Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 12:34:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i7t_4428/05_2023/6i7t_4428.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i7t_4428/05_2023/6i7t_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i7t_4428/05_2023/6i7t_4428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i7t_4428/05_2023/6i7t_4428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i7t_4428/05_2023/6i7t_4428.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i7t_4428/05_2023/6i7t_4428.pdb" } 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 ------------------------------------------------------------------------------- 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 Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 499": "NH1" <-> "NH2" Residue "D ARG 498": "NH1" <-> "NH2" Residue "D ARG 499": "NH1" <-> "NH2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "E ARG 324": "NH1" <-> "NH2" Residue "G ARG 26": "NH1" <-> "NH2" Residue "G ARG 206": "NH1" <-> "NH2" Residue "G ARG 234": "NH1" <-> "NH2" Residue "G ARG 428": "NH1" <-> "NH2" Residue "I ARG 190": "NH1" <-> "NH2" Residue "I ARG 245": "NH1" <-> "NH2" Residue "J ARG 190": "NH1" <-> "NH2" Residue "J ARG 245": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "F ARG 56": "NH1" <-> "NH2" Residue "F ARG 324": "NH1" <-> "NH2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "H ARG 206": "NH1" <-> "NH2" Residue "H ARG 234": "NH1" <-> "NH2" Residue "H ARG 428": "NH1" <-> "NH2" Residue "K ARG 53": "NH1" <-> "NH2" Residue "K TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 209": "OE1" <-> "OE2" Residue "O GLU 231": "OE1" <-> "OE2" Residue "O GLU 383": "OE1" <-> "OE2" Residue "O GLU 494": "OE1" <-> "OE2" Residue "O GLU 506": "OE1" <-> "OE2" Residue "L ARG 53": "NH1" <-> "NH2" Residue "L TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 209": "OE1" <-> "OE2" Residue "P GLU 231": "OE1" <-> "OE2" Residue "P GLU 383": "OE1" <-> "OE2" Residue "P GLU 494": "OE1" <-> "OE2" Residue "P GLU 506": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/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: 18.54, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 14.38 Conformation dependent library (CDL) restraints added in 5.4 seconds 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: 1.85 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: 12.09 Time building geometry restraints manager: 15.64 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: 99.37 - 106.34: 968 106.34 - 113.30: 20386 113.30 - 120.27: 14033 120.27 - 127.23: 15233 127.23 - 134.20: 318 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 2.440 nonbonded pdb=" O ALA F 264 " pdb=" OG1 THR F 271 " model vdw 2.245 2.440 nonbonded pdb=" O GLY F 269 " pdb=" OH TYR F 349 " model vdw 2.269 2.440 nonbonded pdb=" O GLY E 269 " pdb=" OH TYR E 349 " model vdw 2.270 2.440 nonbonded pdb=" OG SER H 80 " pdb=" O PRO H 110 " model vdw 2.280 2.440 ... (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 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: 1.880 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: 0.030 Extract box with map and model: 10.630 Check model and map are aligned: 0.530 Set scattering table: 0.340 Process input model: 86.740 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.320 ------------------------------------------------------------------------------- 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= 0.389 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 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.32 (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 *********************** 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 fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2208 time to fit residues: 12.5325 Evaluate side-chains 24 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3965 Evaluate side-chains 66 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1612 time to fit residues: 12.5810 Evaluate side-chains 31 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.305 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4498 Evaluate side-chains 50 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.335 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2137 time to fit residues: 12.3545 Evaluate side-chains 16 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.338 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4638 Evaluate side-chains 60 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.393 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 0.1908 time to fit residues: 13.6444 Evaluate side-chains 23 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.399 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5303 Evaluate side-chains 37 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 37 average time/residue: 0.1803 time to fit residues: 7.7390 Evaluate side-chains 16 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.283 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3607 Evaluate side-chains 43 residues out of total 224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 0.243 Fit side-chains outliers start: 11 outliers final: 1 residues processed: 43 average time/residue: 0.1837 time to fit residues: 8.9746 Evaluate side-chains 13 residues out of total 224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.225 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0236 time to fit residues: 0.3554 Evaluate side-chains 1 residues out of total 16 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 0 time to evaluate : 0.019 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0619 time to fit residues: 0.0944 Evaluate side-chains 0 residues out of total 16 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0250 Evaluate side-chains 77 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 39 time to evaluate : 0.364 Fit side-chains outliers start: 38 outliers final: 5 residues processed: 75 average time/residue: 0.1684 time to fit residues: 15.0325 Evaluate side-chains 22 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 17 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0328 time to fit residues: 0.7892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 388 optimal weight: 20.0000 chunk 348 optimal weight: 0.0980 chunk 193 optimal weight: 4.9990 chunk 119 optimal weight: 0.2980 chunk 235 optimal weight: 4.9990 chunk 186 optimal weight: 0.0170 chunk 360 optimal weight: 0.0970 chunk 139 optimal weight: 0.0010 chunk 219 optimal weight: 0.6980 chunk 268 optimal weight: 1.9990 chunk 417 optimal weight: 2.9990 overall best weight: 0.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN B 97 ASN 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: C 271 HIS C 301 GLN C 342 ASN 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 E 319 GLN 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: 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 I 293 GLN Total number of N/Q/H flips: 5 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 248 GLN O 422 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5978 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 37642 Z= 0.221 Angle : 0.757 10.873 50938 Z= 0.396 Chirality : 0.049 0.204 5958 Planarity : 0.006 0.087 6490 Dihedral : 7.063 61.709 5022 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.59 % Favored : 90.28 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.11), residues: 4610 helix: -2.28 (0.12), residues: 1400 sheet: -1.90 (0.19), residues: 712 loop : -2.74 (0.11), residues: 2498 *********************** 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 37 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.307 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1332 time to fit residues: 6.1672 Evaluate side-chains 21 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.272 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3944 Evaluate side-chains 48 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 47 average time/residue: 0.2142 time to fit residues: 11.6562 Evaluate side-chains 28 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4147 Evaluate side-chains 22 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.337 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.0981 time to fit residues: 3.1774 Evaluate side-chains 13 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.314 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4689 Evaluate side-chains 42 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.389 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.1769 time to fit residues: 9.1721 Evaluate side-chains 23 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5469 Evaluate side-chains 23 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1629 time to fit residues: 4.5768 Evaluate side-chains 16 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.265 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3616 Evaluate side-chains 24 residues out of total 224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 23 average time/residue: 0.2860 time to fit residues: 7.3342 Evaluate side-chains 12 residues out of total 224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.242 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3413 Evaluate side-chains 3 residues out of total 16 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.017 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.3305 time to fit residues: 1.0264 Evaluate side-chains 0 residues out of total 16 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0264 Evaluate side-chains 22 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.374 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 22 average time/residue: 0.2039 time to fit residues: 5.6206 Evaluate side-chains 12 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0355 time to fit residues: 0.5577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 771, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.7104 > 50: distance: 1 - 2: 5.132 distance: 3 - 4: 28.407 distance: 4 - 5: 31.237 distance: 4 - 7: 13.546 distance: 5 - 6: 12.473 distance: 5 - 14: 36.357 distance: 7 - 8: 27.866 distance: 8 - 9: 25.089 distance: 8 - 10: 20.363 distance: 9 - 11: 24.367 distance: 10 - 12: 33.091 distance: 11 - 13: 18.538 distance: 12 - 13: 28.805 distance: 14 - 15: 44.359 distance: 15 - 16: 42.331 distance: 15 - 18: 32.004 distance: 16 - 17: 24.130 distance: 16 - 22: 40.119 distance: 18 - 19: 20.520 distance: 19 - 20: 18.178 distance: 19 - 21: 19.707 distance: 22 - 23: 39.621 distance: 23 - 24: 27.663 distance: 23 - 26: 15.987 distance: 24 - 25: 5.610 distance: 24 - 30: 25.021 distance: 26 - 27: 18.331 distance: 27 - 28: 4.058 distance: 27 - 29: 23.779 distance: 30 - 31: 21.320 distance: 31 - 32: 47.881 distance: 31 - 34: 30.228 distance: 32 - 33: 35.009 distance: 32 - 36: 33.763 distance: 34 - 35: 22.909 distance: 36 - 37: 22.053 distance: 37 - 38: 20.503 distance: 37 - 40: 21.799 distance: 38 - 39: 33.425 distance: 38 - 42: 16.842 distance: 40 - 41: 14.018 distance: 42 - 43: 37.538 distance: 43 - 44: 18.277 distance: 43 - 46: 37.829 distance: 44 - 45: 11.940 distance: 44 - 50: 29.411 distance: 46 - 47: 21.606 distance: 47 - 48: 8.566 distance: 47 - 49: 13.447 distance: 50 - 51: 34.936 distance: 51 - 52: 26.080 distance: 51 - 54: 10.594 distance: 52 - 53: 13.394 distance: 52 - 58: 30.219 distance: 54 - 55: 25.236 distance: 54 - 56: 15.295 distance: 55 - 57: 10.160 distance: 58 - 59: 32.914 distance: 59 - 60: 29.200 distance: 59 - 62: 30.415 distance: 60 - 61: 21.323 distance: 60 - 64: 36.045 distance: 62 - 63: 23.522 distance: 64 - 65: 41.021 distance: 65 - 66: 31.124 distance: 65 - 68: 17.941 distance: 66 - 67: 23.142 distance: 66 - 70: 25.329 distance: 68 - 69: 49.343 distance: 70 - 71: 9.540 distance: 71 - 72: 8.740 distance: 71 - 74: 17.528 distance: 72 - 73: 11.810 distance: 72 - 77: 6.780 distance: 74 - 75: 13.108 distance: 74 - 76: 11.884 distance: 77 - 78: 9.163 distance: 79 - 80: 6.153