 7.490A pdb=" N VAL M 25 " --> pdb=" O GLN M 265 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLN M 265 " --> pdb=" O VAL M 25 " (cutoff:3.500A) removed outlier: 14.068A pdb=" N LYS M 266 " --> pdb=" O GLU M 313 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N GLU M 313 " --> pdb=" O LYS M 266 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE M 268 " --> pdb=" O VAL M 311 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL M 311 " --> pdb=" O ILE M 268 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TRP M 309 " --> pdb=" O VAL M 304 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL M 304 " --> pdb=" O TRP M 309 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N VAL M 311 " --> pdb=" O ASP M 302 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ASP M 302 " --> pdb=" O VAL M 311 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU M 313 " --> pdb=" O LYS M 300 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA M 283 " --> pdb=" O ILE M 299 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 221 through 225 removed outlier: 3.509A pdb=" N GLU M 223 " --> pdb=" O ARG M 239 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG M 239 " --> pdb=" O GLU M 223 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N SER M 225 " --> pdb=" O THR M 237 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N THR M 237 " --> pdb=" O SER M 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 41 through 42 removed outlier: 3.502A pdb=" N VAL M 167 " --> pdb=" O ALA M 41 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 320 through 322 removed outlier: 3.514A pdb=" N ILE N 321 " --> pdb=" O VAL N 18 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 22 through 28 removed outlier: 3.538A pdb=" N ALA N 267 " --> pdb=" O GLN N 23 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL N 25 " --> pdb=" O GLN N 265 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLN N 265 " --> pdb=" O VAL N 25 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU N 27 " --> pdb=" O VAL N 263 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL N 263 " --> pdb=" O LEU N 27 " (cutoff:3.500A) removed outlier: 14.834A pdb=" N LYS N 266 " --> pdb=" O GLU N 313 " (cutoff:3.500A) removed outlier: 9.798A pdb=" N GLU N 313 " --> pdb=" O LYS N 266 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE N 268 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL N 311 " --> pdb=" O ILE N 268 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG N 303 " --> pdb=" O LEU N 310 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR N 312 " --> pdb=" O ALA N 301 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ALA N 301 " --> pdb=" O THR N 312 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG N 297 " --> pdb=" O ALA N 285 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA N 283 " --> pdb=" O ILE N 299 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 33 through 43 removed outlier: 4.198A pdb=" N PHE N 38 " --> pdb=" O PRO N 172 " (cutoff:3.500A) removed outlier: 10.384A pdb=" N ILE N 40 " --> pdb=" O LEU N 170 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N LEU N 170 " --> pdb=" O ILE N 40 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N GLU N 42 " --> pdb=" O GLN N 168 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N GLN N 168 " --> pdb=" O GLU N 42 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 33 through 43 removed outlier: 4.198A pdb=" N PHE N 38 " --> pdb=" O PRO N 172 " (cutoff:3.500A) removed outlier: 10.384A pdb=" N ILE N 40 " --> pdb=" O LEU N 170 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N LEU N 170 " --> pdb=" O ILE N 40 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N GLU N 42 " --> pdb=" O GLN N 168 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N GLN N 168 " --> pdb=" O GLU N 42 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR N 237 " --> pdb=" O SER N 225 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N SER N 225 " --> pdb=" O THR N 237 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ARG N 239 " --> pdb=" O GLU N 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 69 through 71 removed outlier: 6.755A pdb=" N GLN N 70 " --> pdb=" O LEU N 52 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 124 through 126 removed outlier: 4.102A pdb=" N ILE A 300 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 124 through 126 removed outlier: 4.102A pdb=" N ILE A 300 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 118 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE A 88 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 332 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.804A pdb=" N ALA A 110 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 99 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU B 302 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ALA B 123 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ILE B 88 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 90 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 332 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 330 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE C 300 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 332 through 335 removed outlier: 7.463A pdb=" N ILE C 88 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 118 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 95 through 99 removed outlier: 3.584A pdb=" N GLN B 97 " --> pdb=" O SER B 112 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 128 through 130 removed outlier: 3.508A pdb=" N VAL F 45 " --> pdb=" O ILE F 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR F 89 " --> pdb=" O GLU F 81 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG F 817 " --> pdb=" O SER F 80 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU F 816 " --> pdb=" O ALA F 823 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 172 through 178 removed outlier: 6.443A pdb=" N VAL F 172 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA F 294 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP F 174 " --> pdb=" O LYS F 292 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY F 288 " --> pdb=" O PHE F 178 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU F 293 " --> pdb=" O PHE F 136 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N PHE F 136 " --> pdb=" O LEU F 293 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR F 327 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY F 141 " --> pdb=" O TYR F 325 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR F 325 " --> pdb=" O GLY F 141 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 172 through 178 removed outlier: 6.443A pdb=" N VAL F 172 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA F 294 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP F 174 " --> pdb=" O LYS F 292 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY F 288 " --> pdb=" O PHE F 178 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER F 608 " --> pdb=" O MET F 630 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER F 624 " --> pdb=" O GLY F 614 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN F 577 " --> pdb=" O MET F 662 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET F 662 " --> pdb=" O GLN F 577 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 267 through 272 removed outlier: 3.586A pdb=" N GLY F 271 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N TYR F 182 " --> pdb=" O VAL F 767 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG F 769 " --> pdb=" O TYR F 182 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET F 184 " --> pdb=" O ARG F 769 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR F 771 " --> pdb=" O MET F 184 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG F 766 " --> pdb=" O ASP F 763 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASN F 759 " --> pdb=" O VAL F 770 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU F 772 " --> pdb=" O TYR F 757 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR F 757 " --> pdb=" O LEU F 772 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 250 through 253 removed outlier: 4.431A pdb=" N LYS F 252 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 712 through 717 removed outlier: 5.029A pdb=" N VAL F 715 " --> pdb=" O LEU F 827 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU F 827 " --> pdb=" O VAL F 715 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLU F 825 " --> pdb=" O PRO F 717 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU F 682 " --> pdb=" O ILE F 826 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY F 855 " --> pdb=" O GLN F 685 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 804 through 811 removed outlier: 3.540A pdb=" N GLY F 811 " --> pdb=" O GLU F 723 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ILE E 235 " --> pdb=" O PRO F 724 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TYR F 726 " --> pdb=" O ILE E 235 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 789 through 791 Processing sheet with id=AF3, first strand: chain 'G' and resid 75 through 77 removed outlier: 3.536A pdb=" N VAL G 47 " --> pdb=" O MET G 88 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA G 42 " --> pdb=" O ALA G 132 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 82 through 83 removed outlier: 4.194A pdb=" N GLU G 816 " --> pdb=" O ALA G 823 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 172 through 177 removed outlier: 4.947A pdb=" N ASP G 174 " --> pdb=" O LYS G 292 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS G 292 " --> pdb=" O ASP G 174 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN G 176 " --> pdb=" O ALA G 290 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA G 279 " --> pdb=" O ALA G 286 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN G 278 " --> pdb=" O THR G 613 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER G 608 " --> pdb=" O MET G 630 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 323 through 328 removed outlier: 7.044A pdb=" N VAL G 139 " --> pdb=" O PRO G 326 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP G 328 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N LEU G 137 " --> pdb=" O ASP G 328 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE G 136 " --> pdb=" O LEU G 293 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU G 293 " --> pdb=" O PHE G 136 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET G 138 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA G 279 " --> pdb=" O ALA G 286 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN G 278 " --> pdb=" O THR G 613 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER G 608 " --> pdb=" O MET G 630 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY G 625 " --> pdb=" O VAL G 576 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 183 through 184 Processing sheet with id=AF8, first strand: chain 'G' and resid 266 through 267 Processing sheet with id=AF9, first strand: chain 'G' and resid 234 through 235 removed outlier: 3.687A pdb=" N LEU E 728 " --> pdb=" O ILE G 235 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 250 through 253 removed outlier: 7.180A pdb=" N VAL G 260 " --> pdb=" O LEU G 251 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 712 through 717 removed outlier: 5.135A pdb=" N ARG G 714 " --> pdb=" O GLU G 829 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU G 829 " --> pdb=" O ARG G 714 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG G 716 " --> pdb=" O LEU G 827 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU G 682 " --> pdb=" O ILE G 826 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASP G 681 " --> pdb=" O THR G 859 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR G 859 " --> pdb=" O ASP G 681 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 726 through 730 removed outlier: 3.991A pdb=" N THR G 805 " --> pdb=" O GLU G 729 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 760 through 763 Processing sheet with id=AG5, first strand: chain 'G' and resid 789 through 791 Processing sheet with id=AG6, first strand: chain 'E' and resid 45 through 48 Processing sheet with id=AG7, first strand: chain 'E' and resid 75 through 77 Processing sheet with id=AG8, first strand: chain 'E' and resid 79 through 80 removed outlier: 3.540A pdb=" N ARG E 817 " --> pdb=" O SER E 80 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU E 816 " --> pdb=" O ALA E 823 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 176 through 178 removed outlier: 3.954A pdb=" N GLY E 288 " --> pdb=" O PHE E 178 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL E 139 " --> pdb=" O PRO E 326 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 270 through 272 removed outlier: 8.299A pdb=" N TYR E 182 " --> pdb=" O VAL E 767 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG E 769 " --> pdb=" O TYR E 182 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET E 184 " --> pdb=" O ARG E 769 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR E 771 " --> pdb=" O MET E 184 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASN E 759 " --> pdb=" O VAL E 770 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU E 772 " --> pdb=" O TYR E 757 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR E 757 " --> pdb=" O LEU E 772 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 252 through 254 removed outlier: 3.851A pdb=" N LYS E 252 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN E 254 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N SER E 258 " --> pdb=" O ASN E 254 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 284 through 286 removed outlier: 3.790A pdb=" N ALA E 286 " --> pdb=" O ALA E 279 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA E 279 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN E 278 " --> pdb=" O THR E 613 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N SER E 624 " --> pdb=" O GLY E 614 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU E 572 " --> pdb=" O ILE E 629 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 284 through 286 removed outlier: 3.790A pdb=" N ALA E 286 " --> pdb=" O ALA E 279 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA E 279 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN E 278 " --> pdb=" O THR E 613 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N SER E 624 " --> pdb=" O GLY E 614 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 712 through 713 removed outlier: 3.812A pdb=" N GLY E 828 " --> pdb=" O PHE E 680 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER E 857 " --> pdb=" O PHE E 683 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 790 through 791 2593 hydrogen bonds defined for protein. 7542 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: 28.28 Time building geometry restraints manager: 14.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14766 1.34 - 1.45: 7228 1.45 - 1.57: 27642 1.57 - 1.69: 0 1.69 - 1.81: 270 Bond restraints: 49906 Sorted by residual: bond pdb=" C VAL L 338 " pdb=" N PRO L 339 " ideal model delta sigma weight residual 1.334 1.363 -0.029 8.40e-03 1.42e+04 1.21e+01 bond pdb=" C VAL F 985 " pdb=" N PRO F 986 " ideal model delta sigma weight residual 1.334 1.412 -0.079 2.34e-02 1.83e+03 1.13e+01 bond pdb=" C ASN F 781 " pdb=" N PRO F 782 " ideal model delta sigma weight residual 1.336 1.372 -0.036 1.08e-02 8.57e+03 1.12e+01 bond pdb=" C VAL E 904 " pdb=" N PRO E 905 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.70e+00 bond pdb=" CA THR M 12 " pdb=" C THR M 12 " ideal model delta sigma weight residual 1.525 1.566 -0.041 2.10e-02 2.27e+03 3.77e+00 ... (remaining 49901 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 66336 2.80 - 5.60: 1201 5.60 - 8.41: 227 8.41 - 11.21: 31 11.21 - 14.01: 10 Bond angle restraints: 67805 Sorted by residual: angle pdb=" N PHE B 379 " pdb=" CA PHE B 379 " pdb=" C PHE B 379 " ideal model delta sigma weight residual 114.56 108.26 6.30 1.27e+00 6.20e-01 2.46e+01 angle pdb=" C ASP F 73 " pdb=" N ASN F 74 " pdb=" CA ASN F 74 " ideal model delta sigma weight residual 122.82 129.68 -6.86 1.42e+00 4.96e-01 2.33e+01 angle pdb=" N GLU G 314 " pdb=" CA GLU G 314 " pdb=" C GLU G 314 " ideal model delta sigma weight residual 109.81 119.94 -10.13 2.21e+00 2.05e-01 2.10e+01 angle pdb=" CA LYS L 136 " pdb=" CB LYS L 136 " pdb=" CG LYS L 136 " ideal model delta sigma weight residual 114.10 122.93 -8.83 2.00e+00 2.50e-01 1.95e+01 angle pdb=" C ILE E 438 " pdb=" N GLN E 439 " pdb=" CA GLN E 439 " ideal model delta sigma weight residual 120.54 126.33 -5.79 1.35e+00 5.49e-01 1.84e+01 ... (remaining 67800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 28453 16.17 - 32.35: 1344 32.35 - 48.52: 348 48.52 - 64.69: 6 64.69 - 80.87: 43 Dihedral angle restraints: 30194 sinusoidal: 11698 harmonic: 18496 Sorted by residual: dihedral pdb=" CA ASP J 171 " pdb=" C ASP J 171 " pdb=" N PRO J 172 " pdb=" CA PRO J 172 " ideal model delta harmonic sigma weight residual 180.00 146.31 33.69 0 5.00e+00 4.00e-02 4.54e+01 dihedral pdb=" CA LYS M 136 " pdb=" C LYS M 136 " pdb=" N VAL M 137 " pdb=" CA VAL M 137 " ideal model delta harmonic sigma weight residual -180.00 -146.57 -33.43 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA ASP N 171 " pdb=" C ASP N 171 " pdb=" N PRO N 172 " pdb=" CA PRO N 172 " ideal model delta harmonic sigma weight residual 180.00 147.29 32.71 0 5.00e+00 4.00e-02 4.28e+01 ... (remaining 30191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 6397 0.069 - 0.137: 1321 0.137 - 0.206: 173 0.206 - 0.275: 24 0.275 - 0.343: 5 Chirality restraints: 7920 Sorted by residual: chirality pdb=" CB ILE L 40 " pdb=" CA ILE L 40 " pdb=" CG1 ILE L 40 " pdb=" CG2 ILE L 40 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CB ILE F 289 " pdb=" CA ILE F 289 " pdb=" CG1 ILE F 289 " pdb=" CG2 ILE F 289 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CB ILE G 896 " pdb=" CA ILE G 896 " pdb=" CG1 ILE G 896 " pdb=" CG2 ILE G 896 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 7917 not shown) Planarity restraints: 8865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 164 " -0.051 5.00e-02 4.00e+02 7.67e-02 9.41e+00 pdb=" N PRO E 165 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO E 165 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 165 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN J 70 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.36e+00 pdb=" C GLN J 70 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN J 70 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE J 71 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 224 " -0.018 2.00e-02 2.50e+03 2.18e-02 8.35e+00 pdb=" CG PHE I 224 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE I 224 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE I 224 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE I 224 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE I 224 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE I 224 " -0.004 2.00e-02 2.50e+03 ... (remaining 8862 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3691 2.74 - 3.28: 46642 3.28 - 3.82: 80398 3.82 - 4.36: 90502 4.36 - 4.90: 158879 Nonbonded interactions: 380112 Sorted by model distance: nonbonded pdb=" OH TYR F 467 " pdb=" OE1 GLN F 927 " model vdw 2.201 3.040 nonbonded pdb=" OG SER E 977 " pdb=" OG1 THR E1013 " model vdw 2.226 3.040 nonbonded pdb=" OG SER A 301 " pdb=" O SER A 329 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR G 527 " pdb=" O ILE G1017 " model vdw 2.268 3.040 nonbonded pdb=" OG SER B 310 " pdb=" O GLY B 315 " model vdw 2.277 3.040 ... (remaining 380107 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'E' and (resid 1 through 273 or (resid 274 and (name N or name CA or name \ C or name CB or name CG or name OD1 or name OD2)) or resid 275 through 499 or r \ esid 506 through 1030)) selection = (chain 'F' and (resid 1 through 273 or (resid 274 and (name N or name CA or name \ C or name CB or name CG or name OD1 or name OD2)) or resid 275 through 1030)) selection = (chain 'G' and (resid 1 through 499 or resid 506 through 1030)) } ncs_group { reference = (chain 'I' and (resid 12 through 338 or (resid 339 and (name N or name CA or nam \ e C or name CB or name CG or name CD )) or resid 340 through 343)) selection = (chain 'J' and (resid 12 through 338 or (resid 339 and (name N or name CA or nam \ e C or name CB or name CG or name CD )) or resid 340 through 343)) selection = (chain 'K' and (resid 12 through 338 or (resid 339 and (name N or name CA or nam \ e C or name CB or name CG or name CD )) or resid 340 through 343)) selection = (chain 'L' and (resid 12 through 338 or (resid 339 and (name N or name CA or nam \ e C or name CB or name CG or name CD )) or resid 340 through 343)) selection = (chain 'M' and (resid 12 through 338 or (resid 339 and (name N or name CA or nam \ e C or name CB or name CG or name CD )) or resid 340 through 343)) selection = (chain 'N' and resid 12 through 343) } 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 group one per residue 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: 3.640 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: 0.040 Extract box with map and model: 1.890 Check model and map are aligned: 0.320 Set scattering table: 0.420 Process input model: 117.080 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.300 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: 0.020 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 0.079 49906 Z= 0.311 Angle : 0.968 14.011 67805 Z= 0.491 Chirality : 0.057 0.343 7920 Planarity : 0.007 0.077 8865 Dihedral : 10.772 80.868 18318 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.33 % Allowed : 5.20 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 1.74 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.08), residues: 6424 helix: -2.35 (0.07), residues: 2802 sheet: -3.10 (0.13), residues: 1050 loop : -2.70 (0.10), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 515 HIS 0.008 0.001 HIS E 654 PHE 0.050 0.003 PHE I 224 TYR 0.029 0.002 TYR G 49 ARG 0.011 0.001 ARG G 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 696 time to evaluate : 5.212 Fit side-chains TARDY: cannot create tardy model for: "ASP I 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP J 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP K 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP N 72 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PRO N 339 " (corrupted residue). Skipping it. Corrupt residue: chain: N residue: PRO 339 >>> skipping revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 455 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP G 274 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: J 266 LYS cc_start: 0.8433 (mttp) cc_final: 0.8119 (mmtt) REVERT: K 280 LYS cc_start: 0.8483 (ttmt) cc_final: 0.8082 (tptp) REVERT: K 291 GLN cc_start: 0.8238 (mp10) cc_final: 0.7968 (mp10) REVERT: L 248 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7615 (mt-10) REVERT: M 187 LEU cc_start: 0.8741 (tm) cc_final: 0.8450 (tt) REVERT: M 248 GLU cc_start: 0.7928 (tp30) cc_final: 0.7609 (tt0) REVERT: M 320 LYS cc_start: 0.8117 (ptpt) cc_final: 0.7836 (pttm) REVERT: A 125 GLU cc_start: 0.6666 (pt0) cc_final: 0.6425 (mt-10) REVERT: B 115 TYR cc_start: 0.6604 (p90) cc_final: 0.6213 (p90) REVERT: C 430 THR cc_start: 0.8262 (t) cc_final: 0.8031 (t) REVERT: F 67 GLN cc_start: 0.7653 (tt0) cc_final: 0.7188 (tt0) REVERT: F 583 SER cc_start: 0.9081 (p) cc_final: 0.8871 (t) REVERT: F 729 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6930 (mt-10) REVERT: F 751 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.7924 (mp) REVERT: F 829 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6625 (mt-10) REVERT: F 840 MET cc_start: 0.8138 (ttt) cc_final: 0.7395 (mtt) REVERT: F 902 LEU cc_start: 0.6917 (pp) cc_final: 0.6625 (mp) REVERT: F 975 MET cc_start: 0.7260 (tmm) cc_final: 0.6553 (ttt) REVERT: F 982 LEU cc_start: 0.7268 (mm) cc_final: 0.7021 (mp) REVERT: G 8 ARG cc_start: 0.6632 (mtm180) cc_final: 0.6190 (ptp90) REVERT: G 353 LEU cc_start: 0.8049 (tm) cc_final: 0.7717 (tp) REVERT: G 622 GLN cc_start: 0.8467 (tt0) cc_final: 0.8022 (tt0) REVERT: G 662 MET cc_start: 0.8115 (mtm) cc_final: 0.7745 (mtm) REVERT: G 950 GLU cc_start: 0.7728 (tp30) cc_final: 0.7419 (tp30) REVERT: E 33 ASN cc_start: 0.8865 (m110) cc_final: 0.8585 (m110) REVERT: E 134 LYS cc_start: 0.8901 (mtmt) cc_final: 0.8601 (mtpp) REVERT: E 437 GLN cc_start: 0.6225 (tt0) cc_final: 0.5571 (mm-40) REVERT: E 705 LEU cc_start: 0.8272 (tt) cc_final: 0.8034 (tp) REVERT: E 878 LEU cc_start: 0.8279 (tt) cc_final: 0.7957 (tp) REVERT: E 917 MET cc_start: 0.7171 (mmp) cc_final: 0.6786 (mmm) REVERT: E 1023 PHE cc_start: 0.7431 (m-10) cc_final: 0.7065 (m-80) outliers start: 17 outliers final: 4 residues processed: 709 average time/residue: 0.6289 time to fit residues: 735.4842 Evaluate side-chains 489 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 484 time to evaluate : 5.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 751 ILE Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain E residue 945 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 641 random chunks: chunk 541 optimal weight: 4.9990 chunk 485 optimal weight: 0.3980 chunk 269 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 327 optimal weight: 3.9990 chunk 259 optimal weight: 0.6980 chunk 502 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 305 optimal weight: 0.9980 chunk 373 optimal weight: 3.9990 chunk 582 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 GLN ** I 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 GLN K 168 GLN L 23 GLN L 46 GLN L 110 GLN L 169 GLN M 104 GLN M 256 HIS N 120 GLN N 169 GLN N 195 GLN N 327 GLN A 50 GLN A 354 ASN B 27 ASN B 452 GLN C 48 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN C 386 GLN ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 ASN F 228 GLN F 254 ASN F 439 GLN F 469 GLN F 537 HIS F 622 GLN F 849 GLN G 58 GLN G 248 ASN G 652 GLN G 687 GLN G 998 GLN E 33 ASN E 58 GLN E 210 GLN ** E 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 927 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 49906 Z= 0.211 Angle : 0.652 13.869 67805 Z= 0.329 Chirality : 0.043 0.185 7920 Planarity : 0.005 0.054 8865 Dihedral : 5.331 45.958 6939 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.13 % Allowed : 9.65 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.10), residues: 6424 helix: -0.55 (0.09), residues: 2824 sheet: -2.66 (0.14), residues: 1063 loop : -2.25 (0.10), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 515 HIS 0.005 0.001 HIS G 692 PHE 0.023 0.002 PHE F 556 TYR 0.022 0.002 TYR G 49 ARG 0.005 0.000 ARG M 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 558 time to evaluate : 5.233 Fit side-chains TARDY: cannot create tardy model for: "ASP I 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP J 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP K 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP M 72 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP N 72 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PRO N 339 " (corrupted residue). Skipping it. Corrupt residue: chain: N residue: PRO 339 >>> skipping revert: symmetry clash TARDY: cannot create tardy model for: "VAL A 455 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP G 274 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: J 222 LEU cc_start: 0.8971 (tm) cc_final: 0.8561 (tt) REVERT: J 266 LYS cc_start: 0.8322 (mttp) cc_final: 0.8085 (mmtt) REVERT: K 280 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8136 (tptp) REVERT: K 291 GLN cc_start: 0.8233 (mp10) cc_final: 0.7992 (mp10) REVERT: L 28 ASN cc_start: 0.8077 (m-40) cc_final: 0.7831 (m-40) REVERT: L 185 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7678 (tp) REVERT: M 250 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8374 (pp) REVERT: M 263 VAL cc_start: 0.9044 (m) cc_final: 0.8788 (p) REVERT: M 299 ILE cc_start: 0.8430 (pt) cc_final: 0.8205 (pt) REVERT: A 125 GLU cc_start: 0.7053 (pt0) cc_final: 0.6766 (mt-10) REVERT: B 42 GLU cc_start: 0.7329 (mp0) cc_final: 0.6179 (mp0) REVERT: B 421 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7748 (tt) REVERT: C 96 ARG cc_start: 0.5030 (mtm180) cc_final: 0.4635 (mmm160) REVERT: C 206 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7500 (tm) REVERT: C 409 ASP cc_start: 0.8156 (t0) cc_final: 0.7865 (p0) REVERT: F 67 GLN cc_start: 0.7697 (tt0) cc_final: 0.7329 (tt0) REVERT: F 95 GLU cc_start: 0.7941 (pm20) cc_final: 0.7267 (pt0) REVERT: F 202 ASP cc_start: 0.7490 (t0) cc_final: 0.6967 (t0) REVERT: F 342 LYS cc_start: 0.7491 (tmtt) cc_final: 0.7207 (tmtt) REVERT: F 567 GLU cc_start: 0.7455 (tt0) cc_final: 0.7220 (tt0) REVERT: F 641 GLU cc_start: 0.6750 (tm-30) cc_final: 0.6060 (mp0) REVERT: F 840 MET cc_start: 0.8254 (ttt) cc_final: 0.7612 (mtt) REVERT: F 901 MET cc_start: 0.6992 (mmp) cc_final: 0.6780 (mmt) REVERT: F 902 LEU cc_start: 0.7012 (pp) cc_final: 0.6687 (mp) REVERT: F 982 LEU cc_start: 0.7266 (mm) cc_final: 0.6941 (mp) REVERT: G 8 ARG cc_start: 0.6445 (mtm180) cc_final: 0.6192 (ptp90) REVERT: G 353 LEU cc_start: 0.8093 (tm) cc_final: 0.7856 (tp) REVERT: G 367 ILE cc_start: 0.6927 (OUTLIER) cc_final: 0.6607 (pt) REVERT: G 447 MET cc_start: 0.7470 (mmp) cc_final: 0.6935 (mmm) REVERT: G 622 GLN cc_start: 0.8463 (tt0) cc_final: 0.8026 (tt0) REVERT: G 825 GLU cc_start: 0.7672 (tt0) cc_final: 0.7250 (tt0) REVERT: G 881 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7416 (tp) REVERT: G 950 GLU cc_start: 0.7835 (tp30) cc_final: 0.7617 (tp30) REVERT: E 134 LYS cc_start: 0.8978 (mtmt) cc_final: 0.8632 (mtpp) REVERT: E 317 MET cc_start: 0.8224 (mtt) cc_final: 0.7795 (mtm) REVERT: E 398 MET cc_start: 0.6553 (mtp) cc_final: 0.6293 (mtt) REVERT: E 437 GLN cc_start: 0.6364 (tt0) cc_final: 0.5594 (mm-40) REVERT: E 705 LEU cc_start: 0.8262 (tt) cc_final: 0.8018 (tp) REVERT: E 780 MET cc_start: 0.8112 (mmt) cc_final: 0.7757 (mmm) REVERT: E 791 ARG cc_start: 0.8652 (ttp80) cc_final: 0.8436 (ttm-80) REVERT: E 850 LEU cc_start: 0.8610 (mt) cc_final: 0.8359 (mp) REVERT: E 878 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7915 (tp) REVERT: E 1015 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7347 (pt) outliers start: 111 outliers final: 47 residues processed: 636 average time/residue: 0.5689 time to fit residues: 621.2646 Evaluate side-chains 535 residues out of total 5211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 480 time to evaluate : 4.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 14 GLU Chi-restraints excluded: chain I residue 305 ILE Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 247 ASN Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 207 SER Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 233 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 402 LYS Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 673 GLU Chi-restraints excluded: chain F residue 921 SER Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 367 ILE Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 672 LEU Chi-restraints excluded: chain G residue 703 LEU Chi-restraints excluded: chain G residue 755 SER Chi-restraints excluded: chain G residue 812 SER Chi-restraints excluded: chain G residue 881 LEU Chi-restraints excluded: chain G residue 944 ILE Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 1015 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.3288 > 50: distance: 2 - 18: 5.401 distance: 6 - 24: 20.286 distance: 10 - 29: 13.870 distance: 14 - 18: 3.660 distance: 19 - 22: 5.989 distance: 20 - 21: 8.911 distance: 20 - 24: 18.019 distance: 24 - 25: 19.034 distance: 25 - 26: 12.341 distance: 25 - 28: 22.695 distance: 26 - 27: 27.902 distance: 26 - 29: 7.777 distance: 29 - 30: 13.085 distance: 30 - 31: 23.426 distance: 30 - 33: 15.578 distance: 31 - 32: 14.423 distance: 31 - 36: 37.232 distance: 33 - 34: 28.208 distance: 33 - 35: 34.374 distance: 36 - 37: 32.891 distance: 37 - 38: 19.973 distance: 37 - 40: 24.927 distance: 38 - 39: 28.365 distance: 38 - 47: 28.235 distance: 40 - 41: 22.714 distance: 41 - 42: 22.918 distance: 41 - 43: 18.103 distance: 42 - 44: 18.382 distance: 43 - 45: 18.130 distance: 44 - 46: 20.055 distance: 45 - 46: 22.595 distance: 47 - 48: 13.685 distance: 48 - 49: 16.950 distance: 48 - 51: 27.442 distance: 49 - 50: 35.875 distance: 49 - 55: 18.913 distance: 51 - 52: 14.118 distance: 52 - 53: 36.429 distance: 52 - 54: 38.126 distance: 55 - 56: 26.359 distance: 55 - 61: 32.590 distance: 56 - 57: 13.524 distance: 56 - 59: 28.549 distance: 57 - 58: 28.823 distance: 57 - 62: 26.704 distance: 58 - 75: 16.330 distance: 59 - 60: 15.260 distance: 60 - 61: 48.864 distance: 62 - 63: 17.942 distance: 63 - 64: 17.932 distance: 63 - 66: 8.567 distance: 64 - 65: 19.146 distance: 64 - 70: 21.435 distance: 66 - 67: 18.034 distance: 67 - 68: 7.690 distance: 68 - 69: 16.615 distance: 70 - 71: 11.782 distance: 71 - 74: 13.385 distance: 72 - 73: 11.179 distance: 72 - 75: 9.848 distance: 75 - 76: 4.451 distance: 76 - 77: 11.852 distance: 76 - 79: 4.619 distance: 77 - 78: 15.940 distance: 77 - 86: 14.890 distance: 81 - 83: 3.753 distance: 83 - 85: 3.180 distance: 86 - 87: 9.579 distance: 87 - 88: 24.237 distance: 87 - 90: 12.315 distance: 88 - 89: 8.372 distance: 88 - 97: 21.295 distance: 90 - 91: 12.249 distance: 91 - 92: 4.422 distance: 91 - 93: 10.916 distance: 92 - 94: 10.835 distance: 93 - 95: 12.071 distance: 94 - 96: 7.370 distance: 95 - 96: 7.516