Starting phenix.real_space_refine on Fri Aug 9 22:24:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhs_4264/08_2024/6fhs_4264.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhs_4264/08_2024/6fhs_4264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.754 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhs_4264/08_2024/6fhs_4264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhs_4264/08_2024/6fhs_4264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhs_4264/08_2024/6fhs_4264.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhs_4264/08_2024/6fhs_4264.cif" } resolution = 3.754 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= 0.005 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 123 5.16 5 C 17165 2.51 5 N 4859 2.21 5 O 5221 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 334": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 329": "NH1" <-> "NH2" Residue "D ARG 373": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "E ARG 329": "NH1" <-> "NH2" Residue "E ARG 373": "NH1" <-> "NH2" Residue "E ARG 416": "NH1" <-> "NH2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 329": "NH1" <-> "NH2" Residue "F ARG 373": "NH1" <-> "NH2" Residue "F ARG 416": "NH1" <-> "NH2" Residue "I PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "J ARG 221": "NH1" <-> "NH2" Residue "J ARG 279": "NH1" <-> "NH2" Residue "J ARG 293": "NH1" <-> "NH2" Residue "J ARG 295": "NH1" <-> "NH2" Residue "J ARG 703": "NH1" <-> "NH2" Residue "J ARG 717": "NH1" <-> "NH2" Residue "J ARG 719": "NH1" <-> "NH2" Residue "J ARG 720": "NH1" <-> "NH2" Residue "J ARG 730": "NH1" <-> "NH2" Residue "J ARG 748": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27383 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3432 Classifications: {'peptide': 449} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 429} Chain: "B" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3352 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 419} Chain breaks: 1 Chain: "C" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3511 Classifications: {'peptide': 459} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 439} Chain: "D" Number of atoms: 3383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3383 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 14, 'TRANS': 424} Chain: "E" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3396 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 14, 'TRANS': 426} Chain breaks: 1 Chain: "F" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3376 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 14, 'TRANS': 422} Chain breaks: 1 Chain: "G" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2127 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 21, 'TRANS': 245} Chain: "H" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "I" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 829 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 8, 'TRANS': 94} Chain breaks: 1 Chain: "J" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3521 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 412} Chain breaks: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.25, per 1000 atoms: 0.52 Number of scatterers: 27383 At special positions: 0 Unit cell: (139.92, 163.24, 181.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 123 16.00 P 15 15.00 O 5221 8.00 N 4859 7.00 C 17165 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: 9.15 Conformation dependent library (CDL) restraints added in 4.4 seconds 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6466 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 38 sheets defined 40.9% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'A' and resid 43 through 58 removed outlier: 3.827A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 89 removed outlier: 3.503A pdb=" N ALA A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 120 removed outlier: 3.520A pdb=" N VAL A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 183 Processing helix chain 'A' and resid 208 through 211 Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 273 through 290 removed outlier: 3.806A pdb=" N ASN A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 309 through 321 removed outlier: 3.879A pdb=" N TYR A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 357 removed outlier: 3.692A pdb=" N GLN A 357 " --> pdb=" O ASP A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 354 through 357' Processing helix chain 'A' and resid 370 through 384 Processing helix chain 'A' and resid 388 through 402 Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.982A pdb=" N CYS A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 408' Processing helix chain 'A' and resid 411 through 421 removed outlier: 3.711A pdb=" N ILE A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 438 removed outlier: 3.730A pdb=" N ILE A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'B' and resid 43 through 60 removed outlier: 3.920A pdb=" N HIS B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 89 removed outlier: 3.659A pdb=" N GLY B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 103 removed outlier: 3.719A pdb=" N TYR B 103 " --> pdb=" O SER B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 100 through 103' Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.621A pdb=" N ILE B 121 " --> pdb=" O PHE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 241 through 250 Processing helix chain 'B' and resid 256 through 261 Processing helix chain 'B' and resid 273 through 290 removed outlier: 3.602A pdb=" N ARG B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS B 282 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.536A pdb=" N THR B 314 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 351 Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.932A pdb=" N GLN B 357 " --> pdb=" O PRO B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 371 Processing helix chain 'B' and resid 372 through 384 Processing helix chain 'B' and resid 388 through 402 removed outlier: 3.758A pdb=" N ASP B 393 " --> pdb=" O ASP B 389 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.786A pdb=" N CYS B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 408' Processing helix chain 'B' and resid 410 through 420 removed outlier: 3.658A pdb=" N SER B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 438 removed outlier: 3.819A pdb=" N ILE B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 450 removed outlier: 3.594A pdb=" N SER B 444 " --> pdb=" O ASP B 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 59 Processing helix chain 'C' and resid 76 through 89 removed outlier: 3.538A pdb=" N GLY C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.639A pdb=" N GLU C 101 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE C 102 " --> pdb=" O GLY C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 102' Processing helix chain 'C' and resid 111 through 120 Processing helix chain 'C' and resid 177 through 185 removed outlier: 3.510A pdb=" N LYS C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 273 through 290 removed outlier: 3.747A pdb=" N ARG C 277 " --> pdb=" O THR C 273 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN C 289 " --> pdb=" O GLN C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 removed outlier: 3.671A pdb=" N PHE C 313 " --> pdb=" O ASP C 309 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR C 314 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 318 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 359 Processing helix chain 'C' and resid 371 through 384 Processing helix chain 'C' and resid 388 through 402 Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.837A pdb=" N CYS C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 408' Processing helix chain 'C' and resid 411 through 422 Processing helix chain 'C' and resid 427 through 435 removed outlier: 3.641A pdb=" N ILE C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 451 removed outlier: 3.588A pdb=" N SER C 444 " --> pdb=" O ASP C 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 66 removed outlier: 3.792A pdb=" N GLY D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.905A pdb=" N GLY D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 125 removed outlier: 3.689A pdb=" N LEU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 185 removed outlier: 3.516A pdb=" N LYS D 183 " --> pdb=" O ASP D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 252 removed outlier: 3.760A pdb=" N ARG D 252 " --> pdb=" O VAL D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 285 removed outlier: 3.654A pdb=" N ARG D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR D 277 " --> pdb=" O ASP D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 303 removed outlier: 3.593A pdb=" N MET D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 315 removed outlier: 4.059A pdb=" N TYR D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 315 " --> pdb=" O ILE D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 377 removed outlier: 4.165A pdb=" N GLN D 368 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 397 removed outlier: 3.851A pdb=" N GLU D 395 " --> pdb=" O LYS D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 415 removed outlier: 3.541A pdb=" N ALA D 401 " --> pdb=" O GLY D 397 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'D' and resid 434 through 445 removed outlier: 4.006A pdb=" N ARG D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 64 Processing helix chain 'E' and resid 83 through 93 Processing helix chain 'E' and resid 115 through 125 removed outlier: 3.538A pdb=" N ALA E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 185 removed outlier: 4.346A pdb=" N ALA E 180 " --> pdb=" O LYS E 176 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS E 183 " --> pdb=" O ASP E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 214 removed outlier: 5.309A pdb=" N ARG E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR E 214 " --> pdb=" O SER E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 250 Processing helix chain 'E' and resid 257 through 262 Processing helix chain 'E' and resid 268 through 285 removed outlier: 3.880A pdb=" N ARG E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA E 280 " --> pdb=" O ASN E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 303 Processing helix chain 'E' and resid 304 through 315 removed outlier: 3.521A pdb=" N PHE E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ARG E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 362 through 378 removed outlier: 3.718A pdb=" N GLU E 377 " --> pdb=" O ARG E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 415 removed outlier: 3.803A pdb=" N GLU E 395 " --> pdb=" O LYS E 391 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU E 398 " --> pdb=" O GLN E 394 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N ARG E 399 " --> pdb=" O GLU E 395 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR E 400 " --> pdb=" O ALA E 396 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA E 401 " --> pdb=" O GLY E 397 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR E 406 " --> pdb=" O SER E 402 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU E 410 " --> pdb=" O THR E 406 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG E 415 " --> pdb=" O ILE E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 432 removed outlier: 4.354A pdb=" N ARG E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS E 430 " --> pdb=" O GLN E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 444 Processing helix chain 'F' and resid 49 through 66 removed outlier: 3.785A pdb=" N GLN F 65 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY F 66 " --> pdb=" O MET F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.619A pdb=" N ALA F 87 " --> pdb=" O LYS F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 114 through 126 removed outlier: 3.996A pdb=" N ALA F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE F 123 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 185 removed outlier: 4.183A pdb=" N ASP F 179 " --> pdb=" O SER F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 243 through 250 Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 257 through 262 Processing helix chain 'F' and resid 268 through 285 removed outlier: 3.736A pdb=" N ARG F 272 " --> pdb=" O ARG F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 303 Processing helix chain 'F' and resid 304 through 315 removed outlier: 4.400A pdb=" N TYR F 310 " --> pdb=" O GLU F 306 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG F 313 " --> pdb=" O SER F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 351 Processing helix chain 'F' and resid 362 through 377 removed outlier: 3.902A pdb=" N GLN F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 397 Processing helix chain 'F' and resid 397 through 402 removed outlier: 3.521A pdb=" N ALA F 401 " --> pdb=" O GLY F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 415 Processing helix chain 'F' and resid 421 through 432 Processing helix chain 'F' and resid 434 through 445 removed outlier: 3.839A pdb=" N VAL F 439 " --> pdb=" O PRO F 435 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG F 440 " --> pdb=" O ALA F 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 1334 through 1345 removed outlier: 4.508A pdb=" N PHE G1338 " --> pdb=" O LEU G1334 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER G1340 " --> pdb=" O ALA G1336 " (cutoff:3.500A) Processing helix chain 'G' and resid 1352 through 1357 removed outlier: 3.674A pdb=" N SER G1357 " --> pdb=" O GLU G1353 " (cutoff:3.500A) Processing helix chain 'G' and resid 1365 through 1370 removed outlier: 3.569A pdb=" N LEU G1368 " --> pdb=" O PHE G1365 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG G1369 " --> pdb=" O THR G1366 " (cutoff:3.500A) Processing helix chain 'G' and resid 1374 through 1382 Processing helix chain 'G' and resid 1386 through 1394 Processing helix chain 'G' and resid 1399 through 1407 removed outlier: 4.097A pdb=" N GLN G1404 " --> pdb=" O LEU G1400 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE G1405 " --> pdb=" O GLY G1401 " (cutoff:3.500A) Processing helix chain 'G' and resid 1417 through 1421 removed outlier: 3.530A pdb=" N LEU G1421 " --> pdb=" O VAL G1418 " (cutoff:3.500A) Processing helix chain 'G' and resid 1429 through 1435 removed outlier: 3.815A pdb=" N VAL G1433 " --> pdb=" O ASN G1429 " (cutoff:3.500A) Processing helix chain 'G' and resid 1447 through 1456 removed outlier: 3.687A pdb=" N VAL G1451 " --> pdb=" O ASN G1447 " (cutoff:3.500A) Processing helix chain 'G' and resid 1480 through 1491 removed outlier: 3.705A pdb=" N VAL G1484 " --> pdb=" O SER G1480 " (cutoff:3.500A) Processing helix chain 'G' and resid 1493 through 1502 removed outlier: 3.619A pdb=" N ARG G1497 " --> pdb=" O HIS G1493 " (cutoff:3.500A) Processing helix chain 'G' and resid 1504 through 1513 Processing helix chain 'H' and resid 462 through 466 removed outlier: 3.510A pdb=" N LEU H 465 " --> pdb=" O PRO H 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 470 through 475 removed outlier: 4.567A pdb=" N PHE H 474 " --> pdb=" O ALA H 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 20 Processing helix chain 'I' and resid 43 through 51 Processing helix chain 'I' and resid 190 through 199 Processing helix chain 'I' and resid 204 through 213 removed outlier: 4.051A pdb=" N LEU I 209 " --> pdb=" O GLY I 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 20 removed outlier: 3.548A pdb=" N TRP J 19 " --> pdb=" O ASP J 16 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS J 20 " --> pdb=" O GLU J 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 16 through 20' Processing helix chain 'J' and resid 45 through 50 Processing helix chain 'J' and resid 101 through 105 removed outlier: 3.510A pdb=" N ASP J 104 " --> pdb=" O ALA J 101 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS J 105 " --> pdb=" O GLY J 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 101 through 105' Processing helix chain 'J' and resid 128 through 144 removed outlier: 3.984A pdb=" N HIS J 134 " --> pdb=" O ASP J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 179 Processing helix chain 'J' and resid 190 through 198 Processing helix chain 'J' and resid 234 through 250 removed outlier: 3.580A pdb=" N TYR J 250 " --> pdb=" O LEU J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 271 removed outlier: 3.737A pdb=" N THR J 263 " --> pdb=" O ASN J 259 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP J 269 " --> pdb=" O HIS J 265 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS J 271 " --> pdb=" O VAL J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 283 removed outlier: 4.059A pdb=" N ALA J 282 " --> pdb=" O ASP J 278 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY J 283 " --> pdb=" O ARG J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 294 removed outlier: 3.834A pdb=" N ARG J 293 " --> pdb=" O GLY J 289 " (cutoff:3.500A) Processing helix chain 'J' and resid 607 through 614 removed outlier: 4.142A pdb=" N ALA J 611 " --> pdb=" O SER J 607 " (cutoff:3.500A) Processing helix chain 'J' and resid 623 through 628 removed outlier: 3.866A pdb=" N THR J 627 " --> pdb=" O SER J 623 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N HIS J 628 " --> pdb=" O GLN J 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 623 through 628' Processing helix chain 'J' and resid 634 through 639 removed outlier: 3.794A pdb=" N VAL J 639 " --> pdb=" O GLU J 635 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 642 No H-bonds generated for 'chain 'J' and resid 640 through 642' Processing helix chain 'J' and resid 645 through 650 removed outlier: 3.598A pdb=" N ILE J 649 " --> pdb=" O GLN J 645 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA J 650 " --> pdb=" O PRO J 646 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 645 through 650' Processing helix chain 'J' and resid 656 through 668 removed outlier: 3.716A pdb=" N ARG J 668 " --> pdb=" O ILE J 664 " (cutoff:3.500A) Processing helix chain 'J' and resid 678 through 683 removed outlier: 3.871A pdb=" N PHE J 682 " --> pdb=" O ALA J 678 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU J 683 " --> pdb=" O PRO J 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 678 through 683' Processing helix chain 'J' and resid 698 through 710 Processing helix chain 'J' and resid 726 through 736 removed outlier: 3.969A pdb=" N ALA J 732 " --> pdb=" O ALA J 728 " (cutoff:3.500A) Processing helix chain 'J' and resid 738 through 743 Processing helix chain 'J' and resid 748 through 755 removed outlier: 3.583A pdb=" N GLY J 755 " --> pdb=" O TYR J 751 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 97 removed outlier: 6.516A pdb=" N LEU A 300 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA A 331 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE A 302 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 67 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLY A 66 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE A 362 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU A 68 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 240 Processing sheet with id=AA3, first strand: chain 'A' and resid 131 through 135 removed outlier: 3.940A pdb=" N GLY A 205 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TYR A 193 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG A 203 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU A 195 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N CYS A 201 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 143 Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 338 Processing sheet with id=AA7, first strand: chain 'B' and resid 94 through 98 removed outlier: 5.928A pdb=" N VAL B 67 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLY B 66 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE B 362 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B 68 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.629A pdb=" N LEU B 173 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 158 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 159 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N MET B 139 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY B 161 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 221 through 222 removed outlier: 6.552A pdb=" N VAL B 222 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG B 206 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N CYS B 201 " --> pdb=" O GLU B 195 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLU B 195 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ARG B 203 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR B 193 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY B 205 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASP B 190 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 337 through 338 Processing sheet with id=AB2, first strand: chain 'C' and resid 299 through 303 removed outlier: 6.622A pdb=" N VAL C 67 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY C 66 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE C 362 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU C 68 " --> pdb=" O ILE C 362 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 168 through 173 removed outlier: 6.464A pdb=" N LEU C 159 " --> pdb=" O MET C 139 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N MET C 139 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY C 161 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 202 through 206 removed outlier: 3.700A pdb=" N TYR C 193 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 191 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP C 190 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 155 removed outlier: 6.566A pdb=" N THR D 161 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE D 145 " --> pdb=" O LYS D 159 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS D 159 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE D 147 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN D 157 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY D 158 " --> pdb=" O MET D 173 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 155 removed outlier: 3.580A pdb=" N GLY D 140 " --> pdb=" O ILE D 192 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP D 190 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE D 191 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR D 202 " --> pdb=" O SER D 193 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 336 through 338 Processing sheet with id=AB8, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.108A pdb=" N THR D 101 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASP D 298 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU D 103 " --> pdb=" O ASP D 298 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LEU D 295 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ALA D 326 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE D 297 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL D 73 " --> pdb=" O MET D 325 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 233 through 242 Processing sheet with id=AC1, first strand: chain 'D' and resid 331 through 333 Processing sheet with id=AC2, first strand: chain 'E' and resid 42 through 43 removed outlier: 4.075A pdb=" N SER E 43 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU E 46 " --> pdb=" O SER E 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.688A pdb=" N THR E 101 " --> pdb=" O PHE E 296 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP E 298 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU E 103 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU E 295 " --> pdb=" O ILE E 324 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ALA E 326 " --> pdb=" O LEU E 295 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE E 297 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA E 72 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE E 356 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU E 74 " --> pdb=" O ILE E 356 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 233 through 242 Processing sheet with id=AC5, first strand: chain 'E' and resid 141 through 147 removed outlier: 5.206A pdb=" N VAL E 142 " --> pdb=" O LYS E 163 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LYS E 163 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 190 through 191 removed outlier: 3.673A pdb=" N GLY E 205 " --> pdb=" O ILE E 191 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 331 through 333 Processing sheet with id=AC8, first strand: chain 'F' and resid 42 through 43 removed outlier: 3.612A pdb=" N SER F 43 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU F 46 " --> pdb=" O SER F 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.071A pdb=" N LEU F 295 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA F 326 " --> pdb=" O LEU F 295 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE F 297 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL F 73 " --> pdb=" O MET F 325 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 168 through 173 removed outlier: 7.812A pdb=" N GLN F 157 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE F 147 " --> pdb=" O GLN F 157 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LYS F 159 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE F 145 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR F 161 " --> pdb=" O VAL F 143 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS F 235 " --> pdb=" O SER F 135 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 191 through 195 Processing sheet with id=AD3, first strand: chain 'F' and resid 206 through 207 removed outlier: 6.205A pdb=" N ARG F 206 " --> pdb=" O LEU F 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 331 through 333 Processing sheet with id=AD5, first strand: chain 'G' and resid 1283 through 1284 removed outlier: 6.735A pdb=" N PHE G1283 " --> pdb=" O SER G1470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'G' and resid 1313 through 1314 removed outlier: 6.438A pdb=" N TYR G1313 " --> pdb=" O VAL G1477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'J' and resid 80 through 82 removed outlier: 3.646A pdb=" N LEU J 185 " --> pdb=" O ILE J 746 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE J 746 " --> pdb=" O LEU J 185 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 85 through 86 removed outlier: 3.771A pdb=" N MET J 86 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG J 116 " --> pdb=" O MET J 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'J' and resid 203 through 208 Processing sheet with id=AE1, first strand: chain 'J' and resid 295 through 297 Processing sheet with id=AE2, first strand: chain 'J' and resid 686 through 688 removed outlier: 6.144A pdb=" N VAL J 686 " --> pdb=" O ARG J 719 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 1010 hydrogen bonds defined for protein. 2904 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: 9.13 Time building geometry restraints manager: 10.14 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: 9256 1.34 - 1.46: 5013 1.46 - 1.58: 13339 1.58 - 1.70: 23 1.70 - 1.81: 211 Bond restraints: 27842 Sorted by residual: bond pdb=" C4 ATP J 801 " pdb=" C5 ATP J 801 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.27e+01 bond pdb=" C5 ATP J 801 " pdb=" C6 ATP J 801 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.06e+01 bond pdb=" C4 ATP J 801 " pdb=" N9 ATP J 801 " ideal model delta sigma weight residual 1.374 1.327 0.047 1.00e-02 1.00e+04 2.24e+01 bond pdb=" C8 ATP J 801 " pdb=" N7 ATP J 801 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.19e+01 bond pdb=" C5 ATP J 801 " pdb=" N7 ATP J 801 " ideal model delta sigma weight residual 1.387 1.344 0.043 1.00e-02 1.00e+04 1.81e+01 ... (remaining 27837 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.55: 667 105.55 - 113.25: 15500 113.25 - 120.95: 13263 120.95 - 128.65: 8062 128.65 - 136.35: 156 Bond angle restraints: 37648 Sorted by residual: angle pdb=" PB ATP J 801 " pdb=" O3B ATP J 801 " pdb=" PG ATP J 801 " ideal model delta sigma weight residual 139.87 120.82 19.05 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PA ATP J 801 " pdb=" O3A ATP J 801 " pdb=" PB ATP J 801 " ideal model delta sigma weight residual 136.83 120.42 16.41 1.00e+00 1.00e+00 2.69e+02 angle pdb=" C5 ATP J 801 " pdb=" C4 ATP J 801 " pdb=" N3 ATP J 801 " ideal model delta sigma weight residual 126.80 119.14 7.66 1.00e+00 1.00e+00 5.87e+01 angle pdb=" N3 ATP J 801 " pdb=" C4 ATP J 801 " pdb=" N9 ATP J 801 " ideal model delta sigma weight residual 127.04 134.61 -7.57 1.15e+00 7.59e-01 4.34e+01 angle pdb=" N GLY E 140 " pdb=" CA GLY E 140 " pdb=" C GLY E 140 " ideal model delta sigma weight residual 111.72 118.44 -6.72 1.31e+00 5.83e-01 2.63e+01 ... (remaining 37643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.86: 16908 29.86 - 59.71: 128 59.71 - 89.57: 17 89.57 - 119.42: 6 119.42 - 149.28: 6 Dihedral angle restraints: 17065 sinusoidal: 7021 harmonic: 10044 Sorted by residual: dihedral pdb=" O1B ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PB ADP A 501 " pdb=" PA ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 150.72 149.28 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C5' ADP A 501 " pdb=" O5' ADP A 501 " pdb=" PA ADP A 501 " pdb=" O2A ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 159.87 140.13 1 2.00e+01 2.50e-03 4.24e+01 dihedral pdb=" O1B ADP E 501 " pdb=" O3A ADP E 501 " pdb=" PB ADP E 501 " pdb=" PA ADP E 501 " ideal model delta sinusoidal sigma weight residual 300.00 163.19 136.80 1 2.00e+01 2.50e-03 4.15e+01 ... (remaining 17062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3615 0.073 - 0.147: 619 0.147 - 0.220: 42 0.220 - 0.293: 0 0.293 - 0.366: 3 Chirality restraints: 4279 Sorted by residual: chirality pdb=" CB ILE C 324 " pdb=" CA ILE C 324 " pdb=" CG1 ILE C 324 " pdb=" CG2 ILE C 324 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB ILE J 39 " pdb=" CA ILE J 39 " pdb=" CG1 ILE J 39 " pdb=" CG2 ILE J 39 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CB ILE A 324 " pdb=" CA ILE A 324 " pdb=" CG1 ILE A 324 " pdb=" CG2 ILE A 324 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 4276 not shown) Planarity restraints: 4878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA I 177 " -0.050 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO I 178 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO I 178 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 178 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO J 83 " 0.045 5.00e-02 4.00e+02 6.78e-02 7.35e+00 pdb=" N PRO J 84 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO J 84 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO J 84 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 193 " 0.029 2.00e-02 2.50e+03 1.78e-02 6.34e+00 pdb=" CG TYR A 193 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 193 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 193 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 193 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 193 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 193 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 193 " 0.008 2.00e-02 2.50e+03 ... (remaining 4875 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5661 2.78 - 3.31: 23644 3.31 - 3.84: 42742 3.84 - 4.37: 50039 4.37 - 4.90: 87553 Nonbonded interactions: 209639 Sorted by model distance: nonbonded pdb=" OD2 ASP B 256 " pdb=" OG SER B 259 " model vdw 2.249 3.040 nonbonded pdb=" O SER C 100 " pdb=" OG1 THR F 116 " model vdw 2.271 3.040 nonbonded pdb=" OH TYR A 193 " pdb=" OG1 THR G1279 " model vdw 2.293 3.040 nonbonded pdb=" O LYS I 42 " pdb=" OG SER J 127 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR E 400 " pdb=" O PHE E 432 " model vdw 2.307 3.040 ... (remaining 209634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 144 or resid 156 through 462 or resid 501)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 144 or resid 156 through 462 or resid 501)) } ncs_group { reference = (chain 'D' and (resid 20 through 150 or resid 156 through 458 or resid 501)) selection = (chain 'E' and (resid 20 through 150 or resid 156 through 458 or resid 501)) selection = (chain 'F' and (resid 20 through 458 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 65.710 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 27842 Z= 0.359 Angle : 0.854 19.052 37648 Z= 0.473 Chirality : 0.053 0.366 4279 Planarity : 0.007 0.077 4878 Dihedral : 9.829 149.279 10599 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.11), residues: 3474 helix: -3.17 (0.09), residues: 1349 sheet: -2.14 (0.21), residues: 509 loop : -2.70 (0.13), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP J 236 HIS 0.010 0.002 HIS C 242 PHE 0.033 0.003 PHE B 117 TYR 0.041 0.002 TYR A 193 ARG 0.007 0.001 ARG E 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 732 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8963 (tttt) cc_final: 0.8726 (ttmm) REVERT: A 179 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6920 (mt-10) REVERT: A 245 ASP cc_start: 0.8241 (m-30) cc_final: 0.7872 (t0) REVERT: A 385 VAL cc_start: 0.8772 (t) cc_final: 0.8551 (p) REVERT: A 401 ARG cc_start: 0.6966 (mtt180) cc_final: 0.6679 (mtt-85) REVERT: B 264 LEU cc_start: 0.9040 (tp) cc_final: 0.8646 (mt) REVERT: B 303 ASP cc_start: 0.7467 (t0) cc_final: 0.7034 (t0) REVERT: B 402 ILE cc_start: 0.8936 (mt) cc_final: 0.8735 (mm) REVERT: C 146 ASN cc_start: 0.9027 (m-40) cc_final: 0.8811 (m-40) REVERT: C 260 MET cc_start: 0.8532 (mtt) cc_final: 0.8274 (mtp) REVERT: D 113 MET cc_start: 0.8781 (ptt) cc_final: 0.8440 (ptt) REVERT: D 257 LEU cc_start: 0.6767 (tt) cc_final: 0.6476 (mm) REVERT: D 271 ILE cc_start: 0.8940 (mt) cc_final: 0.8571 (mm) REVERT: D 416 ARG cc_start: 0.8101 (mtt-85) cc_final: 0.7885 (tpp80) REVERT: E 136 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6409 (mt-10) REVERT: F 25 SER cc_start: 0.8739 (m) cc_final: 0.8387 (p) REVERT: F 36 THR cc_start: 0.9189 (p) cc_final: 0.8798 (t) REVERT: F 88 MET cc_start: 0.7896 (mmt) cc_final: 0.7604 (mmt) REVERT: F 201 ILE cc_start: 0.9219 (mt) cc_final: 0.8819 (mt) REVERT: F 247 ASP cc_start: 0.6682 (m-30) cc_final: 0.6360 (m-30) REVERT: F 316 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7699 (mm-30) REVERT: F 331 VAL cc_start: 0.9241 (t) cc_final: 0.8953 (p) REVERT: G 1278 ASP cc_start: 0.7806 (t0) cc_final: 0.7536 (t0) REVERT: G 1305 TYR cc_start: 0.8555 (t80) cc_final: 0.8323 (t80) REVERT: G 1326 LEU cc_start: 0.8448 (mt) cc_final: 0.8175 (mp) REVERT: G 1453 TYR cc_start: 0.8627 (t80) cc_final: 0.8420 (t80) REVERT: G 1534 LYS cc_start: 0.8393 (mttt) cc_final: 0.8059 (mptt) REVERT: I 31 ASN cc_start: 0.8688 (t0) cc_final: 0.8382 (t0) REVERT: I 48 LEU cc_start: 0.8881 (tt) cc_final: 0.8405 (mm) REVERT: I 166 MET cc_start: 0.7316 (ptp) cc_final: 0.7099 (ptt) REVERT: I 173 THR cc_start: 0.9066 (p) cc_final: 0.8775 (t) REVERT: J 128 ASN cc_start: 0.8264 (t0) cc_final: 0.7745 (t0) REVERT: J 145 MET cc_start: 0.7409 (mmm) cc_final: 0.7197 (mmm) REVERT: J 610 HIS cc_start: 0.7963 (t70) cc_final: 0.7749 (t70) outliers start: 0 outliers final: 0 residues processed: 732 average time/residue: 0.4527 time to fit residues: 494.1058 Evaluate side-chains 358 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 0.4980 chunk 261 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 176 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 270 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 201 optimal weight: 0.9980 chunk 313 optimal weight: 0.0050 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 19 HIS ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 HIS B 28 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 HIS C 242 HIS C 421 ASN C 458 HIS D 274 GLN D 394 GLN E 24 HIS E 394 GLN E 409 GLN ** F 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 HIS G1402 HIS ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 GLN J 262 GLN J 633 ASN J 762 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27842 Z= 0.188 Angle : 0.626 10.407 37648 Z= 0.311 Chirality : 0.044 0.159 4279 Planarity : 0.005 0.064 4878 Dihedral : 8.496 134.916 3920 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.61 % Allowed : 7.97 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.13), residues: 3474 helix: -1.46 (0.13), residues: 1365 sheet: -1.84 (0.22), residues: 530 loop : -2.24 (0.14), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 34 HIS 0.011 0.001 HIS J 762 PHE 0.017 0.001 PHE D 223 TYR 0.023 0.002 TYR A 193 ARG 0.007 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 425 time to evaluate : 4.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8921 (tttt) cc_final: 0.8709 (ttmm) REVERT: A 179 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6961 (mt-10) REVERT: A 215 ASP cc_start: 0.6973 (t0) cc_final: 0.6722 (t0) REVERT: A 397 GLU cc_start: 0.7802 (tp30) cc_final: 0.6657 (tp30) REVERT: B 303 ASP cc_start: 0.7294 (t0) cc_final: 0.6956 (t0) REVERT: B 351 ILE cc_start: 0.8729 (mm) cc_final: 0.8287 (mt) REVERT: C 101 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7246 (tm-30) REVERT: C 393 ASP cc_start: 0.7913 (m-30) cc_final: 0.7673 (m-30) REVERT: C 448 LEU cc_start: 0.8832 (tp) cc_final: 0.8566 (tt) REVERT: D 187 MET cc_start: 0.8886 (tpp) cc_final: 0.8592 (mmm) REVERT: D 256 PHE cc_start: 0.6561 (m-80) cc_final: 0.6352 (m-80) REVERT: D 283 LYS cc_start: 0.9101 (tttt) cc_final: 0.8900 (ttpp) REVERT: D 334 ILE cc_start: 0.8523 (mt) cc_final: 0.8246 (mt) REVERT: E 147 ILE cc_start: 0.8523 (mm) cc_final: 0.8209 (mm) REVERT: E 149 ARG cc_start: 0.7076 (ttm110) cc_final: 0.6772 (ptp-110) REVERT: E 313 ARG cc_start: 0.7752 (mpt180) cc_final: 0.7163 (mmt-90) REVERT: F 25 SER cc_start: 0.8615 (m) cc_final: 0.8310 (p) REVERT: F 88 MET cc_start: 0.7977 (mmt) cc_final: 0.7617 (tpp) REVERT: F 245 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7995 (mm-30) REVERT: F 253 THR cc_start: 0.8794 (m) cc_final: 0.8560 (p) REVERT: F 331 VAL cc_start: 0.9206 (t) cc_final: 0.8947 (p) REVERT: F 369 ILE cc_start: 0.8207 (mt) cc_final: 0.7949 (mt) REVERT: G 1453 TYR cc_start: 0.8479 (t80) cc_final: 0.8258 (t80) REVERT: H 464 GLU cc_start: 0.8279 (mp0) cc_final: 0.8061 (mp0) REVERT: H 468 THR cc_start: 0.8885 (p) cc_final: 0.8685 (t) REVERT: I 31 ASN cc_start: 0.8679 (t0) cc_final: 0.8321 (t0) REVERT: I 166 MET cc_start: 0.7384 (ptp) cc_final: 0.7091 (ptm) REVERT: I 173 THR cc_start: 0.9104 (p) cc_final: 0.8875 (t) REVERT: J 128 ASN cc_start: 0.8434 (t0) cc_final: 0.7761 (t0) REVERT: J 132 MET cc_start: 0.9289 (tpp) cc_final: 0.8963 (tpp) REVERT: J 145 MET cc_start: 0.7519 (mmm) cc_final: 0.7289 (mmm) outliers start: 47 outliers final: 25 residues processed: 459 average time/residue: 0.4224 time to fit residues: 308.9831 Evaluate side-chains 357 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 332 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 1303 LEU Chi-restraints excluded: chain G residue 1385 ASP Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 168 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 174 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 86 optimal weight: 0.0970 chunk 313 optimal weight: 5.9990 chunk 339 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 311 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 251 optimal weight: 0.0570 overall best weight: 2.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS D 49 GLN ** F 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 27842 Z= 0.364 Angle : 0.684 10.104 37648 Z= 0.339 Chirality : 0.046 0.167 4279 Planarity : 0.005 0.058 4878 Dihedral : 8.191 122.409 3920 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.30 % Allowed : 9.86 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.13), residues: 3474 helix: -0.89 (0.14), residues: 1375 sheet: -1.78 (0.21), residues: 530 loop : -1.99 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 34 HIS 0.011 0.001 HIS J 762 PHE 0.016 0.002 PHE C 214 TYR 0.025 0.002 TYR A 193 ARG 0.013 0.001 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 352 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8373 (tpp) cc_final: 0.8080 (mmm) REVERT: A 190 ASP cc_start: 0.8395 (m-30) cc_final: 0.7897 (m-30) REVERT: B 264 LEU cc_start: 0.9230 (tp) cc_final: 0.8735 (mt) REVERT: C 448 LEU cc_start: 0.8857 (tp) cc_final: 0.8474 (tt) REVERT: D 263 ASP cc_start: 0.7948 (t0) cc_final: 0.7485 (t0) REVERT: E 310 TYR cc_start: 0.8763 (t80) cc_final: 0.8482 (t80) REVERT: F 25 SER cc_start: 0.8753 (m) cc_final: 0.8373 (p) REVERT: F 88 MET cc_start: 0.7952 (mmt) cc_final: 0.7661 (tpp) REVERT: F 245 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8060 (mm-30) REVERT: F 273 ASP cc_start: 0.7208 (t0) cc_final: 0.6930 (t0) REVERT: F 331 VAL cc_start: 0.9224 (t) cc_final: 0.8978 (p) REVERT: G 1346 MET cc_start: 0.8731 (mmm) cc_final: 0.8344 (mtt) REVERT: H 468 THR cc_start: 0.8975 (p) cc_final: 0.8743 (t) REVERT: I 31 ASN cc_start: 0.8729 (t0) cc_final: 0.8406 (t0) REVERT: I 166 MET cc_start: 0.7548 (ptp) cc_final: 0.7221 (ptm) REVERT: I 173 THR cc_start: 0.9241 (p) cc_final: 0.8956 (t) REVERT: J 128 ASN cc_start: 0.8537 (t0) cc_final: 0.7822 (t0) REVERT: J 145 MET cc_start: 0.7598 (mmm) cc_final: 0.7370 (mmm) outliers start: 67 outliers final: 46 residues processed: 398 average time/residue: 0.3861 time to fit residues: 246.4579 Evaluate side-chains 352 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 306 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 1303 LEU Chi-restraints excluded: chain G residue 1385 ASP Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain J residue 170 LYS Chi-restraints excluded: chain J residue 240 GLU Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 707 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 310 optimal weight: 6.9990 chunk 235 optimal weight: 0.6980 chunk 162 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 210 optimal weight: 0.6980 chunk 314 optimal weight: 0.6980 chunk 333 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS D 368 GLN E 368 GLN ** F 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 HIS G1419 HIS G1423 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27842 Z= 0.183 Angle : 0.588 8.896 37648 Z= 0.287 Chirality : 0.043 0.170 4279 Planarity : 0.004 0.050 4878 Dihedral : 7.708 115.916 3920 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.03 % Allowed : 11.09 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.14), residues: 3474 helix: -0.42 (0.14), residues: 1382 sheet: -1.60 (0.22), residues: 517 loop : -1.81 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 34 HIS 0.008 0.001 HIS J 762 PHE 0.019 0.001 PHE D 223 TYR 0.020 0.001 TYR G1453 ARG 0.007 0.000 ARG C 405 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 345 time to evaluate : 3.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6725 (mt-10) REVERT: A 190 ASP cc_start: 0.8336 (m-30) cc_final: 0.7859 (m-30) REVERT: A 274 ASP cc_start: 0.7533 (t0) cc_final: 0.7327 (t0) REVERT: B 303 ASP cc_start: 0.7614 (t0) cc_final: 0.7185 (t0) REVERT: C 448 LEU cc_start: 0.8834 (tp) cc_final: 0.8474 (tt) REVERT: D 112 GLU cc_start: 0.7233 (tm-30) cc_final: 0.7022 (tm-30) REVERT: D 187 MET cc_start: 0.8851 (tpp) cc_final: 0.8544 (mmm) REVERT: D 263 ASP cc_start: 0.7898 (t0) cc_final: 0.7465 (t0) REVERT: E 115 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8822 (ptmt) REVERT: E 167 MET cc_start: 0.8312 (mmt) cc_final: 0.8082 (mmp) REVERT: E 310 TYR cc_start: 0.8734 (t80) cc_final: 0.8506 (t80) REVERT: F 25 SER cc_start: 0.8668 (m) cc_final: 0.8312 (p) REVERT: F 88 MET cc_start: 0.7897 (mmt) cc_final: 0.7618 (tpp) REVERT: F 245 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7956 (mm-30) REVERT: F 331 VAL cc_start: 0.9174 (t) cc_final: 0.8964 (p) REVERT: F 369 ILE cc_start: 0.8394 (mt) cc_final: 0.8117 (mt) REVERT: G 1305 TYR cc_start: 0.8337 (t80) cc_final: 0.8070 (t80) REVERT: G 1346 MET cc_start: 0.8695 (mmm) cc_final: 0.8151 (ttm) REVERT: H 468 THR cc_start: 0.8914 (p) cc_final: 0.8702 (t) REVERT: I 27 LYS cc_start: 0.8561 (mmtp) cc_final: 0.8319 (mmtp) REVERT: I 31 ASN cc_start: 0.8699 (t0) cc_final: 0.8317 (t0) REVERT: I 166 MET cc_start: 0.7397 (ptp) cc_final: 0.7101 (ptm) REVERT: J 128 ASN cc_start: 0.8480 (t0) cc_final: 0.7744 (t0) REVERT: J 145 MET cc_start: 0.7641 (mmm) cc_final: 0.7379 (mmm) outliers start: 59 outliers final: 37 residues processed: 390 average time/residue: 0.3857 time to fit residues: 238.8268 Evaluate side-chains 335 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 297 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 1303 LEU Chi-restraints excluded: chain G residue 1423 GLN Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1455 GLU Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain J residue 267 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 277 optimal weight: 0.6980 chunk 189 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 284 optimal weight: 4.9990 chunk 230 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 299 optimal weight: 3.9990 chunk 84 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 ASN ** F 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 250 ASN F 368 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27842 Z= 0.175 Angle : 0.571 8.044 37648 Z= 0.279 Chirality : 0.043 0.158 4279 Planarity : 0.004 0.053 4878 Dihedral : 7.423 117.392 3920 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.37 % Allowed : 11.54 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.14), residues: 3474 helix: -0.11 (0.14), residues: 1376 sheet: -1.53 (0.22), residues: 551 loop : -1.68 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP I 34 HIS 0.016 0.001 HIS J 762 PHE 0.014 0.001 PHE C 214 TYR 0.018 0.001 TYR B 178 ARG 0.007 0.000 ARG E 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 330 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6648 (mt-10) REVERT: A 190 ASP cc_start: 0.8303 (m-30) cc_final: 0.7836 (m-30) REVERT: B 109 LYS cc_start: 0.8744 (ptpt) cc_final: 0.8434 (ptpt) REVERT: B 278 MET cc_start: 0.7674 (tpp) cc_final: 0.7437 (tpp) REVERT: C 448 LEU cc_start: 0.8824 (tp) cc_final: 0.8497 (tt) REVERT: D 112 GLU cc_start: 0.7328 (tm-30) cc_final: 0.7067 (tm-30) REVERT: D 187 MET cc_start: 0.8818 (tpp) cc_final: 0.8526 (mmm) REVERT: D 263 ASP cc_start: 0.7892 (t0) cc_final: 0.7431 (t0) REVERT: E 115 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8752 (ptmt) REVERT: F 25 SER cc_start: 0.8671 (m) cc_final: 0.8325 (p) REVERT: F 88 MET cc_start: 0.7871 (mmt) cc_final: 0.7603 (tpp) REVERT: F 138 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8440 (ppp) REVERT: F 196 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8666 (mttp) REVERT: F 245 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7969 (mm-30) REVERT: F 331 VAL cc_start: 0.9177 (t) cc_final: 0.8966 (p) REVERT: G 1346 MET cc_start: 0.8682 (mmm) cc_final: 0.8117 (ttm) REVERT: I 31 ASN cc_start: 0.8587 (t0) cc_final: 0.8293 (t0) REVERT: I 37 ASN cc_start: 0.8245 (t0) cc_final: 0.7905 (t0) REVERT: I 166 MET cc_start: 0.7367 (ptp) cc_final: 0.7080 (ptm) REVERT: J 128 ASN cc_start: 0.8489 (t0) cc_final: 0.7753 (t0) REVERT: J 145 MET cc_start: 0.7638 (mmm) cc_final: 0.7396 (mmm) REVERT: J 238 MET cc_start: 0.8324 (mtt) cc_final: 0.7962 (mtm) outliers start: 69 outliers final: 49 residues processed: 382 average time/residue: 0.3701 time to fit residues: 227.3025 Evaluate side-chains 350 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 298 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 1303 LEU Chi-restraints excluded: chain G residue 1411 GLU Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1455 GLU Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 170 LYS Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 707 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 112 optimal weight: 0.0970 chunk 300 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 195 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 333 optimal weight: 4.9990 chunk 277 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 175 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN E 26 HIS ** F 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27842 Z= 0.165 Angle : 0.566 10.228 37648 Z= 0.275 Chirality : 0.043 0.178 4279 Planarity : 0.004 0.042 4878 Dihedral : 7.168 117.205 3920 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.20 % Allowed : 11.88 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.14), residues: 3474 helix: 0.13 (0.14), residues: 1376 sheet: -1.37 (0.22), residues: 572 loop : -1.61 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP I 34 HIS 0.012 0.001 HIS J 762 PHE 0.019 0.001 PHE D 223 TYR 0.018 0.001 TYR B 178 ARG 0.006 0.000 ARG J 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 318 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8250 (tpp) cc_final: 0.8035 (mmm) REVERT: A 179 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6967 (mt-10) REVERT: A 190 ASP cc_start: 0.8265 (m-30) cc_final: 0.7772 (m-30) REVERT: B 109 LYS cc_start: 0.8727 (ptpt) cc_final: 0.8431 (ptpt) REVERT: B 278 MET cc_start: 0.7714 (tpp) cc_final: 0.7436 (tpp) REVERT: D 112 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7135 (tm-30) REVERT: D 187 MET cc_start: 0.8778 (tpp) cc_final: 0.8522 (mmm) REVERT: D 247 ASP cc_start: 0.8291 (m-30) cc_final: 0.7668 (m-30) REVERT: D 263 ASP cc_start: 0.7868 (t0) cc_final: 0.7385 (t0) REVERT: D 275 ILE cc_start: 0.8918 (mt) cc_final: 0.8691 (mp) REVERT: F 25 SER cc_start: 0.8667 (m) cc_final: 0.8325 (p) REVERT: F 88 MET cc_start: 0.7866 (mmt) cc_final: 0.7596 (tpp) REVERT: F 196 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8668 (mttp) REVERT: F 245 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7952 (mm-30) REVERT: F 312 ASN cc_start: 0.8698 (m-40) cc_final: 0.8389 (t0) REVERT: F 331 VAL cc_start: 0.9170 (t) cc_final: 0.8944 (p) REVERT: G 1305 TYR cc_start: 0.8208 (t80) cc_final: 0.7887 (t80) REVERT: G 1346 MET cc_start: 0.8683 (mmm) cc_final: 0.8141 (ttm) REVERT: I 31 ASN cc_start: 0.8570 (t0) cc_final: 0.8278 (t0) REVERT: I 37 ASN cc_start: 0.8135 (t0) cc_final: 0.7762 (t0) REVERT: I 166 MET cc_start: 0.7290 (ptp) cc_final: 0.7037 (ptm) REVERT: J 128 ASN cc_start: 0.8469 (t0) cc_final: 0.7727 (t0) REVERT: J 238 MET cc_start: 0.8402 (mtt) cc_final: 0.8119 (mtm) outliers start: 64 outliers final: 42 residues processed: 366 average time/residue: 0.3838 time to fit residues: 225.2178 Evaluate side-chains 340 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 297 time to evaluate : 3.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 1303 LEU Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1455 GLU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 170 LYS Chi-restraints excluded: chain J residue 267 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 321 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 243 optimal weight: 0.1980 chunk 188 optimal weight: 10.0000 chunk 280 optimal weight: 7.9990 chunk 186 optimal weight: 2.9990 chunk 332 optimal weight: 0.9980 chunk 208 optimal weight: 0.2980 chunk 202 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1333 ASN I 19 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27842 Z= 0.199 Angle : 0.575 9.328 37648 Z= 0.279 Chirality : 0.043 0.157 4279 Planarity : 0.004 0.043 4878 Dihedral : 7.024 116.308 3920 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.96 % Allowed : 11.98 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.14), residues: 3474 helix: 0.26 (0.14), residues: 1382 sheet: -1.32 (0.22), residues: 569 loop : -1.53 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP I 34 HIS 0.014 0.001 HIS J 762 PHE 0.014 0.001 PHE C 214 TYR 0.026 0.001 TYR E 310 ARG 0.007 0.000 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 318 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6990 (mt-10) REVERT: A 190 ASP cc_start: 0.8275 (m-30) cc_final: 0.7778 (m-30) REVERT: B 278 MET cc_start: 0.7889 (tpp) cc_final: 0.7560 (tpp) REVERT: C 260 MET cc_start: 0.8263 (mtp) cc_final: 0.7961 (ptp) REVERT: D 112 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7158 (tm-30) REVERT: D 167 MET cc_start: 0.8068 (mpp) cc_final: 0.7501 (mpp) REVERT: D 187 MET cc_start: 0.8883 (tpp) cc_final: 0.8593 (mmm) REVERT: D 263 ASP cc_start: 0.7975 (t0) cc_final: 0.7530 (t0) REVERT: F 25 SER cc_start: 0.8707 (m) cc_final: 0.8365 (p) REVERT: F 88 MET cc_start: 0.7965 (mmt) cc_final: 0.7702 (tpp) REVERT: F 138 MET cc_start: 0.8768 (ppp) cc_final: 0.8372 (tmm) REVERT: F 159 LYS cc_start: 0.9027 (mttt) cc_final: 0.8818 (mtmm) REVERT: F 196 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8680 (mttp) REVERT: F 331 VAL cc_start: 0.9182 (t) cc_final: 0.8940 (p) REVERT: G 1346 MET cc_start: 0.8612 (mmm) cc_final: 0.8113 (ttm) REVERT: I 31 ASN cc_start: 0.8559 (t0) cc_final: 0.8251 (t0) REVERT: I 34 TRP cc_start: 0.6994 (t60) cc_final: 0.6722 (t60) REVERT: I 37 ASN cc_start: 0.8107 (t0) cc_final: 0.7757 (t0) REVERT: I 166 MET cc_start: 0.7369 (ptp) cc_final: 0.7078 (ptm) REVERT: J 128 ASN cc_start: 0.8505 (t0) cc_final: 0.7778 (t0) REVERT: J 238 MET cc_start: 0.8522 (mtt) cc_final: 0.8306 (mtm) outliers start: 57 outliers final: 43 residues processed: 361 average time/residue: 0.3668 time to fit residues: 214.0903 Evaluate side-chains 333 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 289 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 1303 LEU Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1455 GLU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 170 LYS Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 754 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 205 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 198 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 211 optimal weight: 0.0270 chunk 226 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 overall best weight: 0.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: