Starting phenix.real_space_refine on Sat Mar 23 12:30:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i7t_4428/03_2024/6i7t_4428.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i7t_4428/03_2024/6i7t_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_4428/03_2024/6i7t_4428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i7t_4428/03_2024/6i7t_4428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i7t_4428/03_2024/6i7t_4428.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i7t_4428/03_2024/6i7t_4428.pdb" } resolution = 4.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 18.98, per 1000 atoms: 0.51 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: 13.34 Conformation dependent library (CDL) restraints added in 6.6 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: 3.65 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: 11.98 Time building geometry restraints manager: 14.47 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 9.010 Check model and map are aligned: 0.540 Set scattering table: 0.370 Process input model: 89.790 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.240 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.510 ------------------------------------------------------------------------------- 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 % 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 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 366 HIS 0.015 0.002 HIS B 234 PHE 0.040 0.003 PHE I 119 TYR 0.035 0.003 TYR K 9 ARG 0.008 0.001 ARG B 157 *********************** 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 : 0.299 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: 0.8547 (t70) REVERT: A 285 THR cc_start: 0.9424 (p) cc_final: 0.8819 (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: 0.2107 time to fit residues: 11.9104 Evaluate side-chains 26 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.227 Evaluate side-chains 66 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.258 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: 0.8462 (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: 0.7695 (t0) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1466 time to fit residues: 11.4239 Evaluate side-chains 37 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.309 Evaluate side-chains 50 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.333 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: 0.8211 (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: 0.1998 time to fit residues: 11.5700 Evaluate side-chains 19 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.331 Evaluate side-chains 60 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: G 52 LEU cc_start: 0.9592 (mt) cc_final: 0.9360 (mt) REVERT: G 108 MET cc_start: 0.8122 (pmm) cc_final: 0.6946 (ppp) REVERT: G 306 LEU cc_start: 0.9568 (tm) cc_final: 0.9290 (tt) outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 0.1884 time to fit residues: 13.4879 Evaluate side-chains 24 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.383 Evaluate side-chains 37 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.261 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: 0.7631 (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: 0.1796 time to fit residues: 7.7144 Evaluate side-chains 16 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.258 Evaluate side-chains 43 residues out of total 224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 0.232 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: 0.8956 (tp) REVERT: K 78 LYS cc_start: 0.9423 (tttt) cc_final: 0.9089 (tppt) 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: 0.1836 time to fit residues: 8.9657 Evaluate side-chains 17 residues out of total 224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 14 time to evaluate : 0.218 Evaluate side-chains 1 residues out of total 16 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 0 time to evaluate : 0.015 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0548 time to fit residues: 0.0831 Evaluate side-chains 0 residues out of total 16 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.021 Evaluate side-chains 77 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 39 time to evaluate : 0.367 Fit side-chains REVERT: O 239 MET cc_start: -0.0056 (mtp) cc_final: -0.0804 (mmt) REVERT: O 307 ARG cc_start: -0.2756 (OUTLIER) cc_final: -0.3411 (mtt90) REVERT: O 512 ILE cc_start: 0.1506 (OUTLIER) cc_final: 0.1206 (mm) outliers start: 38 outliers final: 5 residues processed: 75 average time/residue: 0.1687 time to fit residues: 15.0645 Evaluate side-chains 24 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 17 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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: 20.0000 chunk 139 optimal weight: 0.0010 chunk 219 optimal weight: 0.6980 chunk 268 optimal weight: 1.9990 chunk 417 optimal weight: 6.9990 overall best weight: 0.2224 ------------------------------------------------------------------------------- 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 422 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37642 Z= 0.213 Angle : 0.748 10.611 50938 Z= 0.392 Chirality : 0.049 0.306 5958 Planarity : 0.006 0.078 6490 Dihedral : 7.032 61.672 5022 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.37 % Favored : 90.50 % Rotamer: Outliers : 0.34 % Allowed : 4.70 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.66 (0.11), residues: 4610 helix: -2.26 (0.12), residues: 1406 sheet: -1.90 (0.19), residues: 710 loop : -2.74 (0.11), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP K 132 HIS 0.006 0.001 HIS O 422 PHE 0.019 0.002 PHE H 145 TYR 0.045 0.002 TYR K 82 ARG 0.012 0.001 ARG F 31 *********************** 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 38 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 99 GLN cc_start: 0.8956 (pm20) cc_final: 0.8575 (pp30) REVERT: B 166 TYR cc_start: 0.8765 (t80) cc_final: 0.8494 (t80) REVERT: B 199 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7461 (mt-10) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1217 time to fit residues: 5.8628 Evaluate side-chains 24 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.269 Evaluate side-chains 49 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 296 MET cc_start: 0.8827 (tmm) cc_final: 0.8269 (tmm) REVERT: C 300 PHE cc_start: 0.9017 (m-10) cc_final: 0.8689 (m-10) REVERT: C 439 LYS cc_start: 0.9074 (mtpp) cc_final: 0.8729 (tptt) REVERT: C 465 MET cc_start: 0.7251 (mtm) cc_final: 0.6579 (ttt) REVERT: C 523 PHE cc_start: 0.9091 (t80) cc_final: 0.8313 (t80) REVERT: C 528 ASP cc_start: 0.8041 (t0) cc_final: 0.7815 (t0) outliers start: 2 outliers final: 0 residues processed: 49 average time/residue: 0.2174 time to fit residues: 12.2956 Evaluate side-chains 31 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.379 Evaluate side-chains 24 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: E 63 LEU cc_start: 0.9596 (tp) cc_final: 0.9309 (pp) REVERT: E 65 GLU cc_start: 0.9237 (tp30) cc_final: 0.9022 (tm-30) REVERT: E 104 MET cc_start: 0.8495 (mmp) cc_final: 0.8132 (tpp) REVERT: E 344 GLU cc_start: 0.9054 (mp0) cc_final: 0.8711 (tm-30) outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.1112 time to fit residues: 3.7864 Evaluate side-chains 15 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.373 Evaluate side-chains 42 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: H 52 LEU cc_start: 0.9509 (mt) cc_final: 0.9240 (mt) REVERT: H 108 MET cc_start: 0.8252 (pmm) cc_final: 0.7064 (ppp) outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.1892 time to fit residues: 9.8087 Evaluate side-chains 21 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.405 Evaluate side-chains 23 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 224 THR cc_start: 0.9036 (m) cc_final: 0.8652 (m) REVERT: I 230 GLU cc_start: 0.8850 (tt0) cc_final: 0.7813 (mm-30) REVERT: I 295 MET cc_start: 0.7180 (ttp) cc_final: 0.6613 (ttt) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1632 time to fit residues: 4.6364 Evaluate side-chains 16 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.274 Evaluate side-chains 24 residues out of total 224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 57 ARG cc_start: 0.8557 (mmt180) cc_final: 0.8292 (mmm160) outliers start: 2 outliers final: 0 residues processed: 23 average time/residue: 0.2683 time to fit residues: 6.9470 Evaluate side-chains 13 residues out of total 224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.191 Evaluate side-chains 3 residues out of total 16 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.015 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.2912 time to fit residues: 0.9026 Evaluate side-chains 0 residues out of total 16 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.024 Evaluate side-chains 22 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: O 239 MET cc_start: -0.0038 (mtp) cc_final: -0.0858 (mmt) REVERT: O 310 MET cc_start: 0.2884 (ttt) cc_final: 0.2639 (ttt) outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.2396 time to fit residues: 6.4443 Evaluate side-chains 12 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 232 optimal weight: 20.0000 chunk 129 optimal weight: 0.7980 chunk 347 optimal weight: 0.0060 chunk 284 optimal weight: 0.0870 chunk 115 optimal weight: 0.9990 chunk 418 optimal weight: 50.0000 chunk 452 optimal weight: 0.0670 chunk 372 optimal weight: 0.5980 chunk 414 optimal weight: 0.4980 chunk 142 optimal weight: 0.9980 chunk 335 optimal weight: 1.9990 overall best weight: 0.2512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 HIS ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: D 393 GLN D 416 ASN Total number of N/Q/H flips: 2 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: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 324 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: ** I 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 293 GLN Total number of N/Q/H flips: 1 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.272 37642 Z= 0.602 Angle : 1.259 32.978 50938 Z= 0.643 Chirality : 0.066 0.739 5958 Planarity : 0.014 0.441 6490 Dihedral : 7.303 67.266 5022 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.85 % Favored : 88.85 % Rotamer: Outliers : 0.48 % Allowed : 3.65 % Favored : 95.88 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.81 (0.11), residues: 4610 helix: -2.37 (0.12), residues: 1404 sheet: -1.94 (0.19), residues: 712 loop : -2.86 (0.11), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.004 TRP A 87 HIS 0.046 0.004 HIS A 221 PHE 0.139 0.005 PHE B 4 TYR 0.148 0.005 TYR A 228 ARG 0.141 0.003 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 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: 5 poor density : 32 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.8402 (pt) cc_final: 0.7884 (tt) REVERT: A 166 TYR cc_start: 0.8905 (t80) cc_final: 0.8614 (t80) REVERT: A 199 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7560 (mt-10) REVERT: A 208 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8911 (mm) outliers start: 5 outliers final: 2 residues processed: 33 average time/residue: 0.1010 time to fit residues: 4.5156 Evaluate side-chains 25 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.361 Evaluate side-chains 47 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 253 ASN cc_start: 0.8378 (t0) cc_final: 0.8173 (m-40) REVERT: D 296 MET cc_start: 0.8702 (tmm) cc_final: 0.8172 (tmm) REVERT: D 439 LYS cc_start: 0.9114 (mtpp) cc_final: 0.8721 (tptt) REVERT: D 465 MET cc_start: 0.7126 (mtm) cc_final: 0.6410 (ttt) REVERT: D 523 PHE cc_start: 0.9102 (t80) cc_final: 0.8530 (t80) outliers start: 2 outliers final: 2 residues processed: 46 average time/residue: 0.1467 time to fit residues: 8.3535 Evaluate side-chains 32 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.359 Evaluate side-chains 24 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: E 65 GLU cc_start: 0.9251 (tp30) cc_final: 0.9018 (tm-30) REVERT: E 104 MET cc_start: 0.8502 (mmp) cc_final: 0.8136 (tpp) REVERT: E 344 GLU cc_start: 0.9051 (mp0) cc_final: 0.8752 (tm-30) outliers start: 2 outliers final: 0 residues processed: 24 average time/residue: 0.1072 time to fit residues: 3.6829 Evaluate side-chains 15 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.334 Evaluate side-chains 34 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: H 52 LEU cc_start: 0.9526 (mt) cc_final: 0.9254 (mt) REVERT: H 108 MET cc_start: 0.8247 (pmm) cc_final: 0.7061 (ppp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1210 time to fit residues: 5.7155 Evaluate side-chains 21 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.401 Evaluate side-chains 20 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 230 GLU cc_start: 0.8848 (tt0) cc_final: 0.7813 (mm-30) REVERT: I 295 MET cc_start: 0.7162 (ttp) cc_final: 0.6580 (ttt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1775 time to fit residues: 4.3080 Evaluate side-chains 15 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.269 Evaluate side-chains 15 residues out of total 224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 57 ARG cc_start: 0.8533 (mmt180) cc_final: 0.8289 (mmm160) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.2468 time to fit residues: 4.3178 Evaluate side-chains 11 residues out of total 224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.261 Evaluate side-chains 0 residues out of total 16 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0276 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 Evaluate side-chains 17 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: O 239 MET cc_start: 0.0278 (mtp) cc_final: -0.0624 (mmt) REVERT: O 310 MET cc_start: 0.2879 (ttt) cc_final: 0.2611 (ttt) REVERT: O 482 MET cc_start: -0.1301 (pmm) cc_final: -0.1774 (pmm) outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 0.1982 time to fit residues: 4.3611 Evaluate side-chains 11 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 413 optimal weight: 8.9990 chunk 314 optimal weight: 0.4980 chunk 217 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 199 optimal weight: 2.9990 chunk 281 optimal weight: 0.7980 chunk 419 optimal weight: 0.8980 chunk 444 optimal weight: 20.0000 chunk 219 optimal weight: 0.0470 chunk 398 optimal weight: 1.9990 chunk 119 optimal weight: 40.0000 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 HIS Total number of N/Q/H flips: 1 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: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 293 GLN Total number of N/Q/H flips: 1 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5994 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.272 37642 Z= 0.605 Angle : 1.259 32.978 50938 Z= 0.644 Chirality : 0.066 0.739 5958 Planarity : 0.014 0.441 6490 Dihedral : 7.303 67.266 5022 Min Nonbonded Distance : 1.372 Molprobity Statistics. All-atom Clashscore : 27.85 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.85 % Favored : 88.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.81 (0.11), residues: 4610 helix: -2.37 (0.12), residues: 1404 sheet: -1.94 (0.19), residues: 712 loop : -2.86 (0.11), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.004 TRP A 87 HIS 0.046 0.004 HIS A 221 PHE 0.139 0.005 PHE A 4 TYR 0.148 0.005 TYR B 228 ARG 0.141 0.003 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TYR cc_start: 0.8889 (t80) cc_final: 0.8636 (t80) REVERT: A 199 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7550 (mt-10) REVERT: A 249 MET cc_start: 0.8429 (mpp) cc_final: 0.7507 (mmp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0952 time to fit residues: 3.8750 Evaluate side-chains 23 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.306 Evaluate side-chains 35 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 465 MET cc_start: 0.7225 (mtm) cc_final: 0.6531 (ttt) REVERT: C 523 PHE cc_start: 0.9078 (t80) cc_final: 0.8309 (t80) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1561 time to fit residues: 6.7565 Evaluate side-chains 22 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.357 Evaluate side-chains 24 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 104 MET cc_start: 0.8517 (mmp) cc_final: 0.8165 (tpp) REVERT: F 344 GLU cc_start: 0.9017 (mp0) cc_final: 0.8761 (tm-30) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1052 time to fit residues: 3.6293 Evaluate side-chains 15 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.332 Evaluate side-chains 29 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: H 52 LEU cc_start: 0.9523 (mt) cc_final: 0.9253 (mt) REVERT: H 108 MET cc_start: 0.8241 (pmm) cc_final: 0.7066 (ppp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1161 time to fit residues: 4.7331 Evaluate side-chains 20 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.362 Evaluate side-chains 18 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 230 GLU cc_start: 0.8852 (tt0) cc_final: 0.7811 (mm-30) REVERT: I 295 MET cc_start: 0.7160 (ttp) cc_final: 0.6579 (ttt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1781 time to fit residues: 3.9319 Evaluate side-chains 14 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.242 Evaluate side-chains 15 residues out of total 224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 45 MET cc_start: 0.7312 (ppp) cc_final: 0.7082 (ppp) REVERT: L 57 ARG cc_start: 0.8533 (mmt180) cc_final: 0.8289 (mmm160) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.2437 time to fit residues: 4.2780 Evaluate side-chains 11 residues out of total 224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.247 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 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0301 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 Evaluate side-chains 15 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: O 239 MET cc_start: 0.0299 (mtp) cc_final: -0.0619 (mmt) REVERT: O 310 MET cc_start: 0.2882 (ttt) cc_final: 0.2664 (ttt) REVERT: O 482 MET cc_start: -0.1248 (pmm) cc_final: -0.1887 (pmm) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1632 time to fit residues: 3.4117 Evaluate side-chains 11 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 370 optimal weight: 0.0270 chunk 252 optimal weight: 0.0370 chunk 6 optimal weight: 0.2980 chunk 331 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 379 optimal weight: 0.0970 chunk 307 optimal weight: 40.0000 chunk 0 optimal weight: 0.6980 chunk 227 optimal weight: 20.0000 chunk 399 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 overall best weight: 0.2314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 293 GLN Total number of N/Q/H flips: 1 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.271 37642 Z= 0.603 Angle : 1.257 32.940 50938 Z= 0.643 Chirality : 0.065 0.739 5958 Planarity : 0.014 0.441 6490 Dihedral : 7.303 67.315 5022 Min Nonbonded Distance : 1.379 Molprobity Statistics. All-atom Clashscore : 28.65 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.85 % Favored : 88.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.81 (0.11), residues: 4610 helix: -2.37 (0.12), residues: 1404 sheet: -1.94 (0.19), residues: 712 loop : -2.86 (0.11), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.004 TRP B 87 HIS 0.046 0.004 HIS A 221 PHE 0.139 0.005 PHE A 4 TYR 0.148 0.005 TYR B 228 ARG 0.139 0.003 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TYR cc_start: 0.8897 (t80) cc_final: 0.8662 (t80) REVERT: A 199 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7539 (mt-10) REVERT: A 249 MET cc_start: 0.8426 (mpp) cc_final: 0.7505 (mmp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1001 time to fit residues: 3.8012 Evaluate side-chains 22 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.301 Evaluate side-chains 30 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 465 MET cc_start: 0.7200 (mtm) cc_final: 0.6531 (ttt) REVERT: C 523 PHE cc_start: 0.9078 (t80) cc_final: 0.8309 (t80) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1332 time to fit residues: 5.2075 Evaluate side-chains 22 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.323 Evaluate side-chains 20 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 104 MET cc_start: 0.8513 (mmp) cc_final: 0.8163 (tpp) REVERT: F 344 GLU cc_start: 0.9017 (mp0) cc_final: 0.8760 (tm-30) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1035 time to fit residues: 3.0700 Evaluate side-chains 15 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.348 Evaluate side-chains 29 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: H 52 LEU cc_start: 0.9523 (mt) cc_final: 0.9253 (mt) REVERT: H 108 MET cc_start: 0.8247 (pmm) cc_final: 0.7067 (ppp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1220 time to fit residues: 5.0058 Evaluate side-chains 20 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.403 Evaluate side-chains 18 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 230 GLU cc_start: 0.8852 (tt0) cc_final: 0.7811 (mm-30) REVERT: I 295 MET cc_start: 0.7160 (ttp) cc_final: 0.6579 (ttt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1945 time to fit residues: 4.2817 Evaluate side-chains 14 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.264 Evaluate side-chains 15 residues out of total 224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 45 MET cc_start: 0.7312 (ppp) cc_final: 0.7083 (ppp) REVERT: L 57 ARG cc_start: 0.8533 (mmt180) cc_final: 0.8289 (mmm160) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.2530 time to fit residues: 4.4423 Evaluate side-chains 11 residues out of total 224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.258 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 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0307 Evaluate side-chains 0 residues out of total 16 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.017 Evaluate side-chains 15 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: O 239 MET cc_start: 0.0281 (mtp) cc_final: -0.0621 (mmt) REVERT: O 310 MET cc_start: 0.2883 (ttt) cc_final: 0.2664 (ttt) REVERT: O 482 MET cc_start: -0.1239 (pmm) cc_final: -0.1885 (pmm) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1574 time to fit residues: 3.3316 Evaluate side-chains 11 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 149 optimal weight: 0.3980 chunk 400 optimal weight: 9.9990 chunk 87 optimal weight: 0.0000 chunk 261 optimal weight: 7.9990 chunk 109 optimal weight: 40.0000 chunk 445 optimal weight: 0.0040 chunk 369 optimal weight: 20.0000 chunk 206 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 147 optimal weight: 0.9980 chunk 233 optimal weight: 20.0000 overall best weight: 1.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 293 GLN Total number of N/Q/H flips: 1 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.169 37642 Z= 0.412 Angle : 1.105 27.186 50938 Z= 0.561 Chirality : 0.065 0.669 5958 Planarity : 0.015 0.413 6490 Dihedral : 7.329 61.113 5022 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 22.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.45 % Favored : 88.33 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % 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: -3.89 (0.11), residues: 4610 helix: -2.54 (0.12), residues: 1388 sheet: -2.01 (0.19), residues: 684 loop : -2.84 (0.11), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP B 303 HIS 0.046 0.004 HIS C 280 PHE 0.108 0.005 PHE A 4 TYR 0.088 0.004 TYR A 228 ARG 0.111 0.002 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7188 Ramachandran restraints generated. 3594 Oldfield, 0 Emsley, 3594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.8690 (pt) cc_final: 0.7989 (tt) REVERT: A 249 MET cc_start: 0.8070 (mpp) cc_final: 0.7474 (pmm) REVERT: A 303 TRP cc_start: 0.7795 (m100) cc_final: 0.7390 (m100) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1037 time to fit residues: 3.6792 Evaluate side-chains 23 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.285 Evaluate side-chains 33 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: C 465 MET cc_start: 0.7213 (mtm) cc_final: 0.6528 (ttt) REVERT: C 523 PHE cc_start: 0.9070 (t80) cc_final: 0.8305 (t80) REVERT: C 528 ASP cc_start: 0.7641 (t0) cc_final: 0.7392 (t0) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1644 time to fit residues: 6.6538 Evaluate side-chains 23 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.328 Evaluate side-chains 20 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 104 MET cc_start: 0.8517 (mmp) cc_final: 0.8176 (tpp) REVERT: F 344 GLU cc_start: 0.9023 (mp0) cc_final: 0.8761 (tm-30) REVERT: F 349 TYR cc_start: 0.8234 (m-80) cc_final: 0.7754 (m-80) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0954 time to fit residues: 2.7896 Evaluate side-chains 15 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.336 Evaluate side-chains 30 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: H 52 LEU cc_start: 0.9518 (mt) cc_final: 0.9246 (mt) REVERT: H 108 MET cc_start: 0.8259 (pmm) cc_final: 0.6927 (ppp) REVERT: H 313 GLN cc_start: 0.6637 (pm20) cc_final: 0.6434 (pm20) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1162 time to fit residues: 4.8849 Evaluate side-chains 20 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.357 Evaluate side-chains 18 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 230 GLU cc_start: 0.8861 (tt0) cc_final: 0.7825 (mm-30) REVERT: I 295 MET cc_start: 0.7212 (ttp) cc_final: 0.6619 (ttt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1739 time to fit residues: 3.8184 Evaluate side-chains 13 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.266 Evaluate side-chains 16 residues out of total 224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 45 MET cc_start: 0.7436 (ppp) cc_final: 0.7214 (ppp) REVERT: L 57 ARG cc_start: 0.8548 (mmt180) cc_final: 0.8300 (mmm160) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.2412 time to fit residues: 4.5187 Evaluate side-chains 11 residues out of total 224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.264 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 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0317 Evaluate side-chains 0 residues out of total 16 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.022 Evaluate side-chains 16 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: O 239 MET cc_start: 0.0321 (mtp) cc_final: -0.0703 (mmt) REVERT: O 310 MET cc_start: 0.2902 (ttt) cc_final: 0.2638 (ttt) REVERT: O 431 GLU cc_start: 0.4725 (pm20) cc_final: 0.4318 (pm20) REVERT: O 482 MET cc_start: -0.1129 (pmm) cc_final: -0.1812 (mtt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1512 time to fit residues: 3.3494 Evaluate side-chains 11 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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: 69.5101 > 50: distance: 0 - 1: 16.603 distance: 1 - 2: 8.570 distance: 1 - 4: 13.604 distance: 2 - 3: 17.275 distance: 2 - 5: 13.092 distance: 3 - 28: 42.971 distance: 5 - 6: 17.541 distance: 6 - 7: 17.071 distance: 6 - 9: 23.383 distance: 7 - 8: 27.073 distance: 7 - 15: 23.060 distance: 9 - 10: 15.225 distance: 10 - 11: 8.598 distance: 10 - 12: 15.308 distance: 11 - 13: 13.501 distance: 12 - 14: 10.316 distance: 13 - 14: 14.499 distance: 15 - 16: 14.300 distance: 16 - 17: 22.588 distance: 16 - 19: 43.642 distance: 17 - 18: 31.812 distance: 17 - 23: 25.060 distance: 19 - 20: 20.880 distance: 20 - 21: 29.747 distance: 20 - 22: 33.481 distance: 23 - 24: 46.306 distance: 24 - 25: 40.489 distance: 24 - 27: 49.281 distance: 25 - 26: 41.532 distance: 25 - 28: 44.416 distance: 28 - 29: 44.502 distance: 29 - 30: 23.864 distance: 29 - 32: 46.196 distance: 30 - 31: 32.301 distance: 30 - 39: 37.361 distance: 32 - 33: 54.662 distance: 33 - 34: 36.452 distance: 34 - 35: 34.313 distance: 35 - 36: 16.395 distance: 36 - 37: 12.163 distance: 36 - 38: 13.363 distance: 39 - 40: 40.350 distance: 40 - 41: 20.477 distance: 40 - 43: 10.734 distance: 41 - 42: 34.825 distance: 41 - 48: 22.777 distance: 43 - 44: 16.111 distance: 44 - 45: 40.679 distance: 45 - 46: 50.501 distance: 46 - 47: 39.512 distance: 48 - 49: 25.346 distance: 48 - 54: 36.196 distance: 49 - 50: 14.913 distance: 49 - 52: 32.329 distance: 50 - 51: 30.819 distance: 50 - 55: 21.351 distance: 52 - 53: 50.120 distance: 53 - 54: 39.316 distance: 55 - 56: 35.276 distance: 56 - 57: 22.739 distance: 56 - 59: 40.847 distance: 57 - 58: 17.642 distance: 57 - 66: 46.913 distance: 59 - 60: 35.786 distance: 60 - 61: 14.373 distance: 60 - 62: 49.012 distance: 61 - 63: 19.668 distance: 62 - 64: 20.342 distance: 63 - 65: 49.212 distance: 64 - 65: 39.891 distance: 66 - 67: 59.155 distance: 67 - 68: 23.822 distance: 67 - 70: 58.735 distance: 68 - 69: 42.465 distance: 68 - 78: 33.478 distance: 70 - 71: 30.287 distance: 71 - 72: 18.386 distance: 71 - 73: 43.745 distance: 72 - 74: 32.456 distance: 73 - 75: 69.064 distance: 74 - 76: 42.169 distance: 75 - 76: 42.053 distance: 76 - 77: 50.608 distance: 78 - 79: 30.193 distance: 79 - 80: 30.445 distance: 79 - 82: 23.820 distance: 80 - 81: 55.848 distance: 82 - 83: 32.240 distance: 82 - 84: 26.646