Starting phenix.real_space_refine on Tue Aug 26 13:01:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6i7t_4428/08_2025/6i7t_4428.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i7t_4428/08_2025/6i7t_4428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6i7t_4428/08_2025/6i7t_4428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i7t_4428/08_2025/6i7t_4428.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6i7t_4428/08_2025/6i7t_4428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i7t_4428/08_2025/6i7t_4428.map" } resolution = 4.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 168 5.16 5 C 23570 2.51 5 N 6300 2.21 5 O 6966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37004 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2393 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain: "C" Number of atoms: 2677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2677 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "D" Number of atoms: 2677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2677 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "E" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2797 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 338} Chain breaks: 1 Chain: "G" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3265 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 395} Chain: "I" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2187 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain breaks: 3 Chain: "J" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2187 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain breaks: 3 Chain: "B" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2393 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain: "F" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2797 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 338} Chain breaks: 1 Chain: "H" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3265 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 395} Chain: "K" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2006 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain breaks: 2 Chain: "M" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "O" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3034 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2006 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain breaks: 2 Chain: "N" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "P" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3034 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 7.21, per 1000 atoms: 0.19 Number of scatterers: 37004 At special positions: 0 Unit cell: (176.88, 270.68, 123.28, 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 168 16.00 O 6966 8.00 N 6300 7.00 C 23570 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: 2.90 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8904 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 44 sheets defined 33.0% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 removed outlier: 3.631A pdb=" N ARG A 12 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 37 removed outlier: 3.692A pdb=" N LEU A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 60 removed outlier: 3.689A pdb=" N MET A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 82 removed outlier: 4.310A pdb=" N MET A 74 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.676A pdb=" N ASN A 97 " --> pdb=" O HIS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 116 removed outlier: 3.705A pdb=" N LYS A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.861A pdb=" N PHE A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 removed outlier: 4.077A pdb=" N GLN A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 171 " --> pdb=" O THR A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.734A pdb=" N VAL A 184 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY A 185 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.594A pdb=" N ASN A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.568A pdb=" N LEU A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N MET A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 283 removed outlier: 3.728A pdb=" N LEU C 275 " --> pdb=" O HIS C 271 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 306 removed outlier: 3.730A pdb=" N LEU C 297 " --> pdb=" O CYS C 293 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS C 305 " --> pdb=" O GLN C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 334 removed outlier: 3.767A pdb=" N LEU C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR C 320 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER C 324 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN C 326 " --> pdb=" O TYR C 322 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 329 " --> pdb=" O HIS C 325 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 330 " --> pdb=" O GLN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 353 removed outlier: 4.212A pdb=" N ALA C 343 " --> pdb=" O THR C 339 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP C 346 " --> pdb=" O ASN C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 378 removed outlier: 3.705A pdb=" N GLU C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C 375 " --> pdb=" O ILE C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 392 removed outlier: 3.507A pdb=" N ILE C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP C 388 " --> pdb=" O GLN C 384 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN C 389 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 418 Processing helix chain 'C' and resid 436 through 447 removed outlier: 4.017A pdb=" N MET C 440 " --> pdb=" O GLU C 436 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG C 445 " --> pdb=" O ALA C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 464 removed outlier: 3.662A pdb=" N PHE C 463 " --> pdb=" O LEU C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 499 removed outlier: 4.454A pdb=" N LEU C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS C 497 " --> pdb=" O ALA C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 512 Processing helix chain 'C' and resid 528 through 533 removed outlier: 4.081A pdb=" N LEU C 532 " --> pdb=" O PRO C 529 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 533 " --> pdb=" O ASN C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 643 removed outlier: 3.646A pdb=" N VAL C 640 " --> pdb=" O PRO C 637 " (cutoff:3.500A) Proline residue: C 641 - end of helix Processing helix chain 'D' and resid 271 through 283 removed outlier: 3.728A pdb=" N LEU D 275 " --> pdb=" O HIS D 271 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS D 283 " --> pdb=" O SER D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 306 removed outlier: 3.730A pdb=" N LEU D 297 " --> pdb=" O CYS D 293 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS D 305 " --> pdb=" O GLN D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 334 removed outlier: 3.767A pdb=" N LEU D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR D 320 " --> pdb=" O SER D 316 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER D 321 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN D 326 " --> pdb=" O TYR D 322 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP D 328 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU D 329 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 330 " --> pdb=" O GLN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 353 removed outlier: 4.214A pdb=" N ALA D 343 " --> pdb=" O THR D 339 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP D 346 " --> pdb=" O ASN D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 378 removed outlier: 3.704A pdb=" N GLU D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS D 370 " --> pdb=" O ASP D 366 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA D 375 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 392 removed outlier: 3.507A pdb=" N ILE D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP D 388 " --> pdb=" O GLN D 384 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR D 392 " --> pdb=" O ASP D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 418 Processing helix chain 'D' and resid 436 through 447 removed outlier: 4.017A pdb=" N MET D 440 " --> pdb=" O GLU D 436 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 464 removed outlier: 3.662A pdb=" N PHE D 463 " --> pdb=" O LEU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 499 removed outlier: 4.454A pdb=" N LEU D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS D 497 " --> pdb=" O ALA D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 512 Processing helix chain 'D' and resid 528 through 533 removed outlier: 4.081A pdb=" N LEU D 532 " --> pdb=" O PRO D 529 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 533 " --> pdb=" O ASN D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 643 removed outlier: 3.646A pdb=" N VAL D 640 " --> pdb=" O PRO D 637 " (cutoff:3.500A) Proline residue: D 641 - end of helix Processing helix chain 'E' and resid 17 through 29 removed outlier: 3.515A pdb=" N THR E 21 " --> pdb=" O ASP E 17 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP E 23 " --> pdb=" O ASN E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 54 removed outlier: 3.616A pdb=" N LEU E 42 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 47 " --> pdb=" O GLU E 43 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG E 50 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 73 removed outlier: 3.733A pdb=" N ILE E 64 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU E 70 " --> pdb=" O GLN E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 107 removed outlier: 3.914A pdb=" N LEU E 95 " --> pdb=" O ILE E 91 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU E 98 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU E 100 " --> pdb=" O ARG E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 124 removed outlier: 4.520A pdb=" N LEU E 124 " --> pdb=" O SER E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 166 removed outlier: 3.867A pdb=" N GLN E 152 " --> pdb=" O THR E 148 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU E 161 " --> pdb=" O GLY E 157 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE E 162 " --> pdb=" O ILE E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 removed outlier: 4.081A pdb=" N ILE E 175 " --> pdb=" O GLY E 171 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE E 177 " --> pdb=" O GLN E 173 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP E 178 " --> pdb=" O GLN E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 206 removed outlier: 4.216A pdb=" N ILE E 201 " --> pdb=" O LEU E 197 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR E 202 " --> pdb=" O LYS E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 236 removed outlier: 3.657A pdb=" N HIS E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU E 228 " --> pdb=" O LYS E 224 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS E 231 " --> pdb=" O HIS E 227 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 249 removed outlier: 3.740A pdb=" N VAL E 248 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE E 249 " --> pdb=" O SER E 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 245 through 249' Processing helix chain 'E' and resid 277 through 288 removed outlier: 4.072A pdb=" N VAL E 281 " --> pdb=" O GLY E 277 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE E 288 " --> pdb=" O CYS E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 342 through 346 Processing helix chain 'E' and resid 360 through 366 removed outlier: 3.915A pdb=" N ILE E 364 " --> pdb=" O PHE E 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 71 removed outlier: 4.139A pdb=" N THR G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 92 removed outlier: 4.237A pdb=" N ASN G 87 " --> pdb=" O ALA G 83 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP G 88 " --> pdb=" O ASN G 84 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TYR G 89 " --> pdb=" O GLN G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 126 removed outlier: 3.509A pdb=" N ASP G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 159 removed outlier: 3.670A pdb=" N LEU G 149 " --> pdb=" O PHE G 145 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE G 151 " --> pdb=" O LYS G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 218 removed outlier: 3.799A pdb=" N LEU G 217 " --> pdb=" O ASP G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 249 removed outlier: 3.926A pdb=" N LEU G 244 " --> pdb=" O SER G 240 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU G 248 " --> pdb=" O LEU G 244 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN G 249 " --> pdb=" O ILE G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 263 Processing helix chain 'G' and resid 287 through 300 removed outlier: 3.796A pdb=" N SER G 295 " --> pdb=" O TYR G 291 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN G 296 " --> pdb=" O ASP G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 304 removed outlier: 3.706A pdb=" N TYR G 304 " --> pdb=" O ARG G 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 301 through 304' Processing helix chain 'G' and resid 307 through 311 removed outlier: 3.660A pdb=" N SER G 310 " --> pdb=" O VAL G 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 81 removed outlier: 3.951A pdb=" N VAL I 80 " --> pdb=" O ILE I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 128 removed outlier: 4.248A pdb=" N TYR I 123 " --> pdb=" O PHE I 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA I 125 " --> pdb=" O LEU I 121 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU I 126 " --> pdb=" O ILE I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 157 removed outlier: 3.914A pdb=" N GLN I 156 " --> pdb=" O GLY I 152 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS I 157 " --> pdb=" O GLU I 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 152 through 157' Processing helix chain 'I' and resid 180 through 189 removed outlier: 3.972A pdb=" N ASN I 189 " --> pdb=" O ASP I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 256 through 261 Processing helix chain 'I' and resid 403 through 411 removed outlier: 3.616A pdb=" N VAL I 408 " --> pdb=" O ALA I 404 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU I 409 " --> pdb=" O ASN I 405 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS I 410 " --> pdb=" O ARG I 406 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE I 411 " --> pdb=" O PHE I 407 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 81 removed outlier: 3.950A pdb=" N VAL J 80 " --> pdb=" O ILE J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 128 removed outlier: 4.248A pdb=" N TYR J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA J 125 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU J 126 " --> pdb=" O ILE J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 157 removed outlier: 3.913A pdb=" N GLN J 156 " --> pdb=" O GLY J 152 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS J 157 " --> pdb=" O GLU J 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 152 through 157' Processing helix chain 'J' and resid 180 through 189 removed outlier: 3.972A pdb=" N ASN J 189 " --> pdb=" O ASP J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 403 through 411 removed outlier: 3.616A pdb=" N VAL J 408 " --> pdb=" O ALA J 404 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU J 409 " --> pdb=" O ASN J 405 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS J 410 " --> pdb=" O ARG J 406 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE J 411 " --> pdb=" O PHE J 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 13 removed outlier: 3.630A pdb=" N ARG B 12 " --> pdb=" O THR B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.693A pdb=" N LEU B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 60 removed outlier: 3.689A pdb=" N MET B 45 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B 54 " --> pdb=" O LYS B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 82 removed outlier: 4.309A pdb=" N MET B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG B 79 " --> pdb=" O ARG B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.675A pdb=" N ASN B 97 " --> pdb=" O HIS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 removed outlier: 3.705A pdb=" N LYS B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 146 removed outlier: 3.861A pdb=" N PHE B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 171 removed outlier: 4.078A pdb=" N GLN B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN B 171 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.732A pdb=" N VAL B 184 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY B 185 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 removed outlier: 3.594A pdb=" N ASN B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 302 removed outlier: 3.569A pdb=" N LEU B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N MET B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 29 removed outlier: 3.514A pdb=" N THR F 21 " --> pdb=" O ASP F 17 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP F 23 " --> pdb=" O ASN F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 54 removed outlier: 3.616A pdb=" N LEU F 42 " --> pdb=" O TYR F 38 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU F 47 " --> pdb=" O GLU F 43 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG F 50 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 73 removed outlier: 3.733A pdb=" N ILE F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP F 69 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU F 70 " --> pdb=" O GLN F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 107 removed outlier: 3.915A pdb=" N LEU F 95 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU F 98 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU F 100 " --> pdb=" O ARG F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 124 removed outlier: 4.519A pdb=" N LEU F 124 " --> pdb=" O SER F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 166 removed outlier: 3.867A pdb=" N GLN F 152 " --> pdb=" O THR F 148 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU F 161 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE F 162 " --> pdb=" O ILE F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 180 removed outlier: 4.080A pdb=" N ILE F 175 " --> pdb=" O GLY F 171 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE F 177 " --> pdb=" O GLN F 173 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP F 178 " --> pdb=" O GLN F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 206 removed outlier: 4.217A pdb=" N ILE F 201 " --> pdb=" O LEU F 197 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR F 202 " --> pdb=" O LYS F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 236 removed outlier: 3.658A pdb=" N HIS F 227 " --> pdb=" O THR F 223 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU F 228 " --> pdb=" O LYS F 224 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS F 231 " --> pdb=" O HIS F 227 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 249 removed outlier: 3.741A pdb=" N VAL F 248 " --> pdb=" O ASP F 245 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE F 249 " --> pdb=" O SER F 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 245 through 249' Processing helix chain 'F' and resid 277 through 288 removed outlier: 4.072A pdb=" N VAL F 281 " --> pdb=" O GLY F 277 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE F 288 " --> pdb=" O CYS F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 301 Processing helix chain 'F' and resid 342 through 346 Processing helix chain 'F' and resid 360 through 366 removed outlier: 3.915A pdb=" N ILE F 364 " --> pdb=" O PHE F 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 71 removed outlier: 4.138A pdb=" N THR H 63 " --> pdb=" O LEU H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 92 removed outlier: 4.236A pdb=" N ASN H 87 " --> pdb=" O ALA H 83 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP H 88 " --> pdb=" O ASN H 84 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TYR H 89 " --> pdb=" O GLN H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 126 removed outlier: 3.510A pdb=" N ASP H 121 " --> pdb=" O ASP H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 159 removed outlier: 3.670A pdb=" N LEU H 149 " --> pdb=" O PHE H 145 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE H 151 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 218 removed outlier: 3.800A pdb=" N LEU H 217 " --> pdb=" O ASP H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 249 removed outlier: 3.926A pdb=" N LEU H 244 " --> pdb=" O SER H 240 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU H 248 " --> pdb=" O LEU H 244 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN H 249 " --> pdb=" O ILE H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 263 Processing helix chain 'H' and resid 287 through 300 removed outlier: 3.796A pdb=" N SER H 295 " --> pdb=" O TYR H 291 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN H 296 " --> pdb=" O ASP H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 304 removed outlier: 3.705A pdb=" N TYR H 304 " --> pdb=" O ARG H 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 301 through 304' Processing helix chain 'H' and resid 307 through 311 removed outlier: 3.660A pdb=" N SER H 310 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 51 Processing helix chain 'K' and resid 57 through 62 Processing helix chain 'K' and resid 63 through 65 No H-bonds generated for 'chain 'K' and resid 63 through 65' Processing helix chain 'K' and resid 92 through 115 removed outlier: 3.876A pdb=" N ILE K 96 " --> pdb=" O SER K 92 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU K 99 " --> pdb=" O ILE K 95 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU K 100 " --> pdb=" O ILE K 96 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL K 108 " --> pdb=" O LYS K 104 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS K 109 " --> pdb=" O SER K 105 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG K 113 " --> pdb=" O HIS K 109 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR K 114 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS K 115 " --> pdb=" O ILE K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 135 Processing helix chain 'K' and resid 141 through 146 Processing helix chain 'K' and resid 163 through 173 removed outlier: 3.639A pdb=" N ASP K 167 " --> pdb=" O LYS K 163 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS K 170 " --> pdb=" O LEU K 166 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN K 171 " --> pdb=" O ASP K 167 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR K 172 " --> pdb=" O GLU K 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 209 removed outlier: 3.603A pdb=" N SER K 207 " --> pdb=" O ASP K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 240 through 257 removed outlier: 3.560A pdb=" N GLU K 245 " --> pdb=" O ILE K 241 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER K 246 " --> pdb=" O GLU K 242 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR K 256 " --> pdb=" O THR K 252 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS K 257 " --> pdb=" O GLU K 253 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 141 Processing helix chain 'O' and resid 112 through 121 Processing helix chain 'O' and resid 130 through 135 removed outlier: 4.010A pdb=" N ARG O 134 " --> pdb=" O ASP O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 201 through 209 Processing helix chain 'O' and resid 226 through 239 Processing helix chain 'O' and resid 257 through 270 Processing helix chain 'O' and resid 290 through 301 removed outlier: 4.242A pdb=" N VAL O 294 " --> pdb=" O ASN O 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 51 Processing helix chain 'L' and resid 57 through 62 Processing helix chain 'L' and resid 63 through 65 No H-bonds generated for 'chain 'L' and resid 63 through 65' Processing helix chain 'L' and resid 92 through 115 removed outlier: 3.876A pdb=" N ILE L 96 " --> pdb=" O SER L 92 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU L 99 " --> pdb=" O ILE L 95 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU L 100 " --> pdb=" O ILE L 96 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL L 108 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS L 109 " --> pdb=" O SER L 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG L 113 " --> pdb=" O HIS L 109 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR L 114 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS L 115 " --> pdb=" O ILE L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 135 Processing helix chain 'L' and resid 141 through 146 Processing helix chain 'L' and resid 163 through 173 removed outlier: 3.638A pdb=" N ASP L 167 " --> pdb=" O LYS L 163 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS L 170 " --> pdb=" O LEU L 166 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN L 171 " --> pdb=" O ASP L 167 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR L 172 " --> pdb=" O GLU L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 209 removed outlier: 3.602A pdb=" N SER L 207 " --> pdb=" O ASP L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 257 removed outlier: 3.560A pdb=" N GLU L 245 " --> pdb=" O ILE L 241 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER L 246 " --> pdb=" O GLU L 242 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR L 256 " --> pdb=" O THR L 252 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS L 257 " --> pdb=" O GLU L 253 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 141 Processing helix chain 'P' and resid 112 through 121 Processing helix chain 'P' and resid 130 through 135 removed outlier: 4.012A pdb=" N ARG P 134 " --> pdb=" O ASP P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 209 Processing helix chain 'P' and resid 226 through 239 Processing helix chain 'P' and resid 257 through 270 Processing helix chain 'P' and resid 290 through 301 removed outlier: 4.243A pdb=" N VAL P 294 " --> pdb=" O ASN P 290 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 178 removed outlier: 5.897A pdb=" N ILE A 126 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE A 125 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE A 195 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU A 127 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL A 194 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL A 230 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL A 196 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE A 227 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N ILE A 284 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL A 229 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 398 through 403 removed outlier: 4.320A pdb=" N ASN C 450 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP C 430 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 470 through 472 removed outlier: 6.242A pdb=" N VAL C 470 " --> pdb=" O LEU C 504 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS C 506 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU C 472 " --> pdb=" O CYS C 506 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL C 503 " --> pdb=" O LYS C 627 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE C 629 " --> pdb=" O VAL C 503 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL C 505 " --> pdb=" O ILE C 629 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 476 through 477 Processing sheet with id=AA5, first strand: chain 'D' and resid 398 through 403 removed outlier: 4.320A pdb=" N ASN D 450 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP D 430 " --> pdb=" O ALA D 454 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 470 through 472 removed outlier: 6.242A pdb=" N VAL D 470 " --> pdb=" O LEU D 504 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS D 506 " --> pdb=" O VAL D 470 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU D 472 " --> pdb=" O CYS D 506 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL D 503 " --> pdb=" O LYS D 627 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE D 629 " --> pdb=" O VAL D 503 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL D 505 " --> pdb=" O ILE D 629 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 476 through 477 Processing sheet with id=AA8, first strand: chain 'E' and resid 185 through 188 removed outlier: 6.403A pdb=" N LEU E 186 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL E 213 " --> pdb=" O LEU E 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 258 through 261 removed outlier: 6.547A pdb=" N VAL E 258 " --> pdb=" O PHE E 293 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL E 295 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE E 260 " --> pdb=" O VAL E 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 264 through 265 Processing sheet with id=AB2, first strand: chain 'G' and resid 30 through 31 removed outlier: 4.666A pdb=" N ILE G 235 " --> pdb=" O CYS G 167 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE G 237 " --> pdb=" O THR G 165 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR G 165 " --> pdb=" O ILE G 237 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N HIS G 162 " --> pdb=" O HIS G 272 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N TYR G 274 " --> pdb=" O HIS G 162 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER G 164 " --> pdb=" O TYR G 274 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR G 276 " --> pdb=" O SER G 164 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N MET G 166 " --> pdb=" O TYR G 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 139 through 141 Processing sheet with id=AB4, first strand: chain 'G' and resid 194 through 199 removed outlier: 7.025A pdb=" N VAL G 186 " --> pdb=" O ILE G 195 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TYR G 197 " --> pdb=" O ALA G 184 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA G 184 " --> pdb=" O TYR G 197 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 211 through 212 Processing sheet with id=AB6, first strand: chain 'G' and resid 319 through 321 removed outlier: 6.131A pdb=" N TYR G 326 " --> pdb=" O ILE G 345 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA G 344 " --> pdb=" O ILE G 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 338 through 339 removed outlier: 6.445A pdb=" N LYS G 338 " --> pdb=" O ILE G 357 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS G 356 " --> pdb=" O ILE G 374 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 367 through 368 removed outlier: 7.311A pdb=" N GLN G 367 " --> pdb=" O ILE G 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 279 through 280 removed outlier: 6.439A pdb=" N ALA I 196 " --> pdb=" O ASN I 388 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N THR I 390 " --> pdb=" O ALA I 196 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N THR I 198 " --> pdb=" O THR I 390 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 221 through 222 removed outlier: 3.942A pdb=" N GLN I 221 " --> pdb=" O ASP I 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 254 through 255 Processing sheet with id=AC3, first strand: chain 'I' and resid 266 through 269 removed outlier: 7.694A pdb=" N ALA H 184 " --> pdb=" O TYR H 197 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TYR H 197 " --> pdb=" O ALA H 184 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL H 186 " --> pdb=" O ILE H 195 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 279 through 280 removed outlier: 6.439A pdb=" N ALA J 196 " --> pdb=" O ASN J 388 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N THR J 390 " --> pdb=" O ALA J 196 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N THR J 198 " --> pdb=" O THR J 390 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 221 through 222 removed outlier: 3.943A pdb=" N GLN J 221 " --> pdb=" O ASP J 240 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 176 through 178 removed outlier: 5.897A pdb=" N ILE B 126 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE B 125 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE B 195 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU B 127 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL B 194 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL B 230 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL B 196 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE B 227 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N ILE B 284 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL B 229 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 185 through 188 removed outlier: 6.404A pdb=" N LEU F 186 " --> pdb=" O LEU F 214 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL F 213 " --> pdb=" O LEU F 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 258 through 261 removed outlier: 6.547A pdb=" N VAL F 258 " --> pdb=" O PHE F 293 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL F 295 " --> pdb=" O VAL F 258 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE F 260 " --> pdb=" O VAL F 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 264 through 265 Processing sheet with id=AD1, first strand: chain 'H' and resid 30 through 31 removed outlier: 4.665A pdb=" N ILE H 235 " --> pdb=" O CYS H 167 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE H 237 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR H 165 " --> pdb=" O ILE H 237 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N HIS H 162 " --> pdb=" O HIS H 272 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N TYR H 274 " --> pdb=" O HIS H 162 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER H 164 " --> pdb=" O TYR H 274 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TYR H 276 " --> pdb=" O SER H 164 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N MET H 166 " --> pdb=" O TYR H 276 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 139 through 141 Processing sheet with id=AD3, first strand: chain 'H' and resid 319 through 321 removed outlier: 6.132A pdb=" N TYR H 326 " --> pdb=" O ILE H 345 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA H 344 " --> pdb=" O ILE H 362 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 338 through 339 removed outlier: 6.445A pdb=" N LYS H 338 " --> pdb=" O ILE H 357 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS H 356 " --> pdb=" O ILE H 374 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 367 through 368 removed outlier: 7.311A pdb=" N GLN H 367 " --> pdb=" O ILE H 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'K' and resid 35 through 36 removed outlier: 3.686A pdb=" N LYS K 35 " --> pdb=" O ASN K 23 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN K 23 " --> pdb=" O LYS K 35 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP K 84 " --> pdb=" O LEU K 74 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 219 through 222 Processing sheet with id=AD8, first strand: chain 'O' and resid 144 through 149 removed outlier: 5.732A pdb=" N LYS O 149 " --> pdb=" O LEU O 185 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU O 185 " --> pdb=" O LYS O 149 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 385 through 387 removed outlier: 4.248A pdb=" N ALA O 382 " --> pdb=" O ASN O 385 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU O 387 " --> pdb=" O LEU O 380 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU O 380 " --> pdb=" O LEU O 387 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY O 394 " --> pdb=" O ILE O 342 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL O 337 " --> pdb=" O SER O 320 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER O 320 " --> pdb=" O VAL O 337 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY O 339 " --> pdb=" O ILE O 318 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU O 343 " --> pdb=" O ARG O 314 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG O 314 " --> pdb=" O LEU O 343 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL O 416 " --> pdb=" O ARG O 356 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LYS O 371 " --> pdb=" O PRO O 357 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 347 through 348 Processing sheet with id=AE2, first strand: chain 'O' and resid 425 through 441 removed outlier: 9.812A pdb=" N ILE O 426 " --> pdb=" O SER O 489 " (cutoff:3.500A) removed outlier: 9.866A pdb=" N SER O 489 " --> pdb=" O ILE O 426 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N THR O 428 " --> pdb=" O LEU O 487 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N MET O 482 " --> pdb=" O VAL O 478 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N VAL O 478 " --> pdb=" O MET O 482 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG O 484 " --> pdb=" O VAL O 476 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLY O 472 " --> pdb=" O THR O 488 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ALA O 470 " --> pdb=" O PRO O 490 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL O 461 " --> pdb=" O ARG O 504 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG O 504 " --> pdb=" O VAL O 461 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE O 499 " --> pdb=" O TRP O 514 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TRP O 514 " --> pdb=" O ILE O 499 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU O 501 " --> pdb=" O ILE O 512 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE O 512 " --> pdb=" O LEU O 501 " (cutoff:3.500A) removed outlier: 11.530A pdb=" N ARG O 510 " --> pdb=" O ARG O 439 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N ARG O 439 " --> pdb=" O ARG O 510 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ILE O 512 " --> pdb=" O LEU O 437 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 35 through 36 removed outlier: 3.686A pdb=" N LYS L 35 " --> pdb=" O ASN L 23 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN L 23 " --> pdb=" O LYS L 35 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP L 84 " --> pdb=" O LEU L 74 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 219 through 222 Processing sheet with id=AE5, first strand: chain 'P' and resid 144 through 149 removed outlier: 5.732A pdb=" N LYS P 149 " --> pdb=" O LEU P 185 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU P 185 " --> pdb=" O LYS P 149 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 385 through 387 removed outlier: 4.248A pdb=" N ALA P 382 " --> pdb=" O ASN P 385 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU P 387 " --> pdb=" O LEU P 380 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU P 380 " --> pdb=" O LEU P 387 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY P 394 " --> pdb=" O ILE P 342 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL P 337 " --> pdb=" O SER P 320 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER P 320 " --> pdb=" O VAL P 337 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLY P 339 " --> pdb=" O ILE P 318 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU P 343 " --> pdb=" O ARG P 314 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG P 314 " --> pdb=" O LEU P 343 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL P 416 " --> pdb=" O ARG P 356 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LYS P 371 " --> pdb=" O PRO P 357 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 347 through 348 Processing sheet with id=AE8, first strand: chain 'P' and resid 425 through 441 removed outlier: 9.812A pdb=" N ILE P 426 " --> pdb=" O SER P 489 " (cutoff:3.500A) removed outlier: 9.867A pdb=" N SER P 489 " --> pdb=" O ILE P 426 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N THR P 428 " --> pdb=" O LEU P 487 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N MET P 482 " --> pdb=" O VAL P 478 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N VAL P 478 " --> pdb=" O MET P 482 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG P 484 " --> pdb=" O VAL P 476 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLY P 472 " --> pdb=" O THR P 488 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ALA P 470 " --> pdb=" O PRO P 490 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL P 461 " --> pdb=" O ARG P 504 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG P 504 " --> pdb=" O VAL P 461 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE P 499 " --> pdb=" O TRP P 514 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TRP P 514 " --> pdb=" O ILE P 499 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU P 501 " --> pdb=" O ILE P 512 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE P 512 " --> pdb=" O LEU P 501 " (cutoff:3.500A) removed outlier: 11.530A pdb=" N ARG P 510 " --> pdb=" O ARG P 439 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N ARG P 439 " --> pdb=" O ARG P 510 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ILE P 512 " --> pdb=" O LEU P 437 " (cutoff:3.500A) 1042 hydrogen bonds defined for protein. 2922 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: 6.71 Time building geometry restraints manager: 3.91 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: 11255 1.34 - 1.46: 5951 1.46 - 1.58: 20182 1.58 - 1.70: 0 1.70 - 1.82: 254 Bond restraints: 37642 Sorted by residual: bond pdb=" C ILE J 144 " pdb=" N PRO J 145 " ideal model delta sigma weight residual 1.340 1.425 -0.085 2.76e-02 1.31e+03 9.45e+00 bond pdb=" CZ ARG P 503 " pdb=" NH1 ARG P 503 " ideal model delta sigma weight residual 1.323 1.366 -0.043 1.40e-02 5.10e+03 9.37e+00 bond pdb=" C ILE I 144 " pdb=" N PRO I 145 " ideal model delta sigma weight residual 1.340 1.424 -0.084 2.76e-02 1.31e+03 9.29e+00 bond pdb=" CA VAL P 453 " pdb=" CB VAL P 453 " ideal model delta sigma weight residual 1.530 1.562 -0.031 1.05e-02 9.07e+03 8.94e+00 bond pdb=" CZ ARG O 503 " pdb=" NH1 ARG O 503 " ideal model delta sigma weight residual 1.323 1.365 -0.042 1.40e-02 5.10e+03 8.91e+00 ... (remaining 37637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 49411 2.93 - 5.87: 1289 5.87 - 8.80: 208 8.80 - 11.74: 22 11.74 - 14.67: 8 Bond angle restraints: 50938 Sorted by residual: angle pdb=" N SER K 194 " pdb=" CA SER K 194 " pdb=" C SER K 194 " ideal model delta sigma weight residual 108.07 117.24 -9.17 1.38e+00 5.25e-01 4.41e+01 angle pdb=" N SER L 194 " pdb=" CA SER L 194 " pdb=" C SER L 194 " ideal model delta sigma weight residual 108.07 117.19 -9.12 1.38e+00 5.25e-01 4.37e+01 angle pdb=" N ARG O 356 " pdb=" CA ARG O 356 " pdb=" C ARG O 356 " ideal model delta sigma weight residual 109.81 123.18 -13.37 2.21e+00 2.05e-01 3.66e+01 angle pdb=" N ARG P 356 " pdb=" CA ARG P 356 " pdb=" C ARG P 356 " ideal model delta sigma weight residual 109.81 123.17 -13.36 2.21e+00 2.05e-01 3.65e+01 angle pdb=" N ILE O 430 " pdb=" CA ILE O 430 " pdb=" C ILE O 430 " ideal model delta sigma weight residual 108.48 116.75 -8.27 1.44e+00 4.82e-01 3.30e+01 ... (remaining 50933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 20845 16.19 - 32.38: 1621 32.38 - 48.57: 464 48.57 - 64.76: 74 64.76 - 80.95: 52 Dihedral angle restraints: 23056 sinusoidal: 9364 harmonic: 13692 Sorted by residual: dihedral pdb=" CA HIS K 140 " pdb=" C HIS K 140 " pdb=" N ALA K 141 " pdb=" CA ALA K 141 " ideal model delta harmonic sigma weight residual -180.00 -144.91 -35.09 0 5.00e+00 4.00e-02 4.93e+01 dihedral pdb=" CA HIS L 140 " pdb=" C HIS L 140 " pdb=" N ALA L 141 " pdb=" CA ALA L 141 " ideal model delta harmonic sigma weight residual 180.00 -144.94 -35.06 0 5.00e+00 4.00e-02 4.92e+01 dihedral pdb=" CA ARG H 178 " pdb=" C ARG H 178 " pdb=" N THR H 179 " pdb=" CA THR H 179 " ideal model delta harmonic sigma weight residual 180.00 -147.96 -32.04 0 5.00e+00 4.00e-02 4.11e+01 ... (remaining 23053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 5522 0.122 - 0.244: 396 0.244 - 0.367: 38 0.367 - 0.489: 0 0.489 - 0.611: 2 Chirality restraints: 5958 Sorted by residual: chirality pdb=" CA ARG O 356 " pdb=" N ARG O 356 " pdb=" C ARG O 356 " pdb=" CB ARG O 356 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.33e+00 chirality pdb=" CA ARG P 356 " pdb=" N ARG P 356 " pdb=" C ARG P 356 " pdb=" CB ARG P 356 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.20e+00 chirality pdb=" CA ASP O 130 " pdb=" N ASP O 130 " pdb=" C ASP O 130 " pdb=" CB ASP O 130 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 ... (remaining 5955 not shown) Planarity restraints: 6490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 303 " -0.052 5.00e-02 4.00e+02 7.79e-02 9.71e+00 pdb=" N PRO I 304 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO I 304 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO I 304 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP J 303 " 0.052 5.00e-02 4.00e+02 7.77e-02 9.65e+00 pdb=" N PRO J 304 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO J 304 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO J 304 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY I 291 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.08e+00 pdb=" N PRO I 292 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO I 292 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO I 292 " -0.039 5.00e-02 4.00e+02 ... (remaining 6487 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 6397 2.78 - 3.31: 35232 3.31 - 3.84: 62030 3.84 - 4.37: 72400 4.37 - 4.90: 116550 Nonbonded interactions: 292609 Sorted by model distance: nonbonded pdb=" O ALA E 264 " pdb=" OG1 THR E 271 " model vdw 2.245 3.040 nonbonded pdb=" O ALA F 264 " pdb=" OG1 THR F 271 " model vdw 2.245 3.040 nonbonded pdb=" O GLY F 269 " pdb=" OH TYR F 349 " model vdw 2.269 3.040 nonbonded pdb=" O GLY E 269 " pdb=" OH TYR E 349 " model vdw 2.270 3.040 nonbonded pdb=" OG SER H 80 " pdb=" O PRO H 110 " model vdw 2.280 3.040 ... (remaining 292604 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' } Set up NCS constraints Number of NCS constrained groups: 8 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'I' selection = chain 'J' } pdb_interpretation.ncs_group { reference = chain 'K' selection = chain 'L' } pdb_interpretation.ncs_group { reference = chain 'M' selection = chain 'N' } pdb_interpretation.ncs_group { reference = chain 'O' selection = chain 'P' } Set refine NCS operators NCS operators will be refined. 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: 1.840 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 28.760 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 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 : 0.006 0.085 37642 Z= 0.371 Angle : 1.172 14.669 50938 Z= 0.678 Chirality : 0.069 0.611 5958 Planarity : 0.007 0.078 6490 Dihedral : 13.627 80.951 14152 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.02 % Favored : 87.55 % Rotamer: Outliers : 2.54 % Allowed : 7.91 % Favored : 89.54 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.32 (0.10), residues: 4610 helix: -3.10 (0.10), residues: 1360 sheet: -2.15 (0.19), residues: 618 loop : -3.01 (0.10), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 157 TYR 0.035 0.003 TYR K 9 PHE 0.040 0.003 PHE I 119 TRP 0.017 0.002 TRP E 366 HIS 0.015 0.002 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00591 (37642) covalent geometry : angle 1.17152 (50938) hydrogen bonds : bond 0.27642 ( 1042) hydrogen bonds : angle 9.61994 ( 2922) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TYR cc_start: 0.8662 (t80) cc_final: 0.8264 (t80) REVERT: A 199 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7673 (mt-10) REVERT: A 221 HIS cc_start: 0.9013 (t-90) cc_final: 0.8548 (t70) REVERT: A 285 THR cc_start: 0.9424 (p) cc_final: 0.8820 (p) REVERT: A 302 MET cc_start: 0.8378 (ptm) cc_final: 0.8043 (mpp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0759 time to fit residues: 4.3116 Evaluate side-chains 26 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.067 Evaluate side-chains 66 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 296 MET cc_start: 0.9131 (tmm) cc_final: 0.8527 (tmm) REVERT: C 300 PHE cc_start: 0.9077 (m-10) cc_final: 0.8280 (m-10) REVERT: C 322 TYR cc_start: 0.8155 (t80) cc_final: 0.7913 (t80) REVERT: C 378 LYS cc_start: 0.9256 (mmmt) cc_final: 0.8911 (tppt) REVERT: C 457 THR cc_start: 0.8701 (p) cc_final: 0.8461 (t) REVERT: C 465 MET cc_start: 0.7205 (mtm) cc_final: 0.6569 (ttt) REVERT: C 472 LEU cc_start: 0.9612 (mt) cc_final: 0.9411 (mm) REVERT: C 504 LEU cc_start: 0.9266 (mp) cc_final: 0.9016 (mt) REVERT: C 523 PHE cc_start: 0.9101 (t80) cc_final: 0.8215 (t80) REVERT: C 528 ASP cc_start: 0.8296 (t0) cc_final: 0.7686 (t0) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0683 time to fit residues: 5.3228 Evaluate side-chains 37 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.088 Evaluate side-chains 50 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: E 65 GLU cc_start: 0.9268 (tp30) cc_final: 0.8875 (tm-30) REVERT: E 69 ASP cc_start: 0.8420 (p0) cc_final: 0.8210 (p0) REVERT: E 84 CYS cc_start: 0.7982 (p) cc_final: 0.7709 (p) REVERT: E 88 ILE cc_start: 0.9507 (pt) cc_final: 0.8953 (tt) REVERT: E 158 ILE cc_start: 0.8598 (mm) cc_final: 0.8161 (mm) REVERT: E 344 GLU cc_start: 0.9073 (mp0) cc_final: 0.8738 (tm-30) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0791 time to fit residues: 4.5246 Evaluate side-chains 19 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.072 Evaluate side-chains 60 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: G 52 LEU cc_start: 0.9592 (mt) cc_final: 0.9362 (mt) REVERT: G 108 MET cc_start: 0.8122 (pmm) cc_final: 0.6943 (ppp) REVERT: G 306 LEU cc_start: 0.9568 (tm) cc_final: 0.9292 (tt) REVERT: G 391 ILE cc_start: 0.9564 (mt) cc_final: 0.9108 (tp) outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 0.0634 time to fit residues: 4.5514 Evaluate side-chains 25 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.111 Evaluate side-chains 37 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 224 THR cc_start: 0.9002 (m) cc_final: 0.8770 (m) REVERT: I 230 GLU cc_start: 0.8653 (tt0) cc_final: 0.7632 (mm-30) REVERT: I 295 MET cc_start: 0.7386 (ttp) cc_final: 0.6918 (ttt) outliers start: 2 outliers final: 0 residues processed: 37 average time/residue: 0.0748 time to fit residues: 3.2015 Evaluate side-chains 16 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.053 Evaluate side-chains 43 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.097 Fit side-chains REVERT: K 45 MET cc_start: 0.8406 (ptm) cc_final: 0.8027 (ppp) REVERT: K 63 ILE cc_start: 0.9156 (tt) cc_final: 0.8955 (tp) REVERT: K 78 LYS cc_start: 0.9423 (tttt) cc_final: 0.9089 (tppt) REVERT: K 171 ASN cc_start: 0.8832 (t0) cc_final: 0.8624 (m-40) REVERT: K 185 ARG cc_start: 0.3409 (OUTLIER) cc_final: 0.3040 (ptt-90) REVERT: K 235 LEU cc_start: -0.4104 (OUTLIER) cc_final: -0.4325 (tp) outliers start: 11 outliers final: 1 residues processed: 43 average time/residue: 0.0794 time to fit residues: 3.8393 Evaluate side-chains 17 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.073 Evaluate side-chains 1 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0146 time to fit residues: 0.0240 Evaluate side-chains 0 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 77 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 39 time to evaluate : 0.105 Fit side-chains REVERT: O 239 MET cc_start: -0.0056 (mtp) cc_final: -0.0811 (mmt) REVERT: O 307 ARG cc_start: -0.2756 (OUTLIER) cc_final: -0.3398 (mtt90) REVERT: O 512 ILE cc_start: 0.1506 (OUTLIER) cc_final: 0.1296 (mm) outliers start: 38 outliers final: 5 residues processed: 75 average time/residue: 0.0630 time to fit residues: 5.6617 Evaluate side-chains 24 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 17 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 432 optimal weight: 0.4980 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.0370 chunk 401 optimal weight: 1.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 HIS C 301 GLN C 342 ASN ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN ** E 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 HIS H 85 GLN H 96 ASN H 324 HIS H 376 ASN H 423 ASN Total number of N/Q/H flips: 6 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 131 HIS I 186 GLN I 244 GLN I 258 HIS Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 98 GLN O 221 ASN O 422 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.048775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.041072 restraints weight = 15667.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.042386 restraints weight = 10071.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.043328 restraints weight = 7088.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.044029 restraints weight = 5304.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.044604 restraints weight = 4191.180| |-----------------------------------------------------------------------------| r_work (final): 0.2915 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.051046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.042241 restraints weight = 16983.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.043465 restraints weight = 11095.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.044296 restraints weight = 8014.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.045032 restraints weight = 6254.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.045551 restraints weight = 5068.920| |-----------------------------------------------------------------------------| r_work (final): 0.2965 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.049498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.039597 restraints weight = 19005.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.040700 restraints weight = 12480.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.041535 restraints weight = 9127.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.042078 restraints weight = 7174.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.042547 restraints weight = 6024.195| |-----------------------------------------------------------------------------| r_work (final): 0.2883 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.043108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.036593 restraints weight = 24812.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.037796 restraints weight = 15264.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.038689 restraints weight = 10462.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.039379 restraints weight = 7660.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.039853 restraints weight = 5901.009| |-----------------------------------------------------------------------------| r_work (final): 0.2936 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.068120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.059420 restraints weight = 19500.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.060469 restraints weight = 14597.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.061132 restraints weight = 11721.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.061712 restraints weight = 10027.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.061969 restraints weight = 8791.214| |-----------------------------------------------------------------------------| r_work (final): 0.3619 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.088943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.060748 restraints weight = 21029.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.061782 restraints weight = 13650.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.062647 restraints weight = 9402.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.063124 restraints weight = 7014.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.063535 restraints weight = 5484.185| |-----------------------------------------------------------------------------| r_work (final): 0.3594 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.100787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.097916 restraints weight = 1764.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.098522 restraints weight = 1275.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.098979 restraints weight = 953.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.099318 restraints weight = 708.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.099585 restraints weight = 535.918| |-----------------------------------------------------------------------------| r_work (final): 0.3854 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.078530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.075877 restraints weight = 50209.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.076310 restraints weight = 37918.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.076566 restraints weight = 30384.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.076782 restraints weight = 25732.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.076968 restraints weight = 22302.798| |-----------------------------------------------------------------------------| r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 37642 Z= 0.150 Angle : 0.761 10.112 50938 Z= 0.401 Chirality : 0.049 0.341 5958 Planarity : 0.006 0.102 6490 Dihedral : 7.018 61.340 5022 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.28 % Favored : 90.63 % Rotamer: Outliers : 0.29 % Allowed : 4.94 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.63 (0.11), residues: 4610 helix: -2.24 (0.12), residues: 1406 sheet: -1.95 (0.19), residues: 722 loop : -2.69 (0.11), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 31 TYR 0.030 0.002 TYR K 82 PHE 0.019 0.002 PHE G 145 TRP 0.038 0.002 TRP K 132 HIS 0.006 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00327 (37642) covalent geometry : angle 0.76099 (50938) hydrogen bonds : bond 0.05301 ( 1042) hydrogen bonds : angle 6.38470 ( 2922) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8564 Ramachandran restraints generated. 4282 Oldfield, 0 Emsley, 4282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 GLN cc_start: 0.9172 (pm20) cc_final: 0.8805 (pp30) REVERT: B 153 VAL cc_start: 0.8596 (t) cc_final: 0.8355 (p) REVERT: B 166 TYR cc_start: 0.8962 (t80) cc_final: 0.8596 (t80) REVERT: B 199 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7743 (mt-10) REVERT: B 208 ILE cc_start: 0.9085 (mt) cc_final: 0.8440 (pt) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0360 time to fit residues: 1.7973 Evaluate side-chains 28 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.056 Evaluate side-chains 49 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 296 MET cc_start: 0.8775 (tmm) cc_final: 0.8207 (tmm) REVERT: C 300 PHE cc_start: 0.9067 (m-10) cc_final: 0.8730 (m-10) REVERT: C 439 LYS cc_start: 0.9163 (mtpp) cc_final: 0.8751 (tptt) REVERT: C 465 MET cc_start: 0.7555 (mtm) cc_final: 0.6774 (ttt) REVERT: C 523 PHE cc_start: 0.9156 (t80) cc_final: 0.8294 (t80) REVERT: C 528 ASP cc_start: 0.8145 (t0) cc_final: 0.7880 (t0) outliers start: 2 outliers final: 0 residues processed: 49 average time/residue: 0.0724 time to fit residues: 4.1280 Evaluate side-chains 32 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.075 Evaluate side-chains 26 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: E 63 LEU cc_start: 0.9675 (tp) cc_final: 0.9307 (pp) REVERT: E 65 GLU cc_start: 0.9309 (tp30) cc_final: 0.8995 (tm-30) REVERT: E 104 MET cc_start: 0.8675 (mmp) cc_final: 0.8332 (tpp) REVERT: E 315 PHE cc_start: 0.8442 (m-10) cc_final: 0.8019 (p90) REVERT: E 344 GLU cc_start: 0.9219 (mp0) cc_final: 0.8854 (tm-30) outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.0284 time to fit residues: 1.0925 Evaluate side-chains 17 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.123 Evaluate side-chains 39 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: H 52 LEU cc_start: 0.9580 (mt) cc_final: 0.9315 (mt) REVERT: H 108 MET cc_start: 0.8255 (pmm) cc_final: 0.6956 (ppp) REVERT: H 155 MET cc_start: 0.8464 (ptm) cc_final: 0.8227 (ppp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0493 time to fit residues: 2.5563 Evaluate side-chains 22 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.105 Evaluate side-chains 22 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 221 GLN cc_start: 0.7851 (mp10) cc_final: 0.7196 (mp10) REVERT: I 230 GLU cc_start: 0.8861 (tt0) cc_final: 0.7838 (mm-30) REVERT: I 295 MET cc_start: 0.7291 (ttp) cc_final: 0.6717 (ttt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0719 time to fit residues: 1.8896 Evaluate side-chains 15 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.092 Evaluate side-chains 24 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.084 Fit side-chains REVERT: L 54 ARG cc_start: 0.8919 (mtm180) cc_final: 0.8682 (ptm-80) outliers start: 2 outliers final: 0 residues processed: 23 average time/residue: 0.1139 time to fit residues: 2.8719 Evaluate side-chains 9 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.052 Evaluate side-chains 3 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.1561 time to fit residues: 0.4811 Evaluate side-chains 0 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 22 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 239 MET cc_start: 0.0073 (mtp) cc_final: -0.0902 (mmt) outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.1012 time to fit residues: 2.6396 Evaluate side-chains 15 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.6926 > 50: distance: 0 - 26: 49.328 distance: 1 - 2: 5.114 distance: 2 - 4: 11.332 distance: 5 - 6: 9.854 distance: 6 - 7: 23.300 distance: 6 - 9: 48.185 distance: 7 - 8: 13.036 distance: 7 - 13: 23.571 distance: 8 - 38: 54.888 distance: 9 - 10: 29.019 distance: 10 - 11: 6.594 distance: 10 - 12: 18.221 distance: 13 - 14: 29.650 distance: 14 - 15: 7.949 distance: 14 - 17: 54.181 distance: 15 - 16: 59.786 distance: 15 - 20: 23.293 distance: 17 - 18: 9.530 distance: 17 - 19: 41.209 distance: 21 - 22: 40.320 distance: 22 - 23: 15.708 distance: 22 - 26: 46.294 distance: 23 - 52: 32.456 distance: 26 - 27: 41.575 distance: 27 - 28: 39.847 distance: 27 - 30: 40.060 distance: 28 - 29: 26.107 distance: 28 - 38: 24.611 distance: 31 - 32: 51.585 distance: 31 - 33: 32.268 distance: 32 - 34: 52.878 distance: 33 - 35: 17.802 distance: 34 - 36: 13.564 distance: 35 - 36: 16.683 distance: 36 - 37: 44.343 distance: 39 - 40: 39.505 distance: 39 - 42: 57.493 distance: 40 - 41: 39.114 distance: 40 - 46: 40.989 distance: 42 - 43: 46.860 distance: 43 - 44: 45.192 distance: 43 - 45: 22.898 distance: 46 - 47: 12.401 distance: 47 - 48: 52.623 distance: 47 - 50: 22.908 distance: 48 - 49: 25.711 distance: 48 - 52: 49.771 distance: 50 - 51: 27.454 distance: 52 - 53: 15.262 distance: 53 - 54: 66.986 distance: 53 - 56: 57.616 distance: 54 - 55: 21.735 distance: 54 - 62: 40.739 distance: 56 - 57: 29.277 distance: 57 - 58: 63.432 distance: 57 - 59: 47.298 distance: 59 - 61: 25.493 distance: 63 - 64: 39.036 distance: 63 - 66: 67.238 distance: 64 - 65: 35.873 distance: 66 - 67: 47.924 distance: 67 - 68: 49.984 distance: 68 - 69: 45.289 distance: 68 - 70: 8.789