Starting phenix.real_space_refine on Tue Nov 19 18:15:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/11_2024/5oaf_3773_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/11_2024/5oaf_3773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/11_2024/5oaf_3773.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/11_2024/5oaf_3773.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/11_2024/5oaf_3773_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/11_2024/5oaf_3773_neut.cif" } resolution = 4.06 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= 0.003 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 12 5.49 5 S 92 5.16 5 C 12342 2.51 5 N 3434 2.21 5 O 3868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19748 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3357 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 16, 'TRANS': 419} Chain breaks: 1 Chain: "B" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3232 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "C" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3253 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 16, 'TRANS': 407} Chain breaks: 1 Chain: "D" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3187 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 10, 'TRANS': 400} Chain breaks: 2 Chain: "E" Number of atoms: 3400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3400 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 17, 'TRANS': 424} Chain: "F" Number of atoms: 3157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3157 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 10, 'TRANS': 396} Chain breaks: 2 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} Time building chain proxies: 12.00, per 1000 atoms: 0.61 Number of scatterers: 19748 At special positions: 0 Unit cell: (131.44, 127.2, 132.5, 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 92 16.00 P 12 15.00 O 3868 8.00 N 3434 7.00 C 12342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.74 Conformation dependent library (CDL) restraints added in 2.7 seconds 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4668 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 32 sheets defined 45.9% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.746A pdb=" N ILE A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 53 " --> pdb=" O CYS A 49 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.529A pdb=" N GLY A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 120 removed outlier: 4.012A pdb=" N ILE A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 182 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 256 through 263 removed outlier: 3.827A pdb=" N MET A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 289 removed outlier: 3.586A pdb=" N GLY A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 308 through 320 removed outlier: 3.809A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 383 Processing helix chain 'A' and resid 387 through 401 Processing helix chain 'A' and resid 402 through 421 removed outlier: 3.777A pdb=" N SER A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.957A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 447 Processing helix chain 'B' and resid 49 through 66 removed outlier: 3.560A pdb=" N GLY B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.815A pdb=" N ILE B 86 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 removed outlier: 3.602A pdb=" N ILE B 127 " --> pdb=" O PHE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 185 Processing helix chain 'B' and resid 205 through 211 removed outlier: 4.375A pdb=" N PHE B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 252 Processing helix chain 'B' and resid 254 through 261 removed outlier: 4.452A pdb=" N LEU B 258 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 284 Processing helix chain 'B' and resid 305 through 318 removed outlier: 3.760A pdb=" N ASN B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 346 Processing helix chain 'B' and resid 347 through 354 removed outlier: 3.552A pdb=" N ARG B 353 " --> pdb=" O ASP B 349 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 378 removed outlier: 3.859A pdb=" N LYS B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 398 through 416 removed outlier: 3.608A pdb=" N ALA B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 411 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 433 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 441 through 446 removed outlier: 4.069A pdb=" N LYS B 444 " --> pdb=" O GLN B 441 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU B 445 " --> pdb=" O TYR B 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 removed outlier: 4.032A pdb=" N VAL C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU C 54 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 88 removed outlier: 3.502A pdb=" N GLY C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 120 removed outlier: 3.759A pdb=" N VAL C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 183 removed outlier: 4.088A pdb=" N LYS C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 254 through 263 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 276 through 290 removed outlier: 3.939A pdb=" N GLN C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.590A pdb=" N PHE C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 358 removed outlier: 3.886A pdb=" N ARG C 357 " --> pdb=" O ASP C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 383 removed outlier: 3.559A pdb=" N LYS C 376 " --> pdb=" O LYS C 372 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 381 " --> pdb=" O ILE C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 401 Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.857A pdb=" N SER C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 421 removed outlier: 3.663A pdb=" N ALA C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 437 Processing helix chain 'C' and resid 439 through 447 Processing helix chain 'D' and resid 24 through 28 removed outlier: 4.126A pdb=" N HIS D 27 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE D 28 " --> pdb=" O HIS D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 28' Processing helix chain 'D' and resid 42 through 46 removed outlier: 3.960A pdb=" N GLY D 45 " --> pdb=" O ALA D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 removed outlier: 3.814A pdb=" N GLY D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 93 removed outlier: 3.824A pdb=" N ALA D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 109 removed outlier: 3.506A pdb=" N PHE D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 105 through 109' Processing helix chain 'D' and resid 114 through 127 removed outlier: 3.630A pdb=" N ILE D 127 " --> pdb=" O PHE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 222 through 226 removed outlier: 4.089A pdb=" N VAL D 225 " --> pdb=" O THR D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 252 removed outlier: 3.552A pdb=" N ASN D 251 " --> pdb=" O ILE D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 261 removed outlier: 3.636A pdb=" N LEU D 258 " --> pdb=" O THR D 254 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 286 removed outlier: 3.713A pdb=" N ILE D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA D 281 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.577A pdb=" N PHE D 309 " --> pdb=" O ASP D 305 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 346 Processing helix chain 'D' and resid 347 through 354 Processing helix chain 'D' and resid 363 through 378 removed outlier: 3.636A pdb=" N LYS D 368 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG D 374 " --> pdb=" O ILE D 370 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N CYS D 375 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU D 376 " --> pdb=" O ARG D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 397 removed outlier: 4.120A pdb=" N VAL D 389 " --> pdb=" O ASP D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 416 removed outlier: 3.532A pdb=" N ALA D 402 " --> pdb=" O SER D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 433 Processing helix chain 'D' and resid 435 through 442 Processing helix chain 'D' and resid 443 through 446 Processing helix chain 'E' and resid 42 through 59 removed outlier: 3.917A pdb=" N ILE E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL E 53 " --> pdb=" O CYS E 49 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLU E 54 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU E 55 " --> pdb=" O VAL E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 88 removed outlier: 4.545A pdb=" N ALA E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 102 Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.639A pdb=" N ILE E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 183 removed outlier: 4.078A pdb=" N GLU E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER E 179 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 249 Processing helix chain 'E' and resid 256 through 263 removed outlier: 4.044A pdb=" N MET E 260 " --> pdb=" O ILE E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 290 removed outlier: 3.516A pdb=" N ARG E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL E 282 " --> pdb=" O GLU E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 320 removed outlier: 3.542A pdb=" N PHE E 312 " --> pdb=" O ASP E 308 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR E 313 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 350 Processing helix chain 'E' and resid 351 through 358 removed outlier: 3.998A pdb=" N ARG E 357 " --> pdb=" O ASP E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 383 removed outlier: 4.422A pdb=" N GLN E 373 " --> pdb=" O GLN E 369 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE E 377 " --> pdb=" O GLN E 373 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG E 378 " --> pdb=" O ILE E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 401 Processing helix chain 'E' and resid 402 through 409 removed outlier: 3.816A pdb=" N SER E 406 " --> pdb=" O THR E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 421 removed outlier: 3.841A pdb=" N ALA E 413 " --> pdb=" O LEU E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 437 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 114 through 126 removed outlier: 3.622A pdb=" N ALA F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 185 removed outlier: 4.164A pdb=" N GLU F 180 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER F 181 " --> pdb=" O LYS F 177 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS F 184 " --> pdb=" O GLU F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 252 Processing helix chain 'F' and resid 254 through 261 removed outlier: 4.350A pdb=" N LEU F 258 " --> pdb=" O THR F 254 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE F 261 " --> pdb=" O PHE F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 287 removed outlier: 3.616A pdb=" N VAL F 272 " --> pdb=" O ILE F 268 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE F 276 " --> pdb=" O VAL F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 318 removed outlier: 3.729A pdb=" N ASN F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 346 Processing helix chain 'F' and resid 347 through 352 removed outlier: 3.974A pdb=" N ASP F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 376 removed outlier: 3.818A pdb=" N LYS F 368 " --> pdb=" O GLU F 364 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN F 369 " --> pdb=" O LYS F 365 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU F 376 " --> pdb=" O ARG F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 397 removed outlier: 3.721A pdb=" N VAL F 389 " --> pdb=" O ASP F 385 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU F 396 " --> pdb=" O ARG F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.533A pdb=" N ALA F 402 " --> pdb=" O SER F 398 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU F 411 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 removed outlier: 3.507A pdb=" N SER F 431 " --> pdb=" O LYS F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 442 removed outlier: 3.984A pdb=" N GLN F 441 " --> pdb=" O SER F 437 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR F 442 " --> pdb=" O ARG F 438 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 97 removed outlier: 3.548A pdb=" N CYS A 94 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 300 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU A 299 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ALA A 330 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL A 301 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N SER A 331 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 68 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 172 removed outlier: 3.602A pdb=" N GLU A 134 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 201 removed outlier: 3.696A pdb=" N ASP A 189 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 337 removed outlier: 3.527A pdb=" N CYS A 336 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 104 removed outlier: 6.158A pdb=" N LEU B 296 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA B 327 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 298 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY B 77 " --> pdb=" O THR B 328 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 355 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 239 through 243 Processing sheet with id=AA9, first strand: chain 'B' and resid 162 through 164 Processing sheet with id=AB1, first strand: chain 'B' and resid 193 through 195 removed outlier: 4.044A pdb=" N ILE B 202 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 333 through 334 removed outlier: 3.558A pdb=" N THR B 333 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 342 " --> pdb=" O THR B 333 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB4, first strand: chain 'C' and resid 93 through 97 removed outlier: 6.473A pdb=" N CYS C 94 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ASP C 302 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N MET C 96 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL C 66 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N SER C 331 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU C 68 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 200 through 201 removed outlier: 3.882A pdb=" N VAL C 200 " --> pdb=" O TYR C 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 201 removed outlier: 3.882A pdb=" N VAL C 200 " --> pdb=" O TYR C 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 134 through 137 Processing sheet with id=AB8, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AB9, first strand: chain 'D' and resid 100 through 104 removed outlier: 3.806A pdb=" N ASP D 299 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU D 296 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA D 327 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE D 298 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY D 77 " --> pdb=" O THR D 328 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU D 355 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 240 through 243 removed outlier: 3.562A pdb=" N ILE D 131 " --> pdb=" O HIS D 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 201 through 203 removed outlier: 3.895A pdb=" N ILE D 202 " --> pdb=" O THR D 194 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D 138 " --> pdb=" O ILE D 195 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 141 through 145 removed outlier: 3.685A pdb=" N ILE D 145 " --> pdb=" O LYS D 160 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS D 160 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU D 161 " --> pdb=" O TYR D 172 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR D 172 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 333 through 334 removed outlier: 3.518A pdb=" N SER D 342 " --> pdb=" O THR D 333 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AC6, first strand: chain 'E' and resid 93 through 95 removed outlier: 3.528A pdb=" N CYS E 94 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE E 300 " --> pdb=" O CYS E 94 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU E 299 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ALA E 330 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL E 301 " --> pdb=" O ALA E 330 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL E 66 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER E 331 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU E 68 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET E 359 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 193 through 194 Processing sheet with id=AC8, first strand: chain 'E' and resid 193 through 194 Processing sheet with id=AC9, first strand: chain 'E' and resid 157 through 163 removed outlier: 3.688A pdb=" N VAL E 157 " --> pdb=" O LEU E 172 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 336 through 337 Processing sheet with id=AD2, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.615A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 200 through 203 removed outlier: 3.589A pdb=" N VAL F 238 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS F 236 " --> pdb=" O THR F 135 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 200 through 203 Processing sheet with id=AD5, first strand: chain 'F' and resid 143 through 145 removed outlier: 3.582A pdb=" N LYS F 160 " --> pdb=" O ILE F 145 " (cutoff:3.500A) 845 hydrogen bonds defined for protein. 2382 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: 7.20 Time building geometry restraints manager: 5.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6639 1.34 - 1.46: 3384 1.46 - 1.58: 9789 1.58 - 1.69: 18 1.69 - 1.81: 160 Bond restraints: 19990 Sorted by residual: bond pdb=" C CYS D 227 " pdb=" N PRO D 228 " ideal model delta sigma weight residual 1.334 1.371 -0.038 2.34e-02 1.83e+03 2.58e+00 bond pdb=" C ASP E 273 " pdb=" N LYS E 274 " ideal model delta sigma weight residual 1.335 1.319 0.016 1.38e-02 5.25e+03 1.31e+00 bond pdb=" N GLN E 251 " pdb=" CA GLN E 251 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.14e+00 bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" C GLY A 198 " pdb=" N ALA A 199 " ideal model delta sigma weight residual 1.331 1.319 0.013 1.29e-02 6.01e+03 1.01e+00 ... (remaining 19985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 26698 2.08 - 4.15: 196 4.15 - 6.23: 55 6.23 - 8.31: 0 8.31 - 10.39: 1 Bond angle restraints: 26950 Sorted by residual: angle pdb=" N LEU E 315 " pdb=" CA LEU E 315 " pdb=" C LEU E 315 " ideal model delta sigma weight residual 111.28 106.26 5.02 1.09e+00 8.42e-01 2.12e+01 angle pdb=" CA LEU B 232 " pdb=" CB LEU B 232 " pdb=" CG LEU B 232 " ideal model delta sigma weight residual 116.30 126.69 -10.39 3.50e+00 8.16e-02 8.81e+00 angle pdb=" C ASP A 356 " pdb=" N ARG A 357 " pdb=" CA ARG A 357 " ideal model delta sigma weight residual 121.54 126.97 -5.43 1.91e+00 2.74e-01 8.09e+00 angle pdb=" N ALA F 198 " pdb=" CA ALA F 198 " pdb=" C ALA F 198 " ideal model delta sigma weight residual 113.19 109.84 3.35 1.19e+00 7.06e-01 7.92e+00 angle pdb=" N GLY A 253 " pdb=" CA GLY A 253 " pdb=" C GLY A 253 " ideal model delta sigma weight residual 110.87 114.69 -3.82 1.54e+00 4.22e-01 6.15e+00 ... (remaining 26945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.58: 12275 30.58 - 61.16: 71 61.16 - 91.73: 0 91.73 - 122.31: 4 122.31 - 152.89: 10 Dihedral angle restraints: 12360 sinusoidal: 5113 harmonic: 7247 Sorted by residual: dihedral pdb=" C5' ADP D 501 " pdb=" O5' ADP D 501 " pdb=" PA ADP D 501 " pdb=" O2A ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 92.89 -152.89 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" C5' ADP C 501 " pdb=" O5' ADP C 501 " pdb=" PA ADP C 501 " pdb=" O2A ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 89.33 -149.32 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O2A ADP B 501 " pdb=" O3A ADP B 501 " pdb=" PA ADP B 501 " pdb=" PB ADP B 501 " ideal model delta sinusoidal sigma weight residual -60.00 72.88 -132.88 1 2.00e+01 2.50e-03 4.03e+01 ... (remaining 12357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2172 0.031 - 0.061: 635 0.061 - 0.092: 136 0.092 - 0.123: 215 0.123 - 0.153: 12 Chirality restraints: 3170 Sorted by residual: chirality pdb=" CA TYR E 314 " pdb=" N TYR E 314 " pdb=" C TYR E 314 " pdb=" CB TYR E 314 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CA ILE E 350 " pdb=" N ILE E 350 " pdb=" C ILE E 350 " pdb=" CB ILE E 350 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE A 256 " pdb=" N ILE A 256 " pdb=" C ILE A 256 " pdb=" CB ILE A 256 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 3167 not shown) Planarity restraints: 3434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 139 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO C 140 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 140 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 140 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 295 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO C 296 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 296 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 296 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 98 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO F 99 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO F 99 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 99 " -0.021 5.00e-02 4.00e+02 ... (remaining 3431 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 494 2.71 - 3.26: 20009 3.26 - 3.81: 28601 3.81 - 4.35: 37657 4.35 - 4.90: 61523 Nonbonded interactions: 148284 Sorted by model distance: nonbonded pdb=" OG1 THR A 367 " pdb=" OE1 GLU A 370 " model vdw 2.165 3.040 nonbonded pdb=" O TYR B 387 " pdb=" OG1 THR B 391 " model vdw 2.201 3.040 nonbonded pdb=" O TYR D 387 " pdb=" OG1 THR D 391 " model vdw 2.209 3.040 nonbonded pdb=" NH1 ARG F 400 " pdb=" O2A ADP F 501 " model vdw 2.212 3.120 nonbonded pdb=" OG SER E 99 " pdb=" OG SER F 310 " model vdw 2.235 3.040 ... (remaining 148279 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 11 through 205 or resid 224 through 452 or resid 501)) selection = (chain 'C' and (resid 11 through 144 or resid 151 through 452 or resid 501)) selection = (chain 'E' and (resid 11 through 144 or resid 151 through 205 or resid 224 throu \ gh 452 or resid 501)) } ncs_group { reference = (chain 'B' and (resid 16 through 146 or resid 159 through 210 or resid 228 throu \ gh 449 or resid 501)) selection = (chain 'D' and (resid 16 through 210 or resid 228 through 449 or resid 501)) selection = (chain 'F' and (resid 16 through 449 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=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 45.120 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.100 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 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 : 0.001 0.038 19990 Z= 0.095 Angle : 0.475 10.387 26950 Z= 0.255 Chirality : 0.040 0.153 3170 Planarity : 0.003 0.052 3434 Dihedral : 9.128 152.889 7692 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.28 % Allowed : 0.05 % Favored : 99.67 % 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: -2.75 (0.13), residues: 2512 helix: -2.78 (0.11), residues: 1006 sheet: -0.45 (0.20), residues: 428 loop : -1.20 (0.16), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 283 HIS 0.002 0.000 HIS A 316 PHE 0.007 0.001 PHE D 224 TYR 0.007 0.001 TYR E 314 ARG 0.004 0.000 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 759 time to evaluate : 2.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ARG cc_start: 0.7324 (mpt180) cc_final: 0.6510 (mtp180) REVERT: A 215 LEU cc_start: 0.6942 (mt) cc_final: 0.6441 (tt) REVERT: A 260 MET cc_start: 0.6668 (ptm) cc_final: 0.6126 (ppp) REVERT: A 298 VAL cc_start: 0.6472 (t) cc_final: 0.6113 (t) REVERT: B 117 GLU cc_start: 0.8280 (tm-30) cc_final: 0.8013 (tm-30) REVERT: B 141 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6725 (pp20) REVERT: B 168 MET cc_start: 0.4892 (mmm) cc_final: 0.4655 (ttt) REVERT: B 174 LEU cc_start: 0.7024 (mt) cc_final: 0.6550 (mt) REVERT: B 199 THR cc_start: 0.7066 (p) cc_final: 0.6809 (m) REVERT: B 232 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6750 (pp) REVERT: C 271 ILE cc_start: 0.8453 (mm) cc_final: 0.8242 (mm) REVERT: C 332 ASN cc_start: 0.8119 (t0) cc_final: 0.7834 (t0) REVERT: C 359 MET cc_start: 0.7115 (mtp) cc_final: 0.6752 (mtt) REVERT: C 380 GLN cc_start: 0.8255 (tt0) cc_final: 0.8008 (mt0) REVERT: D 176 THR cc_start: 0.7392 (p) cc_final: 0.6800 (t) REVERT: E 274 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7713 (tmtt) REVERT: E 303 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6564 (mm-30) REVERT: E 308 ASP cc_start: 0.7439 (t0) cc_final: 0.6736 (t0) REVERT: E 380 GLN cc_start: 0.8415 (tt0) cc_final: 0.8198 (tp-100) REVERT: F 135 THR cc_start: 0.8509 (p) cc_final: 0.7695 (p) REVERT: F 277 ASN cc_start: 0.7195 (m-40) cc_final: 0.6611 (m110) REVERT: F 313 ASN cc_start: 0.6645 (t0) cc_final: 0.5792 (t0) outliers start: 6 outliers final: 1 residues processed: 761 average time/residue: 0.3710 time to fit residues: 409.9324 Evaluate side-chains 405 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 402 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 211 optimal weight: 10.0000 chunk 190 optimal weight: 0.0970 chunk 105 optimal weight: 0.6980 chunk 64 optimal weight: 0.2980 chunk 128 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 119 optimal weight: 0.0470 chunk 146 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS A 408 GLN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS B 245 HIS B 251 ASN B 329 ASN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS C 156 HIS C 229 HIS C 414 ASN E 34 GLN E 196 ASN E 305 HIS F 78 GLN F 302 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19990 Z= 0.163 Angle : 0.617 8.250 26950 Z= 0.305 Chirality : 0.044 0.177 3170 Planarity : 0.004 0.093 3434 Dihedral : 9.561 172.760 2788 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: -1.36 (0.14), residues: 2512 helix: -1.14 (0.14), residues: 1034 sheet: 0.10 (0.21), residues: 440 loop : -0.90 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 283 HIS 0.013 0.001 HIS B 245 PHE 0.016 0.001 PHE D 224 TYR 0.014 0.001 TYR C 314 ARG 0.009 0.001 ARG B 130 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8168 (pm20) cc_final: 0.7617 (pp20) REVERT: A 184 ARG cc_start: 0.6992 (mpt180) cc_final: 0.6510 (mtp180) REVERT: A 215 LEU cc_start: 0.7332 (mt) cc_final: 0.6846 (mt) REVERT: A 259 MET cc_start: 0.3014 (mtt) cc_final: 0.2571 (mtm) REVERT: A 260 MET cc_start: 0.6425 (ptm) cc_final: 0.5862 (ppp) REVERT: B 46 MET cc_start: 0.8292 (mmm) cc_final: 0.7893 (mmm) REVERT: B 117 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7812 (tm-30) REVERT: B 174 LEU cc_start: 0.6801 (mt) cc_final: 0.6462 (mt) REVERT: B 443 MET cc_start: 0.7508 (mmp) cc_final: 0.7078 (ppp) REVERT: C 320 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7517 (mt-10) REVERT: C 332 ASN cc_start: 0.8241 (t0) cc_final: 0.8033 (t0) REVERT: C 341 THR cc_start: 0.8091 (p) cc_final: 0.7757 (t) REVERT: C 359 MET cc_start: 0.6942 (mtp) cc_final: 0.6736 (mtt) REVERT: D 141 GLU cc_start: 0.8430 (tt0) cc_final: 0.8142 (tp30) REVERT: D 176 THR cc_start: 0.6852 (p) cc_final: 0.6355 (t) REVERT: D 223 LYS cc_start: 0.7326 (mptt) cc_final: 0.6217 (tttp) REVERT: E 47 GLU cc_start: 0.7360 (pt0) cc_final: 0.7006 (pt0) REVERT: E 376 LYS cc_start: 0.8970 (tptp) cc_final: 0.8748 (tppt) REVERT: E 380 GLN cc_start: 0.8431 (tt0) cc_final: 0.8189 (tp-100) REVERT: F 168 MET cc_start: 0.6080 (ptp) cc_final: 0.5409 (ptt) REVERT: F 313 ASN cc_start: 0.6364 (t0) cc_final: 0.5702 (t0) REVERT: F 368 LYS cc_start: 0.7719 (tttt) cc_final: 0.7332 (tttt) outliers start: 0 outliers final: 0 residues processed: 485 average time/residue: 0.3571 time to fit residues: 256.7493 Evaluate side-chains 329 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 62 optimal weight: 0.2980 chunk 228 optimal weight: 0.2980 chunk 246 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 226 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 183 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN C 156 HIS C 229 HIS C 247 ASN C 414 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 HIS F 245 HIS F 277 ASN ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19990 Z= 0.155 Angle : 0.604 7.838 26950 Z= 0.296 Chirality : 0.043 0.170 3170 Planarity : 0.004 0.061 3434 Dihedral : 9.261 168.715 2788 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.51 % Favored : 97.45 % Rotamer: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.66 % 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: -0.71 (0.15), residues: 2512 helix: -0.39 (0.15), residues: 1045 sheet: 0.44 (0.22), residues: 454 loop : -0.82 (0.17), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 283 HIS 0.013 0.001 HIS F 245 PHE 0.021 0.001 PHE D 261 TYR 0.022 0.002 TYR B 401 ARG 0.006 0.000 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 442 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7997 (pm20) cc_final: 0.7535 (pp20) REVERT: A 184 ARG cc_start: 0.7019 (mpt180) cc_final: 0.6568 (mtp180) REVERT: A 203 GLN cc_start: 0.6008 (tp-100) cc_final: 0.5773 (tp40) REVERT: A 259 MET cc_start: 0.2995 (mtt) cc_final: 0.2659 (mtm) REVERT: A 260 MET cc_start: 0.6464 (ptm) cc_final: 0.6017 (ppp) REVERT: B 443 MET cc_start: 0.7376 (mmp) cc_final: 0.6952 (ppp) REVERT: C 341 THR cc_start: 0.7991 (p) cc_final: 0.7758 (t) REVERT: C 359 MET cc_start: 0.7122 (mtp) cc_final: 0.6910 (mtp) REVERT: D 176 THR cc_start: 0.6986 (p) cc_final: 0.6406 (t) REVERT: D 254 THR cc_start: 0.7704 (p) cc_final: 0.7492 (p) REVERT: D 314 ARG cc_start: 0.7197 (mmt180) cc_final: 0.6773 (mmt90) REVERT: E 47 GLU cc_start: 0.7319 (pt0) cc_final: 0.7019 (pt0) REVERT: E 100 GLU cc_start: 0.8388 (mp0) cc_final: 0.7721 (mp0) REVERT: E 308 ASP cc_start: 0.7362 (t0) cc_final: 0.6764 (t0) REVERT: E 380 GLN cc_start: 0.8466 (tt0) cc_final: 0.8146 (tp-100) REVERT: F 139 GLU cc_start: 0.7990 (pm20) cc_final: 0.7645 (pm20) REVERT: F 311 PHE cc_start: 0.7737 (t80) cc_final: 0.7343 (t80) REVERT: F 314 ARG cc_start: 0.6528 (ptp-110) cc_final: 0.6120 (ttm-80) outliers start: 2 outliers final: 1 residues processed: 444 average time/residue: 0.3322 time to fit residues: 223.7991 Evaluate side-chains 329 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 328 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 225 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 229 optimal weight: 0.0670 chunk 242 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 217 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 overall best weight: 1.0720 ------------------------------------------------------------------------------- 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: